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https://www.readbyqxmd.com/read/29346554/functional-roles-of-sex-biased-growth-hormone-regulated-micrornas-mir-1948-and-mir-802-in-young-adult-mouse-liver
#1
Pengying Hao, David J Waxman
Sex-specific temporal patterns of pituitary GH secretion determine the sex-biased transcription of hundreds of genes in the liver and impart significant sex differences in liver physiology, metabolism and disease. Sex differences in hepatic gene expression vary widely, ranging from <2-fold to >1,000-fold in the mouse. Here, we use small RNA sequencing to discover 24 sex-biased mouse liver miRNAs, and then investigate the roles of two of these miRNAs in GH-regulated liver sex differences. Studies in pre-pubertal and young adult mice, and in mice where pituitary hormones are ablated or where sex-specific hepatic GH signaling is dysregulated, demonstrated that the male-biased miR-1948 and the female-biased miR-802 are both regulated by sex-specific pituitary GH secretory patterns, acquire sex specificity at puberty, and are dependent on the GH-activated transcription factor STAT5 for their sex-specific expression...
January 16, 2018: Endocrinology
https://www.readbyqxmd.com/read/29329439/conserved-proteins-of-the-rna-interference-system-in-the-arbuscular-mycorrhizal-fungus-rhizoglomus-irregulare-provide-new-insight-into-the-evolutionary-history-of-glomeromycota
#2
Soon-Jae Lee, Mengxuan Kong, Paul Harrison, Mohamed Hijri
Horizontal gene transfer (HGT) is an important mechanism in the evolution of many living organisms particularly in Prokaryotes where genes are frequently dispersed between taxa. Although, HGT has been reported in Eukaryotes, its accumulative effect and its frequency has been questioned. Arbuscular mycorrhizal fungi (AMF) are an early diverged fungal lineage belonging to phylum Glomeromycota, whose phylogenetic position is still under debate. The history of AMF and land plant symbiosis dates back to at least 460 million years ago...
January 10, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29327729/h5n1-influenza-virus-specific-mirna-like-small-rna-increases-cytokine-production-and-mouse-mortality-via-targeting-poly-rc-binding-protein-2
#3
Xihan Li, Zheng Fu, Hongwei Liang, Yanbo Wang, Xian Qi, Meng Ding, Xinlei Sun, Zhen Zhou, Ying Huang, Hongwei Gu, Limin Li, Xi Chen, Donghai Li, Quan Zhao, Fenyong Liu, Hua Wang, Jin Wang, Ke Zen, Chen-Yu Zhang
Infection of H5N1 influenza virus causes the highest mortality among all influenza viruses. The mechanisms underlying such high viral pathogenicity are incompletely understood. Here, we report that the H5N1 influenza virus encodes a microRNA-like small RNA, miR-HA-3p, which is processed from a stem loop-containing viral RNA precursor by Argonaute 2, and plays a role in enhancing cytokine production during H5N1 infection. Mechanistic study shows that miR-HA-3p targets poly(rC)-binding protein 2 (PCBP2) and suppresses its expression...
January 12, 2018: Cell Research
https://www.readbyqxmd.com/read/29322451/discovering-circrna-microrna-interactions-from-clip-seq-data
#4
Xiao-Qin Zhang, Jian-Hua Yang
Circular RNAs (circRNAs) represent an abundant group of noncoding RNAs in eukaryotes and are emerging as important regulatory molecules in physiological and pathological processes. However, the precise mechanisms and functions of most of circRNAs remain largely unknown. In this chapter, we describe how to identify circRNA-microRNA interactions from Argonaute (AGO) cross-linking and immunoprecipitation followed by sequencing (CLIP-Seq) and RNA-Seq data using starBase platform and software. We developed three stand-alone computational software, including circSeeker, circAnno, and clipSearch, to identify and annotate circRNAs and their interactions with microRNAs (miRNAs)...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29311329/dysregulation-of-cotranscriptional-alternative-splicing-underlies-charge-syndrome
#5
Catherine Bélanger, Félix-Antoine Bérubé-Simard, Elizabeth Leduc, Guillaume Bernas, Philippe M Campeau, Seema R Lalani, Donna M Martin, Stephanie Bielas, Amanda Moccia, Anshika Srivastava, David W Silversides, Nicolas Pilon
CHARGE syndrome-which stands for coloboma of the eye, heart defects, atresia of choanae, retardation of growth/development, genital abnormalities, and ear anomalies-is a severe developmental disorder with wide phenotypic variability, caused mainly by mutations in CHD7 (chromodomain helicase DNA-binding protein 7), known to encode a chromatin remodeler. The genetic lesions responsible for CHD7 mutation-negative cases are unknown, at least in part because the pathogenic mechanisms underlying CHARGE syndrome remain poorly defined...
