Identification of target genes of microRNAs in retinoic acid-induced neuronal differentiation

2005 ◽  
Vol 77 (1) ◽  
pp. 313-318 ◽  
Author(s):  
Hiroaki Kawasaki ◽  
Kazunari Taira
Keyword(s):  
Retinoic Acid ◽  
Neuronal Differentiation ◽  
Small Rnas ◽  
Target Genes ◽  
Noncoding Rnas ◽  
Messenger Rnas ◽  
Regulate Gene Expression ◽  
Small Noncoding Rnas ◽  
Translational Level ◽  
Regulate Gene

MicroRNAs (miRNAs) are phylogenetically widespread, small noncoding RNAs of 18–25 nucleotides in length, and are expressed in animals and plants. These small RNAs can regulate gene expression at the translational level through interactions with their target messenger RNAs, and have a role in the development of Caenorhabditis elegans, plants, and mammals. Although more than 200 miRNAs have been found in mammals, it is not easy to identify their targets. We investigated the target genes of miRNAs and analyzed the function of these miRNAs during retinoic acid (RA)-induced neuronal differentiation.

scholarly journals Prediction of MicroRNA Precursors Using Parsimonious Feature Sets

2014 ◽  
Vol 13s1 ◽  
pp. CIN.S13877
Author(s):  
Petra Stepanowsky ◽  
Eric Levy ◽  
Jihoon Kim ◽  
Xiaoqian Jiang ◽  
Lucila Ohno-Machado
Keyword(s):  
Noncoding Rnas ◽  
Real Data ◽  
Minimum Free Energy ◽  
Messenger Rnas ◽  
Data Set ◽  
Regulate Gene Expression ◽  
Feature Sets ◽  
Structure Characteristics ◽  
Precursor Mirnas ◽  
Regulate Gene

MicroRNAs (miRNAs) are a class of short noncoding RNAs that regulate gene expression through base pairing with messenger RNAs. Due to the interest in studying miRNA dysregulation in disease and limits of validated miRNA references, identification of novel miRNAs is a critical task. The performance of different models to predict novel miRNAs varies with the features chosen as predictors. However, no study has systematically compared published feature sets. We constructed a comprehensive feature set using the minimum free energy of the secondary structure of precursor miRNAs, a set of nucleotide-structure triplets, and additional extracted sequence and structure characteristics. We then compared the predictive value of our comprehensive feature set to those from three previously published studies, using logistic regression and random forest classifiers. We found that classifiers containing as few as seven highly predictive features are able to predict novel precursor miRNAs as well as classifiers that use larger feature sets. In a real data set, our method correctly identified the holdout miRNAs relevant to renal cancer.

scholarly journals miR in melanoma development: miRNAs and acquired hallmarks of cancer in melanoma

2013 ◽  
Vol 45 (22) ◽  
pp. 1049-1059 ◽  
Author(s):  
Paige E. Bennett ◽  
Lynne Bemis ◽  
David A. Norris ◽  
Yiqun G. Shellman
Keyword(s):  
Gene Expression ◽  
Systematic Review ◽  
Therapeutic Potential ◽  
Noncoding Rnas ◽  
Review Of The Literature ◽  
Cancer Model ◽  
Hallmarks Of Cancer ◽  
Regulate Gene Expression ◽  
Small Noncoding Rnas ◽  
Regulate Gene

Melanoma is a very aggressive skin cancer with increasing incidence worldwide. MicroRNAs are small, noncoding RNAs that regulate gene expression of targeted gene(s). The hallmark of cancer model outlined by Hanahan and Weinberg offers a meaningful framework to consider the roles of microRNAs in melanoma development and progression. In this systematic review of the literature, we associate what is known about deregulation of microRNAs and their targeted genes in melanoma development with the hallmarks and characteristics of cancer. The diagnostic and therapeutic potential of microRNAs for future melanoma management will also be discussed.

The physiological and pathophysiological roles of adipocyte miRNAs

2013 ◽  
Vol 91 (4) ◽  
pp. 195-202 ◽  
Author(s):  
Hongyan Ling ◽  
Xing Li ◽  
Chao Hua Yao ◽  
Bi Hu ◽  
Duanfang Liao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Adipocyte Differentiation ◽  
Noncoding Rnas ◽  
Biological Processes ◽  
Insulin Production ◽  
Regulate Gene Expression ◽  
Small Noncoding Rnas ◽  
And Function ◽  
Posttranscriptional Level ◽  
Regulate Gene

MicroRNAs (miRNAs) are highly conserved, small, noncoding RNAs that regulate gene expression at the posttranscriptional level. Their actions affect numerous important biological processes, including adipocyte differentiation and function, sugar and lipid metabolism, and insulin production and secretion. Recent reports suggest miRNAs may also be involved in the pathogenic processes of obesity, diabetes, and insulin resistance. In this review, we summarize research progresses on adipocyte miRNAs and their physiological and pathological implications.

scholarly journals Small RNAs with 5′-Polyphosphate Termini Associate with a Piwi-Related Protein and Regulate Gene Expression in the Single-Celled Eukaryote Entamoeba histolytica

