We study computational and experimental RNA biology.

@article{nokey,

title = {Cytosine-to-uracil RNA editing is upregulated by pro-inflammatory stimulation of myeloid cells},

author = {Hyomin Seo and Winston H. Cuddleston and Ting Fu and Elisa Navarro and Madison Parks and Amanda Allan and Anastasia G. Efthymiou and Michael S. Breen and Xinshu Xiao and Towfique Raj and Jack Humphrey},

url = {https://www.biorxiv.org/content/10.1101/2025.03.14.643382v1.abstract?%3Fcollection=},

year  = {2025},

date = {2025-03-17},

urldate = {2025-03-17},

journal = {BioRxiv},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid40315057,

title = {Protocol to perform polysome profiling in primary differentiating murine adipocytes},

author = {Mirian Krystel De Siqueira and Zaynab Nouhi and Yutian Zhao and Siqi Wang and Xinshu Xiao and Xia Yang and Laura Hulea and Claudio J Villanueva},

doi = {10.1016/j.xpro.2025.103799},

issn = {2666-1667},

year  = {2025},

date = {2025-04-01},

journal = {STAR Protoc},

volume = {6},

number = {2},

pages = {103799},

abstract = {Here, we present a protocol for polysome profiling in differentiating adipocytes from the mouse stromal vascular fraction. We describe steps for lysate preparation, ultracentrifugation through sucrose gradients, mRNA isolation, RNA sequencing, and motif enrichment. This protocol enables the analysis of actively translating mRNAs and translational gene regulation by isolating polysome-bound mRNA, revealing insights into protein synthesis during adipogenesis or stimuli responses. Applications include studying translational control in adipocytes, metabolic diseases, and obesity, linking translational regulation to cellular and metabolic phenotypes. For complete details on the use and execution of this protocol, please refer to De Siqueira et al..},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid40328247,

title = {DNA methyltransferase 1 modulates mitochondrial function through bridging mC RNA methylation},

author = {Jing Wang and Xiaoqian Deng and Tianshen Jian and Shanshan Yin and Linzhi Chen and Laurent Vergnes and Zhehao Li and Huoyuan Liu and Ryan Lee and Sin Yee Lim and Jae Hoon Bahn and Xinshu Xiao and Xianmin Zhu and Ganlu Hu and Karen Reue and Yizhi Liu and Guoping Fan},

doi = {10.1016/j.molcel.2025.04.019},

issn = {1097-4164},

year  = {2025},

date = {2025-04-01},

journal = {Mol Cell},

abstract = {DNA methyltransferase 1 (DNMT1) is an enzyme known for DNA methylation maintenance. Point mutations in its replication focus targeting sequence (RFTS) domain lead to late-onset neurodegeneration, such as autosomal dominant cerebellar ataxia-deafness and narcolepsy (ADCA-DN) disorder. Here, we demonstrated that DNMT1 has the capability to bind to mRNA transcripts and facilitate 5-methylcytosine (mC) RNA methylation by recruiting NOP2/Sun RNA methyltransferase 2 (NSUN2). RNA mC methylation, in turn, promotes RNA stability for those genes modulating mitochondrial function. When the DNMT1 RFTS domain is mutated in mice, it triggers aberrant DNMT1-RNA interaction and significantly elevated mC RNA methylation and RNA stability for a portion of metabolic genes. Consequently, increased levels of metabolic RNA transcripts contribute to cumulative oxidative stress, mitochondrial dysfunction, and neurological symptoms. Collectively, our results reveal a dual role of DNMT1 in regulating both DNA and RNA methylation, which further modulates mitochondrial function, shedding light on the pathogenic mechanism of DNMT1 mutation-induced neurodegeneration.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Massively parallel screen uncovers many rare 3′ UTR variants regulating mRNA abundance of cancer driver genes},

author = {Ting Fu and Kofi Amoah and Tracey W. Chan and Jae Hoon Bahn and Jae-Hyung Lee and Sari Terrazas and Rockie Chong and Sriram Kosuri and Xinshu Xiao},

url = {https://www.nature.com/articles/s41467-024-46795-7},

year  = {2024},

date = {2024-04-18},

urldate = {2024-04-18},

journal = {Nature Communications},

volume = {15},

number = {3335},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid38702197,

title = {Navigating the landscape of epitranscriptomics and host immunity},

author = {Elaine Huang and Clara Frydman and Xinshu Xiao},

doi = {10.1101/gr.278412.123},

issn = {1549-5469},

year  = {2024},

date = {2024-05-01},

journal = {Genome Res},

volume = {34},

number = {4},

pages = {515--529},

abstract = {RNA modifications, also termed epitranscriptomic marks, encompass chemical alterations to individual nucleotides, including processes such as methylation and editing. These marks contribute to a wide range of biological processes, many of which are related to host immune system defense. The functions of immune-related RNA modifications can be categorized into three main groups: regulation of immunogenic RNAs, control of genes involved in innate immune response, and facilitation of adaptive immunity. Here, we provide an overview of recent research findings that elucidate the contributions of RNA modifications to each of these processes. We also discuss relevant methods for genome-wide identification of RNA modifications and their immunogenic substrates. Finally, we highlight recent advances in cancer immunotherapies that aim to reduce cancer cell viability by targeting the enzymes responsible for RNA modifications. Our presentation of these dynamic research avenues sets the stage for future investigations in this field.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}