January 8, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29309640/a-fungal-argonaute-interferes-with-rna-interference
#6
Quyet Nguyen, Akihide Iritani, Shuhei Ohkita, Ba V Vu, Kana Yokoya, Ai Matsubara, Ken-Ichi Ikeda, Nobuhiro Suzuki, Hitoshi Nakayashiki
Small RNA (sRNA)-mediated gene silencing phenomena, exemplified by RNA interference (RNAi), require a unique class of proteins called Argonautes (AGOs). An AGO protein typically forms a protein-sRNA complex that contributes to gene silencing using the loaded sRNA as a specificity determinant. Here, we show that MoAGO3, one of the three AGO genes in the fungus Pyricularia oryzae (Magnaporthe oryzae) interferes with RNAi. Gene knockout (KO) studies revealed that MoAGO1 and MoAGO2 additively or redundantly played roles in hairpin RNA- and retrotransposon (MAGGY)-triggered RNAi while, surprisingly, the KO mutants of MoAGO3 (Δmoago3) showed elevated levels of gene silencing...
January 4, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29307557/expression-of-alternative-ago2-isoform-associated-with-loss-of-microrna-driven-translational-repression-in-mouse-oocytes
#7
Jacob W Freimer, Raga Krishnakumar, Matthew S Cook, Robert Blelloch
Mouse oocyte maturation, fertilization, and reprogramming occur in the absence of transcription, and thus, changes in mRNA levels and translation rate are regulated through post-transcriptional mechanisms [1]. Surprisingly, microRNA function, which is a major form of post-transcriptional regulation, is absent during this critical period of mammalian development [2, 3]. Here, we investigated the mechanisms underlying the global suppression of microRNA activity. In both mouse and frogs, microRNA function was active in growing oocytes but then absent during oocyte maturation...
January 3, 2018: Current Biology: CB
https://www.readbyqxmd.com/read/29290588/arabidopsis-argonaute-1-binds-chromatin-to-promote-gene-transcription-in-response-to-hormones-and-stresses
#8
Chang Liu, Ying Xin, Le Xu, Zhaokui Cai, Yuanchao Xue, Yong Liu, Daoxin Xie, Yule Liu, Yijun Qi
Conventional RNA interference (RNAi) pathways suppress eukaryotic gene expression at the transcriptional or post-transcriptional level. At the core of RNAi are small RNAs (sRNAs) and effector Argonaute (AGO) proteins. Arabidopsis AGO1 is known to bind microRNAs (miRNAs) and post-transcriptionally repress target genes in the cytoplasm. Here, we report that AGO1 also binds to the chromatin of active genes and promotes their transcription. We show that sRNAs and SWI/SNF complexes associate with nuclear AGO1 and are required for AGO1 binding to chromatin...
December 27, 2017: Developmental Cell
https://www.readbyqxmd.com/read/29286006/altered-piwi-like-1-and-piwi-like-2-mrna-expression-in-ejaculated-spermatozoa-of-men-with-impaired-sperm-characteristics
#9
Maria Giebler, Thomas Greither, Lisa Müller, Carina Mösinger, Hermann M Behre
In about half the cases of involuntary childlessness, a male infertility factor is involved. The PIWI-LIKE genes, a subclade of the Argonaute protein family, are involved in RNA silencing and transposon control in the germline. Knockout of murine Piwi-like 1 and 2 homologs results in complete infertility in males. The aim of this study was to analyze whether the mRNA expression of human PIWI-LIKE 1-4 genes is altered in ejaculated spermatozoa of men with impaired sperm characteristics. Ninety male participants were included in the study, among which 47 were with normozoospermia, 36 with impaired semen characteristics according to the World Health Organization (WHO) manual, 5th edition, and 7 with azoospermia serving as negative control for the PIWI-LIKE 1-4 mRNA expression in somatic cells in the ejaculate...
