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Drosophila mirna

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https://www.readbyqxmd.com/read/29198775/dynamic-mirna-mrna-regulations-are-essential-for-maintaining-drosophila-immune-homeostasis-during-micrococcus-luteus-infection
#1
Guanyun Wei, Lianjie Sun, Ruimin Li, Lei Li, Jiao Xu, Fei Ma
Pathogen bacteria infections can lead to dynamic changes of microRNA (miRNA) and mRNA expression profiles, which may control synergistically the outcome of immune responses. To reveal the role of dynamic miRNA-mRNA regulation in Drosophila innate immune responses, we have detailedly analyzed the paired miRNA and mRNA expression profiles at three time points during Drosophila adult males with Micrococcus luteus (M. luteus) infection using RNA- and small RNA-seq data. Our results demonstrate that differentially expressed miRNAs and mRNAs represent extensively dynamic changes over three time points during Drosophila with M...
November 30, 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/29196461/mirna-suppression-of-a-notch-repressor-directs-non-neuronal-fate-in-drosophila-mechanosensory-organs
#2
Joshua Kavaler, Hong Duan, Rajaguru Aradhya, Luis F de Navas, Brian Joseph, Boris Shklyar, Eric C Lai
Although there is abundant evidence that individual microRNA (miRNA) loci repress large cohorts of targets, large-scale knockout studies suggest that most miRNAs are phenotypically dispensable. Here, we identify a rare case of developmental cell specification that is highly dependent on miRNA control of an individual target. We observe that binary cell fate choice in the Drosophila melanogaster peripheral sensory organ lineage is controlled by the non-neuronally expressed mir-279/996 cluster, with a majority of notum sensory organs exhibiting transformation of sheath cells into ectopic neurons...
December 1, 2017: Journal of Cell Biology
https://www.readbyqxmd.com/read/29191225/landscape-and-evolution-of-tissue-specific-alternative-polyadenylation-across-drosophila-species
#3
Piero Sanfilippo, Jiayu Wen, Eric C Lai
BACKGROUND: Drosophila melanogaster has one of best-described transcriptomes of any multicellular organism. Nevertheless, the paucity of 3'-sequencing data in this species precludes comprehensive assessment of alternative polyadenylation (APA), which is subject to broad tissue-specific control. RESULTS: Here, we generate deep 3'-sequencing data from 23 developmental stages, tissues, and cell lines of D. melanogaster, yielding a comprehensive atlas of ~ 62,000 polyadenylated ends...
November 30, 2017: Genome Biology
https://www.readbyqxmd.com/read/29069479/flyatlas-2-a-new-version-of-the-drosophila-melanogaster-expression-atlas-with-rna-seq-mirna-seq-and-sex-specific-data
#4
David P Leader, Sue A Krause, Aniruddha Pandit, Shireen A Davies, Julian A T Dow
FlyAtlas 2 ( www.flyatlas2.org ) is part successor, part complement to the FlyAtlas database and web application for studying the expression of the genes of Drosophila melanogaster in different tissues of adults and larvae. Although generated in the same lab with the same fly line raised on the same diet as FlyAtlas, the FlyAtlas2 resource employs a completely new set of expression data based on RNA-Seq, rather than microarray analysis, and so it allows the user to obtain information for the expression of different transcripts of a gene...
October 24, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29045748/conserved-asymmetry-underpins-homodimerization-of-dicer-associated-double-stranded-rna-binding-proteins
#5
Alex Heyam, Claire E Coupland, Clément Dégut, Ruth A Haley, Nicola J Baxter, Leonhard Jakob, Pedro M Aguiar, Gunter Meister, Michael P Williamson, Dimitris Lagos, Michael J Plevin
Double-stranded RNA-binding domains (dsRBDs) are commonly found in modular proteins that interact with RNA. Two varieties of dsRBD exist: canonical Type A dsRBDs interact with dsRNA, while non-canonical Type B dsRBDs lack RNA-binding residues and instead interact with other proteins. In higher eukaryotes, the microRNA biogenesis enzyme Dicer forms a 1:1 association with a dsRNA-binding protein (dsRBP). Human Dicer associates with HIV TAR RNA-binding protein (TRBP) or protein activator of PKR (PACT), while Drosophila Dicer-1 associates with Loquacious (Loqs)...
