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Pietrzykowski AZ. The role of microRNAs in drug addiction: a big lesson from tiny molecules. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2010; 91:1-24. [PMID: 20813238 DOI: 10.1016/s0074-7742(10)91001-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Alcoholism is a multifactorial disease of unclear molecular underpinnings. Currently, we are witnessing a major shift in our understanding of the functional elements of the genome, which could help us to discover novel insights into the nature of alcoholism. In humans, the vast majority of the genome encodes non-protein-coding DNA with unclear function. Recent research has started to unveil this mystery by describing the functional relevance of microRNAs, and examining which genes are regulated by non-protein-coding DNA. Here, I describe alcohol regulation of microRNAs and provide examples of microRNAs that control the expression of alcohol-relevant genes. Emphasis is put on the potential of microRNAs in explaining the polygenic nature of alcoholism and prospects of microRNA research and future directions of this burgeoning field.
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102
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Fabian MR, Sundermeier TR, Sonenberg N. Understanding How miRNAs Post-Transcriptionally Regulate Gene Expression. MIRNA REGULATION OF THE TRANSLATIONAL MACHINERY 2010; 50:1-20. [DOI: 10.1007/978-3-642-03103-8_1] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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103
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Vinuesa CG, Rigby RJ, Yu D. Logic and extent of miRNA-mediated control of autoimmune gene expression. Int Rev Immunol 2009; 28:112-38. [PMID: 19811318 DOI: 10.1080/08830180902934909] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Over the past few decades, multiple mechanisms have emerged that operate to prune the lymphocyte repertoire of self-reactive specificities and maintain immunological tolerance. Multiple families of small noncoding RNAs known as microRNAs (miRNAs) target immune transcripts to fine-tune gene expression and turn on negative feedback loops. Both of these actions are crucial to limit co-stimulation, set precise cellular activation thresholds, curtail inflammation, control lymphocyte growth, and maintain regulatory T cell homeostasis and suppressive function. Analysis of predicted miRNA-mediated regulation of 72 lupus susceptibility genes in humans and mice reveals most contain numerous target sites for over 140 miRNAs conserved in mammals. MECP2, ROQUIN/RC3H1, BCL2, BIM, and PTEN contain over 50 miRNA target sites each, highlighting the need to control their final protein products with enormous precision to maintain the balance between immunity and tolerance. Overlap among targets of individual miRNAs is considerable, with each miRNA targeting a median of nine autoimmune genes. Three miRNAs--miR-181, miR-186, and miR-590-3p--together are predicted to target over 50% of all lupus genes. Also, a single miRNA cluster located at 14q32.31 containing 11 miRNAs is predicted to regulate 48 lupus susceptibility genes. Dysregulation of single or a few miRNAs or miRNA clusters can result from genetic variation, hormonal influences, or environmental triggers including EBV infection. In the light of this vast and promiscuous miRNA-mediated regulation of autoimmune genes it is anticipated that changes in miRNA levels or their target sequences will help explain susceptibility to complex autoimmune diseases.
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Affiliation(s)
- Carola G Vinuesa
- John Curtin School of Medical Research, Australian National University, Canberra, Australia.
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104
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Zhao S, Liu MF. Mechanisms of microRNA-mediated gene regulation. ACTA ACUST UNITED AC 2009; 52:1111-6. [PMID: 20016967 DOI: 10.1007/s11427-009-0152-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2008] [Accepted: 11/28/2008] [Indexed: 01/07/2023]
Abstract
microRNAs (miRNAs) are identified as a class of non-protein regulators and a new source for broad control of gene expression in eukaryotes. The past years have witnessed substantial progress in understanding miRNA functions and mechanisms, although a few controversies remain. Various hypotheses and models have been suggested for the mechanisms of miRNA repression, including translational inhibition at the level of initiation or elongation, rapid degradation of the nascent peptide, mRNA degradation, and mRNA sequestration into P bodies (processing bodies) and SGs (stress granules) for degradation or/and storage. Recently, some noncanonical miRNA regulation, such as miRNA activation and de-repression of miRNA inhibition, have been uncovered. This review discusses some recent advances about how miRNAs regulate their targets and various modes of miRNA function.
