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https://www.readbyqxmd.com/read/27900550/biogenesis-of-diverse-plant-phasirnas-involves-an-mirna-trigger-and-dicer-processing
#1
Reina Komiya
It has been almost 30 years since RNA interference (RNAi) was shown to silence genes via double-stranded RNAs (dsRNAs) in Caenorhabditis elegans (Fire et al. 1998). 20-30-nucleotide (nt) small non-coding RNAs are a key element of the RNAi machinery. Recently, phased small interfering RNAs (phasiRNAs), small RNAs that are generated from a long RNA precursor at intervals of 21 to 26-nt, have been identified in plants and animals. In Drosophila, phasiRNAs are generated by the endonuclease, Zucchini (Zuc), in germlines...
November 29, 2016: Journal of Plant Research
https://www.readbyqxmd.com/read/27899625/ym500v3-a-database-for-small-rna-sequencing-in-human-cancer-research
#2
I-Fang Chung, Shing-Jyh Chang, Chen-Yang Chen, Shu-Hsuan Liu, Chia-Yang Li, Chia-Hao Chan, Chuan-Chi Shih, Wei-Chung Cheng
We previously presented the YM500 database, which contains >8000 small RNA sequencing (smRNA-seq) data sets and integrated analysis results for various cancer miRNome studies. In the updated YM500v3 database (http://ngs.ym.edu.tw/ym500/) presented herein, we not only focus on miRNAs but also on other functional small non-coding RNAs (sncRNAs), such as PIWI-interacting RNAs (piRNAs), tRNA-derived fragments (tRFs), small nuclear RNAs (snRNAs) and small nucleolar RNAs (snoRNAs). There is growing knowledge of the role of sncRNAs in gene regulation and tumorigenesis...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27893851/expression-and-regulation-of-piwil-proteins-and-piwi-interacting-rnas-in-rheumatoid-arthritis
#3
Lenka Pleštilová, Michel Neidhart, Giancarlo Russo, Mojca Frank-Bertoncelj, Caroline Ospelt, Adrian Ciurea, Christoph Kolling, Renate E Gay, Beat A Michel, Jiří Vencovský, Steffen Gay, Astrid Jüngel
OBJECTIVE: The PIWIL (P-element induced wimpy testis like protein) subfamily of argonaute proteins is essential for Piwi-interacting RNA (piRNA) biogenesis and their function to silence transposons during germ-line development. Here we explored their presence and regulation in rheumatoid arthritis (RA). METHODS: The expression of PIWIL genes in RA and osteoarthritis (OA) synovial tissues and synovial fibroblasts (SF) was analysed by Real-time PCR, immunofluorescence and Western blot...
2016: PloS One
https://www.readbyqxmd.com/read/27880868/origin-and-evolution-of-the-metazoan-non-coding-regulatory-genome
#4
REVIEW
Federico Gaiti, Andrew D Calcino, Miloš Tanurdžić, Bernard M Degnan
Animals rely on genomic regulatory systems to direct the dynamic spatiotemporal and cell-type specific gene expression that is essential for the development and maintenance of a multicellular lifestyle. Although it is widely appreciated that these systems ultimately evolved from genomic regulatory mechanisms present in single-celled stem metazoans, it remains unclear how this occurred. Here, we focus on the contribution of the non-coding portion of the genome to the evolution of animal gene regulation, specifically on recent insights from non-bilaterian metazoan lineages, and unicellular and colonial holozoan sister taxa...
November 20, 2016: Developmental Biology
https://www.readbyqxmd.com/read/27872309/phosphate-binding-pocket-in-dicer-2-paz-domain-for-high-fidelity-sirna-production
#5
Suresh K Kandasamy, Ryuya Fukunaga
The enzyme Dicer produces small silencing RNAs such as micro-RNAs (miRNAs) and small interfering RNAs (siRNAs). In Drosophila, Dicer-1 produces ∼22-24-nt miRNAs from pre-miRNAs, whereas Dicer-2 makes 21-nt siRNAs from long double-stranded RNAs (dsRNAs). How Dicer-2 precisely makes 21-nt siRNAs with a remarkably high fidelity is unknown. Here we report that recognition of the 5'-monophosphate of a long dsRNA substrate by a phosphate-binding pocket in the Dicer-2 PAZ (Piwi, Argonaute, and Zwille/Pinhead) domain is crucial for the length fidelity, but not the efficiency, in 21-nt siRNA production...