December 26, 2017: Asian Journal of Andrology
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/29246301/profiling-the-mismatch-tolerance-of-argonaute-2-through-deep-sequencing-of-sliced-polymorphic-viral-rnas
#11
Pantazis I Theotokis, Louise Usher, Christopher K Kortschak, Ed Schwalbe, Sterghios A Moschos
Low allelic and clonal variability among endogenous RNAi targets has focused mismatch tolerance studies to RNAi-active guide strands. However, the inherent genomic instability of RNA viruses such as hepatitis C virus (HCV) gives rise to quasi-species mutants within discrete clones: this facilitates mismatch tolerance studies from a target perspective. We recently quantified the slicing imprecision of Argonaute 2 using small interfering RNA (siRNA) analogs of the DNA-directed RNAi drug TT-034 and next-generation sequencing of 5' RNA ligase-mediated rapid amplification of cDNA ends (RACE-SEQ)...
December 15, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/29245946/mir-483-5p-promotes-igf-ii-transcription-and-is-associated-with-poor-prognosis-of-hepatocellular-carcinoma
#12
Shaohui Tang, Yanfang Chen, Shufen Feng, Tingzhuang Yi, Xuyou Liu, Qiang Li, Zhilong Liu, Cuiping Zhu, Jianjun Hu, Xi Yu, Min Wang, Guoli Cao, Hui Tang, Caiqun Bie, Feng Ma, Huijun Tang, Gang Du, Jianwei Huang
The human insulin-like growth factor-II (IGF-II) gene transcribes four mRNAs (P1 mRNA-P4 mRNA), and P3 mRNA overexpression contributes to hepatocarcinogenesis. IGF-II-derived miR-483-5p is implicated in the development of cancers. Here, we investigated the involvement of miR-483-5p in P3 mRNA overexpression regulation and its role in hepatocellular carcinoma. Our results showed that miR-483-5p up-regulated P3 mRNA transcription by targeting the 5'-untranslated region (5'UTR) of P3 mRNA in hepatocellular carcinoma...
November 21, 2017: Oncotarget
https://www.readbyqxmd.com/read/29240875/the-expanding-roles-of-argonautes-rna-interference-splicing-and-beyond
#13
Xiaoxia Ma, Ziwei Zuo, Weishan Shao, Yongfeng Jin, Yijun Meng
Argonaute (AGO) protein family is highly conserved in eukaryotes and prokaryotes, reflecting its evolutionarily indispensible role in maintaining normal life cycle of the organisms. Small RNA-guided, AGO-dependent RNA interference (RNAi) is a well-studied pathway for gene expression regulation, which can be performed at transcriptional, posttranscriptional or translational level. In addition to RNAi, growing pieces of evidence point to a novel role of AGOs in pre-mRNA (messenger RNA precursor) splicing in animals...
December 11, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29236255/identifying-mirna-targets-using-ago-ripseq
#14
Rebecca Petri, Johan Jakobsson
microRNAs (miRNA) are small, noncoding RNAs that bind to messenger RNAs (mRNAs) and regulate their activity. They are, therefore, important posttranscriptional regulators. In recent years it has become clear that miRNAs regulate large genetic networks, rather than single genes, and that one gene can be targeted by several miRNAs. To understand the role of miRNAs in cells or tissues, it is therefore important to analyze the targetome of miRNAs. Here, we present a technique called Argonaute-RNA Immunoprecipitation (AGO-RIP) which takes advantages of the fact that miRNAs and their targets are directly bound by the Argonaute protein family...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29236253/iclip-of-the-piwi-protein-aubergine-in-drosophila-embryos
#15
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/29218749/evidence-for-mirna-mediated-modulation-of-the-host-transcriptome-in-cnidarian-dinoflagellate-symbiosis
#16
Sebastian Baumgarten, Maha J Cziesielski, Ludivine Thomas, Craig T Michell, Lisl Y Esherick, John R Pringle, Manuel Aranda, Christian R Voolstra
Reef-building corals and other cnidarians living in symbiotic relationships with intracellular, photosynthetic dinoflagellates in the genus Symbiodinium undergo transcriptomic changes during infection with the algae and maintenance of the endosymbiont population. However, the precise regulatory mechanisms modulating the host transcriptome are unknown. Here we report apparent post-transcriptional gene regulation by miRNAs in the sea anemone Aiptasia, a model system for cnidarian-dinoflagellate endosymbiosis...
