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https://www.readbyqxmd.com/read/29350289/small-rna-pathways-responsible-for-non-cell-autonomous-regulation-of-plant-reproduction
#1
REVIEW
Ken-Ichi Nonomura
In angiosperms, germline precursors and germ cells are always attached to or engulfed within somatic companion cells until just before fertilization. This is because sperm and egg cells develop as part of the multicellular gametophyte. Thus, the non-cell-autonomous regulation by somatic companions plays important roles in efficient reproduction, in addition to the cell-autonomous regulation. Epigenetic silencing of transposable elements is one of the central events by which the germline transmits the error-free genome to the next generation...
January 19, 2018: Plant Reproduction
https://www.readbyqxmd.com/read/29345184/temperature-dependent-small-rna-expression-in-drosophila-melanogaster
#2
Isabel Fast, David Rosenkranz
Temperature has a major impact on gene expression in ectotherms. But until recently, it was not clear in which way, if any, small non-coding RNAs such as miRNAs or piRNAs contribute to thermosensitive gene regulation. We have recently shown that temperature-responsive miRNAs in Drosophila drive adaptation to different ambient temperatures on the transcriptome level. Moreover, we demonstrated that higher temperatures lead to a more efficient piRNA-dependent transposon silencing, possibly due to heat-induced unfolding of RNA secondary structures...
January 18, 2018: RNA Biology
https://www.readbyqxmd.com/read/29343745/malaria-infected-red-blood-cells-release-small-regulatory-rnas-through-extracellular-vesicles
#3
Kehinde Adebayo Babatunde, Smart Mbagwu, María Andrea Hernández-Castañeda, Swamy R Adapa, Michael Walch, Luis Filgueira, Laurent Falquet, Rays H Y Jiang, Ionita Ghiran, Pierre-Yves Mantel
The parasite Plasmodium falciparum causes the most severe form of malaria. Cell communication between parasites is an important mechanism to control population density and differentiation. The infected red blood cells (iRBCs) release small extracellular vesicles (EVs) that transfer cargoes between cells. The EVs synchronize the differentiation of the asexual parasites into gametocytes to initiate the transmission to the mosquito. Beside their role in parasite communication, EVs regulate vascular function. So far, the exact cargoes responsible for cellular communication remain unknown...
January 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29320577/genome-wide-profiling-of-the-piwi-interacting-rna-mrna-regulatory-networks-in-epithelial-ovarian-cancers
#4
Garima Singh, Jyoti Roy, Pratiti Rout, Bibekanand Mallick
PIWI-interacting (piRNAs), ~23-36 nucleotide-long small non-coding RNAs (sncRNAs), earlier believed to be germline-specific, have now been identified in somatic cells, including cancer cells. These sncRNAs impact critical biological processes by fine-tuning gene expression at post-transcriptional and epigenetic levels. The expression of piRNAs in ovarian cancer, the most lethal gynecologic cancer is largely uncharted. In this study, we investigated the expression of PIWILs by qRT-PCR and western blotting and then identified piRNA transcriptomes in tissues of normal ovary and two most prevalent epithelial ovarian cancer subtypes, serous and endometrioid by small RNA sequencing...
2018: PloS One
https://www.readbyqxmd.com/read/29317756/non-coding-rnas-predict-recurrence-free-survival-of-patients-with-hypoxic-tumours
#5
Victor D Martinez, Natalie S Firmino, Erin A Marshall, Kevin W Ng, Brennan J Wadsworth, Christine Anderson, Wan L Lam, Kevin L Bennewith
Hypoxia promotes tumour aggressiveness and reduces patient survival. A spectrum of poor outcome among patients with hypoxic tumours suggests that additional factors modulate how tumours respond to hypoxia. PIWI-interacting RNAs (piRNAs) are small non-coding RNAs with a pivotal role in genomic stability and epigenetic regulation of gene expression. We reported that cancer type-specific piRNA signatures vary among patients. However, remarkably homogenous piRNA profiles are detected across patients with renal cell carcinoma, a cancer characterized by constitutive upregulation of hypoxia-related signaling induced by common mutation or loss of von Hippel-Lindau factor (VHL)...
January 9, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29317670/tdrd5-binds-pirna-precursors-and-selectively-enhances-pachytene-pirna-processing-in-mice
#6
Deqiang Ding, Jiali Liu, Uros Midic, Yingjie Wu, Kunzhe Dong, Ashley Melnick, Keith E Latham, Chen Chen
Pachytene piRNAs are the most abundant piRNAs in mammalian adult testes. They are generated from long precursor transcripts by the primary piRNA biogenesis pathway but the factors involved in pachytene piRNA precursors processing are poorly understood. Here we show that the Tudor domain-containing 5 (TDRD5) protein is essential for pachytene piRNA biogenesis in mice. Conditional inactivation of TDRD5 in mouse postnatal germ cells reveals that TDRD5 selectively regulates the production of pachytene piRNAs from abundant piRNA-producing precursors, with little effect on low-abundant piRNAs...
