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https://www.readbyqxmd.com/read/29164638/the-piwi-interacting-rna-molecular-pathway-insights-from-cultured-silkworm-germline-cells
#1
Kazuhiro Sakakibara, Mikiko C Siomi
The PIWI-interacting RNA (piRNA) pathway, one of the major eukaryotic small RNA silencing pathways, is a genome surveillance system that silences selfish genes in animal gonads. piRNAs guide PIWI protein to target genes through Watson-Crick RNA-RNA base-parings. Loss of piRNA function causes genome instability, inducing failure in gametogenesis and infertility. Studies using fruit flies and mice as key experimental models have resulted in tremendous progress in understanding the mechanism underlying the piRNA pathway...
November 22, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/29161560/immunity-insect-immune-memory-goes-viral
#2
Petros Ligoxygakis
Adaptive memory in insect immunity has been controversial. In this issue, Andino and co-workers propose that acquisition of viral sequences in the host genome gives rise to anti-sense, anti-viral piRNAs. Such sequences can be regarded as both a genomic archive of past infections and as an armour of potential heritable memory.
November 20, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/29130960/piwi-proteins-and-piwi-interacting-rna-emerging-roles-in-cancer
#3
Yi-Neng Han, Yuan Li, Sheng-Qiang Xia, Yuan-Yuan Zhang, Jun-Hua Zheng, Wei Li
P-Element induced wimpy testis (PIWI)-interacting RNAs (piRNAs) are a type of noncoding RNAs (ncRNAs) and interact with PIWI proteins. piRNAs were primarily described in the germline, but emerging evidence revealed that piRNAs are expressed in a tissue-specific manner among multiple human somatic tissue types as well and play important roles in transposon silencing, epigenetic regulation, gene and protein regulation, genome rearrangement, spermatogenesis and germ stem-cell maintenance. PIWI proteins were first discovered in Drosophila and they play roles in spermatogenesis, germline stem-cell maintenance, self-renewal, retrotransposons silencing and the male germline mobility control...
November 3, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29129531/the-diversity-structure-and-function-of-heritable-adaptive-immunity-sequences-in-the-aedes-aegypti-genome
#4
Zachary J Whitfield, Patrick T Dolan, Mark Kunitomi, Michel Tassetto, Matthew G Seetin, Steve Oh, Cheryl Heiner, Ellen Paxinos, Raul Andino
The Aedes aegypti mosquito transmits arboviruses, including dengue, chikungunya, and Zika virus. Understanding the mechanisms underlying mosquito immunity could provide new tools to control arbovirus spread. Insects exploit two different RNAi pathways to combat viral and transposon infection: short interfering RNAs (siRNAs) and PIWI-interacting RNAs (piRNAs) [1, 2]. Endogenous viral elements (EVEs) are sequences from non-retroviral viruses that are inserted into the mosquito genome and can act as templates for the production of piRNAs [3, 4]...
November 20, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/29127279/the-emergence-of-pirnas-against-transposon-invasion-to-preserve-mammalian-genome-integrity
#5
REVIEW
Christina Ernst, Duncan T Odom, Claudia Kutter
Transposable elements (TEs) contribute to the large amount of repetitive sequences in mammalian genomes and have been linked to species-specific genome innovations by rewiring regulatory circuitries. However, organisms need to restrict TE activity to ensure genome integrity, especially in germline cells to protect the transmission of genetic information to the next generation. This review features our current understandings of mammalian PIWI-interacting RNAs (piRNAs) and their role in TE regulation in spermatogenesis...
November 10, 2017: Nature Communications
https://www.readbyqxmd.com/read/29124009/small-rnaome-sequencing-delineates-the-small-rna-landscape-of-pluripotent-adult-stem-cells-in-the-planarian-schmidtea-mediterranea
#6
Yue Li, An Zeng, Xiao-Shuan Han, Ge Li, Yong-Qin Li, Bairong Shen, Qing Jing
Small noncoding RNAs play a pivotal role in the regulation of gene expression, and are key regulators of animal development. Freshwater planarian exhibits an extraordinary ability to regenerate any missing body parts, representing an emerging model for studying mechanism underlying stem cell regulation and tissue regeneration. Here, we utilized next-generation sequencing (NGS) to identify small RNAs that are expressed in planarian adult stem cells, and are implicated in tissue regeneration. We profiled microRNAs (miRNAs), piwi-interacting RNA (piRNAs), small rDNA-derived RNAs (srRNAs) and endogenous interfering RNAs (endo-siRNAs) population from size 18-30 nt, measured the expression of 244 conserved miRNAs, and identified 41 novel miRNAs and 64 novel endo-siRNAs...
