RNA uridyl transferases TUT4/7 differentially regulate miRNA variants depending on the cancer cell-type

Abstract

The human terminal uridyl transferases TUT4 and TUT7 (TUT4/7) catalyse additions of uridines at the 3' end of RNAs such as the precursors of the tumour suppressor miRNA let-7, upon recruitment by the oncoprotein LIN28A. Consequently, let-7 family miRNAs are downregulated. Disruption of this TUT4/7 activity inhibits tumorigenesis and hence targeting TUT4/7 can be a potential anti-cancer therapy. In this study, we investigate TUT4/7-mediated RNA regulation in two cancer cell lines by establishing catalytic knockout models. Upon TUT4/7 mutation, we observe a significant reduction in miRNA uridylation, which results in defects in cancer cell properties such as cell proliferation and migration. With the loss of TUT4/7-mediated miRNA uridylation, the uridylated miRNA variants are replaced by adenylated isomiRs. Changes in miRNA modification profiles are accompanied by deregulation of expression levels in specific cases. Unlike let-7s, most miRNAs do not depend on LIN28A for TUT4/7-mediated regulation. Additionally, we identify TUT4/7-regulated cell-type-specific miRNA clusters and deregulation in their corresponding mRNA targets. Expression levels of miR-200c-3p and miR-141-3p are regulated by TUT4/7 in a cancer cell type specific manner. Subsequently, BCL2 which is a well-established target of miR-200c is upregulated. Therefore, TUT4/7 loss triggers deregulation of miRNA-mRNA networks in a cell-type-specific manner. Understanding of the underlying biology of such cell-type-specific deregulation will be key when targeting TUT4/7 for cancer therapy. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=198 SRC="FIGDIR/small/451846v2_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@a18bdcorg.highwire.dtl.DTLVardef@1e5534forg.highwire.dtl.DTLVardef@c08e76org.highwire.dtl.DTLVardef@1c90423_HPS_FORMAT_FIGEXP M_FIG C_FIG Highlights TUT4/7 catalyse 3' uridylation of most miRNAs Loss of uridylated isomiRs leads to the gain of adenylated isomiRs TUT4/7-mediated miRNA deregulation and miRNA-mRNA interactions are specific to the cell line type Loss of TUT4/7-mediated RNA uridylation inhibits cancer cell function