October 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29040648/molecular-basis-for-asymmetry-sensing-of-sirnas-by-the-drosophila-loqs-pd-dcr-2-complex-in-rna-interference
#6
Jan-Niklas Tants, Stephanie Fesser, Thomas Kern, Ralf Stehle, Arie Geerlof, Christoph Wunderlich, Michael Juen, Christoph Hartlmüller, Romy Böttcher, Stefan Kunzelmann, Oliver Lange, Christoph Kreutz, Klaus Förstemann, Michael Sattler
RNA interference defends against RNA viruses and retro-elements within an organism's genome. It is triggered by duplex siRNAs, of which one strand is selected to confer sequence-specificity to the RNA induced silencing complex (RISC). In Drosophila, Dicer-2 (Dcr-2) and the double-stranded RNA binding domain (dsRBD) protein R2D2 form the RISC loading complex (RLC) and select one strand of exogenous siRNAs according to the relative thermodynamic stability of base-pairing at either end. Through genome editing we demonstrate that Loqs-PD, the Drosophila homolog of human TAR RNA binding protein (TRBP) and a paralog of R2D2, forms an alternative RLC with Dcr-2 that is required for strand choice of endogenous siRNAs in S2 cells...
October 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29030844/kinetic-analysis-of-small-silencing-rna-production-by%C3%A2-human-and-drosophila-dicer-enzymes-in-vitro
#7
Susan E Liao, Ryuya Fukunaga
Dicer enzymes produce small silencing RNAs such as microRNAs (miRNAs) and small interfering RNAs (siRNAs), which then are loaded into Argonaute proteins and act as sequence-specific guides. A powerful tool to understand the molecular mechanism of small silencing RNA production by Dicers is an in vitro RNA processing assay using recombinant Dicer proteins. Such biochemical analyses have elucidated the substrate specificities and kinetics of Dicers, the mechanism by which the length of small RNAs produced by Dicers is determined, and the effects of Dicer-partner proteins and endogenous small molecules such as ATP and inorganic phosphate on small RNA production by Dicers, among others...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29020923/comparative-analysis-of-mirna-expression-during-the-development-of-insects-of-different-metamorphosis-modes-and-germ-band-types
#8
Guillem Ylla, Maria-Dolors Piulachs, Xavier Belles
BACKGROUND: Do miRNAs contribute to specify the germ-band type and the body structure in the insect embryo? Our goal was to address that issue by studying the changes in miRNA expression along the ontogeny of the German cockroach Blattella germanica, which is a short germ-band and hemimetabolan species. RESULTS: We sequenced small RNA libraries representing 11 developmental stages of B. germanica ontogeny (with especial emphasis on embryogenesis) and the changes in miRNA expression were examined...
October 11, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28979292/drosophila-model-for-the-analysis-of-genesis-of-lim-kinase-1-dependent-williams-beuren-syndrome-cognitive-phenotypes-indels-transposable-elements-of-the-tc1-mariner-superfamily-and-micrornas
#9
Elena V Savvateeva-Popova, Aleksandr V Zhuravlev, Václav Brázda, Gennady A Zakharov, Alena N Kaminskaya, Anna V Medvedeva, Ekaterina A Nikitina, Elena V Tokmatcheva, Julia F Dolgaya, Dina A Kulikova, Olga G Zatsepina, Sergei Y Funikov, Sergei S Ryazansky, Michail B Evgen'ev
Genomic disorders, the syndromes with multiple manifestations, may occur sporadically due to unequal recombination in chromosomal regions with specific architecture. Therefore, each patient may carry an individual structural variant of DNA sequence (SV) with small insertions and deletions (INDELs) sometimes less than 10 bp. The transposable elements of the Tc1/mariner superfamily are often associated with hotspots for homologous recombination involved in human genetic disorders, such as Williams Beuren Syndromes (WBS) with LIM-kinase 1-dependent cognitive defects...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28974923/drosophila-exoribonuclease-nibbler-is-a-tumor-suppressor-acts-within-the-rna-i-machinery-and-is-not-enriched-in-the-nuage-during-early-oogenesis
#10
Casimiro Castillejo-López, Xiaoli Cai, Khalid Fahmy, Stefan Baumgartner
BACKGROUND: micro RNAs (miRNAs) are important regulators of many biological pathways. A plethora of steps are required to form, from a precursor, the mature miRNA that eventually acts on its target RNA to repress its expression or to inhibit translation. Recently, Drosophila nibbler (nbr) has been shown to be an important player in the maturation process of miRNA and piRNA. Nbr is an exoribonuclease which helps to shape the 3' end of miRNAs by trimming the 3' overhang to a final length...