November 21, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27858163/expression-of-piwil3-in-primary-and-metastatic-melanoma
#6
Thilo Gambichler, Christina Kohsik, Ann-Kathrin Höh, Kerstin Lang, Heiko U Käfferlein, Thomas Brüning, Eggert Stockfleth, Markus Stücker, Max Dreißigacker, Michael Sand
PURPOSE: The PIWI-interacting RNA machinery in malignant melanoma (MM) has not been sufficiently studied. We aimed to investigate the PIWIL3 expression profiles in primary melanomas and metastases of MM including a correlation with clinical data. METHODS: We studied 161 primary melanomas, 45 lymph node metastases, and 16 distant metastases of 183 patients with MM. We used immunohistochemistry to assess PIWIL3 protein expression in situ. The relationship between the immunoreactivity of PIWIL3 and clinical data was statistically evaluated...
November 17, 2016: Journal of Cancer Research and Clinical Oncology
https://www.readbyqxmd.com/read/27851737/genetic-and-mechanistic-diversity-of-pirna-3-end-formation
#7
Rippei Hayashi, Jakob Schnabl, Dominik Handler, Fabio Mohn, Stefan L Ameres, Julius Brennecke
Small regulatory RNAs guide Argonaute (Ago) proteins in a sequence-specific manner to their targets and therefore have important roles in eukaryotic gene silencing. Of the three small RNA classes, microRNAs and short interfering RNAs are processed from double-stranded precursors into defined 21- to 23-mers by Dicer, an endoribonuclease with intrinsic ruler function. PIWI-interacting RNAs (piRNAs)-the 22-30-nt-long guides for PIWI-clade Ago proteins that silence transposons in animal gonads-are generated independently of Dicer from single-stranded precursors...
November 16, 2016: Nature
https://www.readbyqxmd.com/read/27845205/comparative-transcriptomic-analyses-of-male-and-female-adult-toxocara-canis
#8
Rong-Qiong Zhou, Guang-Xu Ma, Pasi K Korhonen, Yong-Li Luo, Hong-Hong Zhu, Yong-Fang Luo, Robin B Gasser, Qing-You Xia
Toxocariasis is an important, neglected zoonosis caused mainly by Toxocara canis. Although our knowledge of helminth molecular biology is improving through completed draft genome projects, there is limited detailed information on the molecular biology of Toxocara species. Here, transcriptomic sequencing of male and female adult T. canis and comparative analyses were conducted. For each sex, two-thirds (66-67%) of quality-filtered reads mapped to the gene set of T. canis, and at least five reads mapped to each of 16,196 (87...
November 11, 2016: Gene
https://www.readbyqxmd.com/read/27829231/deregulation-of-small-non-coding-rnas-at-the-dlk1-dio3-imprinted-locus-predicts-lung-cancer-patient-outcome
#9
Katey S S Enfield, Victor D Martinez, Erin A Marshall, Greg L Stewart, Sonia H Y Kung, Jhon R Enterina, Wan L Lam
Deregulation of the imprinted DLK1-DIO3 locus at chromosome 14q32.1-14q32.31 has been associated with developmental and respiratory disorders, including cancer. In lung cancer, deregulation of imprinting at DLK1-DIO3 was recently described in smokers. Deregulated expression of a microRNA (miRNA) cluster mapping to this locus was also associated with patient outcome, suggesting the importance of this locus to lung cancer disease phenotypes. The DLK1-DIO3 locus is complex, and encodes several protein-coding genes, in addition to long and short non-coding RNAs...
