scholarly journals Regulation of gene expression via retrotransposon insertions and the noncoding RNA 4.5S RNA H

2015 ◽  
Vol 20 (11) ◽  
pp. 887-901 ◽  
Author(s):  
Kentaro Ishida ◽  
Kenjyo Miyauchi ◽  
Yuko Kimura ◽  
Mari Mito ◽  
Shunpei Okada ◽  
...  
Keyword(s):  
Gene Expression ◽  
Noncoding Rna ◽  
Regulation Of Gene Expression ◽  
4.5S Rna

scholarly journals The molecular dynamics of long noncoding RNA control of transcription in PTEN and its pseudogene

2017 ◽  
Vol 114 (37) ◽  
pp. 9942-9947 ◽  
Author(s):  
Nicholas Lister ◽  
Galina Shevchenko ◽  
James L. Walshe ◽  
Jessica Groen ◽  
Per Johnsson ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Structure ◽  
Noncoding Rna ◽  
Dna Methyltransferase ◽  
Regulation Of Gene Expression ◽  
Control Of Gene Expression ◽  
Phosphatase And Tensin Homolog ◽  
Tensin Homolog ◽  
Sequence Components ◽  
Antisense Lncrnas

RNA has been found to interact with chromatin and modulate gene transcription. In human cells, little is known about how long noncoding RNAs (lncRNAs) interact with target loci in the context of chromatin. We find here, using the phosphatase and tensin homolog (PTEN) pseudogene as a model system, that antisense lncRNAs interact first with a 5′ UTR-containing promoter-spanning transcript, which is then followed by the recruitment of DNA methyltransferase 3a (DNMT3a), ultimately resulting in the transcriptional and epigenetic control of gene expression. Moreover, we find that the lncRNA and promoter-spanning transcript interaction are based on a combination of structural and sequence components of the antisense lncRNA. These observations suggest, on the basis of this one example, that evolutionary pressures may be placed on RNA structure more so than sequence conservation. Collectively, the observations presented here suggest a much more complex and vibrant RNA regulatory world may be operative in the regulation of gene expression.

scholarly journals Differential Expression of MicroRNAs between Eutopic and Ectopic Endometrium in Ovarian Endometriosis

2010 ◽  
Vol 2010 ◽  
pp. 1-29 ◽  
Author(s):  
Nicoletta Filigheddu ◽  
Ilaria Gregnanin ◽  
Paolo E. Porporato ◽  
Daniela Surico ◽  
Beatrice Perego ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differential Expression ◽  
Posttranscriptional Regulation ◽  
Noncoding Rna ◽  
Critical Role ◽  
Regulation Of Gene Expression ◽  
Differentially Expressed ◽  
Ovarian Endometriosis ◽  
Eutopic Endometrium ◽  
Ectopic Endometrium

Endometriosis, defined as the presence of endometrial tissue outside the uterus, is a common gynecological disease with poorly understood pathogenesis. MicroRNAs are members of a class of small noncoding RNA molecules that have a critical role in posttranscriptional regulation of gene expression by repression of target mRNAs translation. We assessed differentially expressed microRNAs in ectopic endometrium compared with eutopic endometrium in 3 patients through microarray analysis. We identified 50 microRNAs differentially expressed and the differential expression of five microRNAs was validated by real-time RT-PCR in other 13 patients. We identifiedin silicotheir predicted targets, several of which match the genes that have been identified to be differentially expressed in ectopicversuseutopic endometrium in studies of gene expression. A functional analysis of the predicted targets indicates that several of these are involved in molecular pathways implicated in endometriosis, thus strengthening the hypothesis of the role of microRNAs in this pathology.

scholarly journals Long Noncoding RNA Plays a Key Role in Metastasis and Prognosis of Hepatocellular Carcinoma

2014 ◽  
Vol 2014 ◽  
pp. 1-8 ◽  
Author(s):  
Guangbing Li ◽  
Haohai Zhang ◽  
Xueshuai Wan ◽  
Xiaobo Yang ◽  
Chengpei Zhu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Hepatocellular Carcinoma ◽  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Regulation Of Gene Expression ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Comprehensive Review ◽  
Cellular Processes

Long noncoding RNAs (lncRNAs) have been attracting immense research interests. However, only a handful of lncRNAs had been thoroughly characterized. They were involved in fundamental cellular processes including regulation of gene expression at epigenetics as well as tumorogenesis. In this paper, we give a systematic and comprehensive review of existing literature about lncRNA involvement in hepatocellular carcinoma. This review exhibited that lncRNAs played important roles in tumorigenesis and subsequent prognosis and metastasis of hepatocellular carcinoma and elucidated the role of some specific lncRNAs such as MALAT1 and HOTAIR in the pathophysiology of hepatocellular carcinoma and their potential of being therapeutic targets.

