Publications

@article{pmid26975654,

title = {Global analyses of endonucleolytic cleavage in mammals reveal expanded repertoires of cleavage-inducing small RNAs and their targets},

author = {Ashley A Cass and Jae Hoon Bahn and Jae-Hyung Lee and Christopher Greer and Xianzhi Lin and Yong Kim and Yun-Hua Esther Hsiao and Xinshu Xiao},

doi = {10.1093/nar/gkw164},

issn = {1362-4962},

year  = {2016},

date = {2016-04-01},

journal = {Nucleic Acids Res},

volume = {44},

number = {7},

pages = {3253--3263},

abstract = {In mammals, small RNAs are important players in post-transcriptional gene regulation. While their roles in mRNA destabilization and translational repression are well appreciated, their involvement in endonucleolytic cleavage of target RNAs is poorly understood. Very few microRNAs are known to guide RNA cleavage. Endogenous small interfering RNAs are expected to induce target cleavage, but their target genes remain largely unknown. We report a systematic study of small RNA-mediated endonucleolytic cleavage in mouse through integrative analysis of small RNA and degradome sequencing data without imposing any bias toward known small RNAs. Hundreds of small cleavage-inducing RNAs and their cognate target genes were identified, significantly expanding the repertoire of known small RNA-guided cleavage events. Strikingly, both small RNAs and their target sites demonstrated significant overlap with retrotransposons, providing evidence for the long-standing speculation that retrotransposable elements in mRNAs are leveraged as signals for gene targeting. Furthermore, our analysis showed that the RNA cleavage pathway is also present in human cells but affecting a different repertoire of retrotransposons. These results show that small RNA-guided cleavage is more widespread than previously appreciated. Their impact on retrotransposons in non-coding regions shed light on important aspects of mammalian gene regulation.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid26888265,

title = {Alternative splicing modulated by genetic variants demonstrates accelerated evolution regulated by highly conserved proteins},

author = {Yun-Hua Esther Hsiao and Jae Hoon Bahn and Xianzhi Lin and Tak-Ming Chan and Rena Wang and Xinshu Xiao},

doi = {10.1101/gr.193359.115},

issn = {1549-5469},

year  = {2016},

date = {2016-04-01},

journal = {Genome Res},

volume = {26},

number = {4},

pages = {440--450},

abstract = {Identification of functional genetic variants and elucidation of their regulatory mechanisms represent significant challenges of the post-genomic era. A poorly understood topic is the involvement of genetic variants in mediating post-transcriptional RNA processing, including alternative splicing. Thus far, little is known about the genomic, evolutionary, and regulatory features of genetically modulated alternative splicing (GMAS). Here, we systematically identified intronic tag variants for genetic modulation of alternative splicing using RNA-seq data specific to cellular compartments. Combined with our previous method that identifies exonic tags for GMAS, this study yielded 622 GMAS exons. We observed that GMAS events are highly cell type independent, indicating that splicing-altering genetic variants could have widespread function across cell types. Interestingly, GMAS genes, exons, and single-nucleotide variants (SNVs) all demonstrated positive selection or accelerated evolution in primates. We predicted that GMAS SNVs often alter binding of splicing factors, with SRSF1 affecting the most GMAS events and demonstrating global allelic binding bias. However, in contrast to their GMAS targets, the predicted splicing factors are more conserved than expected, suggesting that cis-regulatory variation is the major driving force of splicing evolution. Moreover, GMAS-related splicing factors had stronger consensus motifs than expected, consistent with their susceptibility to SNV disruption. Intriguingly, GMAS SNVs in general do not alter the strongest consensus position of the splicing factor motif, except the more than 100 GMAS SNVs in linkage disequilibrium with polymorphisms reported by genome-wide association studies. Our study reports many GMAS events and enables a better understanding of the evolutionary and regulatory features of this phenomenon.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid26745669,

title = {Research Resource: Hormones, Genes, and Athleticism: Effect of Androgens on the Avian Muscular Transcriptome},

author = {Matthew J Fuxjager and Jae-Hyung Lee and Tak-Ming Chan and Jae Hoon Bahn and Jenifer G Chew and Xinshu Xiao and Barney A Schlinger},

doi = {10.1210/me.2015-1270},

issn = {1944-9917},

year  = {2016},

date = {2016-02-01},

journal = {Mol Endocrinol},

volume = {30},

number = {2},

pages = {254--271},

abstract = {Male vertebrate social displays vary from physically simple to complex, with the latter involving exquisite motor command of the body and appendages. Studies of these displays have, in turn, provided substantial insight into neuromotor mechanisms. The neotropical golden-collared manakin (Manacus vitellinus) has been used previously as a model to investigate intricate motor skills because adult males of this species perform an acrobatic and androgen-dependent courtship display. To support this behavior, these birds express elevated levels of androgen receptors (AR) in their skeletal muscles. Here we use RNA sequencing to explore how testosterone (T) modulates the muscular transcriptome to support male manakin courtship displays. In addition, we explore how androgens influence gene expression in the muscles of the zebra finch (Taenopygia guttata), a model passerine bird with a limited courtship display and minimal muscle AR. We identify androgen-dependent, muscle-specific gene regulation in both species. In addition, we identify manakin-specific effects that are linked to muscle use during the manakin display, including androgenic regulation of genes associated with muscle fiber contractility, cellular homeostasis, and energetic efficiency. Overall, our results point to numerous genes and gene networks impacted by androgens in male birds, including some that underlie optimal muscle function necessary for performing acrobatic display routines. Manakins are excellent models to explore gene regulation promoting athletic ability.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid26619120,

title = {RBFox1-mediated RNA splicing regulates cardiac hypertrophy and heart failure},

author = {Chen Gao and Shuxun Ren and Jae-Hyung Lee and Jinsong Qiu and Douglas J Chapski and Christoph D Rau and Yu Zhou and Maha Abdellatif and Astushi Nakano and Thomas M Vondriska and Xinshu Xiao and Xiang-Dong Fu and Jau-Nian Chen and Yibin Wang},

doi = {10.1172/JCI84015},

issn = {1558-8238},

year  = {2016},

date = {2016-01-01},

journal = {J Clin Invest},

volume = {126},

number = {1},

pages = {195--206},

abstract = {RNA splicing is a major contributor to total transcriptome complexity; however, the functional role and regulation of splicing in heart failure remain poorly understood. Here, we used a total transcriptome profiling and bioinformatic analysis approach and identified a muscle-specific isoform of an RNA splicing regulator, RBFox1 (also known as A2BP1), as a prominent regulator of alternative RNA splicing during heart failure. Evaluation of developing murine and zebrafish hearts revealed that RBFox1 is induced during postnatal cardiac maturation. However, we found that RBFox1 is markedly diminished in failing human and mouse hearts. In a mouse model, RBFox1 deficiency in the heart promoted pressure overload-induced heart failure. We determined that RBFox1 is a potent regulator of RNA splicing and is required for a conserved splicing process of transcription factor MEF2 family members that yields different MEF2 isoforms with differential effects on cardiac hypertrophic gene expression. Finally, induction of RBFox1 expression in murine pressure overload models substantially attenuated cardiac hypertrophy and pathological manifestations. Together, this study identifies regulation of RNA splicing by RBFox1 as an important player in transcriptome reprogramming during heart failure that influence pathogenesis of the disease.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid26323713,

title = {RASER: reads aligner for SNPs and editing sites of RNA},

author = {Jaegyoon Ahn and Xinshu Xiao},

doi = {10.1093/bioinformatics/btv505},

issn = {1367-4811},

year  = {2015},

date = {2015-12-01},

journal = {Bioinformatics},

volume = {31},

number = {24},

pages = {3906--3913},

abstract = {MOTIVATION: Accurate identification of genetic variants such as single-nucleotide polymorphisms (SNPs) or RNA editing sites from RNA-Seq reads is important, yet challenging, because it necessitates a very low false-positive rate in read mapping. Although many read aligners are available, no single aligner was specifically developed or tested as an effective tool for SNP and RNA editing prediction.



RESULTS: We present RASER, an accurate read aligner with novel mapping schemes and index tree structure that aims to reduce false-positive mappings due to existence of highly similar regions. We demonstrate that RASER shows the best mapping accuracy compared with other popular algorithms and highest sensitivity in identifying multiply mapped reads. As a result, RASER displays superb efficacy in unbiased mapping of the alternative alleles of SNPs and in identification of RNA editing sites.



