Small regulatory noncoding RNAs in Drosophila melanogaster: biogenesis and biological functions

2020 ◽  
Vol 19 (4) ◽  
pp. 309-323
Author(s):  
Saeed Soleimani ◽  
Zahra Valizadeh Arshad ◽  
Sharif Moradi ◽  
Ali Ahmadi ◽  
Seyed Javad Davarpanah ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Regulation Of Gene Expression ◽  
Noncoding Rnas ◽  
Critical Discussion ◽  
Rnai Pathway ◽  
Biological Functions ◽  
Small Interfering Rnas ◽  
Heterochromatin Formation ◽  
Small Noncoding Rnas ◽  
Small Ncrnas

Abstract RNA interference (RNAi) is an important phenomenon that has diverse genetic regulatory functions at the pre- and posttranscriptional levels. The major trigger for the RNAi pathway is double-stranded RNA (dsRNA). dsRNA is processed to generate various types of major small noncoding RNAs (ncRNAs) that include microRNAs (miRNAs), small interfering RNAs (siRNAs) and PIWI-interacting RNAs (piRNAs) in Drosophila melanogaster (D. melanogaster). Functionally, these small ncRNAs play critical roles in virtually all biological systems and developmental pathways. Identification and processing of dsRNAs and activation of RNAi machinery are the three major academic interests that surround RNAi research. Mechanistically, some of the important biological functions of RNAi are achieved through: (i) supporting genomic stability via degradation of foreign viral genomes; (ii) suppressing the movement of transposable elements and, most importantly, (iii) post-transcriptional regulation of gene expression by miRNAs that contribute to regulation of epigenetic modifications such as heterochromatin formation and genome imprinting. Here, we review various routes of small ncRNA biogenesis, as well as different RNAi-mediated pathways in D. melanogaster with a particular focus on signaling pathways. In addition, a critical discussion of the most relevant and latest findings that concern the significant contribution of small ncRNAs to the regulation of D. melanogaster physiology and pathophysiology is presented.

scholarly journals Endogenous siRNAs: regulators of internal affairs

2014 ◽  
Vol 42 (4) ◽  
pp. 1174-1179 ◽  
Author(s):  
Monica J. Piatek ◽  
Andreas Werner
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Drosophila Melanogaster ◽  
Transposable Elements ◽  
Essential Role ◽  
Viral Infections ◽  
Biological Functions ◽  
Small Interfering Rnas ◽  
Argonaute Proteins ◽  
Genome Protection

Endo-siRNAs (endogenous small-interfering RNAs) have recently emerged as versatile regulators of gene expression. They derive from double-stranded intrinsic transcripts and are processed by Dicer and associate with Argonaute proteins. In Caenorhabditis elegans, endo-siRNAs are known as 22G and 26G RNAs and are involved in genome protection and gene regulation. Drosophila melanogaster endo-siRNAs are produced with the help of specific Dicer and Argonaute isoforms and play an essential role in transposon control and the protection from viral infections. Biological functions of endo-siRNAs in vertebrates include repression of transposable elements and chromatin organization, as well as gene regulation at the transcriptional and post-transcriptional levels.

scholarly journals The Paramount Role of Drosophila melanogaster in the Study of Epigenetics: From Simple Phenotypes to Molecular Dissection and Higher-Order Genome Organization

Insects ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 884
Author(s):  
Jean-Michel Gibert ◽  
Frédérique Peronnet
Keyword(s):  
Drosophila Melanogaster ◽  
Regulation Of Gene Expression ◽  
Higher Order ◽  
Post Translational Modifications ◽  
Histone Marks ◽  
Heterochromatin Formation ◽  
Regulatory Processes ◽  
Chromatin Regulators ◽  
Chromatin Remodeling Complexes

Drosophila melanogaster has played a paramount role in epigenetics, the study of changes in gene function inherited through mitosis or meiosis that are not due to changes in the DNA sequence. By analyzing simple phenotypes, such as the bristle position or cuticle pigmentation, as read-outs of regulatory processes, the identification of mutated genes led to the discovery of major chromatin regulators. These are often conserved in distantly related organisms such as vertebrates or even plants. Many of them deposit, recognize, or erase post-translational modifications on histones (histone marks). Others are members of chromatin remodeling complexes that move, eject, or exchange nucleosomes. We review the role of D. melanogaster research in three epigenetic fields: Heterochromatin formation and maintenance, the repression of transposable elements by piRNAs, and the regulation of gene expression by the antagonistic Polycomb and Trithorax complexes. We then describe how genetic tools available in D. melanogaster allowed to examine the role of histone marks and show that some histone marks are dispensable for gene regulation, whereas others play essential roles. Next, we describe how D. melanogaster has been particularly important in defining chromatin types, higher-order chromatin structures, and their dynamic changes during development. Lastly, we discuss the role of epigenetics in a changing environment.

