Elucidation of transcriptome-wide microRNA binding sites in human cardiac tissues by Ago2 HITS-CLIP

Spengler, Ryan M; Zhang, Xiaoming; Cheng, Congsheng; McLendon, Jared M.; Skeie, Jessica M.; Johnson, Frances L.; Davidson, Beverly L.; Boudreau, Ryan L.

doi:10.1093/nar/gkw640

Cited by 48 publications

(69 citation statements)

References 48 publications

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“…In order to define both nuclear AGO2 and miRNA target sites on a transcriptome-wide scale, crosslinking immunoprecipitation assays coupled with high throughput sequencing (HITS-CLIP) analyses have been used. Through these assays, AGO2 and miRNA binding sites were identified within intronic sequences, at a frequency ranging from 12%–15% in brain samples of mouse and human, respectively, and up to 3% in human myocardial cells [56,74,75]. These results constitute an important starting point to support the idea of miRNA involvement in the cellular splicing program.…”

Section: Mirnas: Nuclear Functionsmentioning

confidence: 86%

MicroRNA in Control of Gene Expression: An Overview of Nuclear Functions

Catalanotto

Cogoni

Zardo

2016

IJMS

917

668

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The finding that small non-coding RNAs (ncRNAs) are able to control gene expression in a sequence specific manner has had a massive impact on biology. Recent improvements in high throughput sequencing and computational prediction methods have allowed the discovery and classification of several types of ncRNAs. Based on their precursor structures, biogenesis pathways and modes of action, ncRNAs are classified as small interfering RNAs (siRNAs), microRNAs (miRNAs), PIWI-interacting RNAs (piRNAs), endogenous small interfering RNAs (endo-siRNAs or esiRNAs), promoter associate RNAs (pRNAs), small nucleolar RNAs (snoRNAs) and sno-derived RNAs. Among these, miRNAs appear as important cytoplasmic regulators of gene expression. miRNAs act as post-transcriptional regulators of their messenger RNA (mRNA) targets via mRNA degradation and/or translational repression. However, it is becoming evident that miRNAs also have specific nuclear functions. Among these, the most studied and debated activity is the miRNA-guided transcriptional control of gene expression. Although available data detail quite precisely the effectors of this activity, the mechanisms by which miRNAs identify their gene targets to control transcription are still a matter of debate. Here, we focus on nuclear functions of miRNAs and on alternative mechanisms of target recognition, at the promoter lavel, by miRNAs in carrying out transcriptional gene silencing.

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Section: Mirnas: Nuclear Functionsmentioning

confidence: 86%

MicroRNA in Control of Gene Expression: An Overview of Nuclear Functions

Catalanotto

Cogoni

Zardo

2016

IJMS

917

668

View full text Add to dashboard Cite

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“…We have shown that an RBP heterogeneous ribonucleoprotein L (hnRNP L) forms a complex with miR-574-3p via binding a CA-rich element and inactivates Ago2 loading and the miRNA activity in monocytes 48 . Intriguingly, Ago2 CLIP-Seq barely detected any miR-574-5p and miR-574-3p binding to Ago2 in advanced cardiomyopathy patients, despite its induced expression in both ischemic and non-ischemic HF patients, as indicated by comparative miRNA-Seq analyses of myocardial miRNAs 51,52 . This finding implies that both strands of miR-574 may be eliminated from the RISC by an unknown mechanism.…”

Section: Discussionmentioning

confidence: 92%

MicroRNA-574 Regulates FAM210A Expression and Influences Pathological Cardiac Remodeling

Subbaiah

Jiang

et al. 2020

Preprint

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Aberrant synthesis of mitochondrial proteins impairs cardiac function and causes heart disease. However, the mechanism of regulation of mitochondria encoded protein expression during cardiac disease remains underexplored. Here, we have shown that multiple pathogenic cardiac stressors induce the expression of miR-574 guide and passenger strands (miR-574-5p/3p) in both humans and mice. miR-574 knockout mice exhibit severe cardiac disorder under heart disease-triggering stresses. miR-574-5p/3p mimics that are delivered systematically using nanoparticles reduce cardiac pathogenesis under disease insults.Transcriptome analysis of miR-574-null hearts uncovers FAM210A as a common target mRNA for both strands of miR-574. The interactome capture and translational state analyses suggest that FAM210A interacts with mitochondrial translation factors and regulates the protein expression of mitochondrial encoded electron transport chain genes. Using a human cardiomyocyte cell culture system, we discover that miR-574 regulates FAM210A expression and modulates mitochondrial encoded protein expression, which influences cardiac remodeling in heart failure.Abbreviations of key terms: ACM, adult cardiomyocytes; CF, cardiac fibroblasts; CM, cardiomyocytes; ETC, electron transport chain; FAM210A, family with sequence similarity 210 member A; HF, heart failure; ISO, isoproterenol; MEG, mitochondrial encoded gene; MI, myocardial infarction; NEMG, nuclear-encoded mitochondrial gene; RBP, RNA-binding protein; RISC, RNA-induced silencing complex; TAC, transverse aortic constriction; UTR, untranslated region Results Cardiac stress induces miR-574-5p and miR-574-3p in human and mouse heartsFrom data mining of unbiased screening data from four laboratories, the guide strand miR-574-5p has been identified as a miRNA that is robustly induced in the heart in response to pathological cardiac remodeling, which included the cardiac tissues of patients during the initial stages following MI onset 33 , a mouse model of left coronary artery occlusion-derived MI 24 , and aged murine hearts ( Fig. 1a) 26 . On the other hand, the passenger strand miR-574-3p is increased in the human hearts after MI and more remarkably induced by exercise training in murine hearts 34 . The cardiac functions of complementary strands of miR-574-5p and miR-574-3p remain unknown. miR-574 is conserved in 43 animal species (10 primates and 33 mammals, UCSC Genome Browser). In mammals, miR-574 is located in intron 1 of the host gene FAM114A1 (Family with sequence similarity 114 member A1) ( Fig. 1b). We confirmed that both miR-574-5p and miR-574-3p were significantly induced in heart tissues of chronic HF patients, with the expression level of miR-574-5p even higher than that of miR-574-3p (Fig. 1c). Northern blot analysis showed that both miR-574-5p and miR-574-3p were expressed in the normal murine heart ( Supplementary Fig. 1a). miR-574-5p and miR-574-3p were both significantly induced in isoproterenol (ISO)-or transverse aortic constriction (TAC)-treated mouse hearts, compar...