AVAILABILITY AND IMPLEMENTATION: RASER is written in C++ and freely available for download at https://github.com/jaegyoonahn/RASER.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid26531099,

title = {ESRP2 controls an adult splicing programme in hepatocytes to support postnatal liver maturation},

author = {Amruta Bhate and Darren J Parker and Thomas W Bebee and Jaegyoon Ahn and Waqar Arif and Edrees H Rashan and Sandip Chorghade and Anthony Chau and Jae-Hyung Lee and Sayeepriyadarshini Anakk and Russ P Carstens and Xinshu Xiao and Auinash Kalsotra},

doi = {10.1038/ncomms9768},

issn = {2041-1723},

year  = {2015},

date = {2015-11-01},

journal = {Nat Commun},

volume = {6},

pages = {8768},

abstract = {Although major genetic networks controlling early liver specification and morphogenesis are known, the mechanisms responsible for postnatal hepatic maturation are poorly understood. Here we employ global analyses of the mouse liver transcriptome to demonstrate that postnatal remodelling of the liver is accompanied by large-scale transcriptional and post-transcriptional transitions that are cell-type-specific and temporally coordinated. Combining detailed expression analyses with gain- and loss-of-function studies, we identify epithelial splicing regulatory protein 2 (ESRP2) as a conserved regulatory factor that controls the neonatal-to-adult switch of ∼20% of splice isoforms in mouse and human hepatocytes. The normal shift in splicing coincides tightly with dramatic postnatal induction of ESRP2 in hepatocytes. We further demonstrate that forced expression of ESRP2 in immature mouse and human hepatocytes is sufficient to drive a reciprocal shift in splicing and causes various physiological abnormalities. These findings define a direct role for ESRP2 in the generation of conserved repertoires of adult splice isoforms that facilitate terminal differentiation and maturation of hepatocytes.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid25730491,

title = {Genome sequence-independent identification of RNA editing sites},

author = {Qing Zhang and Xinshu Xiao},

doi = {10.1038/nmeth.3314},

issn = {1548-7105},

year  = {2015},

date = {2015-04-01},

journal = {Nat Methods},

volume = {12},

number = {4},

pages = {347--350},

abstract = {RNA editing generates post-transcriptional sequence changes that can be deduced from RNA-seq data, but detection typically requires matched genomic sequence or multiple related expression data sets. We developed the GIREMI tool (genome-independent identification of RNA editing by mutual information; https://www.ibp.ucla.edu/research/xiao/GIREMI.html) to predict adenosine-to-inosine editing accurately and sensitively from a single RNA-seq data set of modest sequencing depth. Using GIREMI on existing data, we observed tissue-specific and evolutionary patterns in editing sites in the human population.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid25519955,

title = {The Sm protein methyltransferase PRMT5 is not required for primordial germ cell specification in mice},

author = {Ziwei Li and Juehua Yu and Linzi Hosohama and Kevin Nee and Sofia Gkountela and Sonal Chaudhari and Ashley A Cass and Xinshu Xiao and Amander T Clark},

doi = {10.15252/embj.201489319},

issn = {1460-2075},

year  = {2015},

date = {2015-03-01},

journal = {EMBO J},

volume = {34},

number = {6},

pages = {748--758},

abstract = {PRMT5 is a type II protein arginine methyltransferase with roles in stem cell biology, reprograming, cancer and neurogenesis. During embryogenesis in the mouse, it was hypothesized that PRMT5 functions with the master germline determinant BLIMP1 to promote primordial germ cell (PGC) specification. Using a Blimp1-Cre germline conditional knockout, we discovered that Prmt5 has no major role in murine germline specification, or the first global epigenetic reprograming event involving depletion of cytosine methylation from DNA and histone H3 lysine 9 dimethylation from chromatin. Instead, we discovered that PRMT5 functions at the conclusion of PGC reprograming I to promote proliferation, survival and expression of the gonadal germline program as marked by MVH. We show that PRMT5 regulates gene expression by promoting methylation of the Sm spliceosomal proteins and significantly altering the spliced repertoire of RNAs in mammalian embryonic cells and primordial cells.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid25751603,

title = {Genomic analysis of ADAR1 binding and its involvement in multiple RNA processing pathways},

author = {Jae Hoon Bahn and Jaegyoon Ahn and Xianzhi Lin and Qing Zhang and Jae-Hyung Lee and Mete Civelek and Xinshu Xiao},

doi = {10.1038/ncomms7355},

issn = {2041-1723},

year  = {2015},

date = {2015-03-01},

journal = {Nat Commun},

volume = {6},

pages = {6355},

abstract = {Adenosine deaminases acting on RNA (ADARs) are the primary factors underlying adenosine to inosine (A-to-I) editing in metazoans. Here we report the first global study of ADAR1-RNA interaction in human cells using CLIP-seq. A large number of CLIP sites are observed in Alu repeats, consistent with ADAR1's function in RNA editing. Surprisingly, thousands of other CLIP sites are located in non-Alu regions, revealing functional and biophysical targets of ADAR1 in the regulation of alternative 3' UTR usage and miRNA biogenesis. We observe that binding of ADAR1 to 3' UTRs precludes binding by other factors, causing 3' UTR lengthening. Similarly, ADAR1 interacts with DROSHA and DGCR8 in the nucleus and possibly out-competes DGCR8 in primary miRNA binding, which enhances mature miRNA expression. These functions are dependent on ADAR1's editing activity, at least for a subset of targets. Our study unfolds a broad landscape of the functional roles of ADAR1.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid25999984,

title = {Noncoding RNAs in human saliva as potential disease biomarkers},

author = {Xianzhi Lin and Hsien-Chun Lo and David T W Wong and Xinshu Xiao},

doi = {10.3389/fgene.2015.00175},

issn = {1664-8021},

year  = {2015},

date = {2015-01-01},

journal = {Front Genet},

volume = {6},

pages = {175},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid25376581,

title = {The landscape of microRNA, Piwi-interacting RNA, and circular RNA in human saliva},

author = {Jae Hoon Bahn and Qing Zhang and Feng Li and Tak-Ming Chan and Xianzhi Lin and Yong Kim and David T W Wong and Xinshu Xiao},

doi = {10.1373/clinchem.2014.230433},

issn = {1530-8561},

year  = {2015},

date = {2015-01-01},

journal = {Clin Chem},

volume = {61},

number = {1},

pages = {221--230},

abstract = {BACKGROUND: Extracellular RNAs (exRNAs) in human body fluids are emerging as effective biomarkers for detection of diseases. Saliva, as the most accessible and noninvasive body fluid, has been shown to harbor exRNA biomarkers for several human diseases. However, the entire spectrum of exRNA from saliva has not been fully characterized.



METHODS: Using high-throughput RNA sequencing (RNA-Seq), we conducted an in-depth bioinformatic analysis of noncoding RNAs (ncRNAs) in human cell-free saliva (CFS) from healthy individuals, with a focus on microRNAs (miRNAs), piwi-interacting RNAs (piRNAs), and circular RNAs (circRNAs).



RESULTS: Our data demonstrated robust reproducibility of miRNA and piRNA profiles across individuals. Furthermore, individual variability of these salivary RNA species was highly similar to those in other body fluids or cellular samples, despite the direct exposure of saliva to environmental impacts. By comparative analysis of >90 RNA-Seq data sets of different origins, we observed that piRNAs were surprisingly abundant in CFS compared with other body fluid or intracellular samples, with expression levels in CFS comparable to those found in embryonic stem cells and skin cells. Conversely, miRNA expression profiles in CFS were highly similar to those in serum and cerebrospinal fluid. Using a customized bioinformatics method, we identified >400 circRNAs in CFS. These data represent the first global characterization and experimental validation of circRNAs in any type of extracellular body fluid.



CONCLUSIONS: Our study provides a comprehensive landscape of ncRNA species in human saliva that will facilitate further biomarker discoveries and lay a foundation for future studies related to ncRNAs in human saliva.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid25327529,

title = {Regulation of NF-κB signaling by oxidized glycerophospholipid and IL-1β induced miRs-21-3p and -27a-5p in human aortic endothelial cells},

author = {Milagros C Romay and Nam Che and Scott N Becker and Delila Pouldar and Raffi Hagopian and Xinshu Xiao and Aldons J Lusis and Judith A Berliner and Mete Civelek},

doi = {10.1194/jlr.M052670},

issn = {1539-7262},

year  = {2015},

date = {2015-01-01},

journal = {J Lipid Res},

volume = {56},

number = {1},

pages = {38--50},

abstract = {Exposure of endothelial cells (ECs) to agents such as oxidized glycerophospholipids (oxGPs) and cytokines, known to accumulate in atherosclerotic lesions, perturbs the expression of hundreds of genes in ECs involved in inflammatory and other biological processes. We hypothesized that microRNAs (miRNAs) are involved in regulating the inflammatory response in human aortic endothelial cells (HAECs) in response to oxGPs and interleukin 1β (IL-1β). Using next-generation sequencing and RT-quantitative PCR, we characterized the profile of expressed miRNAs in HAECs pre- and postexposure to oxGPs. Using this data, we identified miR-21-3p and miR-27a-5p to be induced 3- to 4-fold in response to oxGP and IL-1β treatment compared with control treatment. Transient overexpression of miR-21-3p and miR-27a-5p resulted in the downregulation of 1,253 genes with 922 genes overlapping between the two miRNAs. Gene Ontology functional enrichment analysis predicted that the two miRNAs were involved in the regulation of nuclear factor κB (NF-κB) signaling. Overexpression of these two miRNAs leads to changes in p65 nuclear translocation. Using 3' untranslated region luciferase assay, we identified 20 genes within the NF-κB signaling cascade as putative targets of miRs-21-3p and -27a-5p, implicating these two miRNAs as modulators of NF-κB signaling in ECs.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid24840202,