January 9, 2018: Nature Communications
https://www.readbyqxmd.com/read/29317647/investigation-of-piwi-interacting-rna-pathway-genes-role-in-idiopathic-non-obstructive-azoospermia
#7
Zeeba Kamaliyan, Sara Pouriamanesh, Mohsen Soosanabadi, Milad Gholami, Reza Mirfakhraie
Genes involved in piwi-interacting RNAs (piRNAs) pathway have an essential role in spermatogenesis. HIWI and TDRD proteins are critical for piRNA biogenesis and function. Therefore, Mutations and polymorphisms in HIWI and TDRD genes may play role in male infertility. The aim of the present study was to investigate the role of HIWI2 rs508485 (T>C) and HIWI3 rs11703684 (C>T) polymorphisms and mutational analysis of TDRD5 gene in idiopathic non-obstructive azoospermia in a case-control study including 226 non-obstructive azoospermia patients and 200 fertile males...
January 9, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29301509/assessment-of-pirna-biogenesis-and-function-in-testicular-germ-cell-tumors-and-their-precursor-germ-cell-neoplasia-in-situ
#8
Ildar V Gainetdinov, Yulia V Skvortsova, Sofia A Kondratieva, Alexey Klimov, Alexey A Tryakin, Tatyana L Azhikina
BACKGROUND: Aberrant overexpression of PIWI/piRNA pathway proteins is shown for many types of tumors. Interestingly, these proteins are downregulated in testicular germ cell tumors (TGCTs) compared to normal testis tissues. Here, we used germline and TGCT markers to assess the piRNA biogenesis and function in TGCTs and their precursor germ cell neoplasia in situ (GCNIS). METHODS: We used small RNA deep sequencing, qRT-PCR, and mining public RNAseq/small RNA-seq datasets to examine PIWI/piRNA gene expression and piRNA biogenesis at four stages of TGCT development: (i) germ cells in healthy testis tissues, (ii) germ cells in testis tissues adjacent to TGCTs, (iii) GCNIS cells and (iv) TGCT cells...
January 4, 2018: BMC Cancer
https://www.readbyqxmd.com/read/29297285/effective-computational-detection-of-pirnas-using-n-gram-models-and-support-vector-machine
#9
Chun-Chi Chen, Xiaoning Qian, Byung-Jun Yoon
BACKGROUND: Piwi-interacting RNAs (piRNAs) are a new class of small non-coding RNAs that are known to be associated with RNA silencing. The piRNAs play an important role in protecting the genome from invasive transposons in the germline. Recent studies have shown that piRNAs are linked to the genome stability and a variety of human cancers. Due to their clinical importance, there is a pressing need for effective computational methods that can be used for computational identification of piRNAs...
December 28, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29281264/piwi-interacting-rna-in-drosophila-biogenesis-transposon-regulation-and-beyond
#10
Haruna Yamashiro, Mikiko C Siomi
PIWI-interacting RNAs (piRNAs) are germline-enriched small RNAs that control transposons to maintain genome integrity. To achieve this, upon being processed from piRNA precursors, most of which are transcripts of intergenic piRNA clusters, piRNAs bind PIWI proteins, germline-specific Argonaute proteins, to form effector complexes. The mechanism of this piRNA-mediated transposon silencing pathway is fundamentally similar to that of siRNA/miRNA-dependent gene silencing in that a small RNA guides its partner Argonaute protein to target gene transcripts for repression via RNA-RNA base pairing...
December 27, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/29237021/human-specific-subcellular-compartmentalization-of-p-element-induced-wimpy-testis-like-piwil-granules-during-germ-cell-development-and-spermatogenesis
#11
Maria Gomes Fernandes, Nannan He, Fang Wang, Liesbeth Van Iperen, Cristina Eguizabal, Roberto Matorras, Bernard A J Roelen, Susana M Chuva De Sousa Lopes
STUDY QUESTION: What is the dynamics of expression of P-element induced wimpy testis-like (PIWIL) proteins in the germline during human fetal development and spermatogenesis? SUMMARY ANSWER: PIWIL1, PIWIL2, PIWIL3 and PIWIL4 were expressed in a sex-specific fashion in human germ cells (GC) during development and adulthood. PIWILs showed a mutually exclusive pattern of subcellular localization. PIWILs were present in the intermitochondrial cement and a single large granule in meiotic GC and their expression was different from that observed in mice, highlighting species-differences...