November 5, 2016: Oncotarget
https://www.readbyqxmd.com/read/27799346/pirnas-and-their-diverse-roles-a-transposable-element-driven-tactic-for-gene-regulation
#10
REVIEW
Arpita Sarkar, Jean-Nicolas Volff, Chantal Vaury
P-element-induced wimpy testis (PIWI)-interacting RNAs (piRNAs) are small, noncoding RNAs known for silencing transposable elements (TEs) in the germline of animals. Most genomes host TEs, which are notorious for mobilizing themselves and endangering survival of the host if not controlled. By silencing TEs in the germline, piRNAs prevent harmful mutations from being passed on to the next generation. How piRNAs are generated and how they silence TEs were the focus of researchers ever since their discovery. Now a spate of recent papers are beginning to tell us that piRNAs can play roles beyond TE silencing and are involved in diverse cellular processes from mRNA regulation to development or genome rearrangement...
October 31, 2016: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/27791114/roles-for-small-noncoding-rnas-in-silencing-of-retrotransposons-in-the-mammalian-brain
#11
Sayan Nandi, Dhruva Chandramohan, Luana Fioriti, Ari M Melnick, Jean M Hébert, Christopher E Mason, Priyamvada Rajasethupathy, Eric R Kandel
Piwi-interacting RNAs (piRNAs), long thought to be restricted to germline, have recently been discovered in neurons of Aplysia, with a role in the epigenetic regulation of gene expression underlying long-term memory. We here ask whether piwi/piRNAs are also expressed and have functional roles in the mammalian brain. Large-scale RNA sequencing and subsequent analysis of protein expression revealed the presence in brain of several piRNA biogenesis factors including a mouse piwi (Mili), as well as small RNAs, albeit at low levels, resembling conserved piRNAs in mouse testes [primarily LINE1 (long interspersed nuclear element1) retrotransposon-derived]...
October 24, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27789612/kc167-a-widely-used-drosophila-cell-line-contains-an-active-primary-pirna-pathway
#12
Nicholas Vrettos, Manolis Maragkakis, Panagiotis Alexiou, Zissimos Mourelatos
PIWI family proteins bind to small RNAs known as PIWI-interacting RNAs (piRNAs) and play essential roles in the germline by silencing transposons and by promoting germ cell specification and function. Cell lines that endogenously express piRNAs and PIWI proteins are an invaluable complement to whole-organism studies as they facilitate molecular and biochemical investigations of piRNAs. Here we report that the widely used Kc167 cell line, derived from Drosophila melanogaster embryos, expresses piRNAs that are loaded to Aub and Piwi...
October 27, 2016: RNA
https://www.readbyqxmd.com/read/27786269/genome-wide-identification-of-endogenous-rna-directed-dna-methylation-loci-associated-with-abundant-21-nucleotide-sirnas-in-arabidopsis
#13
Jian-Hua Zhao, Yuan-Yuan Fang, Cheng-Guo Duan, Rong-Xiang Fang, Shou-Wei Ding, Hui-Shan Guo
In Arabidopsis, the 24-nucleotide (nt) small interfering RNAs (siRNAs) mediates RNA-directed DNA methylation (RdDM) and transcriptional gene silencing (TGS) of transposable elements (TEs). In the present study, we examined genome-wide changes in DNA methylation and siRNA accumulation in Arabidopsis induced by expression of the Cucumber mosaic virus silencing suppressor protein 2b known to directly bind to both the 21/24-nt siRNAs as well as their associated Argonaute proteins. We demonstrated a genome-wide reduction of CHH and CHG methylation in the 2b-transgenic plants...
October 27, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27777367/artificial-ping-pong-cascade-of-piwi-interacting-rna-in-silkworm-cells
#14
Keisuke Shoji, Yutaka Suzuki, Sumio Sugano, Toru Shimada, Susumu Katsuma
PIWI-interacting RNAs (piRNAs) play essential roles in the defense system against selfish elements in animal germ line cells by cooperating with PIWI proteins. A subset of piRNAs is predicted to be generated via the "ping-pong" cascade, which is mainly controlled by two different PIWI proteins. Here we established a cell-based artificial piRNA production system using a silkworm ovarian cultured cell line that is believed to possess a complete piRNA pathway. In addition, we took advantage of a unique silkworm sex-determining one-to-one ping-pong piRNA pair, which enabled us to precisely monitor the behaviour of individual artificial piRNAs...