December 8, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29195056/rna-interference-mediated-gene-silencing-by-branched-tripodal-rnas-does-not-require-dicer-processing
#17
Yanghee Kim, Young Gyu Kang, Jeong Yong Choe, Dooyoung Lee, Chanseok Shin, Sun Woo Hong, Dong-Ki Lee
Specific gene silencing through RNA interference (RNAi) holds great promise as the next-generation therapeutic development platform. Previously, we have shown that branched, tripodal interfering RNA (tiRNA) structures could simultaneously trigger RNAi-mediated gene silencing of three target genes with 38 nt-long guide strands associated with Argonaute 2. Herein, we show that the branched RNA structure can trigger effective gene silencing in Dicer knockout cell line, demonstrating that the Dicer-mediated processing is not required for tiRNA activity...
December 1, 2017: Nucleic Acid Therapeutics
https://www.readbyqxmd.com/read/29167236/p-body-induced-inactivation-of-let-7a-mirnp-prevents-the-death-of-growth-factor-deprived-neuronal-cells
#18
Somi Patranabis, Suvendra Nath Bhattacharyya
RNA processing bodies (P-bodies) are cytoplasmic RNA granules in eukaryotic cells that regulate gene expression by executing the translation suppression and degradation of mRNAs that are targeted to these bodies. P-bodies can also serve as storage sites for translationally repressed mRNAs both in mammalian cells and yeast cells. In this report, a unique role of mammalian P-bodies is documented. Depletion of P-body components dedifferentiate nerve growth factor-treated PC12 cells, whereas ectopic expression of P-body components induces the neuronal differentiation of precursor cells...
November 22, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/29150439/suppression-of-fip200-and-autophagy-by-tumor-derived-lactate-promotes-na%C3%A3-ve-t-cell-apoptosis-and-affects-tumor-immunity
#19
Houjun Xia, Wei Wang, Joel Crespo, Ilona Kryczek, Wei Li, Shuang Wei, Zhaoqun Bian, Tomasz Maj, Mingxiao He, Rebecca J Liu, Youwen He, Ramandeep Rattan, Adnan Munkarah, Jun-Lin Guan, Weiping Zou
Naïve T cells are poorly studied in cancer patients. We report that naïve T cells are prone to undergo apoptosis due to a selective loss of FAK family-interacting protein of 200 kDa (FIP200) in ovarian cancer patients and tumor-bearing mice. This results in poor antitumor immunity via autophagy deficiency, mitochondria overactivation, and high reactive oxygen species production in T cells. Mechanistically, loss of FIP200 disables the balance between proapoptotic and antiapoptotic Bcl-2 family members via enhanced argonaute 2 (Ago2) degradation, reduced Ago2 and microRNA1198-5p complex formation, less microRNA1198-5p maturation, and consequently abolished microRNA1198-5p-mediated repression on apoptotic gene Bak1 Bcl-2 overexpression and mitochondria complex I inhibition rescue T cell apoptosis and promoted tumor immunity...
November 17, 2017: Science Immunology
https://www.readbyqxmd.com/read/29133395/rna-stem-structure-governs-coupling-of-dicing-and-gene-silencing-in-rna-interference
#20
Hye Ran Koh, Amirhossein Ghanbariniaki, Sua Myong
PremicroRNAs (premiRNAs) possess secondary structures consisting of a loop and a stem with multiple mismatches. Despite the well-characterized RNAi pathway, how the structural features of premiRNA contribute to dicing and subsequent gene-silencing efficiency remains unclear. Using single-molecule FISH, we demonstrate that cytoplasmic mRNA, but not nuclear mRNA, is reduced during RNAi. The dicing rate and silencing efficiency both increase in a correlated manner as a function of the loop length. In contrast, mismatches in the stem drastically diminish the silencing efficiency without impacting the dicing rate...
November 13, 2017: Proceedings of the National Academy of Sciences of the United States of America
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