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{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}

}

@article{pmid38815579,

title = {hnRNPM protects against the dsRNA-mediated interferon response by repressing LINE-associated cryptic splicing},

author = {Rong Zheng and Mikayla Dunlap and Georg O M Bobkov and Carlos Gonzalez-Figueroa and Khushali J Patel and Jingyi Lyu and Samuel E Harvey and Tracey W Chan and Giovanni Quinones-Valdez and Mudra Choudhury and Charlotte A Le Roux and Mason D Bartels and Amy Vuong and Ryan A Flynn and Howard Y Chang and Eric L Van Nostrand and Xinshu Xiao and Chonghui Cheng},

doi = {10.1016/j.molcel.2024.05.004},

issn = {1097-4164},

year  = {2024},

date = {2024-05-01},

journal = {Mol Cell},

abstract = {RNA splicing is pivotal in post-transcriptional gene regulation, yet the exponential expansion of intron length in humans poses a challenge for accurate splicing. Here, we identify hnRNPM as an essential RNA-binding protein that suppresses cryptic splicing through binding to deep introns, maintaining human transcriptome integrity. Long interspersed nuclear elements (LINEs) in introns harbor numerous pseudo splice sites. hnRNPM preferentially binds at intronic LINEs to repress pseudo splice site usage for cryptic splicing. Remarkably, cryptic exons can generate long dsRNAs through base-pairing of inverted ALU transposable elements interspersed among LINEs and consequently trigger an interferon response, a well-known antiviral defense mechanism. Significantly, hnRNPM-deficient tumors show upregulated interferon-associated pathways and elevated immune cell infiltration. These findings unveil hnRNPM as a guardian of transcriptome integrity by repressing cryptic splicing and suggest that targeting hnRNPM in tumors may be used to trigger an inflammatory immune response, thereby boosting cancer surveillance.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}