title = {Cell type-restricted activity of hnRNPM promotes breast cancer metastasis via regulating alternative splicing},

author = {Yilin Xu and Xin D Gao and Jae-Hyung Lee and Huilin Huang and Haiyan Tan and Jaegyoon Ahn and Lauren M Reinke and Marcus E Peter and Yue Feng and David Gius and Kalliopi P Siziopikou and Junmin Peng and Xinshu Xiao and Chonghui Cheng},

doi = {10.1101/gad.241968.114},

issn = {1549-5477},

year  = {2014},

date = {2014-06-01},

journal = {Genes Dev},

volume = {28},

number = {11},

pages = {1191--1203},

abstract = {Tumor metastasis remains the major cause of cancer-related death, but its molecular basis is still not well understood. Here we uncovered a splicing-mediated pathway that is essential for breast cancer metastasis. We show that the RNA-binding protein heterogeneous nuclear ribonucleoprotein M (hnRNPM) promotes breast cancer metastasis by activating the switch of alternative splicing that occurs during epithelial-mesenchymal transition (EMT). Genome-wide deep sequencing analysis suggests that hnRNPM potentiates TGFβ signaling and identifies CD44 as a key downstream target of hnRNPM. hnRNPM ablation prevents TGFβ-induced EMT and inhibits breast cancer metastasis in mice, whereas enforced expression of the specific CD44 standard (CD44s) splice isoform overrides the loss of hnRNPM and permits EMT and metastasis. Mechanistically, we demonstrate that the ubiquitously expressed hnRNPM acts in a mesenchymal-specific manner to precisely control CD44 splice isoform switching during EMT. This restricted cell-type activity of hnRNPM is achieved by competition with ESRP1, an epithelial splicing regulator that binds to the same cis-regulatory RNA elements as hnRNPM and is repressed during EMT. Importantly, hnRNPM is associated with aggressive breast cancer and correlates with increased CD44s in patient specimens. These findings demonstrate a novel molecular mechanism through which tumor metastasis is endowed by the hnRNPM-mediated splicing program.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid23598527,

title = {Analysis and design of RNA sequencing experiments for identifying RNA editing and other single-nucleotide variants},

author = {Jae-Hyung Lee and Jason K Ang and Xinshu Xiao},

doi = {10.1261/rna.037903.112},

issn = {1469-9001},

year  = {2013},

date = {2013-06-01},

journal = {RNA},

volume = {19},

number = {6},

pages = {725--732},

abstract = {RNA-sequencing (RNA-Seq) technologies hold enormous promise for novel discoveries in genomics and transcriptomics. In the past year, a surge of reports has analyzed RNA-Seq data to gain a global view of the RNA editome. Opposing results have been presented, giving rise to extensive debate surrounding one of the first such studies in which a daunting list of all 12 types of RNA-DNA differences (RDDs) were identified. Although a consensus is forming that some of the initial "paradigm-shifting" results of this study may be questionable, recent reports on this topic differed in terms of the number and relative abundance of each type of RDD. Many outstanding issues exist, most importantly, the choice of bioinformatic approaches. Here we discuss the critical data analysis and experimental design issues of such studies to enable improved systematic investigation of the largely unexplored frontier of single-nucleotide variants in RNA.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid24091402,

title = {Modeling associated protein-DNA pattern discovery with unified scores},

author = {Tak-Ming Chan and Leung-Yau Lo and Ho-Yin Sze-To and Kwong-Sak Leung and Xinshu Xiao and Man-Hon Wong},

doi = {10.1109/TCBB.2013.60},

issn = {1557-9964},

year  = {2013},

date = {2013-01-01},

journal = {IEEE/ACM Trans Comput Biol Bioinform},

volume = {10},

number = {3},

pages = {696--707},

abstract = {Understanding protein-DNA interactions, specifically transcription factor (TF) and transcription factor binding site (TFBS) bindings, is crucial in deciphering gene regulation. The recent associated TF-TFBS pattern discovery combines one-sided motif discovery on both the TF and the TFBS sides. Using sequences only, it identifies the short protein-DNA binding cores available only in high-resolution 3D structures. The discovered patterns lead to promising subtype and disease analysis applications. While the related studies use either association rule mining or existing TFBS annotations, none has proposed any formal unified (both-sided) model to prioritize the top verifiable associated patterns. We propose the unified scores and develop an effective pipeline for associated TF-TFBS pattern discovery. Our stringent instance-level evaluations show that the patterns with the top unified scores match with the binding cores in 3D structures considerably better than the previous works, where up to 90 percent of the top 20 scored patterns are verified. We also introduce extended verification from literature surveys, where the high unified scores correspond to even higher verification percentage. The top scored patterns are confirmed to match the known WRKY binding cores with no available 3D structures and agree well with the top binding affinities of in vivo experiments.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid23241926,

title = {A complex network of factors with overlapping affinities represses splicing through intronic elements},

author = {Yang Wang and Xinshu Xiao and Jianming Zhang and Rajarshi Choudhury and Alex Robertson and Kai Li and Meng Ma and Christopher B Burge and Zefeng Wang},

doi = {10.1038/nsmb.2459},

issn = {1545-9985},

year  = {2013},

date = {2013-01-01},

journal = {Nat Struct Mol Biol},

volume = {20},

number = {1},

pages = {36--45},

abstract = {To better understand splicing regulation, we used a cell-based screen to identify ten diverse motifs that inhibit splicing from introns. Motifs were validated in another human cell type and gene context, and their presence correlated with in vivo splicing changes. All motifs exhibited exonic splicing enhancer or silencer activity, and grouping these motifs according to their distributions yielded clusters with distinct patterns of context-dependent activity. Candidate regulatory factors associated with each motif were identified, to recover 24 known and new splicing regulators. Specific domains in selected factors were sufficient to confer intronic-splicing-silencer activity. Many factors bound multiple distinct motifs with similar affinity, and all motifs were recognized by multiple factors, which revealed a complex overlapping network of protein-RNA interactions. This arrangement enables individual cis elements to function differently in distinct cellular contexts, depending on the spectrum of regulatory factors present.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid22983564,

title = {Intronic splicing enhancers, cognate splicing factors and context-dependent regulation rules},

author = {Yang Wang and Meng Ma and Xinshu Xiao and Zefeng Wang},

doi = {10.1038/nsmb.2377},

issn = {1545-9985},

year  = {2012},

date = {2012-10-01},

journal = {Nat Struct Mol Biol},

volume = {19},

number = {10},

pages = {1044--1052},

abstract = {Most human genes produce multiple splicing isoforms with distinct functions. To systematically understand splicing regulation, we conducted an unbiased screen and identified >100 intronic splicing enhancers (ISEs), clustered by sequence similarity. All ISEs functioned in multiple cell types and in heterologous introns, and patterns of distribution and conservation across pre-mRNA regions were similar to those of exonic splicing silencers. Consistently, all ISEs inhibited use of splice sites from exons. Putative trans-factors of each ISE group were identified and validated. Five distinct groups were recognized by hnRNP H and hnRNP F, whose C-terminal domains were sufficient to render context-dependent activities of ISEs. The sixth group was controlled by factors that either activate or suppress splicing. We provide a comprehensive picture of general ISE activities and suggest new models of how single elements can function oppositely, depending on locations and binding factors.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid22467206,

title = {Identification of allele-specific alternative mRNA processing via transcriptome sequencing},

author = {Gang Li and Jae Hoon Bahn and Jae-Hyung Lee and Guangdun Peng and Zugen Chen and Stanley F Nelson and Xinshu Xiao},

doi = {10.1093/nar/gks280},

issn = {1362-4962},

year  = {2012},

date = {2012-07-01},

journal = {Nucleic Acids Res},

volume = {40},

number = {13},

pages = {e104},

abstract = {Establishing the functional roles of genetic variants remains a significant challenge in the post-genomic era. Here, we present a method, allele-specific alternative mRNA processing (ASARP), to identify genetically influenced mRNA processing events using transcriptome sequencing (RNA-Seq) data. The method examines RNA-Seq data at both single-nucleotide and whole-gene/isoform levels to identify allele-specific expression (ASE) and existence of allele-specific regulation of mRNA processing. We applied the methods to data obtained from the human glioblastoma cell line U87MG and primary breast cancer tissues and found that 26-45% of all genes with sufficient read coverage demonstrated ASE, with significant overlap between the two cell types. Our methods predicted potential mechanisms underlying ASE due to regulations affecting either whole-gene-level expression or alternative mRNA processing, including alternative splicing, alternative polyadenylation and alternative transcriptional initiation. Allele-specific alternative splicing and alternative polyadenylation may explain ASE in hundreds of genes in each cell type. Reporter studies following these predictions identified the causal single nucleotide variants (SNVs) for several allele-specific alternative splicing events. Finally, many genes identified in our study were also reported as disease/phenotype-associated genes in genome-wide association studies. Future applications of our approach may provide ample insights for a better understanding of the genetic basis of gene regulation underlying phenotypic diversity and disease mechanisms.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid22456266,