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Affiliation(s)
- Shuang Zhao
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, the Chinese Academy of Sciences, Shanghai, China
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105
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MicroRNA mir-346 targets the 5′-untranslated region of receptor-interacting protein 140 (RIP140) mRNA and up-regulates its protein expression. Biochem J 2009; 424:411-8. [DOI: 10.1042/bj20090915] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
RIP140 (receptor-interacting protein 140) is a transcriptional co-repressor that regulates diverse genes such as those responsive to hormones and involved in metabolic processes. The expression of RIP140 is regulated by multiple hormonal activities in adipose tissue and cancer cell lines. However, it is unclear whether and how RIP140 is regulated post-transcriptionally. Using 5′RACE (rapid amplification of 5′ cDNA ends), we have identified a novel 5′ splice variant of RIP140 mRNA in mouse brain and P19 cells. A target sequence for miRNA (microRNA) mir-346 was found in the 5′UTR (5′-untranslated region) of RIP140 mRNA; this miRNA is also expressed endogenously in mouse brain and P19 cells. Gain- and loss-of-function studies demonstrated that mir-346 elevates RIP140 protein levels by facilitating association of its mRNA with the polysome fraction. Furthermore, the activity of mir346 does not require Ago-2 (Argonaute 2). The expression of mir-346 enhances the gene repressive activity of RIP140. This is the first report demonstrating post-transcriptional regulation of RIP140 mRNA, involving the enhancing effect of a specific miRNA that targets RIP140's 5′UTR.
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106
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Hu Z. Insight into microRNA regulation by analyzing the characteristics of their targets in humans. BMC Genomics 2009; 10:594. [PMID: 20003303 PMCID: PMC2799441 DOI: 10.1186/1471-2164-10-594] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2009] [Accepted: 12/10/2009] [Indexed: 01/24/2023] Open
Abstract
Background microRNAs (miRNAs) are believed to regulate their targets through posttranscriptional gene regulation and have the potential to silence gene expression via multiple mechanisms. Despite previous advances on miRNA regulation of gene expression, little has been investigated from a genome scale. Results To gain new insight into miRNA regulation in humans, we used large scale data and carried out a series of studies to compare various features of miRNA target genes to that of non-miRNA target genes. We observed significant differences between miRNA and non-miRNA target genes for a number of characteristics, including higher and broader mRNA expression, faster mRNA decay rate, longer protein half-life, and longer gene structures. Based on these features and by analyzing their relationships we found that miRNA target genes, other than having miRNA repression, were most likely under more complex regulation than non-miRNA target genes, which was evidenced by their higher and broader gene expression but longer gene structures. Our results of higher and broader gene expression but fast mRNA decay rates also provide evidence that miRNA dampening of the output of preexisting transcripts facilitates a more rapid and robust transition to new expression programs. This could be achieved by enhancing mRNA degradation through an additive effect from multiple miRNA targeting. Conclusion Genome-scale analysis on the nature of miRNA target genes has revealed a general mechanism for miRNA regulation of human gene expression. The results of this study also indicate that miRNA target genes, other than having miRNA repression, are under more complex gene regulation than non-miRNA target genes. These findings provide novel insight into miRNA regulation of human gene expression.
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Affiliation(s)
- Zihua Hu
- Center for Computational Research, New York State Center of Excellence in Bioinformatics & Life Sciences, Department of Biostatistics, Department of Medicine, State University of New York (SUNY), Buffalo, NY 14260, USA.
