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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. MicroRNAs regulate gene expression by targeting mRNAs via complementarity with seed sequences. Rudensky and colleagues provide genome-wide profiles of the microRNA miR-155 in multiple immune cell lineages and identify its cell-type effects on gene expression.

MicroRNA-155 (miR-155) is involved in differentiation and regulation of responses of multiple haematopoietic cell types. Its dysregulation is implicated in many human malignancies, e.g. Hodgkin, diffuse large B lymphomas, and breast cancer. Many microRNAs and their target mRNAs are co-expressed in diverse types of cells and tissues. To what extent the interaction between a specific microRNA and its target mRNAs is preserved in different cellular context is largely unknown. We employed genome-wide approaches to investigate whether regulation of commonly expressed mRNA by miR-155 operates in a cell type-specific manner in analogy to cell-context dependent regulation by transcription factors. We first performed RNA-Seq to quantitatively measure mRNA expression levels in primary B cells, dendritic cells, macrophages, and CD4+ T cells from wild type and miR-155 knockout mice. We found many miR-155 target mRNAs that contain seed matches in 3' untranslated regions (3'UTRs) were differentially repressed between four types of primary immune cells. Next, we performed iCLIP (individual-nucleotide resolution UV crosslinking and immunoprecipitation) to precisely map Argonaute 2 binding. Quantitative analysis of iCLIP in both wild type and miR-155 KO primary cells uncovered hundreds of miR-155 bound genes, a large number of which overlapped the cohorts of genes that were identified by RNA-Seq as differentially regulated by miR-155. Most mRNAs are alternatively polyadenylated, and through alternative polyadenylation (ApA) mRNAs can acquire or lose microRNA sites. To account for ApA, we carried out PolyA-Seq to measure polyadenylation site usage, and found that ApA contributed to differential miR-155 regulation of a number of genes. However, in many cases the same target 3'UTR isoforms were differentially regulated between cell types, suggesting ApA-independent mechanisms of miR-155 specificity, and cellular context dependent miR-155-mediated regulation of gene expression. This research will elucidate mechanistic underpinning of cell-context dependent microRNA function, and help understand miR-155 functions in disease, specifically in lymphomas and other cancers. Citation Format: Jing-Ping Hsin, Yuheng Lu, Christina S. Leslie, Alexander Y. Rudensky. The effects of cellular context on miR-155 mediated regulation of gene expression [abstract]. In: Proceedings of the Second CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; 2016 Sept 25-28; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(11 Suppl):Abstract nr A062.