title = {The cardiotonic steroid digitoxin regulates alternative splicing through depletion of the splicing factors SRSF3 and TRA2B},

author = {Erik S Anderson and Chia-Ho Lin and Xinshu Xiao and Peter Stoilov and Christopher B Burge and Douglas L Black},

doi = {10.1261/rna.032912.112},

issn = {1469-9001},

year  = {2012},

date = {2012-05-01},

journal = {RNA},

volume = {18},

number = {5},

pages = {1041--1049},

abstract = {Modulation of alternative pre-mRNA splicing is a potential approach to therapeutic targeting for a variety of human diseases. We investigated the mechanism by which digitoxin, a member of the cardiotonic steroid class of drugs, regulates alternative splicing. Transcriptome-wide analysis identified a large set of alternative splicing events that change after digitoxin treatment. Within and adjacent to these regulated exons, we identified enrichment of potential binding sites for the splicing factors SRp20 (SRSF3/SFRS3) and Tra2-β (SFRS10/TRA2B). We further find that both of these proteins are depleted from cells by digitoxin treatment. Characterization of SRp20 and Tra2-β splicing targets revealed that many, but not all, digitoxin-induced splicing changes can be attributed to the depletion of one or both of these factors. Re-expression of SRp20 or Tra2-β after digitoxin treatment restores normal splicing of their targets, indicating that the digitoxin effect is directly due to these factors. These results demonstrate that cardiotonic steroids, long prescribed in the clinical treatment of heart failure, have broad effects on the cellular transcriptome through these and likely other RNA binding proteins. The approach described here can be used to identify targets of other potential therapeutics that act as alternative splicing modulators.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid22438865,

title = {Identification of vascular and hematopoietic genes downstream of etsrp by deep sequencing in zebrafish},

author = {Gustavo Gomez and Jae-Hyung Lee and Matthew B Veldman and Jing Lu and Xinshu Xiao and Shuo Lin},

doi = {10.1371/journal.pone.0031658},

issn = {1932-6203},

year  = {2012},

date = {2012-01-01},

journal = {PLoS One},

volume = {7},

number = {3},

pages = {e31658},

abstract = {The transcription factor etsrp/Er71/Etv2 is a master control gene for vasculogenesis in all species studied to date. It is also required for hematopoiesis in zebrafish and mice. Several novel genes expressed in vasculature have been identified through transcriptional profiling of zebrafish embryos overexpressing etsrp by microarrays. Here we re-examined this transcriptional profile by Illumina RNA-sequencing technology, revealing a substantially increased number of candidate genes regulated by etsrp. Expression studies of 50 selected candidate genes from this dataset resulted in the identification of 39 new genes that are expressed in vascular cells. Regulation of these genes by etsrp was confirmed by their ectopic induction in etsrp overexpressing and decreased expression in etsrp deficient embryos. Our studies demonstrate the effectiveness of the RNA-sequencing technology to identify biologically relevant genes in zebrfish and produced a comprehensive profile of genes previously unexplored in vascular endothelial cell biology.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid21960545,

title = {Accurate identification of A-to-I RNA editing in human by transcriptome sequencing},

author = {Jae Hoon Bahn and Jae-Hyung Lee and Gang Li and Christopher Greer and Guangdun Peng and Xinshu Xiao},

doi = {10.1101/gr.124107.111},

issn = {1549-5469},

year  = {2012},

date = {2012-01-01},

journal = {Genome Res},

volume = {22},

number = {1},

pages = {142--150},

abstract = {RNA editing enhances the diversity of gene products at the post-transcriptional level. Approaches for genome-wide identification of RNA editing face two main challenges: separating true editing sites from false discoveries and accurate estimation of editing levels. We developed an approach to analyze transcriptome sequencing data (RNA-seq) for global identification of RNA editing in cells for which whole-genome sequencing data are available. We applied the method to analyze RNA-seq data of a human glioblastoma cell line, U87MG. Around 10,000 DNA-RNA differences were identified, the majority being putative A-to-I editing sites. These predicted A-to-I events were associated with a low false-discovery rate (∼5%). Moreover, the estimated editing levels from RNA-seq correlated well with those based on traditional clonal sequencing. Our results further facilitated unbiased characterization of the sequence and evolutionary features flanking predicted A-to-I editing sites and discovery of a conserved RNA structural motif that may be functionally relevant to editing. Genes with predicted A-to-I editing were significantly enriched with those known to be involved in cancer, supporting the potential importance of cancer-specific RNA editing. A similar profile of DNA-RNA differences as in U87MG was predicted for another RNA-seq data set obtained from primary breast cancer samples. Remarkably, significant overlap exists between the putative editing sites of the two transcriptomes despite their difference in cell type, cancer type, and genomic backgrounds. Our approach enabled de novo identification of the RNA editome, which sets the stage for further mechanistic studies of this important step of post-transcriptional regulation.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid22034492,

title = {Analysis of transcriptome complexity through RNA sequencing in normal and failing murine hearts},

author = {Jae-Hyung Lee and Chen Gao and Guangdun Peng and Christopher Greer and Shuxun Ren and Yibin Wang and Xinshu Xiao},

doi = {10.1161/CIRCRESAHA.111.249433},

issn = {1524-4571},

year  = {2011},

date = {2011-12-01},

journal = {Circ Res},

volume = {109},

number = {12},

pages = {1332--1341},

abstract = {RATIONALE: Accurate and comprehensive de novo transcriptome profiling in heart is a central issue to better understand cardiac physiology and diseases. Although significant progress has been made in genome-wide profiling for quantitative changes in cardiac gene expression, current knowledge offers limited insights to the total complexity in cardiac transcriptome at individual exon level.



OBJECTIVE: To develop more robust bioinformatic approaches to analyze high-throughput RNA sequencing (RNA-Seq) data, with the focus on the investigation of transcriptome complexity at individual exon and transcript levels.



METHODS AND RESULTS: In addition to overall gene expression analysis, the methods developed in this study were used to analyze RNA-Seq data with respect to individual transcript isoforms, novel spliced exons, novel alternative terminal exons, novel transcript clusters (ie, novel genes), and long noncoding RNA genes. We applied these approaches to RNA-Seq data obtained from mouse hearts after pressure-overload-induced by transaortic constriction. Based on experimental validations, analyses of the features of the identified exons/transcripts, and expression analyses including previously published RNA-Seq data, we demonstrate that the methods are highly effective in detecting and quantifying individual exons and transcripts. Novel insights inferred from the examined aspects of the cardiac transcriptome open ways to further experimental investigations.



CONCLUSIONS: Our work provided a comprehensive set of methods to analyze mouse cardiac transcriptome complexity at individual exon and transcript levels. Applications of the methods may infer important new insights to gene regulation in normal and disease hearts in terms of exon utilization and potential involvement of novel components of cardiac transcriptome.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid20209111,

title = {Detection of two distinct forms of apoC-I in great apes},

author = {Donald L Puppione and Christopher M Ryan and Sara Bassilian and Puneet Souda and Xinshu Xiao and Oliver A Ryder and Julian P Whitelegge},

doi = {10.1016/j.cbd.2009.12.003},

issn = {1878-0407},

year  = {2010},

date = {2010-03-01},

journal = {Comp Biochem Physiol Part D Genomics Proteomics},

volume = {5},

number = {1},

pages = {73--79},

abstract = {ApoC-I, the smallest of the soluble apolipoproteins, associates with both TG-rich lipoproteins and HDL. Mass spectral analyses of human apoC-I previously had demonstrated that in the circulation there are two forms, either a 57 amino acid protein or a 55 amino acid protein, due to the loss of two amino acids from the N-terminus. In our analyses of the apolipoproteins of the other great apes by mass spectrometry, four forms of apoC-I were detected. Two of these showed a high degree of identity to the mature and truncated forms of human apoC-I. The other two were homologous to the virtual protein and its truncated form that are encoded by a human pseudogene. In humans, the genes for apoC-I and its pseudogene are located on chromosome 19, the pseudogene being 2.5 kb downstream from the apoC-I gene. Based on the similarity between the apoC-I gene and the pseudogene, it has been concluded that the latter arose from the former as a result of gene duplication approximately 35 million years ago. Interestingly, the virtual protein encoded by the pseudogene is acidic, not basic like apoC-I. In the chimpanzee, there also are two genes for apoC-I, the one upstream encodes a basic protein and the downstream gene, rather than being a pseudogene, encodes an acidic protein (P86336). In addition to reporting on the molecular masses of great ape apoC-I, we were able to clearly demonstrate by "Top-down" sequencing that the acidic form arose from a separate gene. In our analyses, we have measured the molecular masses of apoC-I associated with the HDL of the following great apes: bonobo (Pan paniscus), chimpanzee (Pan troglodytes), and the Sumatran orangutan (Pongo abelii). Genomic variations in chromosome 19 among great apes, baboons and macaques as they relate to both genes for apoC-I and the pseudogene are compared and discussed.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid20836047,