December 11, 2017: Human Reproduction
https://www.readbyqxmd.com/read/29236253/iclip-of-the-piwi-protein-aubergine-in-drosophila-embryos
#12
Bridlin Barckmann, Jérémy Dufourt, Martine Simonelig
Piwi-interacting RNAs (piRNAs) are a class of small noncoding RNAs bound to specific Argonaute proteins, the PIWI proteins. piRNAs target mRNAs by complementarity to silence them; they play an important role in the repression of transposable elements in the germ line of many species. piRNAs and PIWI proteins are also involved in diverse biological processes through their role in the regulation of cellular mRNAs. In the Drosophila embryo, they contribute to the maternal mRNA decay occurring during the maternal-to-zygotic transition...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29219730/a-comprehensive-profile-of-circulating-rnas-in-human-serum
#13
Sinan Uğur Umu, Hilde Langseth, Cecilie Bucher-Johannessen, Bastian Fromm, Andreas Keller, Eckart Meese, Marianne Lauritzen, Magnus Leithaug, Robert Lyle, Trine B Rounge
Non-coding RNA (ncRNA) molecules have fundamental roles in cells and many are also stable in body fluids as extracellular RNAs. In this study, we used RNA sequencing (RNA-seq) to investigate the profile of small non-coding RNA (sncRNA) in human serum. We analyzed 10 billion Illumina reads from 477 serum samples, included in the Norwegian population-based Janus Serum Bank (JSB). We found that the core serum RNA repertoire includes 258 micro RNAs (miRNA), 441 piwi-interacting RNAs (piRNA), 411 transfer RNAs (tRNA), 24 small nucleolar RNAs (snoRNA), 125 small nuclear RNAs (snRNA) and 123 miscellaneous RNAs (misc-RNA)...
December 8, 2017: RNA Biology
https://www.readbyqxmd.com/read/29211718/pirna-mediated-regulation-of-transposon-alternative-splicing-in-the-soma-and-germ-line
#14
Felipe Karam Teixeira, Martyna Okuniewska, Colin D Malone, Rémi-Xavier Coux, Donald C Rio, Ruth Lehmann
Transposable elements can drive genome evolution, but their enhanced activity is detrimental to the host and therefore must be tightly regulated. The Piwi-interacting small RNA (piRNA) pathway is vital for the regulation of transposable elements, by inducing transcriptional silencing or post-transcriptional decay of mRNAs. Here we show that piRNAs and piRNA biogenesis components regulate precursor mRNA splicing of P-transposable element transcripts in vivo, leading to the production of the non-transposase-encoding mature mRNA isoform in Drosophila germ cells...
December 6, 2017: Nature
https://www.readbyqxmd.com/read/29203920/pan-arthropod-analysis-reveals-somatic-pirnas-as-an-ancestral-defence-against-transposable-elements
#15
Samuel H Lewis, Kaycee A Quarles, Yujing Yang, Melanie Tanguy, Lise Frézal, Stephen A Smith, Prashant P Sharma, Richard Cordaux, Clément Gilbert, Isabelle Giraud, David H Collins, Phillip D Zamore, Eric A Miska, Peter Sarkies, Francis M Jiggins
In animals, small RNA molecules termed PIWI-interacting RNAs (piRNAs) silence transposable elements (TEs), protecting the germline from genomic instability and mutation. piRNAs have been detected in the soma in a few animals, but these are believed to be specific adaptations of individual species. Here, we report that somatic piRNAs were probably present in the ancestral arthropod more than 500 million years ago. Analysis of 20 species across the arthropod phylum suggests that somatic piRNAs targeting TEs and messenger RNAs are common among arthropods...
January 2018: Nature Ecology & Evolution
https://www.readbyqxmd.com/read/29179434/growth-of-malignant-extracranial-tumors-alters-micrornaome-in-the-prefrontal-cortex-of-tumorgraft-mice
#16
Anna Kovalchuk, Yaroslav Ilnytskyy, Rocio Rodriguez-Juarez, Amanda Katz, David Sidransky, Bryan Kolb, Olga Kovalchuk
A wide array of central nervous system complications, neurological deficits, and cognitive impairments occur and persist as a result of systemic cancer and cancer treatments. This condition is known as chemo brain and it affects over half of cancer survivors. Recent studies reported that cognitive impairments manifest before chemotherapy and are much broader than chemo brain alone, thereby adding in tumor brain as a component. The molecular mechanisms of chemo brain are under-investigated, and the mechanisms of tumor brain have not been analyzed at all...
October 24, 2017: Oncotarget
https://www.readbyqxmd.com/read/29164638/the-piwi-interacting-rna-molecular-pathway-insights-from-cultured-silkworm-germline-cells
#17
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
#18
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
#19
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
#20
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
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