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107
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Abstract
TNFalpha (tumour necrosis factor alpha) mRNA bears in its 3'-UTR (untranslated region) a conserved ARE (AU-rich element), a signal that exerts tight post-transcriptional control over the expression of TNFalpha and other cytokines. We found that the TNFalpha ARE increases translational efficiency when cell growth is arrested, a physiologically relevant state occurring during inflammation, angiogenesis and monocyte differentiation. Under these conditions, called quiescence, the miRNP (microribonucleoprotein)-associated proteins FXR1 (Fragile X mental retardation-related protein 1) and AGO2 (Argonaute 2), which are usually considered negative regulators, are transformed into effector molecules that bind the ARE to activate translation. We then identified a specific miRNA (microRNA) that directs the association of AGO2 and FXR1 with the ARE during translational up-regulation. Two other well-characterized miRNAs likewise promote translation activation in quiescent or in contact-inhibited cells; yet, they repress translation in proliferating cells in the late S/G(2)-phase. We conclude that translational regulation by miRNPs oscillates between repression and activation as a function of the cell cycle. The activating role of miRNAs is now being confirmed in the immature Xenopus oocyte, which mimics the quiescent state.
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108
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Greither T, Grochola LF, Udelnow A, Lautenschläger C, Würl P, Taubert H. Elevated expression of microRNAs 155, 203, 210 and 222 in pancreatic tumors is associated with poorer survival. Int J Cancer 2009; 126:73-80. [PMID: 19551852 DOI: 10.1002/ijc.24687] [Citation(s) in RCA: 360] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Pancreatic cancer is the eighth most common cancer and has an overall 5-year survival rate lower than 10%. Because of their ability to regulate gene expression, microRNAs can act as oncogenes or tumor-suppressor genes and so have garnered interest as possible prognostic and therapeutic markers during the last decade. However, the prognostic value of microRNA expression in pancreatic cancer has not been thoroughly investigated. We measured the levels of miR-155, miR-203, miR-210, miR-216, miR-217 and miR-222 by quantitative RT-PCR in a cohort of 56 microdissected pancreatic ductal adenocarcinomas (PDAC). These microRNAs were chosen as they had previously been shown to be differentially expressed in pancreatic tumors compared to normal tissues. The possible association of microRNA expression and patients' survival was examined using multivariate Cox's regression hazard analyses. Interestingly, significant correlations between elevated microRNA expression and overall survival were observed for miR-155 (RR = 2.50; p = 0.005), miR-203 (RR = 2.21; p = 0.017), miR-210 (RR = 2.48; p = 0.005) and miR-222 (RR = 2.05; p = 0.035). Furthermore, tumors from patients demonstrating elevated expression levels of all 4 microRNAs possessed a 6.2-fold increased risk of tumor-related death compared to patients whose tumors showed a lower expression of these microRNAs. This study provides the first evidence for an oncogenic activity of miR-155, miR-203, miR-210 and miR-222 in the development of pancreatic cancer as has been reported for other tumor types. Furthermore, the putative target genes for these microRNAs suggest a complex signaling network that can affect PDAC tumorigenesis and tumor progression.
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Affiliation(s)
- Thomas Greither
- Clinic of Radiation Therapy, Martin-Luther University, Halle, Wittenberg, Germany
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109
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Eacker SM, Dawson TM, Dawson VL. Understanding microRNAs in neurodegeneration. Nat Rev Neurosci 2009; 10:837-41. [PMID: 19904280 DOI: 10.1038/nrn2726] [Citation(s) in RCA: 227] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Interest in the functions of microRNAs (miRNAs) in the nervous system has recently expanded to include their roles in neurodegeneration. Investigations have begun to reveal the influence of miRNAs on both neuronal survival and the accumulation of toxic proteins that are associated with neurodegeneration, and are providing clues as to how these toxic proteins can influence miRNA expression.
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Affiliation(s)
- Stephen M Eacker
- Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.