December 2017: Genomics Data
https://www.readbyqxmd.com/read/29118143/structural-basis-for-arginine-methylation-independent-recognition-of-piwil1-by-tdrd2
#7
Heng Zhang, Ke Liu, Natsuko Izumi, Haiming Huang, Deqiang Ding, Zuyao Ni, Sachdev S Sidhu, Chen Chen, Yukihide Tomari, Jinrong Min
The P-element-induced wimpy testis (PIWI)-interacting RNA (piRNA) pathway plays a central role in transposon silencing and genome protection in the animal germline. A family of Tudor domain proteins regulates the piRNA pathway through direct Tudor domain-PIWI interactions. Tudor domains are known to fulfill this function by binding to methylated PIWI proteins in an arginine methylation-dependent manner. Here, we report a mechanism of methylation-independent Tudor domain-PIWI interaction. Unlike most other Tudor domains, the extended Tudor domain of mammalian Tudor domain-containing protein 2 (TDRD2) preferentially recognizes an unmethylated arginine-rich sequence from PIWI-like protein 1 (PIWIL1)...
November 8, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29116069/-participation-of-the-pirna-pathway-in-recruiting-a-component-of-rna-polymerase-i-transcription-initiation-complex-to-germline-cell-nucleoli
#8
E A Fefelova, A D Stolyarenko, E Y Yakushev, V A Gvozdev, M S Klenov
Proteins of the Piwi family and short Piwi-interacting RNAs (piRNAs) ensure the protection of the genome from transposable elements. We have previously shown that nuclear Piwi protein tends to concentrate in the nucleoli of the cells of Drosophila melanogaster ovaries. It could be hypothesized that the function of Piwi in the nucleolus is associated with the repression of R1 and R2 retrotransposons inserted into the rDNA cluster. Here, we show that Piwi participates in recruiting Udd protein to nucleoli. Udd is a component of the conserved Selectivity Factor I-like (SL1-like) complex, which is required for transcription initiation by RNA polymerase I...
September 2017: Molekuliarnaia Biologiia
https://www.readbyqxmd.com/read/29109362/papolb-tpap-regulates-spermiogenesis-independently-of-chromatoid-body-associated-factors
#9
Shin-Ichi Kashiwabara, Satsuki Tsuruta, Yutaro Yamaoka, Kanako Oyama, Chieko Iwazaki, Tadashi Baba
Mutant mice lacking a testis-specific cytoplasmic poly(A) polymerase, PAPOLB/TPAP, exhibit spermiogenesis arrest and male infertility. However, the mechanism by which PAPOLB regulates spermiogenesis remains unclear. In this study, we examined the relationships between PAPOLB and other spermiogenesis regulators present in the chromatoid body (CB). The loss of PAPOLB had no impact either on the abundance of CB components such as PIWIL1, TDRD6, YBX2, and piRNAs, or on retrotransposon expression. In addition, localization of CB proteins and CB architecture were both normal in PAPOLB-null mice...
November 3, 2017: Journal of Reproduction and Development
https://www.readbyqxmd.com/read/29106639/mndr-v2-0-an-updated-resource-of-ncrna-disease-associations-in-mammals
#10
Tianyu Cui, Lin Zhang, Yan Huang, Ying Yi, Puwen Tan, Yue Zhao, Yongfei Hu, Liyan Xu, Enmin Li, Dong Wang
Accumulating evidence suggests that diverse non-coding RNAs (ncRNAs) are involved in the progression of a wide variety of diseases. In recent years, abundant ncRNA-disease associations have been found and predicted according to experiments and prediction algorithms. Diverse ncRNA-disease associations are scattered over many resources and mammals, whereas a global view of diverse ncRNA-disease associations is not available for any mammals. Hence, we have updated the MNDR v2.0 database (www.rna-society.org/mndr/) by integrating experimental and prediction associations from manual literature curation and other resources under one common framework...