Noncoding RNAs and Colorectal Cancer:A General Overview

MicroRNA ◽  
2020 ◽  
Vol 09 ◽  
Author(s):  
Jonathan Souza Sarraf ◽  
Taynah Cascaes Puty ◽  
Emanuely Magno da Silva ◽  
Thais Suellen Ramos Allen ◽  
Yasmim Souza Sarraf ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Clinical Practice ◽  
Noncoding Rnas ◽  
Target Prediction ◽  
Small Interfering Rnas ◽  
Noncoding Regions ◽  
Rna Molecules ◽  
Small Noncoding Rnas ◽  
Non Coding Rnas ◽  
Nucleolar Rnas

Background: Colorectal cancer (CRC) is the second most prevalent cancer in the world when nonmelanoma skin cases are not considered. Different epigenetic mechanisms play a role in the development of cancer. Noncoding RNAs (ncRNAs) are RNA molecules transcribed from noncoding regions of the genome. These are divided into sncRNAs (small noncoding RNAs: <200 nucleotides - including miRNAs [microRNAs], siRNAs [small interfering RNAs], piRNAs [piwi-interacting RNAs], snoRNAs [small nucleolar RNAs]) and lncRNAs (long noncoding RNAs: >200 nucleotides – includingcircular RNAs [circRNAs]). NcRNAs can act as oncogenes or as tumor suppressor genes in CRC and are potential biomarkers of diagnosis, with possible clinical implications. Objective: This article aims to make a general review around all types of non-coding RNAs and influence in colorectal cancer, focus in biomarkesof CRC and their possible applications in clinical practice, as well as review their biogenesis and functions. Furthermore, we seek to summarize possible databases available for new searches and studies that require sequence annotation, comparison sequences and target prediction for ncRNAs with the hope ofgathering information that can aid in the process of understanding and translating the use of ncRNAs into clinical practice.

scholarly journals Fixation of transposable elements in the Drosophila melanogaster genome

2005 ◽  
Vol 85 (3) ◽  
pp. 195-203 ◽  
Author(s):  
XULIO MASIDE ◽  
STAVROULA ASSIMACOPOULOS ◽  
BRIAN CHARLESWORTH
Keyword(s):  
Drosophila Melanogaster ◽  
Transposable Elements ◽  
Genomic Dna ◽  
Molecular Level ◽  
Hybridization Technique ◽  
Small Interfering Rnas ◽  
Heterochromatin Formation ◽  
Large Clusters

We have investigated at the molecular level four cases in which D. melanogaster middle repetitive DNA probes consistently hybridized to a particular band on chromosomes sampled from a D. melanogaster natural population. Two corresponded to true fixations of a roo and a Stalker element, and the others were artefacts of the in situ hybridization technique caused by the presence of genomic DNA flanking the transposable elements (TEs) in the probes. The two fixed elements are located in the β-heterochromatin (20A and 80B, respectively) and are embedded in large clusters of other elements, many of which may also be fixed. We also found evidence that this accumulation is an ongoing process. These results support the hypothesis that TEs accumulate in the non-recombining part of the genome. Their implications for the effects of TEs on determining the chromatin structure of the host genomes are discussed in the light of recent evidence for the role of TE-derived small interfering-RNAs as cis-acting determinants of heterochromatin formation.

