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https://www.readbyqxmd.com/read/28646211/increasing-cell-density-globally-enhances-the-biogenesis-of-piwi-interacting-rnas-in-bombyx-mori-germ-cells
#1
Shozo Honda, Phillipe Loher, Keisuke Morichika, Megumi Shigematsu, Takuya Kawamura, Yoriko Kirino, Isidore Rigoutsos, Yohei Kirino
Piwi proteins and their bound Piwi-interacting RNAs (piRNAs) are predominantly expressed in the germline and play crucial roles in germline development by silencing transposons and other targets. Bombyx mori BmN4 cells are culturable germ cells that equip the piRNA pathway. Because of the scarcity of piRNA-expressing culturable cells, BmN4 cells are being utilized for the analyses of piRNA biogenesis. We here report that the piRNA biogenesis in BmN4 cells is regulated by cell density. As cell density increased, the abundance of Piwi proteins and piRNA biogenesis factors was commonly upregulated, resulting in an increased number of perinuclear nuage-like granules where Piwi proteins localize...
June 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28645172/the-biogenesis-pathway-of-trna-derived-pirnas-in-bombyx-germ-cells
#2
Shozo Honda, Takuya Kawamura, Phillipe Loher, Keisuke Morichika, Isidore Rigoutsos, Yohei Kirino
Transfer RNAs (tRNAs) function in translational machinery and further serves as a source of short non-coding RNAs (ncRNAs). tRNA-derived ncRNAs show differential expression profiles and play roles in many biological processes beyond translation. Molecular mechanisms that shape and regulate their expression profiles are largely unknown. Here, we report the mechanism of biogenesis for tRNA-derived Piwi-interacting RNAs (td-piRNAs) expressed in Bombyx BmN4 cells. In the cells, two cytoplasmic tRNA species, tRNAAspGUC and tRNAHisGUG, served as major sources for td-piRNAs, which were derived from the 5΄-part of the respective tRNAs...
June 22, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28642363/nuclear-phosphorylated-dicer-processes-double-stranded-rna-in-response-to-dna-damage
#3
Kaspar Burger, Margarita Schlackow, Martin Potts, Svenja Hester, Shabaz Mohammed, Monika Gullerova
The endoribonuclease Dicer is a key component of the human RNA interference pathway and is known for its role in cytoplasmic microRNA production. Recent findings suggest that noncanonical Dicer generates small noncoding RNA to mediate the DNA damage response (DDR). Here, we show that human Dicer is phosphorylated in the platform-Piwi/Argonaute/Zwille-connector helix cassette (S1016) upon induction of DNA damage. Phosphorylated Dicer (p-Dicer) accumulates in the nucleus and is recruited to DNA double-strand breaks...
June 22, 2017: Journal of Cell Biology
https://www.readbyqxmd.com/read/28642173/protein-functional-effector-sncrnas-pfernas-in-lung-cancer
#4
Malcolm Brock, Yuping Mei
PIWI-interacting RNA Likes (piR-Ls) were recently reported to regulate functions of their target phospho-Proteins (p-Proteins) in somatic lung cells. However, the mechanism underlying this functionality remains unclear. piR-Ls interact with their targets through direct binding but do not follow base-pairing rules, known to have important roles at levels of transcription, RNA processing and translation for small non-coding RNA (sncRNA). These observations imply a fundamentally different type of sncRNA with behavior that causes a molecular response in their target p-Proteins...
June 19, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28634417/expression-status-of-piwil1-as-a-prognostic-marker-of-colorectal-cancer
#5
Rui Sun, Chun-Li Gao, Dong-Hai Li, Bo-Jun Li, Yan-Hong Ding
The PIWI-like protein 1 (PIWIL1) plays a crucial role in stem cell proliferation, embryogenesis, growth, and development, as well as differentiation and maturation in multiple organisms. The relationships between PIWIL1 expression and clinicopathological features of colorectal cancer (CRC) patients were analyzed by us. Survival analysis was performed using the Kaplan-Meier method and Cox's proportional hazards model. The high expression rate of PIWIL1 in the cancer tissue was obviously higher than that in the corresponding adjacent tissue...
2017: Disease Markers
https://www.readbyqxmd.com/read/28633017/distinct-roles-of-rna-helicases-mvh-and-tdrd9-in-piwi-slicing-triggered-mammalian-pirna-biogenesis-and-function
#6
Joanna M Wenda, David Homolka, Zhaolin Yang, Pietro Spinelli, Ravi Sachidanandam, Radha Raman Pandey, Ramesh S Pillai
Small RNAs called PIWI-interacting RNAs (piRNAs) act as an immune system to suppress transposable elements in the animal gonads. A poorly understood adaptive pathway links cytoplasmic slicing of target RNA by the PIWI protein MILI to loading of target-derived piRNAs into nuclear MIWI2. Here we demonstrate that MILI slicing generates a 16-nt by-product that is discarded and a pre-piRNA intermediate that is used for phased piRNA production. The ATPase activity of Mouse Vasa Homolog (MVH) is essential for processing the intermediate into piRNAs, ensuring transposon silencing and male fertility...
