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https://www.readbyqxmd.com/read/28463242/exercise-alters-mouse-sperm-small-noncoding-rnas-and-induces-a-transgenerational-modification-of-male-offspring-conditioned-fear-and-anxiety
#1
A K Short, S Yeshurun, R Powell, V M Perreau, A Fox, J H Kim, T Y Pang, A J Hannan
There is growing evidence that the preconceptual lifestyle and other environmental exposures of a father can significantly alter the physiological and behavioral phenotypes of their children. We and others have shown that paternal preconception stress, regardless of whether the stress was experienced during early-life or adulthood, results in offspring with altered anxiety and depression-related behaviors, attributed to hypothalamic-pituitary-adrenal axis dysregulation. The transgenerational response to paternal preconceptual stress is believed to be mediated by sperm-borne small noncoding RNAs, specifically microRNAs...
May 2, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28449079/small-non-coding-rna-and-cancer
#2
Giulia Romano, Dario Veneziano, Mario Acunzo, Carlo M Croce
The ENCODE project has reported that at least 80% of the human genome is biologically active, yet only a small part of human DNA encodes for protein. The massive amount of RNA transcribed but not translated into protein can be classified as housekeeping RNA (such as rRNA, tRNA) and regulatory RNA (such as miRNA, piRNA, lncRNA). Small non-coding RNAs, in particular, have been the focus of many studies in the last 20 years and their fundamental role in many human diseases is currently well established. Inter alia, their role in cancer development and progression, as well as in drug resistance, is being increasingly investigated...
May 1, 2017: Carcinogenesis
https://www.readbyqxmd.com/read/28446464/trf-mir-1280-suppresses-stem-cell-like-cells-and-metastasis-in-colorectal-cancer
#3
Bingqing Huang, Huipeng Yang, Xixi Cheng, Dan Wang, Shuyu Fu, Wencui Shen, Qi Zhang, Lijuan Zhang, Zhenyi Xue, Yan Li, Yurong Da, Qing Yang, Zesong Li, Li Liu, Liang Qiao, Ying Kong, Zhi Yao, Peng Zhao, Min Li, Rongxin Zhang
Several studies have shown that tRNAs can be enzymatically cleaved to generate distinct classes of tRNA-derived fragments (tRF). Here we report that tRF/miR-1280, a 17bp fragment derived from tRNA(Leu) and pre-miRNA, influences Notch signaling pathways that support the function of cancer stem-like cells (CSC) in colorectal cancer progression. tRF/miR-1280 expression was decreased in human specimens of colorectal cancer (CRC). Ectopic expression of tRF/miR-1280 reduced cell proliferation and colony formation, whereas its suppression reversed these effects...
April 26, 2017: Cancer Research
https://www.readbyqxmd.com/read/28378898/trf-leu-cag-promotes-cell-proliferation-and-cell-cycle-in-non-small-cell-lung-cancer
#4
Yang Shao, Qiangling Sun, Xiaomin Liu, Ping Wang, Renqi Wu, Zhongliang Ma
tRNA-derived RNA fragments (tRFs), non-coding single-stranded RNAs with 14-35 nt in length, were found to play important roles in gene regulation, even in carcinogenesis. In this study, we investigated the expression of tRF-Leu-CAG in human non-small cell lung cancer (NSCLC) and its function in the cell proliferation and cell cycle of NSCLC. The expression level of tRF-Leu-CAG was detected in NSCLC tissues, cell lines, and sera. tRF-Leu-CAG RNA levels were higher in NSCLC tumor tissues than in normal tissues, and also upregulated in NSCLC cell lines...