Genome-Wide Analysis of Long Intergenic Noncoding RNAs Responding to Low-Nutrient Conditions in Arabidopsis thaliana: Possible Involvement of Trans-Acting siRNA3 in Response to Low Nitrogen

2019 ◽  
Vol 60 (9) ◽  
pp. 1961-1973 ◽  
Author(s):  
Makiha Fukuda ◽  
Sho Nishida ◽  
Yusuke Kakei ◽  
Yukihisa Shimada ◽  
Toru Fujiwara
Keyword(s):  
Arabidopsis Thaliana ◽  
Root Development ◽  
Expression Patterns ◽  
Regulation Of Gene Expression ◽  
Noncoding Rnas ◽  
Small Interfering Rnas ◽  
Sequencing Data ◽  
Genome Wide ◽  
A Genome ◽  
Nutrient Conditions

Abstract Long intergenic noncoding RNAs (lincRNAs) play critical roles in transcriptional and post-transcriptional regulation of gene expression in a wide variety of organisms. Thousands of lincRNAs have been identified in plant genomes, although their functions remain mostly uncharacterized. Here, we report a genome-wide survey of lincRNAs involved in the response to low-nutrient conditions in Arabidopsis thaliana. We used RNA sequencing data derived from A. thaliana roots exposed to low levels of 12 different nutrients. Using bioinformatics approaches, 60 differentially expressed lincRNAs were identified that were significantly upregulated or downregulated under deficiency of at least one nutrient. To clarify their roles in nutrient response, correlations of expression patterns between lincRNAs and reference genes were examined across the 13 conditions (12 low-nutrient conditions and control). This analysis allowed us to identify lincRNA-RNA pairs with highly positive or negative correlations. In addition, calculating interaction energies of those pairs showed lincRNAs that may act as regulatory interactors; e.g. small interfering RNAs (siRNAs). Among them, trans-acting siRNA3 (TAS3), which is known to promote lateral root development by producing siRNA against Auxin response factor 2, 3, and 4, was revealed as a nitrogen (N)-responsive lincRNA. Furthermore, nitrate transporter 2 was identified as a potential target of TAS3-derived siRNA, suggesting that TAS3 participates in multiple pathways by regulating N transport and root development under low-N conditions. This study provides the first resource for candidate lincRNAs involved in multiple nutrient responses in plants.

scholarly journals MicroRNA biogenesis and variability

2013 ◽  
Vol 4 (4) ◽  
pp. 367-380 ◽  
Author(s):  
Jesús García-López ◽  
Miguel A. Brieño-Enríquez ◽  
Jesús del Mazo
Keyword(s):  
Gene Expression ◽  
Posttranscriptional Regulation ◽  
Regulation Of Gene Expression ◽  
Noncoding Rnas ◽  
High Variability ◽  
Regulate Gene Expression ◽  
Alternative Pathways ◽  
Small Noncoding Rnas ◽  
Fine Regulation ◽  
And Function

AbstractMicroRNAs (miRNAs) are cell-endogenous small noncoding RNAs that, through RNA interference, are involved in the posttranscriptional regulation of mRNAs. The biogenesis and function of miRNAs entail multiple elements with different alternative pathways. These confer a high versatility of regulation and a high variability to generate different miRNAs and hence possess a broad potential to regulate gene expression. Here we review the different mechanisms, both canonical and noncanonical, that generate miRNAs in animals. The ‘miRNome’ panorama enhances our knowledge regarding the fine regulation of gene expression and provides new insights concerning normal, as opposed to pathological, cell differentiation and development.

Life without RNAi: noncoding RNAs and their functions in Saccharomyces cerevisiaeThis paper is one of a selection of papers published in this Special Issue, entitled 30th Annual International Asilomar Chromatin and Chromosomes Conference, and has undergone the Journal’s usual peer review process.

2009 ◽  
Vol 87 (5) ◽  
pp. 767-779 ◽  
Author(s):  
Benjamin R. Harrison ◽  
Oya Yazgan ◽  
Jocelyn E. Krebs
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Chromatin Structure ◽  
Messenger Rna ◽  
Peer Review Process ◽  
Regulation Of Gene Expression ◽  
Noncoding Rnas ◽  
Rna Degradation ◽  
Small Interfering Rnas ◽  
Ideal System

There are a number of well-characterized and fundamental roles for noncoding RNAs (ncRNAs) in gene regulation in all kingdoms of life. ncRNAs, such as ribosomal RNAs, transfer RNAs, small nuclear RNAs, small nucleolar RNAs, and small interfering RNAs, can serve catalytic and scaffolding functions in transcription, messenger RNA processing, translation, and RNA degradation. Recently, our understanding of gene expression has been dramatically challenged by the identification of large and diverse populations of novel ncRNAs in the eukaryotic genomes surveyed thus far. Studies carried out using the budding yeast Saccharomyces cerevisiae indicate that at least some coding genes are regulated by these novel ncRNAs. S. cerevisiae lacks RNA interference (RNAi) and, thus, provides an ideal system for studying the RNAi-independent mechanisms of ncRNA-based gene regulation. The current picture of gene regulation is one of great unknowns, in which the transcriptional environment surrounding a given locus may have as much to do with its regulation as its DNA sequence or local chromatin structure. Drawing on the recent research in S. cerevisiae and other organisms, this review will discuss the identification of ncRNAs, their origins and processing, and several models that incorporate ncRNAs into the regulation of gene expression and chromatin structure.

