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https://www.readbyqxmd.com/read/28448516/natural-variation-of-pirna-expression-affects-immunity-to-transposable-elements
#1
Sergei Ryazansky, Elizaveta Radion, Anastasia Mironova, Natalia Akulenko, Yuri Abramov, Valeriya Morgunova, Maria Y Kordyukova, Ivan Olovnikov, Alla Kalmykova
In the Drosophila germline, transposable elements (TEs) are silenced by PIWI-interacting RNA (piRNA) that originate from distinct genomic regions termed piRNA clusters and are processed by PIWI-subfamily Argonaute proteins. Here, we explore the variation in the ability to restrain an alien TE in different Drosophila strains. The I-element is a retrotransposon involved in the phenomenon of I-R hybrid dysgenesis in Drosophila melanogaster. Genomes of R strains do not contain active I-elements, but harbour remnants of ancestral I-related elements...
April 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28445427/small-rna-pathways-that-protect-the-somatic-genome
#2
REVIEW
Seogang Hyun
Transposable elements (TEs) are DNA elements that can change their position within the genome, with the potential to create mutations and destabilize the genome. As such, special molecular systems have been adopted in animals to control TE activity in order to protect the genome. PIWI proteins, in collaboration with PIWI-interacting RNAs (piRNAs), are well known to play a critical role in silencing germline TEs. Although initially thought to be germline-specific, the role of PIWI-piRNA pathways in controlling TEs in somatic cells has recently begun to be explored in various organisms, together with the role of endogenous small interfering RNAs (endo-siRNAs)...
April 26, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28441530/aubergine-controls-germline-stem-cell-self-renewal-and-progeny-differentiation-via-distinct-mechanisms
#3
Xing Ma, Xiujuan Zhu, Yingying Han, Benjamin Story, Trieu Do, Xiaoqing Song, Su Wang, Ying Zhang, Marco Blanchette, Madelaine Gogol, Kate Hall, Allison Peak, Perera Anoja, Ting Xie
Piwi family protein Aubergine (Aub) maintains genome integrity in late germ cells of the Drosophila ovary through Piwi-associated RNA-mediated repression of transposon activities. Although it is highly expressed in germline stem cells (GSCs) and early progeny, it remains unclear whether it plays any roles in early GSC lineage development. Here we report that Aub promotes GSC self-renewal and GSC progeny differentiation. RNA-iCLIP results show that Aub binds the mRNAs encoding self-renewal and differentiation factors in cultured GSCs...
April 24, 2017: Developmental Cell
https://www.readbyqxmd.com/read/28438683/identification-and-expression-of-piwil2-in-turbot-scophthalmus-maximus-with-implications-of-the-involvement-in-embryonic-and-gonadal-development
#4
Huizhen Wang, Bo Wang, Xiaobing Liu, Yuezhong Liu, Xinxin Du, Quanqi Zhang, XuBo Wang
Piwil2, a member of the Argonaute family, is involved in the biogenesis of PIWI-interacting RNAs (piRNAs) and plays an important role in regulating gametogenesis. In the present study, we identified turbot Scophthalmus maximus piwil2 gene, named Smpiwil2, which contained a PAZ domain and a PIWI domain. Sequence comparison, genomic structure and phylogenetic analyses showed that Smpiwil2 is homologous to that of teleosts and tetrapods. The Smpiwil2 transcript showed higher expression in ovary than in testis, demonstrating a sexually dimorphic gene expression pattern...
April 21, 2017: Comparative Biochemistry and Physiology. Part B, Biochemistry & Molecular Biology
https://www.readbyqxmd.com/read/28423657/identification-and-characterization-of-rassf1c-pirna-target-genes-in-lung-cancer-cells
#5
Mark E Reeves, Mathew Firek, Abdullaati Jliedi, Yousef G Amaar
RASSF1C up-regulates important genes involved in lung cancer cell growth, including a stem cell self-renewal gene, piwil1. In this article, we report the identification of small noncoding PIWI-interacting RNAs (piRNAs) in lung cancer cells over-expressing RASSF1C. A piRNA microarray screen was performed using RNA isolated from the lung cancer cell line H1299 stably over-expressing RASSF1C and corresponding control. The piRNA microarray screen identified several piRNAs that are regulated by RASSF1C and we have validated the expression of two up-regulated piRNAs (piR-34871 and piR-52200) and two down-regulated piRNAs (piR-35127 and piR-46545) in lung cancer cells with silenced and over-expressed RASSF1C using RT-PCR...