June 19, 2017: Developmental Cell
https://www.readbyqxmd.com/read/28632173/gene-expression-profiling-reveals-potential-players-of-left-right-asymmetry-in-female-chicken-gonads
#7
Zhiyi Wan, Yanan Lu, Lei Rui, Xiaoxue Yu, Fang Yang, Chengfang Tu, Zandong Li
Most female birds develop only a left ovary, whereas males develop bilateral testes. The mechanism underlying this process is still not completely understood. Here, we provide a comprehensive transcriptional analysis of female chicken gonads and identify novel candidate side-biased genes. RNA-Seq analysis was carried out on total RNA harvested from the left and right gonads on embryonic day 6 (E6), E12, and post-hatching day 1 (D1). By comparing the gene expression profiles between the left and right gonads, 347 differentially expressed genes (DEGs) were obtained on E6, 3730 were obtained on E12, and 2787 were obtained on D1...
June 20, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28630288/intact-pirna-pathway-prevents-l1-mobilization-in-male-meiosis
#8
Simon J Newkirk, Suman Lee, Fiorella C Grandi, Valeriya Gaysinskaya, James M Rosser, Nicole Vanden Berg, Cathryn A Hogarth, Maria C N Marchetto, Alysson R Muotri, Michael D Griswold, Ping Ye, Alex Bortvin, Fred H Gage, Jef D Boeke, Wenfeng An
The PIWI-interacting RNA (piRNA) pathway is essential for retrotransposon silencing. In piRNA-deficient mice, L1-overexpressing male germ cells exhibit excessive DNA damage and meiotic defects. It remains unknown whether L1 expression simply highlights piRNA deficiency or actually drives the germ-cell demise. Specifically, the sheer abundance of genomic L1 copies prevents reliable quantification of new insertions. Here, we developed a codon-optimized L1 transgene that is controlled by an endogenous mouse L1 promoter...
June 19, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28630141/temperature-responsive-mirnas-in-drosophila-orchestrate-adaptation-to-different-ambient-temperatures
#9
Isabel Fast, Charlotte Hewel, Laura Wester, Julia Schumacher, Daniel Gebert, Hans Zischler, Christian Berger, David Rosenkranz
The majority of Drosophila genes are expressed in a temperature-dependent manner, but the way in which small RNAs may contribute to this effect is completely unknown as we currently lack an idea of how small RNA transcriptomes change as a function of temperature. Applying high throughput sequencing techniques complemented by quantitative real-time PCR experiments, we demonstrate that altered ambient temperature induces drastic, but reversible changes in sequence composition and total abundance of both, miRNA- and piRNA populations...
June 19, 2017: RNA
https://www.readbyqxmd.com/read/28624202/2l-pirna-a-two-layer-ensemble-classifier-for-identifying-piwi-interacting-rnas-and-their-function
#10
Bin Liu, Fan Yang, Kuo-Chen Chou
Involved with important cellular or gene functions and implicated with many kinds of cancers, piRNAs, or piwi-interacting RNAs, are of small non-coding RNA with around 19-33 nt in length. Given a small non-coding RNA molecule, can we predict whether it is of piRNA according to its sequence information alone? Furthermore, there are two types of piRNA: one has the function of instructing target mRNA deadenylation, and the other does not. Can we discriminate one from the other? With the avalanche of RNA sequences emerging in the postgenomic age, it is urgent to address the two problems for both basic research and drug development...
June 16, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28618124/pir-823-contributes-to-colorectal-tumorigenesis-by-enhancing-the-transcriptional-activity-of-hsf1
#11
Jie Yin, Xiao-Yu Jiang, Wei Qi, Chen-Guang Ji, Xiao-Li Xie, Dong-Xuan Zhang, Zi-Jin Cui, Cun-Kai Wang, Yun Bai, Jia Wang, Hui-Qing Jiang
Piwi-interacting RNAs (piRNAs), a novel class of small non-coding RNA, were first discovered in germline cells and are thought to silence transposons in spermatogenesis. Recently, piRNAs have also been identified in somatic tissues, and aberrant expression of piRNAs in tumor tissues may be implicated in carcinogenesis. However, the function of piR-823 in colorectal cancer (CRC) remains unclear. Here, we first found that piR-823 was significantly up-regulated in CRC tissues compared with its expression in the adjacent tissues...
June 15, 2017: Cancer Science
https://www.readbyqxmd.com/read/28607498/male-factor-infertility-piwi-hiwi-miwi-essential-genes-for-effective-spermiogenesis
#12
Annette Fenner
No abstract text is available yet for this article.
June 13, 2017: Nature Reviews. Urology
https://www.readbyqxmd.com/read/28602845/silencing-of-transposable-elements-by-pirnas-in-drosophila-an-evolutionary-perspective
#13
REVIEW
Shiqi Luo, Jian Lu
Transposable elements (TEs) are DNA sequences that can move within the genome. TEs have greatly shaped the genomes, transcriptomes, and proteomes of the host organisms through a variety of mechanisms. However, TEs generally disrupt genes and destabilize the host genomes, which substantially reduce fitness of the host organisms. Understanding the genomic distribution and evolutionary dynamics of TEs will greatly deepen our understanding of the TE-mediated biological processes. Most TE insertions are highly polymorphic in Drosophila melanogaster, providing us a good system to investigate the evolution of TEs at the population level...