2008 ◽  
Vol 4 (11) ◽  
pp. e1000219 ◽  
Author(s):  
Hanbang Zhang ◽  
Gretchen M. Ehrenkaufer ◽  
Justine M. Pompey ◽  
Jason A. Hackney ◽  
Upinder Singh
Keyword(s):  
Gene Expression ◽  
Entamoeba Histolytica ◽  
Small Rnas ◽  
Related Protein ◽  
Regulate Gene Expression ◽  
Regulate Gene

scholarly journals 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) and Polychlorinated Biphenyl Coexposure Alters the Expression Profile of MicroRNAs in the Liver Associated with Atherosclerosis

2020 ◽  
Vol 2020 ◽  
pp. 1-12
Author(s):  
Qiuli Shan ◽  
Fan Qu ◽  
Ningning Chen
Keyword(s):  
Small Rnas ◽  
Polychlorinated Biphenyl ◽  
System Development ◽  
Complex Mixtures ◽  
Regulate Gene Expression ◽  
Significant Expression ◽  
And Function ◽  
Function Network ◽  
Regulate Gene

MicroRNAs (miRNAs) are a class of small RNAs that regulate gene expression. 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) and polychlorinated biphenyls (PCBs) are persistent organic pollutants that exist as complex mixtures in vivo. When humans are simultaneously exposed to these compounds, the development of atherosclerosis is known to be enhanced. However, the roles of miRNA in TCDD- and PCB-induced atherosclerosis are largely unknown. Therefore, the present study is aimed at elucidating the possible dysregulation of miRNAs in atherogenesis induced by coexposure to TCDD and PCBs. Eight-week-old male ApoE-/- mice were coexposed to TCDD (15 μg/kg) and Aroclor1254 (55 mg/kg, a representative mixture of PCBs) by intraperitoneal injection four times over a 6-week period. Microarray analysis of miRNAs and mRNAs in the liver of ApoE-/- mice with or without TCDD and Aroclor1254 coexposure was performed. We discovered that 68 miRNAs and 1312 mRNAs exhibited significant expression changes in response to TCDD and PCB coexposure and revealed that both changed miRNAs and mRNAs are involved in cardiovascular disease processes. An integrated miRNA-mRNA approach indicated that miRNA-26a-5p, miRNA-193a-3p, and miRNA-30c-5p participated in specific TCDD and Aroclor1254 coresponsive networks which are relevant to the cardiovascular system development and function network. Furthermore, our results also indicated that miRNA-130a-3p and miRNA-376a-3p were novel players in the regulation of TCDD- and Aroclor1254-induced atherosclerosis pathways. In summary, our finding provided new insights into the mechanism of atherosclerosis in response to TCDD and PCB coexposure.

scholarly journals Dietary microRNA—A Novel Functional Component of Food

2019 ◽  
Vol 10 (4) ◽  
pp. 711-721 ◽  
Author(s):  
Lin Zhang ◽  
Ting Chen ◽  
Yulong Yin ◽  
Chen-Yu Zhang ◽  
Yong-Liang Zhang
Keyword(s):  
Gene Expression ◽  
Small Rnas ◽  
Biological Significance ◽  
Circulatory System ◽  
Physiological Effects ◽  
Biological Processes ◽  
Regulate Gene Expression ◽  
Functional Component ◽  
Health And Disease ◽  
Regulate Gene

ABSTRACT MicroRNAs are a class of small RNAs that play essential roles in various biological processes by silencing genes. Evidence emerging in recent years suggests that microRNAs in food can be absorbed into the circulatory system and organs of humans and other animals, where they regulate gene expression and biological processes. These food-derived dietary microRNAs may serve as a novel functional component of food, a role that has been neglected to date. However, a significant amount of evidence challenges this new concept. The absorption, stability, and physiological effects of dietary microRNA in recipients, especially in mammals, are currently under heavy debate. In this review, we summarize our current understanding of the unique characteristics of dietary microRNAs and concerns about both the mechanistic and methodological basis for studying the biological significance of dietary microRNAs. Such efforts will benefit continuing investigations and offer new perspectives for the interpretation of the roles of dietary microRNA with respect to the health and disease of humans and animals.

scholarly journals miR-615 Fine-Tunes Growth and Development and Has a Role in Cancer and in Neural Repair

Cells ◽  
2020 ◽  
Vol 9 (7) ◽  
pp. 1566 ◽  
Author(s):  
Marisol Godínez-Rubí ◽  
Daniel Ortuño-Sahagún
Keyword(s):  
Growth And Development ◽  
Target Genes ◽  
Noncoding Rnas ◽  
Tumor Promoter ◽  
Neural Repair ◽  
Small Noncoding Rnas ◽  
Physiological Processes ◽  
And Migration ◽  
Migration Of Cells ◽  
Regulation Of Growth