March 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/28423565/identification-and-characterization-of-l1-specific-endo-sirnas-essential-for-early-embryonic-development-in-pig
#6
Heng Zhang, Jilong Liu, Yurong Tai, Xiaolei Zhang, Jiaming Zhang, Shichao Liu, Jiawei Lv, Zhonghua Liu, Qingran Kong
Small noncoding RNAs (sncRNAs) play important roles in RNA interference (RNAi). In addition to microRNA (miRNA) and Piwi-interacting RNA (piRNA), one key member of sncRNAs group is endogenous small interfering RNA (endo-siRNA). Some studies do show the role of endo-siRNAs in Dicer and/or Ago mutants, however, the biological functions of specific endo-siRNAs remains mostly unanswered. In the study, we have performed a comparative analysis of endo-siRNAs present in porcine sperms, oocytes and zygotes, identified by deep sequencing and bioinformatics analysis...
April 4, 2017: Oncotarget
https://www.readbyqxmd.com/read/28422722/the-clinical-value-regulatory-mechanisms-and-gene-network-of-the-cancer-testis-gene-stk31-in-pancreatic-cancer
#7
Kai Zhang, Zipeng Lu, Yi Zhu, Lei Tian, Jingjing Zhang, Chunhua Xi, Wentao Gao, Kuirong Jiang, Yi Miao
We aimed to identify STK31 as a cancer-testis (CT) gene and to explore its potential clinical value, regulatory mechanisms, and gene network in pancreatic cancer (PC). Gene expression data were generated from normal organ samples and pancreatic cancer samples from three public databases. STK31 expression patterns in normal and PC tissues were identified, and we explored its regulatory mechanisms. Gene ontology (GO) and pathway analyses of STK31-related genes were performed and an STK31 protein-protein interaction (PPI) network was constructed...
April 4, 2017: Oncotarget
https://www.readbyqxmd.com/read/28420675/integrative-analysis-unveils-new-functions-for-the-drosophila-cutoff-protein-in-non-coding-rna-biogenesis-and-gene-regulation
#8
Yuri Pritykin, Tarcisio Brito, Trudi Schupbach, Mona Singh, Attilio Pane
Piwi-Interacting RNAs (piRNAs) are central components of the piRNA pathway, which directs transposon silencing and guarantees genome integrity in the germ cells of several metazoans. In Drosophila, piRNAs are produced from discrete regions of the genome termed piRNA clusters, whose expression relies on the RDC complex comprised of the core proteins Rhino, Deadlock and Cutoff. To date, the RDC complex has been exclusively implicated in the regulation of the piRNA loci. Here we further elucidate the function of Cutoff and the RDC complex by performing genome-wide ChIP-seq and RNA-seq assays in the Drosophila germline and analyzing these data together with other publicly available data sets...
April 18, 2017: RNA
https://www.readbyqxmd.com/read/28414124/roles-of-pirnas-in-microcystin-leucine-arginine-mc-lr-induced-reproductive-toxicity-in-testis-on-male-offspring
#9
Ling Zhang, Hui Zhang, Huan Zhang, Mikael Benson, Xiaodong Han, Dongmei Li
In the present study, we evaluated the toxic effects on the testis of the male offspring of MC-LR exposure during fetal and lactational periods. Pregnant females were distributed into two experimental groups: control group and MC-LR group which were exposed to 0 and 10 μg/L of MC-LR, respectively, through drinking water separately during fetal and lactational periods. At the age of 30 days after birth, the male offspring were euthanized. The body weight, testis index, and histomorphology change were observed and the global changes of piwi-interacting RNA (piRNA) expression were evaluated...
April 13, 2017: Food and Chemical Toxicology
https://www.readbyqxmd.com/read/28399266/pirna-3312-a-putative-role-for-pyrethroid-resistance-in-culex-pipiens-pallens-diptera-culicidae
#10
Juxin Guo, Wenyun Ye, Xianmiao Liu, Xueli Sun, Qin Guo, Yun Huang, Lei Ma, Yan Sun, Bo Shen, Dan Zhou, Changliang Zhu
Piwi-interacting RNAs (piRNAs) are a newly identified class of small noncoding RNAs. They are associated with chromatin organization, messenger RNA stability, and genome structure. Although the overexpression of piRNA-3312 in deltamethrin-susceptible (DS) strain of Culex pipiens pallens (L.) was observed in our previous large-scale transcriptome data, the roles of piRNA in insecticide resistance have not been clearly defined. The aim of the present study was to investigate how piRNA-3312 is involved in insecticide resistance...
