MERIT: Systematic Analysis and Characterization of Mutational Effect on RNA Interactome Topology

Hepatology : Official Journal of the American Association for the Study of Liver Diseases
Yongsheng LiNidhi Sahni

Abstract

The interaction between RNA-binding proteins (RBPs) and RNA plays an important role in regulating cellular function. However, decoding genome-wide protein-RNA regulatory networks as well as how cancer-related mutations impair RNA regulatory activities in hepatocellular carcinoma (HCC) remains mostly undetermined. We explored the genetic alteration patterns of RBPs and found that deleterious mutations are likely to occur on the surface of RBPs. We then constructed protein-RNA interactome networks by integration of target binding screens and expression profiles. Network analysis highlights regulatory principles among interacting RBPs. In addition, somatic mutations selectively target functionally important genes (cancer genes, core fitness genes, or conserved genes) and perturb the RBP-gene regulatory networks in cancer. These regulatory patterns were further validated using independent data. A computational method (Mutational Effect on RNA Interactome Topology) and a web-based, user-friendly resource were further proposed to analyze the RBP-gene regulatory networks across cancer types. Pan-cancer analysis also suggests that cancer cells selectively target "vulnerability" genes to perturb protein-RNA interactome that is involved ...Continue Reading

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Citations

Apr 14, 2019·Cellular and Molecular Life Sciences : CMLS·Jozef Nahalka
Feb 13, 2020·Frontiers in Genetics·Jianjun WangXianzeng Hou
Feb 13, 2021·Frontiers in Cell and Developmental Biology·Ya ZhangYongsheng Li
Feb 16, 2020·Molecular Therapy : the Journal of the American Society of Gene Therapy·Jiwei ZhangYongsheng Li
Jul 13, 2021·Frontiers in Genetics·Yongsheng Li, Juan Xu
Nov 11, 2021·Nucleic Acids Research·Tiantongfei JiangXia Li

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Methods Mentioned

BETA
GTPase
CLIP
transfection
Immunoprecipitation

Software Mentioned

MERIT
CADD
R

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