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110
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Alternative splicing in the differentiation of human embryonic stem cells into cardiac precursors. PLoS Comput Biol 2009; 5:e1000553. [PMID: 19893621 PMCID: PMC2764345 DOI: 10.1371/journal.pcbi.1000553] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2008] [Accepted: 10/02/2009] [Indexed: 12/21/2022] Open
Abstract
The role of alternative splicing in self-renewal, pluripotency and tissue lineage specification of human embryonic stem cells (hESCs) is largely unknown. To better define these regulatory cues, we modified the H9 hESC line to allow selection of pluripotent hESCs by neomycin resistance and cardiac progenitors by puromycin resistance. Exon-level microarray expression data from undifferentiated hESCs and cardiac and neural precursors were used to identify splice isoforms with cardiac-restricted or common cardiac/neural differentiation expression patterns. Splice events for these groups corresponded to the pathways of cytoskeletal remodeling, RNA splicing, muscle specification, and cell cycle checkpoint control as well as genes with serine/threonine kinase and helicase activity. Using a new program named AltAnalyze (http://www.AltAnalyze.org), we identified novel changes in protein domain and microRNA binding site architecture that were predicted to affect protein function and expression. These included an enrichment of splice isoforms that oppose cell-cycle arrest in hESCs and that promote calcium signaling and cardiac development in cardiac precursors. By combining genome-wide predictions of alternative splicing with new functional annotations, our data suggest potential mechanisms that may influence lineage commitment and hESC maintenance at the level of specific splice isoforms and microRNA regulation. The reprogramming of pluripotent stem cells from adult cells is a crucial step toward producing patient-specific cells for transplant therapy. Critical to this goal is the ability to reproducibly drive the differentiation of these cells to specific fates, such as cardiac and neural cells. While gene expression is important in tissue specific differentiation, the impact of alternative splicing on the biology of differentiating cells has not been fully realized. To identify specific splicing events that may determine cell-type-specific differentiation, we compared splicing profiles of human embryonic stem cells (ESCs) and derived cardiac and neural precursors using Affymetrix exon tiling arrays. Segregation of splicing profiles into cardiac-restricted and common cardiac/neural differentiation pattern groups revealed unique groups of genes with clear implications for the biology of cardiomyocyte function and the maintenance of pluripotent ESCs. Alternative splicing of many of these genes, notably regulators of cell death and proliferation, were often predicted to impact protein domain or microRNA binding site inclusion, suggesting that the function or expression of these proteins is altered during differentiation. These results provide further evidence that alternative splicing is important in shaping the functional repertoire of ESCs and differentiated cells.
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111
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MicroRNAs and epigenetic regulation in the mammalian inner ear: implications for deafness. Mamm Genome 2009; 20:581-603. [PMID: 19876605 DOI: 10.1007/s00335-009-9230-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2009] [Accepted: 09/30/2009] [Indexed: 01/19/2023]
Abstract
Sensorineural hearing loss is the most common sensory disorder in humans and derives, in most cases, from inner-ear defects or degeneration of the cochlear sensory neuroepithelial hair cells. Genetic factors make a significant contribution to hearing impairment. While mutations in 51 genes have been associated with hereditary sensorineural nonsyndromic hearing loss (NSHL) in humans, the responsible mutations in many other chromosomal loci linked with NSHL have not been identified yet. Recently, mutations in a noncoding microRNA (miRNA) gene, MIR96, which is expressed specifically in the inner-ear hair cells, were linked with progressive hearing loss in humans and mice. Furthermore, additional miRNAs were found to have essential roles in the development and survival of inner-ear hair cells. Epigenetic mechanisms, in particular, DNA methylation and histone modifications, have also been implicated in human deafness, suggesting that several layers of noncoding genes that have never been studied systematically in the inner-ear sensory epithelia are required for normal hearing. This review aims to summarize the current knowledge about the roles of miRNAs and epigenetic regulatory mechanisms in the development, survival, and function of the inner ear, specifically in the sensory epithelia, tectorial membrane, and innervation, and their contribution to hearing.