title = {Systems analysis of alternative splicing and its regulation},

author = {Xinshu Xiao and Jae-Hyung Lee},

doi = {10.1002/wsbm.84},

issn = {1939-005X},

year  = {2010},

date = {2010-01-01},

journal = {Wiley Interdiscip Rev Syst Biol Med},

volume = {2},

number = {5},

pages = {550--565},

abstract = {Alternative splicing (AS) has emerged as a key mechanism that accounts for gene expression diversity in metazoan organisms. Splicing is tightly regulated by a repertoire of RNA and protein factors and RNA sequence elements that function in a cooperative manner. Systems-level experimental and computational approaches have been instrumental in establishing comprehensive profiles of transcript variants generated by AS. In addition, systems biology approaches are starting to define how combinatorial splicing regulation shapes the complex splicing phenotypes observed in different tissue types and developmental stages and under different conditions. Here, we review recent progress in these areas.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid19749754,

title = {Splice site strength-dependent activity and genetic buffering by poly-G runs},

author = {Xinshu Xiao and Zefeng Wang and Minyoung Jang and Razvan Nutiu and Eric T Wang and Christopher B Burge},

doi = {10.1038/nsmb.1661},

issn = {1545-9985},

year  = {2009},

date = {2009-10-01},

journal = {Nat Struct Mol Biol},

volume = {16},

number = {10},

pages = {1094--1100},

abstract = {Pre-mRNA splicing is regulated through the combinatorial activity of RNA motifs, including splice sites and splicing regulatory elements. Here we show that the activity of the G-run (polyguanine sequence) class of splicing enhancer elements is approximately 4-fold higher when adjacent to intermediate strength 5' splice sites (ss) than when adjacent to weak 5' ss, and approximately 1.3-fold higher relative to strong 5' ss. We observed this dependence on 5' ss strength in both splicing reporters and in global microarray and mRNA-Seq analyses of splicing changes following RNA interference against heterogeneous nuclear ribonucleoprotein (hnRNP) H, which cross-linked to G-runs adjacent to many regulated exons. An exon's responsiveness to changes in hnRNP H levels therefore depends in a complex way on G-run abundance and 5' ss strength. This pattern of activity enables G-runs and hnRNP H to buffer the effects of 5' ss mutations, augmenting both the frequency of 5' ss polymorphism and the evolution of new splicing patterns. Certain other splicing factors may function similarly.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid19075228,

title = {A postnatal switch of CELF and MBNL proteins reprograms alternative splicing in the developing heart},

author = {Auinash Kalsotra and Xinshu Xiao and Amanda J Ward and John C Castle and Jason M Johnson and Christopher B Burge and Thomas A Cooper},

doi = {10.1073/pnas.0809045105},

issn = {1091-6490},

year  = {2008},

date = {2008-12-01},

journal = {Proc Natl Acad Sci U S A},

volume = {105},

number = {51},

pages = {20333--20338},

abstract = {From a large-scale screen using splicing microarrays and RT-PCR, we identified 63 alternative splicing (AS) events that are coordinated in 3 distinct temporal patterns during mouse heart development. More than half of these splicing transitions are evolutionarily conserved between mouse and chicken. Computational analysis of the introns flanking these splicing events identified enriched and conserved motifs including binding sites for CUGBP and ETR-3-like factors (CELF), muscleblind-like (MBNL) and Fox proteins. We show that CELF proteins are down-regulated >10-fold during heart development, and MBNL1 protein is concomitantly up-regulated nearly 4-fold. Using transgenic and knockout mice, we show that reproducing the embryonic expression patterns for CUGBP1 and MBNL1 in adult heart induces the embryonic splicing patterns for more than half of the developmentally regulated AS transitions. These findings indicate that CELF and MBNL proteins are determinative for a large subset of splicing transitions that occur during postnatal heart development.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid17998536,

title = {Coevolutionary networks of splicing cis-regulatory elements},

author = {Xinshu Xiao and Zefeng Wang and Minyoung Jang and Christopher B Burge},

doi = {10.1073/pnas.0707349104},

issn = {1091-6490},

year  = {2007},

date = {2007-11-01},

journal = {Proc Natl Acad Sci U S A},

volume = {104},

number = {47},

pages = {18583--18588},

abstract = {Accurate and efficient splicing of eukaryotic pre-mRNAs requires recognition by trans-acting factors of a complex array of cis-acting RNA elements. Here, we developed a generalized Bayesian network to model the coevolution of splicing cis elements in diverse eukaryotic taxa. Cross-exon but not cross-intron compensatory interactions between the 5' splice site (5'ss) and 3' splice site (3'ss) were observed in human/mouse, indicating that the exon is the primary evolutionary unit in mammals. Studied plants, fungi, and invertebrates exhibited exclusively cross-intron interactions, suggesting that intron definition drives evolution in these organisms. In mammals, 5'ss strength and the strength of several classes of exonic splicing silencers (ESSs) evolved in a correlated way, whereas specific exonic splicing enhancers (ESEs), including motifs associated with hTra2, SRp55, and SRp20, evolved in a compensatory manner relative to the 5'ss and 3'ss. Interactions between specific ESS or ESE motifs were not observed, suggesting that elements bound by different factors are not commonly interchangeable. Thus, the splicing elements defining exons coevolve in a way that preserves overall exon strength, allowing specific elements to substitute for loss or weakening of others.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid17978102,

title = {Global analysis of alternative splicing differences between humans and chimpanzees},

author = {John A Calarco and Yi Xing and Mario Cáceres and Joseph P Calarco and Xinshu Xiao and Qun Pan and Christopher Lee and Todd M Preuss and Benjamin J Blencowe},

doi = {10.1101/gad.1606907},

issn = {0890-9369},

year  = {2007},

date = {2007-11-01},

journal = {Genes Dev},

volume = {21},

number = {22},

pages = {2963--2975},

abstract = {Alternative splicing is a powerful mechanism affording extensive proteomic and regulatory diversity from a limited repertoire of genes. However, the extent to which alternative splicing has contributed to the evolution of primate species-specific characteristics has not been assessed previously. Using comparative genomics and quantitative microarray profiling, we performed the first global analysis of alternative splicing differences between humans and chimpanzees. Surprisingly, 6%-8% of profiled orthologous exons display pronounced splicing level differences in the corresponding tissues from the two species. Little overlap is observed between the genes associated with alternative splicing differences and the genes that display steady-state transcript level differences, indicating that these layers of regulation have evolved rapidly to affect distinct subsets of genes in humans and chimpanzees. The alternative splicing differences we detected are predicted to affect diverse functions including gene expression, signal transduction, cell death, immune defense, and susceptibility to diseases. Differences in expression at the protein level of the major splice variant of Glutathione S-transferase omega-2 (GSTO2), which functions in the protection against oxidative stress and is associated with human aging-related diseases, suggests that this enzyme is less active in human cells compared with chimpanzee cells. The results of this study thus support an important role for alternative splicing in establishing differences between humans and chimpanzees.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid17121466,

title = {Inference of splicing regulatory activities by sequence neighborhood analysis},

author = {Michael B Stadler and Noam Shomron and Gene W Yeo and Aniket Schneider and Xinshu Xiao and Christopher B Burge},

doi = {10.1371/journal.pgen.0020191},

issn = {1553-7404},

year  = {2006},

date = {2006-11-01},

journal = {PLoS Genet},

volume = {2},

number = {11},

pages = {e191},

abstract = {Sequence-specific recognition of nucleic-acid motifs is critical to many cellular processes. We have developed a new and general method called Neighborhood Inference (NI) that predicts sequences with activity in regulating a biochemical process based on the local density of known sites in sequence space. Applied to the problem of RNA splicing regulation, NI was used to predict hundreds of new exonic splicing enhancer (ESE) and silencer (ESS) hexanucleotides from known human ESEs and ESSs. These predictions were supported by cross-validation analysis, by analysis of published splicing regulatory activity data, by sequence-conservation analysis, and by measurement of the splicing regulatory activity of 24 novel predicted ESEs, ESSs, and neutral sequences using an in vivo splicing reporter assay. These results demonstrate the ability of NI to accurately predict splicing regulatory activity and show that the scope of exonic splicing regulatory elements is substantially larger than previously anticipated. Analysis of orthologous exons in four mammals showed that the NI score of ESEs, a measure of function, is much more highly conserved above background than ESE primary sequence. This observation indicates a high degree of selection for ESE activity in mammalian exons, with surprisingly frequent interchangeability between ESE sequences.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid16916086,

