The Integrator complex regulates microRNA abundance through RISC loading

Abstract

MicroRNA (miRNA) homeostasis is crucial for the post-transcriptional regulation of their target genes and miRNA dysregulation has been linked to multiple diseases, including cancer. The molecular mechanisms underlying miRNA biogenesis from processing of primary miRNA transcripts to formation of mature miRNA duplex are well understood. Loading of miRNA duplex into members of the Argonaute (Ago) protein family, representing the core of the RNA-induced silencing complex (RISC), is pivotal to miRNA-mediated gene silencing. The Integrator complex has been previously shown to be an important regulator of RNA maturation, RNA polymerase II pause-release, and premature transcriptional termination. Here, we report that loss of Integrator results in global diminution of mature miRNAs. By incorporating 4-Thiouridine (s4U) in nascent transcripts, we traced miRNA fate from biogenesis to stabilization and identified Integrator to be essential for proper miRNA assembly into RISC. Enhanced UV crosslinking and immunoprecipitation (eCLIP) of Integrator confirms a robust association with mature miRNAs. Indeed, Integrator potentiates Ago2-mediated cleavage of target RNAs. These findings highlight an essential role for Integrator in miRNA abundance and RISC function.

Transcriptome-wide analysis of primary human endothelial cell responses to 1 hour of protein translation inhibition identify nonsense mediated decay targets and a non-codingSLC11A2exon as an acute biomarker

“…Identification of the integrator complex is highly relevant to recent data indicating that the integrator complex regulates production of full length coding and non-coding RNAs by mechanisms including RNA cleavage, [53] RNA polymerase II pausing, [54] premature transcriptional termination, [55] and RISC loading of miRNAs. [56] ATP is relevant particularly to UPF1 which has both ATPase and RNA helicase activities. [7] Additional biological functions were elucidated by examining the targets of miRNAs differentially expressed in cycloheximide and media treated cells -phosphorylation, phosphatidylinositol signalling, transcription, and cell adhesion were in-keeping with more recent data in other cell types that is leading to more targeted therapeutics.…”

Rapid Adaptation of Cellular Metabolic Rate to the MicroRNA Complements of Mammals and its Relevance to the Evolution of Endothermy

“…Given the potential for microRNA regulation to increase the heritability of adaptive traits (Peterson et al, 2009), the enlargement of microRNA and target repertoires has been proposed as a key mechanism in the diversification of animal cell types and morphologies (Makeyev and Maniatis, 2008;Erwin et al, 2011;Deline et al, 2018;Dexheimer and Cochella, 2020;Peterson et al, 2021;Jenike et al, 2023;Taylor et al, 2023). However, relatively little attention has been paid to the nature of global microRNA activity (Reichholf et al, 2019;Kingston and Bartel, 2019;Tarbier et al, 2020;Kirstein et al, 2023) or its impact on energy metabolism (Schwanhäusser et al, 2011;Cassidy et al, 2019). Our model predicts that compensatory noise suppression by microRNAs should be proportional to body temperature, since temperature is the primary determinant of the rate of protein synthesis, and therefore of intrinsic stochastic translation noise (Thattai and van Oudenaarden, 2001;Ozbudak et al, 2002).…”

MicroRNA Signatures in Cartilage Ageing and Osteoarthritis

“…In the nucleus, miRNAs genes are first transcribed into long primary miRNA (pri-miRNA) transcripts, which are double-stranded stems with hairpin structures. Pri-miRNAs undergo cleavage by the microprocessor complex which consists of two proteins: Drosha, a ribonuclease III (RNase III) enzyme, and DiGeorge critical region 8 (DGCR8) [ 9 , 10 ]. This gives rise to the precursor-miRNA (pre-miRNA), which is a ~70 nt stem-loop structure.…”

“…Pre-miRNAs exit the nucleus and are exported to the cytoplasm via exportin-5. There, they are cleaved further by another endoribonucleolytic enzyme with RNase III activity, Dicer [ 10 ]. After cleavage, there is a ~22 nt RNA duplex left.…”

“…This RNA duplex is loaded into an Argonaute (Ago) protein to form the RNA-induced silencing complex (RISC). One strand, called the guide strand, is stabilised within the complex, while the remaining strand, called the passenger strand, is degraded [ 9 , 10 , 11 ]. Mature miRNAs exert their function by pairing with their mRNA targets.…”