scholarly journals Circular RNAs in Cardiovascular Disease: An Overview

2017 ◽  
Vol 2017 ◽  
pp. 1-9 ◽  
Author(s):  
Ximin Fan ◽  
Xinyu Weng ◽  
Yifan Zhao ◽  
Wei Chen ◽  
Tianyi Gan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cardiovascular Disease ◽  
Cardiovascular Diseases ◽  
Noncoding Rna ◽  
Essential Role ◽  
Closed Loop ◽  
Regulation Of Gene Expression ◽  
Circular Rna ◽  
Circular Rnas ◽  
Mirna Sponges

Circular RNA (circRNA), a novel type of endogenous noncoding RNA (ncRNA), has become a research hotspot in recent years. CircRNAs are abundant and stably exist in creatures, and they are found with covalently closed loop structures in which they are quite different from linear RNAs. Nowadays, an increasing number of scientists have demonstrated that circRNAs may have played an essential role in the regulation of gene expression, especially acting as miRNA sponges, and have described the potential mechanisms of several circRNAs in diseases, hinting at their clinical therapeutic values. In this review, the authors summarized the current understandings of the biogenesis and properties of circRNAs and their functions and role as biomarkers in cardiovascular diseases.

scholarly journals Long Noncoding RNA-Directed Epigenetic Regulation of Gene Expression Is Associated With Anxiety-like Behavior in Mice

2015 ◽  
Vol 78 (12) ◽  
pp. 848-859 ◽  
Author(s):  
Paola A. Spadaro ◽  
Charlotte R. Flavell ◽  
Jocelyn Widagdo ◽  
Vikram S. Ratnu ◽  
Michael Troup ◽  
...  
Keyword(s):  
Gene Expression ◽  
Epigenetic Regulation ◽  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Regulation Of Gene Expression

scholarly journals Epigenetic Regulation and Measurement of Epigenetic Changes

2012 ◽  
Vol 15 (4) ◽  
pp. 373-381 ◽  
Author(s):  
Kimberly E. Stephens ◽  
Christine A. Miaskowski ◽  
Jon D. Levine ◽  
Clive R. Pullinger ◽  
Bradley E. Aouizerat
Keyword(s):  
Gene Expression ◽  
Epigenetic Regulation ◽  
Noncoding Rna ◽  
Regulation Of Gene Expression ◽  
Epigenetic Changes ◽  
Small Noncoding Rna ◽  
Transcript Stability ◽  
Functional Consequences ◽  
Specific Tissue

Epigenetic mechanisms provide an adaptive layer of control in the regulation of gene expression that enables an organism to adjust to a changing environment. Epigenetic regulation increases the functional complexity of deoxyribonucleic acid (DNA) by altering chromatin structure, nuclear organization, and transcript stability. These changes may additively or synergistically influence gene expression and result in long-term molecular and functional consequences independent of the DNA sequence that may ultimately define an individual’s phenotype. This article (1) describes histone modification, DNA methylation, and expression of small noncoding RNA species; (2) reviews the most common methods used to measure these epigenetic changes; and (3) presents factors that need to be considered when choosing a specific tissue to evaluate for epigenetic changes.

scholarly journals Small Molecule, Big Prospects: MicroRNA in Pregnancy and Its Complications

2017 ◽  
Vol 2017 ◽  
pp. 1-15 ◽  
Author(s):  
Meng Cai ◽  
Gopi K. Kolluru ◽  
Asif Ahmed
Keyword(s):  
Gene Expression ◽  
Preterm Labor ◽  
Noncoding Rna ◽  
Molecular Mechanisms ◽  
Regulation Of Gene Expression ◽  
Disease Process ◽  
Rna Molecules ◽  
Small Noncoding Rna ◽  
Posttranscriptional Level ◽  
In Pregnancy

MicroRNAs are small, noncoding RNA molecules that regulate target gene expression in the posttranscriptional level. Unlike siRNA, microRNAs are “fine-tuners” rather than “switches” in the regulation of gene expression; thus they play key roles in maintaining tissue homeostasis. The aberrant microRNA expression is implicated in the disease process. To date, numerous studies have demonstrated the regulatory roles of microRNAs in various pathophysiological conditions. In contrast, the study of microRNA in pregnancy and its associated complications, such as preeclampsia (PE), fetal growth restriction (FGR), and preterm labor, is a young field. Over the last decade, the knowledge of pregnancy-related microRNAs has increased and the molecular mechanisms by which microRNAs regulate pregnancy or its associated complications are emerging. In this review, we focus on the recent advances in the research of pregnancy-related microRNAs, especially their function in pregnancy-associated complications and the potential clinical applications. Here microRNAs that associate with pregnancy are classified as placenta-specific, placenta-associated, placenta-derived circulating, and uterine microRNA according to their localization and origin. MicroRNAs offer a great potential for developing diagnostic and therapeutic targets in pregnancy-related disorders.