title = {A weighted-principal component regression method for the identification of physiologic systems},

author = {Xinshu Xiao and Ramakrishna Mukkamala and Richard J Cohen},

doi = {10.1109/TBME.2006.876623},

issn = {0018-9294},

year  = {2006},

date = {2006-08-01},

journal = {IEEE Trans Biomed Eng},

volume = {53},

number = {8},

pages = {1521--1530},

abstract = {We introduce a system identification method based on weighted-principal component regression (WPCR). This approach aims to identify the dynamics in a linear time-invariant (LTI) model which may represent a resting physiologic system. It tackles the time-domain system identification problem by considering, asymptotically, frequency information inherent in the given data. By including in the model only dominant frequency components of the input signal(s), this method enables construction of candidate models that are specific to the data and facilitates a reduction in parameter estimation error when the signals are colored (as are most physiologic signals). Additionally, this method allows incorporation of preknowledge about the system through a weighting scheme. We present the method in the context of single-input and multi-input single-output systems operating in open-loop and closed-loop. In each scenario, we compare the WPCR method with conventional approaches and approaches that also build data-specific candidate models. Through both simulated and experimental data, we show that the WPCR method enables more accurate identification of the system impulse response function than the other methods when the input signal(s) is colored.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid16797197,

title = {General and specific functions of exonic splicing silencers in splicing control},

author = {Zefeng Wang and Xinshu Xiao and Eric Van Nostrand and Christopher B Burge},

doi = {10.1016/j.molcel.2006.05.018},

issn = {1097-2765},

year  = {2006},

date = {2006-07-01},

journal = {Mol Cell},

volume = {23},

number = {1},

pages = {61--70},

abstract = {Correct splice site recognition is critical in pre-mRNA splicing. We find that almost all of a diverse panel of exonic splicing silencer (ESS) elements alter splice site choice when placed between competing sites, consistently inhibiting use of intron-proximal 5' and 3' splice sites. Supporting a general role for ESSs in splice site definition, we found that ESSs are both abundant and highly conserved between alternative splice site pairs and that mutation of ESSs located between natural alternative splice site pairs consistently shifted splicing toward the intron-proximal site. Some exonic splicing enhancers (ESEs) promoted use of intron-proximal 5' splice sites, and tethering of hnRNP A1 and SF2/ASF proteins between competing splice sites mimicked the effects of ESS and ESE elements, respectively. Further, we observed that specific subsets of ESSs had distinct effects on a multifunctional intron retention reporter and that one of these subsets is likely preferred for regulation of endogenous intron retention events. Together, our findings provide a comprehensive picture of the functions of ESSs in the control of diverse types of splicing decisions.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid17152857,

title = {Why is orthostatic tolerance lower in women than in men? Renal and cardiovascular responses to simulated microgravity and the role of midodrine},

author = {S Marlene Grenon and Xinshu Xiao and Shelley Hurwitz and Natalie Sheynberg and Christine Kim and Ellen W Seely and Richard J Cohen and Gordon H Williams},

doi = {10.2310/6650.2006.05064},

issn = {1081-5589},

year  = {2006},

date = {2006-05-01},

journal = {J Investig Med},

volume = {54},

number = {4},

pages = {180--190},

abstract = {BACKGROUND: Exposure to microgravity induces cardiovascular deconditioning, manifested by orthostatic intolerance (OI). We assessed the renal, cardioendocrine, and cardiovascular responses of women and men to simulated microgravity to examine the impact of gender on OI.



METHODS: Fifteen healthy female and 14 healthy male subjects were given a constant diet for 3 to 5 days, after which they underwent a tilt-stand test (pre-TST) and began 14 to 16 days of head-down tilt bed rest (HDTB), followed by a repeat tilt-stand test (post-TST). Female subjects began HDTB so that the post-TST was at the same time in their menstrual cycle as their pre-TST. Twenty-four-hour urine collections (daily), hormonal measurements, plethysmography, and cardiovascular system identification were performed.



RESULTS: The times to presyncope were significantly different for men and women before (p= .005) and after HDTB (p= .001), with all of the women but only 50% of the men experiencing presyncope during the pre-TST (p= .002) and all of the women but only 64% of the men experiencing presyncope during the post-TST. At baseline, the following differences between women and men were observed: women had higher serum aldosterone levels (p = .02), higher parasympathetic responsiveness (p = .01), lower sympathetic responsiveness (p = .05), and lower venous compliance (p = .05). Several parameters changed with HDTB in both men and women. In a double-blinded randomized trial, midodrine (5 mg orally) or placebo given to female subjects 1 hour before post-TST was ineffective in preventing 01.



CONCLUSION: In conclusion, the frequency of OI is higher in women than in men and is not modified by midodrine at the dose used. This increased susceptibility is likely secondary to intrinsic basal differences in the activity of volume-mediated parasympathetic and adrenergic systems and in venous tone. Thus, approaches to reduce OI in women are likely to differ from those effective in men.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid16315396,

title = {Bed rest effects on human calf hemodynamics and orthostatic intolerance: a model-based analysis},

author = {Xinshu Xiao and S Marlene Grenon and Christine Kim and Natalie Sheynberg and Shelly Hurwitz and Gordon H Williams and Richard J Cohen},

issn = {0095-6562},

year  = {2005},

date = {2005-11-01},

journal = {Aviat Space Environ Med},

volume = {76},

number = {11},

pages = {1037--1045},

abstract = {INTRODUCTION: Microgravity-induced orthostatic intolerance continues to be a primary problem after space missions. Its etiology remains uncertain despite significant research efforts over the past years. We hypothesized that calf hemodynamic parameters (compliance and resistance) are significantly affected by 14 to 16-d head-down bed rest (simulated microgravity), and their alterations play a role in the pathogenesis of orthostatic intolerance (OI) following bed rest.



METHODS: To estimate these parameters, we developed a model-based approach to quantitatively simulate calf vascular response to venous occlusion, which only necessitates measurement of plethysmography data. In this study, plethysmography data were obtained from 29 subjects before and after 14-16 d of head-down bed rest. The subjects also underwent a tilt/stand test before and after bed rest.



RESULTS: Statistical analyses demonstrated an increase in calf compliance (1.87 +/- 0.08, mean +/- SE, pre-bed rest; 2.16 +/- 0.10, end-bed rest) but no significant change in vascular resistance following bed rest. Compared with the tilt-intolerant subjects, those who were tilt-tolerant before bed rest had significantly higher calf compliance [2.00 +/- 0.09 (tolerant); 1.58 +/- 0.09 (intolerant)] and higher vascular resistance [7.79 +/- 0.18 (tolerant); 6.91 +/- 0.40 (intolerant)]. After bed rest, no such difference was detected.



DISCUSSION: Based on these results, we validated the hypothesis that, instead of causing orthostatic intolerance, higher calf compliance before bed rest leads to recruitment of compensatory mechanisms (validated by the enhanced vascular resistance during venous occlusion) for a better toleration of orthostatic stress. With the absence of orthostatic challenge during bed rest, the difference in calf hemodynamic parameters is attenuated between the tilt-tolerant and tilt-intolerant groups.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid16029389,

title = {Simulated microgravity induces microvolt T wave alternans},

author = {S Marlene Grenon and Xinshu Xiao and Shelley Hurwitz and Craig D Ramsdell and Natalie Sheynberg and Christine Kim and Gordon H Williams and Richard J Cohen},

doi = {10.1111/j.1542-474X.2005.00654.x},

issn = {1082-720X},

year  = {2005},

date = {2005-07-01},

journal = {Ann Noninvasive Electrocardiol},

volume = {10},

number = {3},

pages = {363--370},

abstract = {BACKGROUND: There are numerous anecdotal reports of ventricular arrhythmias during spaceflight; however, it is not known whether spaceflight or microgravity systematically increases the risk of cardiac dysrhythmias. Microvolt T wave alternans (MTWA) testing compares favorably with other noninvasive risk stratifiers and invasive electrophysiological testing in patients as a predictor of sudden cardiac death, ventricular tachycardia, and ventricular fibrillation. We hypothesized that simulated microgravity leads to an increase in MTWA.



METHODS: Twenty-four healthy male subjects underwent 9 to 16 days of head-down tilt bed rest (HDTB). MTWA was measured before and after the bed rest period during bicycle exercise stress. For the purposes of this study, we defined MTWA outcome to be positive if sustained MTWA was present with an onset heart rate


RESULTS: Before HDTB, 17% of the subjects were MTWA positive [95%CI: (0.6%, 37%)]; after HDTB, 42% of the subjects were MTWA positive [95%CI: (23%, 63%)] (P=0.03). The subjects who were MTWA positive after HDTB compared with MTWA negative subjects had an increased versus decreased sympathetic responsiveness (P=0.03) and serum norepinephrine levels (P=0.05), and a trend toward higher potassium excretion (P=0.06) after bed rest compared to baseline.