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112
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MicroRNAs in brain development and physiology. Curr Opin Neurobiol 2009; 19:461-70. [DOI: 10.1016/j.conb.2009.09.006] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2009] [Accepted: 09/18/2009] [Indexed: 01/06/2023]
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113
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Breving K, Esquela-Kerscher A. The complexities of microRNA regulation: mirandering around the rules. Int J Biochem Cell Biol 2009; 42:1316-29. [PMID: 19800023 DOI: 10.1016/j.biocel.2009.09.016] [Citation(s) in RCA: 175] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2009] [Revised: 09/21/2009] [Accepted: 09/22/2009] [Indexed: 02/06/2023]
Abstract
MicroRNAs (miRNAs) are an important class of non-coding small RNAs that possess a large range of biological activities in a variety of organisms and are linked to human diseases such as cancer. Initially, miRNAs were thought to act solely as negative regulators of gene expression and exert their effects by binding to regions within the 3'UTR of their target protein-coding messenger RNAs (mRNAs) in a sequence dependent manner. However, recent data reveals that miRNA regulation entails a far more complex system of post-transcriptional control than initially appreciated. An evolving consensus has emerged of how miRNAs can repress as well as activate gene expression by interacting with complementary regions found in the promoter, coding region, as well as the 3'UTR of their mRNA targets. Furthermore, miRNAs are extensively regulated at the levels of miRNA promoter transcription, methylation, miRNA processing, RNA editing, and miRNA-target interactions. This review will discuss new insights into miRNA-based mechanisms and the role specific DNA- and RNA-binding factors play in fine-tuning gene expression in both negative and positive ways by directing miRNA biogenesis and activity. We will also discuss the influence that cellular context and environmental cues have on miRNA function. In the future, a clear understanding of miRNA regulation will be essential when understanding the role miRNAs play during animal development and in maintaining adult homeostasis as well as exploring the use of small RNAs for diagnostic and therapeutic purposes.
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Affiliation(s)
- Kimberly Breving
- Department of Microbiology and Molecular Cell Biology, 700 West Olney Road, Eastern Virginia Medical School, Norfolk, VA 23507, USA
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114
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Multivesicular bodies associate with components of miRNA effector complexes and modulate miRNA activity. Nat Cell Biol 2009; 11:1143-9. [PMID: 19684575 DOI: 10.1038/ncb1929] [Citation(s) in RCA: 784] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2009] [Accepted: 05/28/2009] [Indexed: 12/11/2022]
Abstract
In animals, P-bodies or GW-bodies appear to cause the congregation of proteins involved in microRNA (miRNA)-mediated post-transcriptional silencing. The localization of P-bodies does not overlap with that of known organelles and are thus considered independent of lipid bilayers. Nonetheless, an miRNA effector protein, argonaute 2 (AGO2), was initially identified as membrane-associated, and some miRNAs have been found in secreted vesicles (exosomes) that derive from endo-lysosomal compartments called multivesicular bodies (MVBs). Proteins can be sorted in a ubiquitin-dependent manner into MVBs by three heteromeric subcomplexes, collectively termed ESCRT (endosomal sorting complex required for transport), to be further secreted in exosomes and/or degraded by the lysosome. Here we show that GW-bodies containing GW182 and AGO2, two main components of the RNA-induced silencing complex (RISC), are distinct from P-bodies due to their congregation with endosomes and MVBs. Moreover, miRNAs and miRNA-repressible mRNAs are enriched at these cellular membranes, suggesting that endosomes and/or MVBs are sites of miRNA-loaded RISC (miRISC) accumulation and, possibly, action. We further show that purified exosome-like vesicles secreted by MVBs are considerably enriched in GW182, but not P-body components, AGO2 or miRNA-repressible mRNA. Moreover, cells depleted of some ESCRT components show compromised miRNA-mediated gene silencing and over-accumulate GW182, which associates with ubiquitylated proteins. Therefore, GW182, possibly in association with a fraction of miRNA-loaded AGO2, is sorted into MVBs for secretion and/or lysosomal degradation. We propose that this process promotes continuous assembly or disassembly of membrane-associated miRISCs, which is possibly required for miRNA loading or target recognition and subsequent silencing.