November 2, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29101389/pirnas-and-aubergine-cooperate-with-wispy-poly-a-polymerase-to-stabilize-mrnas-in-the-germ-plasm
#11
Jérémy Dufourt, Gwénaëlle Bontonou, Aymeric Chartier, Camille Jahan, Anne-Cécile Meunier, Stéphanie Pierson, Paul F Harrison, Catherine Papin, Traude H Beilharz, Martine Simonelig
Piwi-interacting RNAs (piRNAs) and PIWI proteins play a crucial role in germ cells by repressing transposable elements and regulating gene expression. In Drosophila, maternal piRNAs are loaded into the embryo mostly bound to the PIWI protein Aubergine (Aub). Aub targets maternal mRNAs through incomplete base-pairing with piRNAs and can induce their destabilization in the somatic part of the embryo. Paradoxically, these Aub-dependent unstable mRNAs encode germ cell determinants that are selectively stabilized in the germ plasm...
November 3, 2017: Nature Communications
https://www.readbyqxmd.com/read/29101267/identification-and-verification-of-potential-pirnas-from-domesticated-yak-testis
#12
Jishang Gong, Quanwei Zhang, Qi Wang, Youji Ma, Jiaxiang Du, Yong Zhang, Xingxu Zhao
PIWI-interacting RNAs (piRNA) are small non-coding RNA molecules expressed in animal germ cells that interact with PIWI family proteins to form RNA- protein complexes involved in epigenetic and post- transcriptional gene silencing of retrotransposons and other genetic elements in germ line cells, including reproductive stem cell self- sustainment, differentiation, meiosis and spermatogenesis. In the present study, weperformed high- throughput sequencing of piRNAs in testis samples from yaks in different stages of sexual maturity...
November 3, 2017: Reproduction: the Official Journal of the Society for the Study of Fertility
https://www.readbyqxmd.com/read/29093734/double-stranded-rna-in-human-seminal-plasma
#13
Maxim V Zagoskin, Richard E Davis, Dmitry V Mukha
Recently, human semen was shown to contain cell-free nucleic acids, such as DNA, long single stranded RNA, and small RNAs-miRNA and piRNA. The RNAs have been suggested to have potential biological roles as communication molecules between cells and in the temporal and spatial regulation of gene expression in the male reproductive system. Here we demonstrate that human seminal plasma contains a variety of cell-free dsRNAs, describe a robust method to isolate this type of nucleic acid in preparative amounts, and discuss the potential biological roles of these molecules in inheritance...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/29075336/diversity-of-p-element-pirna-production-among-m-and-q-strains-and-its-association-with-p-m-hybrid-dysgenesis-in-drosophila-melanogaster
#14
Keiko Tsuji Wakisaka, Kenji Ichiyanagi, Seiko Ohno, Masanobu Itoh
BACKGROUND: Transposition of P elements in the genome causes P-M hybrid dysgenesis in Drosophila melanogaster. For the P strain, the P-M phenotypes are associated with the ability to express a class of small RNAs, called piwi-interacting small RNAs (piRNAs), that suppress the P elements in female gonads. However, little is known about the extent to which piRNAs are involved in the P-M hybrid dysgenesis in M' and Q strains, which show different abilities to regulate the P elements from P strains...
2017: Mobile DNA
https://www.readbyqxmd.com/read/29064465/small-non-coding-rna-transcriptome-of-the-nci-60-cell-line-panel
#15
Erin A Marshall, Adam P Sage, Kevin W Ng, Victor D Martinez, Natalie S Firmino, Kevin L Bennewith, Wan L Lam
Only 3% of the transcribed human genome is translated into protein, and small non-coding RNAs from these untranslated regions have demonstrated critical roles in transcriptional and translational regulation of proteins. Here, we provide a resource that will facilitate cell line selection for gene expression studies involving sncRNAs in cancer research. As the most accessible and tractable models of tumours, cancer cell lines are widely used to study cancer development and progression. The NCI-60 panel of 59 cancer cell lines was curated to provide common models for drug screening in 9 tissue types; however, its prominence has extended to use in gene regulation, xenograft models, and beyond...
