Direct measurement of pervasive weak repression by microRNAs and their role at the network level

BMC Genomics
Fuqiang MaChung-I Wu

Abstract

A gene regulatory network (GRN) comprises many weak links that are often regulated by microRNAs. Since miRNAs rarely repress their target genes by more than 30%, doubts have been expressed about the biological relevance of such weak effects. These doubts raise the possibility of under-estimation as miRNA repression is usually estimated indirectly from equilibrium expression levels. To measure miRNA repression directly, we inhibited transcript synthesis in Drosophila larvae and collected time-course data on mRNA abundance, the decline of which reflects transcript degradation. The rate of target degradation in the absence of miR310s, a moderately expressed miRNA family, was found to decrease by 5 to 15%. A conventional analysis that does not remove transcript synthesis yields an estimate of 6.5%, within the range of the new estimates. These data permit further examinations of the repression mechanisms by miRNAs including seed matching types, APA (alternative polyadenylation) sites, effects of other highly-expressed miRNAs and the length of 3'UTR. Our direct measurements suggest the latter two factors have a measurable effect on decay rate. The direct measurement confirms pervasive weak repression by miRNAs, supporting the conclus...Continue Reading

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Citations

Nov 23, 2018·The Plant Journal : for Cell and Molecular Biology·Kathleen BeilsmithJoy Bergelson
Nov 21, 2019·Cells·Bruna Cristine de AlmeidaKatia Candido Carvalho
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Mar 7, 2021·Non-coding RNA·Elena López-Jiménez, Eduardo Andrés-León

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Datasets Mentioned

BETA
PRJCA000381

Methods Mentioned

BETA
RNA-Seq
reverse transcription PCR
electrophoresis

Software Mentioned

tophat
TargetScan
GO
Ensembl
Cufflinks
TermFinder

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