CONCLUSIONS: HDTB leads to an increase in MTWA, providing the first evidence that simulated microgravity has a measurable effect on electrical repolarization processes. Possible contributing factors include loss in potassium and changes in sympathetic function.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid15798289,

title = {System identification: a multi-signal approach for probing neural cardiovascular regulation},

author = {Xinshu Xiao and Thomas J Mullen and Ramakrishna Mukkamala},

doi = {10.1088/0967-3334/26/3/R01},

issn = {0967-3334},

year  = {2005},

date = {2005-06-01},

journal = {Physiol Meas},

volume = {26},

number = {3},

pages = {R41--R71},

abstract = {Short-term, beat-to-beat cardiovascular variability reflects the dynamic interplay between ongoing perturbations to the circulation and the compensatory response of neurally mediated regulatory mechanisms. This physiologic information may be deciphered from the subtle, beat-to-beat variations by using digital signal processing techniques. While single signal analysis techniques (e.g., power spectral analysis) may be employed to quantify the variability itself, the multi-signal approach of system identification permits the dynamic characterization of the neural regulatory mechanisms responsible for coupling the variability between signals. In this review, we provide an overview of applications of system identification to beat-to-beat variability for the quantitative characterization of cardiovascular regulatory mechanisms. After briefly summarizing the history of the field and basic principles, we take a didactic approach to describe the practice of system identification in the context of probing neural cardiovascular regulation. We then review studies in the literature over the past two decades that have applied system identification for characterizing the dynamical properties of the sinoatrial node, respiratory sinus arrhythmia, and the baroreflex control of sympathetic nerve activity, heart rate and total peripheral resistance. Based on this literature review, we conclude by advocating specific methods of practice and that future research should focus on nonlinear and time-varying behaviors, validation of identification methods, and less understood neural regulatory mechanisms. Ultimately, we hope that this review stimulates such future investigations by both new and experienced system identification researchers.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid15759574,

title = {A model order selection criterion with applications to cardio-respiratory-renal systems},

author = {Xinshu Xiao and Ying Li and Ramakrishna Mukkamala},

doi = {10.1109/TBME.2004.843285},

issn = {0018-9294},

year  = {2005},

date = {2005-03-01},

journal = {IEEE Trans Biomed Eng},

volume = {52},

number = {3},

pages = {445--453},

abstract = {We introduce a model order selection criterion called signal prediction error (SPE) for the identification of a linear regression model, which can be an adequate representation of a resting physiologic system. SPE is an estimate of the prediction error variance due only to model estimation error and not unobserved noise, which distinguishes it from the widely used final prediction error (FPE). We then present a theoretical analysis of SPE, which predicts that its ability to select correctly the model order is more dependent on the signal-to-noise ratio (SNR) and less dependent on the number of data samples available for analysis. We next propose a heuristic procedure based on SPE (called SPE(D)) to improve its robustness to SNR levels. We then demonstrate, through simulated physiologic data at high SNR levels, that SPE will be equivalent to consistent model order selection criteria for long data records but will become superior to FPE and other model order selection criteria as the size of the data record decreases. The simulated data results also show that SPE(D) is indeed a significant improvement over SPE in terms of robustness to SNR. Finally, we demonstrate the applicability of SPE and SPE(D) to actual cardio-respiratory-renal data.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid15810494,

title = {Readaptation from simulated microgravity as a stimulus for improved orthostatic tolerance: role of the renal, cardioendocrine, and cardiovascular systems},

author = {S Marlene Grenon and Shelley Hurwitz and Xinshu Xiao and Natalie Sheynberg and Craig D Ramsdell and Christine Kim and Richard J Cohen and Gordon H Williams},

doi = {10.2310/6650.2005.00203},

issn = {1081-5589},

year  = {2005},

date = {2005-03-01},

journal = {J Investig Med},

volume = {53},

number = {2},

pages = {82--91},

abstract = {BACKGROUND: Microgravity and simulated microgravity (SM) lead to important changes in orthostatic tolerance (OT), the autonomic nervous system (ANS), and the volume-regulating systems. After one is exposed to microgravity or SM, a period of readaptation to gravity is known to take place, but it is not certain if orthostatic function returns to baseline within the initial recovery and what mechanisms are involved. We hypothesized that after a period of recovery, OT, ANS, and volume-regulating systems would return to pre-SM levels.



METHODS: To test this hypothesis, 24 healthy men were placed on a constant diet for 3 to 5 days, after which a tilt-stand test (pre-TST) was performed. The TST was repeated after 14 to 16 days of head-down tilt bed rest (HDTB) (post-TST) and a 3-day period of recovery (rec-TST), at which times measurements of renal, cardioendocrine, and cardiovascular systems were conducted.



RESULTS: Presyncope occurred in 46% of subjects pre-TST, in 72% post-TST, and in 23% during rec-TST. OT was significantly better during the recovery period than at baseline (p = .03). There was a significant decrease in urinary sodium and potassium excretion, along with a decrease in plasma renin activity and serum and urine aldosterone compared with baseline. Serum norepinephrine and sympathetic responsiveness remained below baseline values.



CONCLUSION: In summary, OT improved compared with baseline after a period of readaptation. Retention of electrolytes (sodium, potassium) could be involved. These findings indicate that recovery after SM is not simply a gradual return to baseline values but is instead a dynamic process reflecting interaction of multiple regulatory systems.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid15234956,

title = {Sleep restriction does not affect orthostatic tolerance in the simulated microgravity environment},

author = {S Marlene Grenon and Shelley Hurwitz and Natalie Sheynberg and Xinshu Xiao and Brad Judson and Craig D Ramsdell and Christine Kim and Richard J Cohen and Gordon H Williams},

doi = {10.1152/japplphysiol.00328.2004},

issn = {8750-7587},

year  = {2004},

date = {2004-11-01},

journal = {J Appl Physiol (1985)},

volume = {97},

number = {5},

pages = {1660--1666},

abstract = {Orthostatic intolerance (OI) is a major problem following spaceflight, and, during flight, astronauts also experience sleep restriction. We hypothesized that sleep restriction will compound the risk and severity of OI following simulated microgravity and exaggerate the renal, cardioendocrine, and cardiovascular adaptive responses to it. Nineteen healthy men were equilibrated on a constant diet, after which they underwent a tilt-stand test. They then completed 14-16 days of simulated microgravity [head-down tilt bed rest (HDTB)], followed by repeat tilt-stand test. During HDTB, 11 subjects were assigned to an 8-h sleep protocol (non-sleep restricted), and 8 were assigned to a sleep-restricted protocol with 6 h of sleep per night. During various phases, the following were performed: 24-h urine collections, hormonal measurements, and cardiovascular system identification. Development of presyncope or syncope defined OI. There was a significant decrease in time free of OI (P = 0.02) and an increase in OI occurrence (P = 0.06) after HDTB among all subjects. However, the increase in OI occurrence did not differ significantly between the two groups (P = 0.60). The two groups also experienced similar physiological changes with HDTB (initial increase in sodium excretion; increased excretion of potassium at the end of HDTB; increase in plasma renin activity secretion without a change in serum or urine aldosterone). No significant change in autonomic function or catecholamines was noted. Simulated microgravity leads to increased OI, and sleep restriction does not additively worsen OI in simulated microgravity. Furthermore, conditions of sleep restriction and nonsleep restriction are similar with respect to renal, cardioendocrine, and cardiovascular responses to simulated microgravity.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid15075309,

title = {Role of individual predisposition in orthostatic intolerance before and after simulated microgravity},

author = {S M Grenon and S Hurwitz and N Sheynberg and X Xiao and C D Ramsdell and C L Mai and C Kim and R J Cohen and G H Williams},

doi = {10.1152/japplphysiol.01274.2003},

issn = {8750-7587},

year  = {2004},

date = {2004-05-01},

journal = {J Appl Physiol (1985)},

volume = {96},

number = {5},

pages = {1714--1722},

abstract = {Orthostatic intolerance (OI) is a major problem after spaceflight. Its etiology remains uncertain, but reports have pointed toward an individual susceptibility to OI. We hypothesized that individual predisposition plays an important role in post-bed rest OI. Twenty-four healthy male subjects were equilibrated on a constant diet, after which they underwent tilt-stand test (pre-TST). They then completed 14-16 days of head-down-tilt bed rest, and 14 of the subjects underwent repeat tilt-stand test (post-TST). During various phases, the following were performed: 24-h urine collections and hormonal measurements, plethysmography, and cardiovascular system identification (a noninvasive method to assess autonomic function and separately quantify parasympathetic and sympathetic responsiveness). Development of presyncope or syncope defined OI. During pre-TST, 11 subjects were intolerant and 13 were tolerant. At baseline, intolerant subjects had lower serum aldosterone (P < 0.01), higher excretion of potassium (P = 0.01), lower leg venous compliance (P = 0.03), higher supine parasympathetic responsiveness (P = 0.02), and lower standing sympathetic responsiveness (P = 0.048). Of the 14 subjects who completed post-TST, 9 were intolerant and 5 were tolerant. Intolerant subjects had lower baseline serum cortisol (P = 0.03) and a higher sodium level (P = 0.02) compared with tolerant subjects. Thus several physiological characteristics were associated with increased susceptibility to OI. We propose a new model for OI, whereby individuals with greater leg venous compliance recruit compensatory mechanisms (activation of the renin-angiotensin-aldosterone system and sympathetic nervous system, and withdrawal of the parasympathetic nervous system) in the face of daily postural challenges, which places them at an advantage to face orthostatic stress. With head-down-tilt bed rest, the stimulus to recruit compensatory mechanisms disappears, and differences between the two subgroups attenuate.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid15068228,