2018: Hereditas
https://www.readbyqxmd.com/read/28964526/pirna-biogenesis-in-drosophila-melanogaster
#11
REVIEW
Xiawei Huang, Katalin Fejes Tóth, Alexei A Aravin
The PIWI-interacting RNA (piRNA) pathway is a conserved defense system that protects the genome integrity of the animal germline from deleterious transposable elements. Targets of silencing are recognized by small noncoding piRNAs that are processed from long precursor molecules. Although piRNAs and other classes of small noncoding RNAs, such as miRNAs and small interfering (si)RNAs, interact with members of the same family of Argonaute (Ago) proteins and their function in target repression is similar, the biogenesis of piRNAs differs from those of the other two small RNAs...
November 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28963741/micrornas-mir-184-and-let-7-alter-drosophila-metabolism-and-longevity
#12
Christi M Gendron, Scott D Pletcher
MicroRNAs (miRNAs) are small RNA molecules that regulate gene expression associated with many complex biological processes. By comparing miRNA expression between long-lived cohorts of Drosophila melanogaster that were fed a low-nutrient diet with normal-lived control animals fed a high-nutrient diet, we identified miR-184, let-7, miR-125, and miR-100 as candidate miRNAs involved in modulating aging. We found that ubiquitous, adult-specific overexpression of these individual miRNAs led to significant changes in fat metabolism and/or lifespan...
December 2017: Aging Cell
https://www.readbyqxmd.com/read/28954229/microprocessor-recruitment-to-elongating-rna-polymerase-ii-is-required-for-differential-expression-of-micrornas
#13
Victoria A Church, Sigal Pressman, Mamiko Isaji, Mary Truscott, Nihal Terzi Cizmecioglu, Stephen Buratowski, Maxim V Frolov, Richard W Carthew
The cellular abundance of mature microRNAs (miRNAs) is dictated by the efficiency of nuclear processing of primary miRNA transcripts (pri-miRNAs) into pre-miRNA intermediates. The Microprocessor complex of Drosha and DGCR8 carries this out, but it has been unclear what controls Microprocessor's differential processing of various pri-miRNAs. Here, we show that Drosophila DGCR8 (Pasha) directly associates with the C-terminal domain of the RNA polymerase II elongation complex when it is phosphorylated by the Cdk9 kinase (pTEFb)...
September 26, 2017: Cell Reports
https://www.readbyqxmd.com/read/28942151/molecular-characterization-of-mitochondrial-zucchini-and-its-relation-to-nuage-pirna-pathway-components-in-bombyx-mori-ovary-derived-bmn4-cells
#14
Anandrao Ashok Patil, Tsuneyuki Tatsuke, Hiroaki Mon, Jae Man Lee, Daisuke Morokuma, Masato Hino, Takahiro Kusakabe
Piwi-interacting RNAs (piRNAs) are a class of small non-coding RNAs that associate with PIWI subfamily proteins, which play an important role in transposon silencing in animal germ cell. The piRNAs biogenesis is divided into two major pathways: primary and secondary, and both pathways are independent of double-stranded RNA-processing enzyme Dicer, which processes the single-stranded RNA transcripts in microRNA (miRNA) and siRNA (small interfering RNA) pathway. Primary piRNAs are processed from long non-coding RNA precursors transcribed from piRNA clusters...
November 18, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28904014/redundant-and-incoherent-regulations-of-multiple-phenotypes-suggest-micrornas-role-in-stability-control
#15
Zhongqi Liufu, Yixin Zhao, Li Guo, Guangxia Miao, Juan Xiao, Yang Lyu, Yuxin Chen, Suhua Shi, Tian Tang, Chung-I Wu
Each microRNA (miRNA) represses a web of target genes and, through them, controls multiple phenotypes. The difficulties inherent in such controls cast doubt on how effective miRNAs are in driving phenotypic changes. A "simple regulation" model posits "one target-one phenotype" control under which most targeting is nonfunctional. In an alternative "coordinate regulation" model, multiple targets are assumed to control the same phenotypes coherently, and most targeting is functional. Both models have some empirical support but pose different conceptual challenges...