October 24, 2017: Scientific Data
https://www.readbyqxmd.com/read/29052331/piwis-pirnas-and-retrotransposons-complex-battles-during-reprogramming-in-gametes-and-early-embryos
#16
REVIEW
S J Russell, L Stalker, J LaMarre
Gamete and embryo development are indispensable processes for successful reproduction. Cells involved in these processes acquire pluripotency, the ability to differentiate into multiple different cell types, through a series of events known as reprogramming that lead to profound changes in histone and DNA methylation. While essential for pluripotency, this epigenetic remodelling removes constraints that normally limit the expression of genomic sequences known as transposable elements (TEs). Unconstrained TE expression can lead to many deleterious consequences including infertility, so organisms have evolved complex and potent mechanistic arsenals to target and suppress TE expression during reprogramming...
October 2017: Reproduction in Domestic Animals, Zuchthygiene
https://www.readbyqxmd.com/read/29044429/dynamic-expression-of-long-noncoding-rnas-reveals-their-potential-roles-in-spermatogenesis-and-fertility
#17
Lauren Wichman, Saigopal Somasundaram, Christine Breindel, Dana M Valerio, John R McCarrey, Craig A Hodges, Ahmad M Khalil
Mammalian reproduction requires that males and females produce functional haploid germ cells through complex cellular differentiation processes known as spermatogenesis and oogenesis, respectively. While numerous studies have functionally characterized protein-coding genes and small noncoding RNAs (microRNAs and piRNAs) that are essential for gametogenesis, the roles of regulatory long noncoding RNAs (lncRNAs) are yet to be fully characterized. Previously, we and others have demonstrated that intergenic regions of the mammalian genome encode thousands of long noncoding RNAs, and many studies have now demonstrated their critical roles in key biological processes...
August 1, 2017: Biology of Reproduction
https://www.readbyqxmd.com/read/29040791/roles-of-mmu_pir_003399-in-microcystin-leucine-arginine-mc-lr-induced-reproductive-toxicity-in-the-spermatogonial-cells-and-testis
#18
Ling Zhang, Xiannan Meng, Zou Xiang, Dongmei Li, Xiaodong Han
Our previous work has demonstrated that microcystin-leucine arginine (MC-LR) is a potent toxin for the reproductive system of male mice and it exerts cytotoxicity in spermatogonial cells, resulting in the constitutional and functional changes of the mouse testis. The present study was designed to investigate the functions of P-element-induced wimpy (piwi)-interacting RNAs (piRNAs) in MC-LR-induced reproductive toxicity in male mice. We observed an increase in the mmu_piR_003399 level in spermatogonial cells and mouse testicular tissues following treatment with MC-LR...
October 12, 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/29040304/characterization-of-the-zika-virus-induced-small-rna-response-in-aedes-aegypti-cells
#19
Margus Varjak, Claire L Donald, Timothy J Mottram, Vattipally B Sreenu, Andres Merits, Kevin Maringer, Esther Schnettler, Alain Kohl
RNA interference (RNAi) controls arbovirus infections in mosquitoes. Two different RNAi pathways are involved in antiviral responses: the PIWI-interacting RNA (piRNA) and exogenous short interfering RNA (exo-siRNA) pathways, which are characterized by the production of virus-derived small RNAs of 25-29 and 21 nucleotides, respectively. The exo-siRNA pathway is considered to be the key mosquito antiviral response mechanism. In Aedes aegypti-derived cells, Zika virus (ZIKV)-specific siRNAs were produced and loaded into the exo-siRNA pathway effector protein Argonaute 2 (Ago2); although the knockdown of Ago2 did not enhance virus replication...
October 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/29038333/germ-granule-mediated-rna-regulation-in-male-germ-cells
#20
Tiina Lehtiniemi, Noora Kotaja
Germ cells have exceptionally diverse transcriptomes. Furthermore, the progress of spermatogenesis is accompanied by dramatic changes in gene expression patterns, the most drastic of them being near-to-complete transcriptional silencing during the final steps of differentiation. Therefore, accurate RNA regulatory mechanisms are critical for normal spermatogenesis. Cytoplasmic germ cell-specific ribonucleoprotein (RNP) granules, known as germ granules, participate in posttranscriptional regulation in developing male germ cells...
October 16, 2017: Reproduction: the Official Journal of the Society for the Study of Fertility
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