scholarly journals The miRNome of Depression

2021 ◽  
Vol 22 (21) ◽  
pp. 11312
Author(s):  
Dariusz Żurawek ◽  
Gustavo Turecki
Keyword(s):  
Gene Expression ◽  
Stress Responses ◽  
Posttranscriptional Regulation ◽  
Noncoding Rna ◽  
Regulation Of Gene Expression ◽  
Rna Transcripts ◽  
Complex Interactions ◽  
Post Mortem Brain ◽  
Fine Tune

Depression is an effect of complex interactions between genetic, epigenetic and environmental factors. It is well established that stress responses are associated with multiple modest and often dynamic molecular changes in the homeostatic balance, rather than with a single genetic factor that has a strong phenotypic penetration. As depression is a multifaceted phenotype, it is important to study biochemical pathways that can regulate the overall allostasis of the brain. One such biological system that has the potential to fine-tune a multitude of diverse molecular processes is RNA interference (RNAi). RNAi is an epigenetic process showing a very low level of evolutionary diversity, and relies on the posttranscriptional regulation of gene expression using, in the case of mammals, primarily short (17–23 nucleotides) noncoding RNA transcripts called microRNAs (miRNA). In this review, our objective was to examine, summarize and discuss recent advances in the field of biomedical and clinical research on the role of miRNA-mediated regulation of gene expression in the development of depression. We focused on studies investigating post-mortem brain tissue of individuals with depression, as well as research aiming to elucidate the biomarker potential of miRNAs in depression and antidepressant response.

scholarly journals Noncoding RNA participation in gene expression regulation in yeast Saccharomyces cerevisiae

2011 ◽  
Vol 9 (1) ◽  
pp. 3-14
Author(s):  
Olga V Kochenova
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Gene Regulation ◽  
Antisense Rna ◽  
Noncoding Rna ◽  
Gene Expression Regulation ◽  
Regulation Of Gene Expression ◽  
Yeast Genome ◽  
Yeast Saccharomyces Cerevisiae ◽  
Main Components

Saccharomyces cerevisiae lacks the main components of RNAi-dependent gene silencing. Nevertheless, regulation of gene expression in S. cerevisiae could be accomplished via some other types of noncoding RNA, particularly via antisense RNA. Although, there is a high percent of untranslated RNA in yeast genome only few evidences of noncoding RNA gene regulation exist in yeast S. cerevisiae, some of them are reviewed in the present paper. 

scholarly journals Epigenetic Modulation of Chromatin States and Gene Expression by G-Quadruplex Structures

2020 ◽  
Vol 21 (11) ◽  
pp. 4172 ◽  
Author(s):  
Chiara Reina ◽  
Vincenzo Cavalieri
Keyword(s):  
Gene Expression ◽  
Noncoding Rna ◽  
Biological Activities ◽  
Regulation Of Gene Expression ◽  
Three Dimensional ◽  
Structural Features ◽  
Rna Molecules ◽  
Dna And Rna ◽  
G Quadruplex ◽  
Epigenetic Modulation

G-quadruplexes are four-stranded helical nucleic acid structures formed by guanine-rich sequences. A considerable number of studies have revealed that these noncanonical structural motifs are widespread throughout the genome and transcriptome of numerous organisms, including humans. In particular, G-quadruplexes occupy strategic locations in genomic DNA and both coding and noncoding RNA molecules, being involved in many essential cellular and organismal functions. In this review, we first outline the fundamental structural features of G-quadruplexes and then focus on the concept that these DNA and RNA structures convey a distinctive layer of epigenetic information that is critical for the complex regulation, either positive or negative, of biological activities in different contexts. In this framework, we summarize and discuss the proposed mechanisms underlying the functions of G-quadruplexes and their interacting factors. Furthermore, we give special emphasis to the interplay between G-quadruplex formation/disruption and other epigenetic marks, including biochemical modifications of DNA bases and histones, nucleosome positioning, and three-dimensional organization of chromatin. Finally, epigenetic roles of RNA G-quadruplexes in post-transcriptional regulation of gene expression are also discussed. Undoubtedly, the issues addressed in this review take on particular importance in the field of comparative epigenetics, as well as in translational research.

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