scholarly journals Ago1 and Dcr1, Two Core Components of the RNA Interference Pathway, Functionally Diverge from Rdp1 in Regulating Cell Cycle Events in Schizosaccharomyces pombe

2004 ◽  
Vol 15 (3) ◽  
pp. 1425-1435 ◽  
Author(s):  
Jon B. Carmichael ◽  
Patrick Provost ◽  
Karl Ekwall ◽  
Tom C. Hobman
Keyword(s):  
Cell Cycle ◽  
Rna Interference ◽  
Schizosaccharomyces Pombe ◽  
Fission Yeast ◽  
Chromosome Segregation ◽  
Control Cell ◽  
Cell Cycle Checkpoints ◽  
Rnai Pathway ◽  
Small Interfering Rnas ◽  
Heterochromatin Formation

In the fission yeast Schizosaccharomyces pombe, three genes that function in the RNA interference (RNAi) pathway, ago1+, dcr1+, and rdp1+, have recently been shown to be important for timely formation of heterochromatin and accurate chromosome segregation. In the present study, we present evidence that null mutants for ago1+ and dcr1+ but not rdp1+, exhibit abnormal cytokinesis, cell cycle arrest deficiencies, and mating defects. Subsequent analyses showed that ago1+ and dcr1+ are required for regulated hyperphosphorylation of Cdc2 when encountering genotoxic insults. Because rdp1+ is dispensable for this process, the functions of ago1+ and dcr1+ in this pathway are presumably independent of their roles in RNAi-mediated heterochromatin formation and chromosome segregation. This was further supported by the finding that ago1+ is a multicopy suppressor of the S-M checkpoint deficiency and cytokinesis defects associated with loss of Dcr1 function, but not for the chromosome segregation defects of this mutant. Accordingly, we conclude that Dcr1-dependent production of small interfering RNAs is not required for enactment and/or maintenance of certain cell cycle checkpoints and that Ago1 and Dcr1 functionally diverge from Rdp1 to control cell cycle events in fission yeast. Finally, exogenous expression of hGERp95/EIF2C2/hAgo2, a human Ago1 homolog implicated in posttranscriptional gene silencing, compensated for the loss of ago1+ function in S. pombe. This suggests that PPD proteins may also be important for regulation of cell cycle events in higher eukaryotes.

scholarly journals Production of Small Noncoding RNAs from the flamenco Locus Is Regulated by the gypsy Retrotransposon of Drosophila melanogaster

Genetics ◽  
2016 ◽  
Vol 204 (2) ◽  
pp. 631-644 ◽  
Author(s):  
V. Guida ◽  
F. M. Cernilogar ◽  
A. Filograna ◽  
R. De Gregorio ◽  
H. Ishizu ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Noncoding Rnas ◽  
Small Noncoding Rnas ◽  
Gypsy Retrotransposon

scholarly journals Exosomal miRNAs in Heart Disease

Physiology ◽  
2016 ◽  
Vol 31 (1) ◽  
pp. 16-24 ◽  
Author(s):  
Claudio Iaconetti ◽  
Sabato Sorrentino ◽  
Salvatore De Rosa ◽  
Ciro Indolfi
Keyword(s):  
Heart Disease ◽  
Posttranscriptional Regulation ◽  
Functional Role ◽  
Regulation Of Gene Expression ◽  
Noncoding Rnas ◽  
Small Noncoding Rnas ◽  
Micro Rnas ◽  
Exosomal Mirnas ◽  
New Biomarkers ◽  
Potential Use

Micro-RNAs (miRNAs) are small noncoding RNAs involved in the posttranscriptional regulation of gene expression. Exosomes have recently emerged as novel elements of intercellular communication in the cardiovascular system. Exosomal miRNAs could be key players in intercellular cross-talk, particularly during different diseases such as myocardial infarction (MI) and heart failure (HF). This review addresses the functional role played by exosomal miRNAs in heart disease and their potential use as new biomarkers.

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