October 24, 2016: RNA
https://www.readbyqxmd.com/read/27754357/microrna-in-control-of-gene-expression-an-overview-of-nuclear-functions
#15
Caterina Catalanotto, Carlo Cogoni, Giuseppe Zardo
The finding that small non-coding RNAs (ncRNAs) are able to control gene expression in a sequence specific manner has had a massive impact on biology. Recent improvements in high throughput sequencing and computational prediction methods have allowed the discovery and classification of several types of ncRNAs. Based on their precursor structures, biogenesis pathways and modes of action, ncRNAs are classified as small interfering RNAs (siRNAs), microRNAs (miRNAs), PIWI-interacting RNAs (piRNAs), endogenous small interfering RNAs (endo-siRNAs or esiRNAs), promoter associate RNAs (pRNAs), small nucleolar RNAs (snoRNAs) and sno-derived RNAs...
October 13, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27743003/small-rnas-from-a-big-genome-the-pirna-pathway-and-transposable-elements-in-the-salamander-species-desmognathus-fuscus
#16
M J Madison-Villar, Cheng Sun, Nelson C Lau, Matthew L Settles, Rachel Lockridge Mueller
Most of the largest vertebrate genomes are found in salamanders, a clade of amphibians that includes 686 species. Salamander genomes range in size from 14 to 120 Gb, reflecting the accumulation of large numbers of transposable element (TE) sequences from all three TE classes. Although DNA loss rates are slow in salamanders relative to other vertebrates, high levels of TE insertion are also likely required to explain such high TE loads. Across the Tree of Life, novel TE insertions are suppressed by several pathways involving small RNA molecules...
October 2016: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/27734358/identification-of-mouse-pirna-pathway-components-using-anti-miwi2-antibodies
#17
Takamasa Hirano, Hidetoshi Hasuwa, Haruhiko Siomi
The mouse testis has served as a popular model system to study a wide range of biological processes, including germ cell development, meiosis, epigenetic changes of chromatin, transposon silencing, and small RNA-mediated epigenetic modifications. PIWI-interacting RNAs (piRNAs) are a class of small RNAs that are almost exclusively expressed in animal gonads. They repress transposons by forming effector complexes with PIWI proteins to maintain genome integrity of the germline. Here we describe detailed procedures of how to produce monoclonal antibodies against a mouse nuclear PIWI protein, MIWI2, which functions in de novo DNA methylation of target transposon loci...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27725823/vat-an-amazing-gene-conferring-resistance-to-aphids-and-viruses-they-carry-from-molecular-structure-to-field-effects
#18
Nathalie Boissot, Alexandra Schoeny, Flavie Vanlerberghe-Masutti
We review half a century of research on Cucumis melo resistance to Aphis gossypii from molecular to field levels. The Vat gene is unique in conferring resistance to both A. gossypii and the viruses it transmits. This double phenotype is aphid clone-dependent and has been observed in 25 melon accessions, mostly from Asia. It is controlled by a cluster of genes including CC-NLR, which has been characterized in detail. Copy-number polymorphisms (for the whole gene and for a domain that stands out in the LLR region) and single-nucleotide polymorphisms have been identified in the Vat cluster...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27716504/piwi-takes-a-giant-step
#19
COMMENT
Yibei Xiao, Ailong Ke
piRNA guides the action of PIWI proteins to silence deleterious transposons in animal reproductive tissues. Biogenesis of piRNA-induced silencing complex (piRISC) involves a multi-step process. In this issue, Matsumoto et al. report the first crystal structure of a PIWI-clade protein displaying a guide RNA, ready for action.
October 6, 2016: Cell
https://www.readbyqxmd.com/read/27698791/micrornas-and-piwi-interacting-rnas-in-oncology
#20
Yong Liu
RNA molecules that are unable to translate into proteins are classified as non-coding RNA. Non-coding RNA (ncRNA) genes include highly abundant and functionally important RNAs such as transfer RNAs, microRNAs (miRNAs), siRNAs, snRNAs, exRNAs and piRNAs. The number of ncRNAs encoded within the human genome is unknown; however, recent transcriptomic and bioinformatic studies suggest the existence of thousands of ncRNAs. Furthermore, small ncRNAs, including miRNAs and PIWI-interacting RNAs (piRNAs), play an imperative role in the regulation of gene expression of numerous biological and pathological processes...
October 2016: Oncology Letters
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