Principles of RNA Processing From Analysis of Enhanced Clip Maps for 150 RNA Binding Proteins

Authors

Eric L Van Nostrand
Gabriel A Pratt
Brian A Yee
Emily C Wheeler
Steven M Blue
Jasmine Mueller
Samuel S Park
Keri E Garcia
Chelsea Gelboin-Burkhart
Thai B Nguyen
Ines Rabano
Rebecca Stanton
Balaji Sundararaman
Ruth Wang
Xiang-Dong Fu
Brenton R Graveley
Gene W Yeo

Publication Date

4-6-2020

Journal

Genome Biology

DOI

10.1186/s13059-020-01982-9

PMID

32252787

PMCID

PMC7137325

PubMedCentral® Posted Date

4-6-2021

PubMedCentral® Full Text Version

Post-print

Published Open-Access

yes

Keywords

Binding Sites, Hep G2 Cells, Humans, Immunoprecipitation, Introns, K562 Cells, RNA, RNA Processing, Post-Transcriptional, RNA Splicing, RNA, Ribosomal, RNA-Binding Proteins, Repetitive Sequences, Nucleic Acid, Retroelements, Spliceosomes, eCLIP, CLIP-seq, RNA binding protein, RNA processing

Abstract

BACKGROUND: A critical step in uncovering rules of RNA processing is to study the in vivo regulatory networks of RNA binding proteins (RBPs). Crosslinking and immunoprecipitation (CLIP) methods enable mapping RBP targets transcriptome-wide, but methodological differences present challenges to large-scale analysis across datasets. The development of enhanced CLIP (eCLIP) enabled the mapping of targets for 150 RBPs in K562 and HepG2, creating a unique resource of RBP interactomes profiled with a standardized methodology in the same cell types.

RESULTS: Our analysis of 223 eCLIP datasets reveals a range of binding modalities, including highly resolved positioning around splicing signals and mRNA untranslated regions that associate with distinct RBP functions. Quantification of enrichment for repetitive and abundant multicopy elements reveals 70% of RBPs have enrichment for non-mRNA element classes, enables identification of novel ribosomal RNA processing factors and sites, and suggests that association with retrotransposable elements reflects multiple RBP mechanisms of action. Analysis of spliceosomal RBPs indicates that eCLIP resolves AQR association after intronic lariat formation, enabling identification of branch points with single-nucleotide resolution, and provides genome-wide validation for a branch point-based scanning model for 3' splice site recognition. Finally, we show that eCLIP peak co-occurrences across RBPs enable the discovery of novel co-interacting RBPs.

CONCLUSIONS: This work reveals novel insights into RNA biology by integrated analysis of eCLIP profiling of 150 RBPs with distinct functions. Further, our quantification of both mRNA and other element association will enable further research to identify novel roles of RBPs in regulating RNA processing.

Comments

Associated Data