June 8, 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28601066/induction-of-transposon-silencing-in-the-drosophila-germline
#14
REVIEW
S S Ryazansky, A D Stolyarenko, M S Klenov, V A Gvozdev
In this review we consider the role of the piRNA system in transposable element silencing in the Drosophila melanogaster germline. We focus on new data that demonstrate the mechanisms of initiation of piRNA biogenesis in ovarian germinal cells and the role of Piwi protein in this process, including our own results.
May 2017: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/28595904/characterization-of-armitage-and-yb-containing-granules-and-their-relationship-to-nuage-in-ovary-derived-cultured-silkworm-cell
#15
Anandrao Ashok Patil, Tsuneyuki Tatsuke, Hiroaki Mon, Jae Man Lee, Daisuke Morokuma, Masato Hino, Takahiro Kusakabe
PIWI-interacting RNAs (piRNAs) are a class of endogenous small non-coding RNAs, which are mostly 24-32 nucleotides in length and interact specifically with PIWI subfamily of argonaute proteins. Despite the significant research progress in germ line piRNA pathway, its role in somatic cell is not well known. In Drosophila ovarian somatic cell, maturation of primary piRNA and its loading onto Piwi occurs at perinuclear Yb body. The Armitage (Armi) and Yb proteins are the major components of Yb body and specially expressed in ovarian somatic cell...
June 5, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28595264/male-infertility-caused-by-dominant-point-mutations-in-the-d-box-domain-reveals-a-novel-role-of-murine-and-human-piwi-proteins
#16
Wei Yan
No abstract text is available yet for this article.
June 8, 2017: Biology of Reproduction
https://www.readbyqxmd.com/read/28590408/tdrd12-is-essential-for-germ-cell-development-and-maintenance-in-zebrafish
#17
Xiangyan Dai, Yuqin Shu, Qiyong Lou, Qiang Tian, Gang Zhai, Jia Song, Suxiang Lu, Hong Yu, Jiangyan He, Zhan Yin
The regularity of Piwi-interacting RNA (piRNA) biogenesis is crucial to germline development. Functioning as Piwi-interacting proteins, Tudor domain-related proteins (Tdrds) have been demonstrated to be involved in spermatogenesis and the piRNA pathway. In this study, zebrafish tdrd12 was identified, and the maternal and germ cell-specific expression patterns of zebrafish tdrd12 were observed. Utilizing TALEN (transcription activator-like effector nuclease) techniques, two independent tdrd12 mutant zebrafish lines were generated...
June 7, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28587209/variability-in-the-content-of-trans-resveratrol-trans-%C3%AE%C2%B5-viniferin-and-r2-viniferin-in-grape-cane-of-seven-vitis-vinifera-l-varieties-during-a-three-year-study
#18
Jan Tříska, Naděžda Vrchotová, Josef Balík, Ivo Soural, Radek Sotolář
Grape canes are a waste product from viticulture that show potential as an industrially extractable source of stilbenes, which are valuable for medical and other purposes. In this work, grape canes collected in three consecutive years (2014-2016) at six different places in South Moravia, Czech Republic were extracted, and the contents of trans-resveratrol, trans-ε-viniferin, and r2-viniferin were determined by high-performance liquid chromatography. The study included three blue grape varieties of Vitis vinifera L...
June 3, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28585968/isonucleotide-incorporation-into-middle-and-terminal-sirna-duplexes-exhibits-high-gene-silencing-efficacy-and-nuclease-resistance
#19
Yuan Ma, Shuang Liu, Yusi Wang, Yuanhe Zhao, Ye Huang, Lijun Zhong, Zhu Guan, Lihe Zhang, Zhenjun Yang
In this study, we introduced a pair of nucleotide enantiomers, d-/l-isonucleotides (d-/l-isoNA), to examine the interactions between siRNAs and their related proteins. The serum stability and gene-silencing activity of the modified siRNAs were systematically evaluated. Gene-silencing activity had a site-specific effect, and the incorporation of a single d-isoNA at the 8th position (counting from the 5'-terminus) in the antisense strand improved the gene-silencing activity by improving RISC loading and affecting the movement of the PIWI domain...
June 21, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28552546/use-of-the-crispr-cas9-system-for-genome-editing-in-cultured-drosophila-ovarian-somatic-cells
#20
Hirotsugu Ishizu, Tetsutaro Sumiyoshi, Mikiko C Siomi
The CRISPR-Cas9 system can be used for genome engineering in many organisms. PIWI-interacting RNAs (piRNAs) play a crucial role in repressing transposons to maintain genome integrity in Drosophila ovaries, and cultured ovarian somatic cells (OSCs) are widely used to elucidate the molecular mechanisms underlying the piRNA pathway. However, the germline-specific piRNA amplification system known as the ping-pong machinery does not occur in OSCs, making them unsuitable for elucidating the underlying mechanisms...
May 25, 2017: Methods: a Companion to Methods in Enzymology
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