MicroRNAs (miRNAs) are small noncoding RNAs that function as epigenetic modulators regulating almost any gene expression. Similarly, other noncoding RNAs, as well as epigenetic modifications, can regulate miRNAs. This reciprocal interaction forms a miRNA-epigenetic feedback loop, the deregulation of which affects physiological processes and contributes to a great diversity of diseases. In the present review, we focus on miR-615, a miRNA highly conserved across eutherian mammals. It is involved not only during embryogenesis in the regulation of growth and development, for instance during osteogenesis and angiogenesis, but also in the regulation of cell growth and the proliferation and migration of cells, acting as a tumor suppressor or tumor promoter. It therefore serves as a biomarker for several types of cancer, and recently has also been found to be involved in reparative processes and neural repair. In addition, we present the pleiad of functions in which miR-615 is involved, as well as their multiple target genes and the multiple regulatory molecules involved in its own expression. We do this by introducing in a comprehensible way the reported knowledge of their actions and interactions and proposing an integral view of its regulatory mechanisms.

scholarly journals An Evolutionary Perspective of Animal MicroRNAs and Their Targets

2009 ◽  
Vol 2009 ◽  
pp. 1-9 ◽  
Author(s):  
Noam Shomron ◽  
David Golan ◽  
Eran Hornstein
Keyword(s):  
Gene Expression ◽  
Posttranscriptional Regulation ◽  
Noncoding Rnas ◽  
Mrna Degradation ◽  
Evolutionary Perspective ◽  
Mirna Regulation ◽  
Regulate Gene Expression ◽  
Mirna Genes ◽  
Genomic Architecture ◽  
Regulate Gene

MicroRNAs (miRNAs) are short noncoding RNAs that regulate gene expression through translational inhibition or mRNA degradation by binding to sequences on the target mRNA. miRNA regulation appears to be the most abundant mode of posttranscriptional regulation affecting 50% of the transcriptome. miRNA genes are often clustered and/or located in introns, and each targets a variable and often large number of mRNAs. Here we discuss the genomic architecture of animal miRNA genes and their evolving interaction with their target mRNAs.

scholarly journals H3K27me3-rich genomic regions can function as silencers to repress gene expression via chromatin interactions

2019 ◽  
Author(s):  
Yichao Cai ◽  
Ying Zhang ◽  
Yan Ping Loh ◽  
Jia Qi Tng ◽  
Mei Chee Lim ◽  
...  
Keyword(s):  
Gene Expression ◽  
Tumor Growth ◽  
Target Genes ◽  
Gene Repression ◽  
Xenograft Tumor ◽  
Regulate Gene Expression ◽  
Chromatin Interactions ◽  
Genomic Regions ◽  
Xenograft Tumor Growth ◽  
Regulate Gene

AbstractGene repression and silencers are poorly understood. We reasoned that H3K27me3-rich regions (MRRs) of the genome defined from clusters of H3K27me3 peaks may be used to identify silencers that can regulate gene expression via proximity or looping. MRRs were associated with chromatin interactions and interact preferentially with each other. MRR component removal at interaction anchors by CRISPR led to upregulation of interacting target genes, altered H3K27me3 and H3K27ac levels at interacting regions, and altered chromatin interactions. Chromatin interactions did not change at regions with high H3K27me3, but regions with low H3K27me3 and high H3K27ac levels showed changes in chromatin interactions. The MRR knockout cells also showed changes in phenotype associated with cell identity, and altered xenograft tumor growth. MRR-associated genes and long-range chromatin interactions were susceptible to H3K27me3 depletion. Our results characterized H3K27me3-rich regions and their mechanisms of functioning via looping.

scholarly journals The interplay between small RNA pathways shapes chromatin landscapes in C. elegans

2018 ◽  
Author(s):  
Ekaterina Gushchanskaia ◽  
Ruben Esse ◽  
Qicheng Ma ◽  
Nelson Lau ◽  
Alla Grishok
Keyword(s):  
Small Rnas ◽  
Target Genes ◽  
Noncoding Rnas ◽  
Small Interfering Rnas ◽  
Loss Of Function ◽  
Partial Loss ◽  
Rna Dependent Rna Polymerase ◽  
C Elegans ◽  
Highly Expressed Genes ◽  
Rna Pathways

ABSTRACTThe nematode C. elegans contains several types of endogenous small interfering RNAs (endo-siRNAs) produced by RNA-dependent RNA polymerase (RdRP) complexes. Both “silencing” siRNAs bound by Worm-specific Argonautes (WAGO) and “activating” siRNAs bound by the CSR-1 Argonaute require the DRH-3 helicase, an RdRP component. Here we show that, in the drh-3(ne4253) mutant deficient in RdRP-produced secondary endo-siRNAs, the silencing histone mark H3K9me3 is largely depleted, whereas in the csr-1 partial loss-of-function mutant this mark is ectopically deposited on CSR-1 target genes. Moreover, we observe ectopic H3K9me3 at enhancer elements in both drh-3 and csr-1 partial loss-of-function mutants and describe small RNAs matching enhancers. Finally, we detect accumulation of H3K27me3 at highly expressed genes in the drh-3(ne4253) mutant, which correlates with their reduced transcription. Our study shows that when abundant RdRP-produced siRNAs are depleted, there is ectopic elevation of noncoding RNAs linked to increase in silencing chromatin marks. Moreover, our results suggest that enhancer small RNAs may guide local H3K9 methylation.

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