March 7, 2017: Journal of Medical Entomology
https://www.readbyqxmd.com/read/28393858/hili-destabilizes-microtubules-by-suppressing-phosphorylation-and-gigaxonin-mediated-degradation-of-tbcb
#11
Hao Tan, Hua Liao, Lianfang Zhao, Yilu Lu, Siyuan Jiang, Dachang Tao, Yunqiang Liu, Yongxin Ma
Human PIWIL2, aka HILI, is a member of PIWI protein family and overexpresses in various tumors. However, the underlying mechanisms of HILI in tumorigenesis remain largely unknown. TBCB has a critical role in regulating microtubule dynamics and is overexpressed in many cancers. Here we report that HILI inhibits Gigaxonin-mediated TBCB ubiquitination and degradation by interacting with TBCB, promoting the binding between HSP90 and TBCB, and suppressing the interaction between Gigaxonin and TBCB. Meanwhile, HILI can also reduce phosphorylation level of TBCB induced by PAK1...
April 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28388001/exploring-the-rna-bound-and-rna-free-human-argonaute-2-by-molecular-dynamics-simulation-method
#12
Ren Kong, Lei Xu, Lianhua Piao, Dawei Zhang, Ting-Jun Hou, Shan Chang
Argonaute 2 (Ago2) protein is the major vehicle of MicroRNAs (miRNAs) guided gene repression and silencing processes. Although the crystal structure of human Ago2 (hAgo2) has recently been disclosed but the information of dynamically structural character of protein-RNA recognition is still lacking. Molecular dynamics simulations were used to systematically explore hAgo2 in the presence and absence of RNA duplex. Stable direct and water-mediated hydrogen bonds were observed between guide RNA backbone atoms and hAgo2, especially for nucleotides 2-7...
April 7, 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/28384097/domestic-chickens-activate-a-pirna-defense-against-avian-leukosis-virus
#13
Yu Huining Sun, Li Huitong Xie, Xiaoyu Zhuo, Qiang Chen, Dalia Ghoneim, Bin Zhang, Jarra Jagne, Chengbo Yang, Xin Zhiguo Li
PIWI-interacting RNAs (piRNAs) protect the germ line by targeting transposable elements (TEs) through the base-pair complementarity. We do not know how piRNAs co-evolve with TEs in chickens. Here we reported that all active TEs in the chicken germ line are targeted by piRNAs, and as TEs lose their activity, the corresponding piRNAs erode away. We observed de novo piRNA birth as host responds to a recent retroviral invasion. Avian leukosis virus (ALV) has endogenized prior to chicken domestication, remains infectious, and threatens poultry industry...
April 6, 2017: ELife
https://www.readbyqxmd.com/read/28367472/hiwi2-rs508485-polymorphism-is-associated-with-non-obstructive-azoospermia-in-iranian-patients
#14
Zeeba Kamaliyan, Sara Pouriamanesh, Mona Amin-Beidokhti, Amir Rezagholizadeh, Reza Mirfakhraie
BACKGROUND: The PIWI-interacting RNA (piRNA) pathway has an essential role in transposon silencing, meiosis progression, spermatogenesis, and germline maintenance. HIWI genes are critical for piRNA biogenesis and function. Therefore, polymorphisms in HIWI genes contribute to spermatogenesis defects and can be considered as risk factors for male infertility. The aim of the present study was to investigate the association between the HIWI2 gene rs508485 polymorphism and non-obstructive azoospermia...
April 2017: Reports of Biochemistry & Molecular Biology
https://www.readbyqxmd.com/read/28348640/exploration-of-small-rna-seq-data-for-small-non-coding-rnas-in-human-colorectal-cancer
#15
Srinivas V Koduru, Amit K Tiwari, Sprague W Hazard, Milind Mahajan, Dino J Ravnic
Background: Improved healthcare and recent breakthroughs in technology have substantially reduced cancer mortality rates worldwide. Recent advancements in next-generation sequencing (NGS) have allowed genomic analysis of the human transcriptome. Now, using NGS we can further look into small non-coding regions of RNAs (sncRNAs) such as microRNAs (miRNAs), Piwi-interacting-RNAs (piRNAs), long non-coding RNAs (lncRNAs), and small nuclear/nucleolar RNAs (sn/snoRNAs) among others. Recent studies looking at sncRNAs indicate their role in important biological processes such as cancer progression and predict their role as biomarkers for disease diagnosis, prognosis, and therapy...
