The effect of cellular context on miR-155-mediated gene regulation in four major immune cell types

JP Hsin, Y Lu, GB Loeb, CS Leslie, AY Rudensky - Nature immunology, 2018 - nature.com
Nature immunology, 2018nature.com
Numerous microRNAs and their target mRNAs are coexpressed across diverse cell types.
However, it is unknown whether they are regulated in a manner independent of or
dependent on cellular context. Here, we explored transcriptome-wide targeting and gene
regulation by miR-155, whose activation-induced expression plays important roles in innate
and adaptive immunity. Through mapping of miR-155 targets through differential iCLIP,
mRNA quantification with RNA-seq, and 3′ untranslated region (UTR)-usage analysis with …
Abstract
Numerous microRNAs and their target mRNAs are coexpressed across diverse cell types. However, it is unknown whether they are regulated in a manner independent of or dependent on cellular context. Here, we explored transcriptome-wide targeting and gene regulation by miR-155, whose activation-induced expression plays important roles in innate and adaptive immunity. Through mapping of miR-155 targets through differential iCLIP, mRNA quantification with RNA-seq, and 3′ untranslated region (UTR)-usage analysis with poly(A)-seq in macrophages, dendritic cells, and T and B lymphocytes either sufficient or deficient in activated miR-155, we identified numerous targets differentially bound by miR-155. Whereas alternative cleavage and polyadenylation (ApA) contributed to differential miR-155 binding to some transcripts, in most cases, identical 3′-UTR isoforms were differentially regulated across cell types, thus suggesting ApA-independent and cellular-context-dependent miR-155-mediated gene regulation. Our study provides comprehensive maps of miR-155 regulatory networks and offers a valuable resource for dissecting context-dependent and context-independent miRNA-mediated gene regulation in key immune cell types.
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