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115
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Roush SF, Slack FJ. Transcription of the C. elegans let-7 microRNA is temporally regulated by one of its targets, hbl-1. Dev Biol 2009; 334:523-34. [PMID: 19627983 DOI: 10.1016/j.ydbio.2009.07.012] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2009] [Revised: 07/10/2009] [Accepted: 07/12/2009] [Indexed: 11/26/2022]
Abstract
The let-7 family of microRNAs (miRNAs) are important regulators of developmental timing and cell differentiation and are often misexpressed in human cancer. In C. elegans, let-7 controls cell fate transitions from larval stage 4 (L4) to adulthood by post-transcriptionally down-regulating lineage-abnormal 41 (lin-41) and hunchback-like 1 (hbl-1). Primary let-7 (pri-let-7) transcripts are up-regulated in the L3, yet little is known about what controls this transcriptional up-regulation. We sought factors that either turn on let-7 transcription or keep it repressed until the correct time. Here we report that one of let-7's targets, the transcription factor Hunchback-like 1 (HBL-1), is responsible for inhibiting the transcription of let-7 in specific tissues until the L3. hbl-1 is a known developmental timing regulator and inhibits adult development in larval stages. Therefore, one important function of HBL-1 in maintaining larval stage fates is inhibition of let-7. Indeed, our results reveal let-7 as the first known target of the HBL-1 transcription factor in C. elegans and suggest a negative feedback loop mechanism for let-7 and HBL-1 regulation.
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Affiliation(s)
- Sarah F Roush
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
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116
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Abstract
This review is focused on current findings implicating miRNAs in the polycystic liver diseases, which we categorized as cholangiociliopathies. Our recent data suggest that deregulation of miRNA pathways is emerging as a novel mechanism in the development of cholangiociliopathies. Experimental evidence demonstrates that miRNAs (i.e., miR-15a) influence hepatic cyst growth by affecting the expression of the cell cycle regulator, Cdc25A. Given that abnormalities in many cellular processes (i.e., cell cycle regulation, cell proliferation, cAMP and calcium signaling, the EGF-stimulated mitogen-activated protein kinase (MAPK) pathway and fluid secretion) contribute to the hepatic cystogenesis, the potential role of miRNAs in regulation of these processes is discussed.
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Affiliation(s)
- Tatyana Masyuk
- Miles and Shirley Fiterman Center for Digestive Diseases, Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
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117
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Zipprich JT, Bhattacharyya S, Mathys H, Filipowicz W. Importance of the C-terminal domain of the human GW182 protein TNRC6C for translational repression. RNA (NEW YORK, N.Y.) 2009; 15:781-93. [PMID: 19304925 PMCID: PMC2673060 DOI: 10.1261/rna.1448009] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Proteins of the GW182 family play an important role in the execution of microRNA repression in metazoa. They interact directly with Argonaute proteins, components of microRNPs, and also form part of P-bodies, structures implicated in translational repression and mRNA degradation. Recent results demonstrated that Drosophila GW182 has the potential to both repress translation and accelerate mRNA deadenylation and decay. In contrast to a single GW182 protein in Drosophila, the three GW182 paralogs TNRC6A, TNRC6B, and TNRC6C are encoded in mammalian genomes. In this study, we provide evidence that TNRC6C, like TNRC6A and TNRC6B, is important for efficient miRNA repression. We further demonstrate that tethering of each of the human TNRC6 proteins to a reporter mRNA has a dramatic inhibitory effect on protein synthesis. The repression is due to a combination of effects on the mRNA level and mRNA translation. Through deletion and mutagenesis, we identified the C-terminal part of TNRC6C encompassing the RRM RNA-binding motif as a key effector domain mediating protein synthesis repression by TNRC6C.