2017: Journal of Genomics
https://www.readbyqxmd.com/read/28325293/a-pirna-like-small-rna-induces-chemoresistance-to-cisplatin-based-therapy-by-inhibiting-apoptosis-in-lung-squamous-cell-carcinoma
#16
Yuyan Wang, Tyler Gable, Mark Z Ma, David Clark, Jun Zhao, Yi Zhang, Wei Liu, Li Mao, Yuping Mei
Lung cancer is the leading cause of cancer-related death worldwide. Although advanced drugs have benefitted patients, therapeutic success has largely been hampered because of rapid development of resistance. Here we report that PIWI-interacting RNA likes (piR-Ls), a novel type of functional sncRNAs, play key roles in chemoresistance to cisplatin (CDDP)-based chemotherapy in lung squamous cell carcinoma (LSCC). piR-L-138 was upregulated upon CDDP-based chemotherapy both in LSCC cells and in patient-derived xenograft (PDX) LSCC models...
March 17, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28323037/a-phosphorylation-wide-sncrna-screen-reveals-protein-functional-effector-sncrnas-pfernas-in-human-lung-somatic-cells
#17
Tyler Gable, Yuyan Wang, David Clark, Priti Kumari, Amol Carl Shetty, Mao Li, Yuping Mei
We recently reported that PIWI-interacting RNAs likes (piR-Ls) could regulate functions of the interacting phosphorylated proteins (p-Proteins). In addition, except for writers and erasers, functional efficacy of p-Proteins on their readers still remains unknown. We, therefore, reasoned there was a type of sncRNAs which could regulate functional efficacy of p-Proteins. Here, we profiled sncRNAs interacting with phosphorylated -Ser, -Thr and -Tyr residues in 3 HBE and 4 lung SCC cell lines, investigated effects and mechanisms of phosphorylated-residue-interacting sncRNAs...
March 16, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28292424/btbd18-regulates-a-subset-of-pirna-generating-loci-through-transcription-elongation-in-mice
#18
Liquan Zhou, Bertram Canagarajah, Yangu Zhao, Boris Baibakov, Keizo Tokuhiro, Dragan Maric, Jurrien Dean
PIWI-interacting RNAs (piRNAs) are small non-coding RNAs essential for animal germ cell development. Despite intense investigation of post-transcriptional processing, chromatin regulators for piRNA biogenesis in mammals remain largely unexplored. Here we document that BTBD18 is a pachytene nuclear protein in mouse testes that occupies a subset of pachytene piRNA-producing loci. Ablation of Btbd18 in mice disrupts piRNA biogenesis, prevents spermiogenesis, and results in male sterility. Transcriptome profiling, chromatin accessibility, and RNA polymerase II occupancy demonstrate that BTBD18 facilitates expression of pachytene piRNA precursors by promoting transcription elongation...
March 13, 2017: Developmental Cell
https://www.readbyqxmd.com/read/28289238/stroke-and-circulating-extracellular-rnas
#19
Eric Mick, Ravi Shah, Kahraman Tanriverdi, Venkatesh Murthy, Mark Gerstein, Joel Rozowsky, Robert Kitchen, Martin G Larson, Daniel Levy, Jane E Freedman
BACKGROUND AND PURPOSE: There is increasing interest in extracellular RNAs (ex-RNAs), with numerous reports of associations between selected microRNAs (miRNAs) and a variety of cardiovascular disease phenotypes. Previous studies of ex-RNAs in relation to risk for cardiovascular disease have investigated small numbers of patients and assayed only candidate miRNAs. No human studies have investigated links between novel ex-RNAs and stroke. METHODS: We conducted unbiased next-generation sequencing using plasma from 40 participants of the FHS (Framingham Heart Study; Offspring Cohort Exam 8) followed by high-throughput polymerase chain reaction of 471 ex-RNAs...
April 2017: Stroke; a Journal of Cerebral Circulation
https://www.readbyqxmd.com/read/28283070/circular-concatemers-of-ultra-short-dna-segments-produce-regulatory-rnas
#20
Sarah E Allen, Iris Hug, Sylwia Pabian, Iwona Rzeszutek, Cristina Hoehener, Mariusz Nowacki
In the ciliated protozoan Paramecium tetraurelia, Piwi-associated small RNAs are generated upon the elimination of tens of thousands of short transposon-derived DNA segments as part of development. These RNAs then target complementary DNA for elimination in a positive feedback process, contributing to germline defense and genome stability. In this work, we investigate the formation of these RNAs, which we show to be transcribed directly from the short (length mode 27 bp) excised DNA segments. Our data support a mechanism whereby the concatenation and circularization of excised DNA segments provides a template for RNA production...
March 9, 2017: Cell
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