October 2017: Genome Research
https://www.readbyqxmd.com/read/28866639/overexpression-of-mirna-9-generates-muscle-hypercontraction-through-translational-repression-of-troponin-t-in-drosophila-melanogaster-indirect-flight-muscles
#16
Prasanna Katti, Divesh Thimmaya, Aditi Madan, Upendra Nongthomba
MicroRNAs (miRNAs) are small noncoding endogenous RNAs, typically 21-23 nucleotides long, that regulate gene expression, usually post-transcriptionally, by binding to the 3'-UTR of target mRNA, thus blocking translation. The expression of several miRNAs is significantly altered during cardiac hypertrophy, myocardial ischemia, fibrosis, heart failure, and other cardiac myopathies. Recent studies have implicated miRNA-9 (miR-9) in myocardial hypertrophy. However, a detailed mechanism remains obscure. In this study, we have addressed the roles of miR-9 in muscle development and function using a genetically tractable model system, the indirect flight muscles (IFMs) of Drosophila melanogaster Bioinformatics analysis identified 135 potential miR-9a targets, of which 27 genes were associated with Drosophila muscle development...
October 5, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28859623/ancient-human-mirnas-are-more-likely-to-have-broad-functions-and-disease-associations-than-young-mirnas
#17
Vir D Patel, John A Capra
BACKGROUND: microRNAs (miRNAs) are essential to the regulation of gene expression in eukaryotes, and improper expression of miRNAs contributes to hundreds of diseases. Despite the essential functions of miRNAs, the evolutionary dynamics of how they are integrated into existing gene regulatory and functional networks is not well understood. Knowledge of the origin and evolutionary history a gene has proven informative about its functions and disease associations; we hypothesize that incorporating the evolutionary origins of miRNAs into analyses will help resolve differences in their functional dynamics and how they influence disease...
August 31, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28859085/plant-micrornas-in-larval-food-regulate-honeybee-caste-development
#18
Kegan Zhu, Minghui Liu, Zheng Fu, Zhen Zhou, Yan Kong, Hongwei Liang, Zheguang Lin, Jun Luo, Huoqing Zheng, Ping Wan, Junfeng Zhang, Ke Zen, Jiong Chen, Fuliang Hu, Chen-Yu Zhang, Jie Ren, Xi Chen
The major environmental determinants of honeybee caste development come from larval nutrients: royal jelly stimulates the differentiation of larvae into queens, whereas beebread leads to worker bee fate. However, these determinants are not fully characterized. Here we report that plant RNAs, particularly miRNAs, which are more enriched in beebread than in royal jelly, delay development and decrease body and ovary size in honeybees, thereby preventing larval differentiation into queens and inducing development into worker bees...
August 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28728902/role-of-mirnas-in-development-and-disease-lessons-learnt-from-small-organisms
#19
REVIEW
Swati Chandra, Divya Vimal, Divya Sharma, Vipin Rai, Subash Chandra Gupta, D Kar Chowdhuri
MicroRNAs (miRNAs) constitute a class of small (18-22 nucleotides) non-coding RNAs that regulate gene expression at the post-transcriptional level. Caenorhabditis elegans, Drosophila melanogaster, and many other small organisms have been instrumental in deciphering the biological functions of miRNAs. While some miRNAs from small organisms are highly conserved across the taxa, others are organism specific. The miRNAs are known to play a crucial role during development and in various cellular functions such as cell survival, cell proliferation, and differentiation...
September 15, 2017: Life Sciences
https://www.readbyqxmd.com/read/28708823/notch-dependent-epithelial-fold-determines-boundary-formation-between-developmental-fields-in-the-drosophila-antenna
#20
Hui-Yu Ku, Y Henry Sun
Compartment boundary formation plays an important role in development by separating adjacent developmental fields. Drosophila imaginal discs have proven valuable for studying the mechanisms of boundary formation. We studied the boundary separating the proximal A1 segment and the distal segments, defined respectively by Lim1 and Dll expression in the eye-antenna disc. Sharp segregation of the Lim1 and Dll expression domains precedes activation of Notch at the Dll/Lim1 interface. By repressing bantam miRNA and elevating the actin regulator Enable, Notch signaling then induces actomyosin-dependent apical constriction and epithelial fold...
July 2017: PLoS Genetics
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