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Affiliation(s)
- Jakob T Zipprich
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
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118
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MicroRNAs are essential for development and function of inner ear hair cells in vertebrates. Proc Natl Acad Sci U S A 2009; 106:7915-20. [PMID: 19416898 DOI: 10.1073/pnas.0812446106] [Citation(s) in RCA: 149] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
MicroRNAs (miRNAs) inhibit the translation of target mRNAs and affect, directly or indirectly, the expression of a large portion of the protein-coding genes. This study focuses on miRNAs that are expressed in the mouse cochlea and vestibule, the 2 inner ear compartments. A conditional knock-out mouse for Dicer1 demonstrated that miRNAs are crucial for postnatal survival of functional hair cells of the inner ear. We identified miRNAs that have a role in the vertebrate developing inner ear by combining miRNA transcriptome analysis, spatial and temporal expression patterns, and bioinformatics. Microarrays revealed similar miRNA profiles in newborn-mouse whole cochleae and vestibules, but different temporal and spatial expression patterns of six miRNAs (miR-15a, miR-18a, miR-30b, miR-99a, miR-182, and miR-199a) may reflect their roles. Two of these miRNAs, miR-15a-1 and miR-18a, were also shown to be crucial for zebrafish inner ear development and morphogenesis. To suggest putative target mRNAs whose translation may be inhibited by selected miRNAs, we combined bioinformatics-based predictions and mRNA expression data. Finally, we present indirect evidence that Slc12a2, Cldn12, and Bdnf mRNAs may be targets for miR-15a. Our data support the hypothesis that inner ear tissue differentiation and maintenance are regulated and controlled by conserved sets of cell-specific miRNAs in both mouse and zebrafish.
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119
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Chang S, Wen S, Chen D, Jin P. Small regulatory RNAs in neurodevelopmental disorders. Hum Mol Genet 2009; 18:R18-26. [PMID: 19297398 DOI: 10.1093/hmg/ddp072] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Increasingly complex networks of small RNAs act through RNA interference pathway to regulate gene expression. Recent evidence suggests that both development and proper function of central nervous system require intricate spatiotemporal expression of a wide repertoire of small regulatory RNAs. Misregulation of these small regulatory RNAs could contribute to the abnormalities in brain development that are associated with neurodevelopmental disorders. Here, we will review recent progress made toward understanding roles of small regulatory RNAs in neurodevelopmental disorders and discuss the potential involvement of newly discovered classes of small RNAs in these disorders.
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Affiliation(s)
- Shuang Chang
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
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120
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Nimmo RA, Slack FJ. An elegant miRror: microRNAs in stem cells, developmental timing and cancer. Chromosoma 2009; 118:405-18. [PMID: 19340450 DOI: 10.1007/s00412-009-0210-z] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2008] [Revised: 03/17/2009] [Accepted: 03/17/2009] [Indexed: 12/27/2022]
Abstract
MicroRNAs (miRNAs) were first discovered in genetic screens for regulators of developmental timing in the stem-cell-like seam cell lineage in Caenorhabditis elegans. As members of the heterochronic pathway, the lin-4 and let-7 miRNAs are required in the seam cells for the correct progression of stage-specific events and to ensure that cell cycle exit and terminal differentiation occur at the correct time. Other heterochronic genes such as lin-28 and lin-41 are direct targets of the lin-4 and let-7 miRNAs. Recent findings on the functions of the let-7 and lin-4/mir-125 miRNA families and lin-28 and lin-41 orthologs from a variety of organisms suggest that core elements of the heterochronic pathway are retained in mammalian stem cells and development. In particular, these genes appear to form bistable switches via double-negative feedback loops in both nematode and mammalian stem cell development, the functional relevance of which is finally becoming clear. let-7 inhibits stem cell self-renewal in both normal and cancer stem cells of the breast and acts as a tumor suppressor in lung and breast cancer. let-7 also promotes terminal differentiation at the larval to adult transition in both nematode stem cells and fly wing imaginal discs and inhibits proliferation of human lung and liver cancer cells. Conversely, LIN-28 is a highly specific embryonic stem cell marker and is one of four "stemness" factors used to reprogram adult fibroblasts into induced pluripotent stem cells; furthermore, lin-28 is oncogenic in hepatocellular carcinomas. Therefore, a core module of heterochronic genes--lin-28, lin-41, let-7, and lin-4/mir-125-acts as an ancient regulatory switch for differentiation in stem cells (and in some cancers), illustrating that nematode seam cells mirror miRNA regulatory networks in mammalian stem cells during both normal development and cancer.