title = {Renal, endocrine, and cardiovascular responses to bed rest in male subjects on a constant diet},

author = {S Marlene Grenon and Natalie Sheynberg and Shelley Hurwitz and Grace Xiao and Craig D Ramsdell and Michael D Ehrman and C Lan Mai and Siri Rostoft Kristjansson and Grete H Sundby and Richard J Cohen and Gordon H Williams},

doi = {10.1136/jim-52-02-21},

issn = {1081-5589},

year  = {2004},

date = {2004-03-01},

journal = {J Investig Med},

volume = {52},

number = {2},

pages = {117--128},

abstract = {BACKGROUND: Exposure to actual and simulated microgravity induces cardiovascular deconditioning through a variety of factors. Although the mechanisms involved remain uncertain, one involves alterations in volume-regulating systems--the hypothesis being tested in this study. To maximize our ability to detect subtle changes in the volume-regulating systems, subjects were studied on a high-average salt intake to maximally suppress these systems basally.



METHODS: Fourteen healthy male subjects underwent 14-day head-down tilt bed rest (HDTB) during which a constant 200 mEq sodium, 100 mEq potassium diet was maintained. Daily 24-hour urine collection was performed; plasma renin activity, serum aldosterone, plethysmography, and cardiovascular system identification were performed during a control period (pre-HDTB) and at the end of HDTB (end HDTB).



RESULTS: Sodium excretion increased initially (pre-HDTB = 182.8 +/- 10.4 mEq/total volume; early HDTB = 236.4 +/- 13.0; p = .002) and then returned to baseline values. Potassium excretion increased 4 days after the initiation of HDTB and remained elevated thereafter (pre-HDTB = 82.2 +/- 2.4/total volume; mid- to late HDTB = 89.4 +/- 2.1; p = .02). Plasma renin activity increased significantly with HDTB (pre-HDTB = 1.28 +/- 0.21 ng/mL/h; end HDTB = 1.69 +/- 0.18; p = .01), but serum aldosterone did not change. A significant decrease in autonomic responsiveness and an increase in leg compliance were observed.



CONCLUSIONS: We conclude that even in the presence of a high-average salt intake diet, simulated microgravity leads to renal, cardioendocrine, and cardiovascular system alterations that likely contribute to cardiovascular deconditioning.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid14514703,

title = {Effects of simulated microgravity on closed-loop cardiovascular regulation and orthostatic intolerance: analysis by means of system identification},

author = {Xinshu Xiao and Ramakrishna Mukkamala and Natalie Sheynberg and S Marlene Grenon and Michael D Ehrman and Thomas J Mullen and Craig D Ramsdell and Gordon H Williams and Richard J Cohen},

doi = {10.1152/japplphysiol.00602.2003},

issn = {8750-7587},

year  = {2004},

date = {2004-02-01},

journal = {J Appl Physiol (1985)},

volume = {96},

number = {2},

pages = {489--497},

abstract = {Microgravity-induced orthostatic intolerance (OI) continues to be a primary concern for the human space program. To test the hypothesis that exposure to simulated microgravity significantly alters autonomic nervous control and, thus, contributes to increased incidence of OI, we employed the cardiovascular system identification (CSI) technique to evaluate quantitatively parasympathetic and sympathetic regulation of heart rate (HR). The CSI method analyzes second-to-second fluctuations in noninvasively measured HR, arterial blood pressure, and instantaneous lung volume. The coupling mechanisms between these signals are characterized by using a closed-loop model. Parameters reflecting parasympathetic and sympathetic responsiveness with regard to HR regulation can be extracted from the identified coupling mechanisms. We analyzed data collected from 29 human subjects before and after 16 days of head-down-tilt bed rest (simulated microgravity). Statistical analyses showed that parasympathetic and sympathetic responsiveness was impaired by bed rest. A lower sympathetic responsiveness and a higher parasympathetic responsiveness measured before bed rest identified individuals at greater risk of OI before and after bed rest. We propose an algorithm to predict OI after bed rest from measures obtained before bed rest.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid12108836,

title = {Model-based assessment of cardiovascular health from noninvasive measurements},

author = {Xinshu Xiao and Edwin T Ozawa and Yaqi Huang and Roger D Kamm},

doi = {10.1114/1.1484217},

issn = {0090-6964},

year  = {2002},

date = {2002-05-01},

journal = {Ann Biomed Eng},

volume = {30},

number = {5},

pages = {612--623},

abstract = {Cardiovascular health is currently assessed through a variety of hemodynamic parameters, many of which can only be determined by invasive measurement often requiring hospitalization. A noninvasive method of evaluating several of these parameters such as systemic vascular resistance (SVR), maximum left ventricular elasticity (E(LV)), end diastolic volume (VED), and cardiac output, is presented. The method has three elements: (1) a distributed model of the human cardiovascular system (Ozawa et aL, Ann. Biomed. Eng. 29:284-297, 2001) to generate a solution library that spans the anticipated range of parameter values, (2) a method for establishing the multidimensional relationship between features computed from the arterial blood pressure and/or flow traces (e.g., mean arterial pressure, pulse amplitude, mean flow velocity) and the critical hemodynamic parameters, and (3) a parameter estimation method that yields the best fit between measured and computed data. Sensitivity analyses were used to determine the critical parameters, and the influence of fixed model parameters. Using computer-generated brachial pressure and velocity profiles (which can be measured noninvasively), the error associated with this method was found to be less than 3% for SVR, and less than 10% for E(LV) and V(ED). Simulations were also performed to test the ability of the approach to predict changes in SVR and E(LV) from an initial base line state.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid14686446,

title = {Effects of prolonged bed rest on the total peripheral resistance baroreflex},

author = {X Xiao and R Mukkamala and N Sheynberg and G H Williams and R J Cohen},

issn = {0276-6574},

year  = {2002},

date = {2002-01-01},

journal = {Comput Cardiol},

volume = {29},

pages = {53--56},

abstract = {Orthostatic intolerance following prolonged exposure to microgravity continues to be a primary concern of the human space program. Reduced autonomic tone has been demonstrated to contribute to this phenomenon, and the heart rate baroreflex, in particular, has been repeatedly shown to be impaired. However, only the works of Yelle et al. have attempted to address the role of the total peripheral resistance (TPR) baroreflex, a potentially more significant contributor to blood pressure regulation. We applied a previously developed method for estimating the static gains of both the arterial and cardiopulmonary TPR baroreflexes to data obtained before and after 16-day bed rest. Reductions in the estimated static gains of the arterial (statistically significant) and cardiopulmonary TPR baroreflexes were found after bed rest. This study supports the works of Yelle et al, which imply that the TPR baroreflex is reduced after spaceflight.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid11339326,

title = {Numerical simulation of enhanced external counterpulsation},

author = {E T Ozawa and K E Bottom and X Xiao and R D Kamm},

doi = {10.1114/1.1359448},

issn = {0090-6964},

year  = {2001},

date = {2001-04-01},

journal = {Ann Biomed Eng},

volume = {29},

number = {4},

pages = {284--297},

abstract = {Enhanced external counterpulsation (EECP) is a noninvasive, counterpulsative method to provide temporary aid to the failing heart by sequentially inflating cuffs on the lower extremity out-of-phase with the left ventricle. Optimization of the method necessitates consideration of the hemodynamics created by EECP and the mode of action providing patient benefit. A computational model based on the governing one-dimensional equations is developed that simulates cardiovascular hemodynamics during EECP. The model includes a 30-element arterial system including the left ventricle, bifurcations, and peripheral arterial vessels. Effects of vessel collapse as external pressure is applied, arterial refilling on pressure release, changes in aortic pressure, and shear stress generated in the arteries are each investigated. Device parameters are systematically varied to determine their effect on system performance. Results show the potential for significant collapse and shear augmentation throughout the arteries of the lower extremity. Performance is strongly influenced by the mean level of external pressurization and the timing of cuff inflation, but less so by the relative timing and pressure differences between cuff segments.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {dsRID: Editing-free in silico identification of dsRNA region using long-read RNA-seq data},

author = {Ryo Yamamoto},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {LINE-associated cryptic splicing induces dsRNA-mediated interferon response and tumor immunity},

keywords = {},

pubstate = {published},

tppubtype = {article}

}