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“…These studies, and most others in adipose tissue, rely on computational predictions and low-throughput validation to identify miRNA targets. Although high-throughput crosslinking techniques to map the miRNA targetome have been applied to liver, brain, heart and other tissues 11,12,13 , thus far, no comprehensive targetome has been described for adipose tissue.…”

Section: Figmentioning

confidence: 99%

AGO HITS-CLIP in Adipose Tissue Reveals miR-29 as a Post-Transcriptional Regulator of Leptin

O’Connor

Murphy

et al. 2020

Preprint

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MicroRNAs (miRNAs) are short, non-coding RNAs that associate with Argonaute (AGO) to regulate mRNA stability and translation. While individual miRNAs have been shown to play important roles in white and brown adipose tissue in normal physiology and disease 1,2,3 , a comprehensive analysis of miRNA activity in these tissues has not been performed. We used high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP) to comprehensively characterize the network of high-confidence, in vivo mRNA:miRNA interactions across white and brown fat, revealing over 100,000 unique miRNA binding sites. Targets for each miRNA were ranked to generate a catalog of miRNA binding activity, and the miR-29 family emerged as a top regulator of adipose tissue gene expression. Among the top targets of miR-29 was leptin, an adipocyte-derived hormone that acts on the brain to regulate food intake and energy expenditure 4 . Two independent miR-29 binding sites in the leptin 3'-UTR were validated using luciferase assays, and miR-29 gain and loss-of-function modulated leptin mRNA and protein secretion in primary adipocytes. In mice, miR-29 abundance inversely correlated with leptin levels in two independent models of obesity. This work represents the only experimentally generated miRNA targetome in adipose tissue and identifies the first known post-transcriptional regulator of leptin. Future work aimed at manipulating miR-29:leptin binding may provide a therapeutic opportunity to treat obesity and its sequelae.Much of the work on adipocyte development and function over the last several decades has focused on transcriptional regulators. These include PPARG2, which is necessary and sufficient for the development and maintenance of white and brown adipocytes 5 , and PRDM16, which regulates brown and beige adipocyte identity 6,7 . More recently, it has become clear that post-transcriptional regulators also play 3 a key role in influencing adipocyte phenotype. Studies with adipose-specific dicer KO mice demonstrate that microRNAs (miRNAs) are essential in regulating adipogenesis, insulin sensitivity and non-shivering thermogenesis 8,9 . Several individual miRNAs have been shown to contribute to these phenotypic effects.miR-133 represses BAT function by directly targeting Prdm16 and inhibiting expression of thermogenic genes 2 . miR-196a induces browning of WAT by targeting Hoxc8 1 , and miR-26 protects mice from dietinduced obesity by blocking adipogenesis 10 . These studies, and most others in adipose tissue, rely on computational predictions and low-throughput validation to identify miRNA targets. Although highthroughput crosslinking techniques to map the miRNA targetome have been applied to liver, brain, heart and other tissues 11,12,13 , thus far, no comprehensive targetome has been described for adipose tissue.To profile the complete network of in vivo, adipose-specific miRNA binding activity across both brown and white fat, we used AGO HITS-CLIP on interscapular brown adipose tissue (iBAT) and epididymal white a...

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Elucidation of transcriptome-wide microRNA binding sites in human cardiac tissues by Ago2 HITS-CLIP

Cited by 48 publications

References 48 publications

MicroRNA in Control of Gene Expression: An Overview of Nuclear Functions

MicroRNA in Control of Gene Expression: An Overview of Nuclear Functions

MicroRNA-574 Regulates FAM210A Expression and Influences Pathological Cardiac Remodeling

AGO HITS-CLIP in Adipose Tissue Reveals miR-29 as a Post-Transcriptional Regulator of Leptin

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