The influence of microRNAs and poly(A) tail length on endogenous mRNA-protein complexes

Genome Biology
Olivia S RisslandDavid P Bartel

Abstract

All mRNAs are bound in vivo by proteins to form mRNA-protein complexes (mRNPs), but changes in the composition of mRNPs during posttranscriptional regulation remain largely unexplored. Here, we have analyzed, on a transcriptome-wide scale, how microRNA-mediated repression modulates the associations of the core mRNP components eIF4E, eIF4G, and PABP and of the decay factor DDX6 in human cells. Despite the transient nature of repressed intermediates, we detect significant changes in mRNP composition, marked by dissociation of eIF4G and PABP, and by recruitment of DDX6. Furthermore, although poly(A)-tail length has been considered critical in post-transcriptional regulation, differences in steady-state tail length explain little of the variation in either PABP association or mRNP organization more generally. Instead, relative occupancy of core components correlates best with gene expression. These results indicate that posttranscriptional regulatory factors, such as microRNAs, influence the associations of PABP and other core factors, and do so without substantially affecting steady-state tail length.

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Citations

Dec 1, 2017·Genome Biology·Jeremy R Sanford, Luiz O F Penalva
Dec 1, 2017·Genome Biology·Mihaela Zavolan, Brenton R Graveley
Jul 1, 2018·Cold Spring Harbor Perspectives in Biology·Thomas F Duchaine, Marc R Fabian
Jun 11, 2019·Nucleic Acids Research·Hedda A MeijerMartin Bushell
Sep 19, 2019·RNA·Ashrut NarulaOlivia S Rissland
Apr 5, 2018·Frontiers in Neurology·Yuhai Zhao, Walter J Lukiw
Aug 28, 2020·Biomedicine & Pharmacotherapy = Biomédecine & Pharmacothérapie·Nutthapoom Pathomthongtaweechai, Somchai Chutipongtanate
Oct 2, 2021·Nature Reviews. Molecular Cell Biology·Lori A Passmore, Jeff Coller
Nov 19, 2021·Biochemical Genetics·Hao WuHaichao Xu

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Methods Mentioned

BETA
RIPs
RIP
pull-down
transfection
RIP-seq
RNA-seq
pull-downs
immunoprecipitations
PAL-seq
transfections

Software Mentioned

Cufflinks
STAR
nSolver
bcl2fastq2
Metagene
R

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