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Affiliation(s)
- Rachael A Nimmo
- Department of Molecular, Cellular and Developmental Biology, Yale University, P.O. Box 208103, New Haven, CT 06520, USA
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121
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Abstract
Recent genome-wide interrogations of transcribed RNA have yielded compelling evidence for pervasive and complex transcription throughout a large majority of the human genome. Tens of thousands of noncoding RNA transcripts have been identified, most of which have yet to be functionally characterized. Along with the revelation that noncoding RNAs in the human genome are surprisingly abundant, there has been a surge in molecular and genetic data showing important and diverse regulatory roles for noncoding RNA. In this report, we summarize the potential roles that noncoding RNAs may play in the molecular pathogenesis of different mental retardation disorders. We suspect that these findings are just the tip of the iceberg, with noncoding RNAs possibly being involved in disease pathogenesis at different levels and through multiple distinct mechanisms.
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Affiliation(s)
- K E Szulwach
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
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122
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Jeffries CD, Fried HM, Perkins DO. Additional layers of gene regulatory complexity from recently discovered microRNA mechanisms. Int J Biochem Cell Biol 2009; 42:1236-42. [PMID: 20460095 DOI: 10.1016/j.biocel.2009.02.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2008] [Revised: 01/30/2009] [Accepted: 02/09/2009] [Indexed: 01/07/2023]
Abstract
In recent years microRNAs have become recognized as pervasive, versatile agents of gene regulation. Some widely embraced rules involving Watson-Crick hybridization of microRNAs with mRNAs have generated great interest as scientists envision potential RNA cargoes for gene therapy and other experimental systems. However, while researchers ardently seek simplifying principles, nature seems very uncooperative. This article reviews some small RNA mechanisms that potentially regulate genes and which are not covered by previous microRNAs characterizations. In addition, we report here results of fluorescence microscopy experiments to directly demonstrate nuclear import of small RNAs equal in length to typical mature microRNAs, implying that gene regulation at the locus of transcription might be possible.
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Affiliation(s)
- Clark D Jeffries
- Renaissance Computing Institute and Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, CB 360, Chapel Hill, NC 27599, USA.
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123
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Abstract
MicroRNAs (miRNAs) are endogenous approximately 23 nt RNAs that play important gene-regulatory roles in animals and plants by pairing to the mRNAs of protein-coding genes to direct their posttranscriptional repression. This review outlines the current understanding of miRNA target recognition in animals and discusses the widespread impact of miRNAs on both the expression and evolution of protein-coding genes.
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Affiliation(s)
- David P Bartel
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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124
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Abstract
MicroRNAs (miRNAs) are endogenous approximately 23 nt RNAs that play important gene-regulatory roles in animals and plants by pairing to the mRNAs of protein-coding genes to direct their posttranscriptional repression. This review outlines the current understanding of miRNA target recognition in animals and discusses the widespread impact of miRNAs on both the expression and evolution of protein-coding genes.
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Affiliation(s)
- David P Bartel
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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125
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Havelange V, Heaphy CEA, Garzon R. MicroRNAs in the diagnosis, prognosis and treatment of cancer. Oncol Rev 2008. [DOI: 10.1007/s12156-008-0076-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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126
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Abstract
MicroRNAs (miRNAs) are a family of endogenous small noncoding RNA molecules, of 19–28 nucleotides in length. In humans, up to 3% of all genes are estimated to encode these evolutionarily conserved sequences. miRNAs are thought to control expression of thousands of target mRNAs. Mammalian miRNAs generally negatively regulate gene expression by repressing translation, possibly through effects on mRNA stability and compartmentalisation, and/or the translation process itself. An extensive range of in silico and experimental techniques have been applied to our understanding of the occurrence and functional relevance of such sequences, and antisense technologies have been successfully used to control miRNA expression in vitro and in vivo. Interestingly, miRNAs have been identified in both normal and pathological conditions, including differentiation and development, metabolism, proliferation, cell death, viral infection and cancer. Of specific relevance and excitement to the area of diabetes research, miRNA regulation has been implicated in insulin secretion from pancreatic β-cells, diabetic heart conditions and nephropathy. Further analyses of miRNAs in vitro and in vivo will, undoubtedly, enable us determine their potential to be exploited as therapeutic targets in diabetes.
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