Two novel RNA-binding proteins identification through computational prediction and experimental validation

Genomics. 2022 Jan;114(1):149-160. doi: 10.1016/j.ygeno.2021.12.003. Epub 2021 Dec 16.

Abstract

Since RBPs play important roles in the cell, it's particularly important to find new RBPs. We performed iRIP-seq and CLIP-seq to verify two proteins, CLIP1 and DMD, predicted by RBPPred whether are RBPs or not. The experimental results confirm that these two proteins have RNA-binding activity. We identified significantly enriched binding motifs UGGGGAGG, CUUCCG and CCCGU for CLIP1 (iRIP-seq), DMD (iRIP-seq) and DMD (CLIP-seq), respectively. The computational KEGG and GO analysis show that the CLIP1 and DMD share some biological processes and functions. Besides, we found that the SNPs between DMD and its RNA partners may be associated with Becker muscular dystrophy, Duchenne muscular dystrophy, Dilated cardiomyopathy 3B and Cardiovascular phenotype. Among the thirteen cancers data, CLIP1 and another 300 oncogenes always co-occur, and 123 of these 300 genes interact with CLIP1. These cancers may be associated with the mutations occurred in both CLIP1 and the genes it interacts with.

Keywords: CLIP-seq; CLIP1; Cancer; ClinVar; DMD; RBPPred; RNA-binding protein; iRIP-seq.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cardiomyopathy, Dilated / diagnosis
  • Cardiomyopathy, Dilated / genetics
  • Computational Biology
  • Dystrophin / genetics
  • Humans
  • Muscular Dystrophy, Duchenne / diagnosis
  • Muscular Dystrophy, Duchenne / genetics
  • RNA
  • RNA-Binding Proteins* / genetics
  • RNA-Binding Proteins* / metabolism

Substances

  • DMD protein, human
  • Dystrophin
  • RNA-Binding Proteins
  • RNA