April 5, 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/28349464/high-throughput-small-rna-sequencing-enhanced-by-alkb-facilitated-rna-de-methylation-arm-seq
#5
Eva Hrabeta-Robinson, Erin Marcus, Aaron E Cozen, Eric M Phizicky, Todd M Lowe
N (1)-methyladenosine (m(1)A), N (3)-methylcytidine (m(3)C), and N (1)-methylguanosine (m(1)G) are common in transfer RNA (tRNA) and tRNA-derived fragments. These modifications alter Watson-Crick base-pairing, and cause pauses or stops during reverse transcription required for most high-throughput RNA sequencing protocols, resulting in inefficient detection of methyl-modified RNAs. Here, we describe a procedure to demethylate RNAs containing m(1)A, m(3)C, or m(1)G using the Escherichia coli dealkylating enzyme AlkB, along with instructions for subsequent processing with widely used protocols for small RNA sequencing...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28335016/trna-derived-small-rnas-target-transposable-element-transcripts
#6
German Martinez, Sarah G Choudury, R Keith Slotkin
tRNA-derived RNA fragments (tRFs) are 18-26 nucleotide small RNAs that are not random degradation products, but are rather specifically cleaved from mature tRNA transcripts. Abundant in stressed or viral-infected cells, the function and potential targets of tRFs are not known. We identified that in the unstressed wild-type male gamete containing pollen of flowering plants, and analogous reproductive structure in non-flowering plant species, tRFs accumulate to high levels. In the reference plant Arabidopsis thaliana, tRFs are processed by Dicer-like 1 and incorporated into Argonaute1 (AGO1), akin to a microRNA...
May 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28203519/the-widespread-occurrence-of-trna-derived-fragments-in-saccharomyces-cerevisiae
#7
Kamilla Bąkowska-Żywicka, Anna M Mleczko, Marta Kasprzyk, Piotr Machtel, Marek Żywicki, Tomasz Twardowski
Short RNAs derived from the cleavage of tRNA molecules are observed in most organisms. Their occurrence seems to be induced by stress conditions, but still little is known about their biogenesis and functions. We find that the recovery of tRNA fragments depends on the RNA isolation method. Using an optimized RNA extraction protocol and northern blot hybridization technique, we show that the tRNA-derived fragments in yeast are widespread in 12 different growth conditions. We did not observe significant stress-dependent changes in the amounts of tRNA fragments pool...
December 2016: FEBS Open Bio
https://www.readbyqxmd.com/read/28127696/angiogenin-prevents-progranulin-a9d-mutation-induced-neuronal-like-cell-apoptosis-through-cleaving-trnas-into-tirnas
#8
Siqi Li, Yongdui Chen, Desen Sun, Rongpai Bai, Xiangwei Gao, Yi Yang, Jinghao Sheng, Zhengping Xu
Gene defects have been recognized as prominent factors in the etiology and pathogenesis of neurodegeneration. Among 60 neurodegeneration-related mutations in progranulin (PGRN), a mutation in PGRN gene exon 1 introduces a charged amino acid in the hydrophobic core of its signal peptide at residue 9 (named PGRN A9D) and results in incorrect cytoplasmic sorting. However, the pathogenesis of this mutation remains elusive. To address this issue, we first examined the subcellular distribution of PGRN A9D in human neuronal-like cells (SH-SY5Y)...
January 27, 2017: Molecular Neurobiology
https://www.readbyqxmd.com/read/28061744/comprehensive-evaluation-of-extracellular-small-rna-isolation-methods-from-serum-in-high-throughput-sequencing
#9
Yan Guo, Kasey Vickers, Yanhua Xiong, Shilin Zhao, Quanhu Sheng, Pan Zhang, Wanding Zhou, Charles R Flynn
BACKGROUND: DNA and RNA fractions from whole blood, serum and plasma are increasingly popular analytes that are currently under investigation for their utility in the diagnosis and staging of disease. Small non-coding ribonucleic acids (sRNAs), specifically microRNAs (miRNAs) and their variant isoforms (isomiRs), and transfer RNA (tRNA)-derived small RNAs (tDRs) comprise a repertoire of molecules particularly promising in this regard. RESULTS: In this designed study, we compared the performance of various methods and kits for isolating circulating extracellular sRNAs (ex-sRNAs)...
January 7, 2017: BMC Genomics
https://www.readbyqxmd.com/read/27936807/trna-derived-rna-fragments-associate-with-human-multisynthetase-complex-msc-and-modulate-ribosomal-protein-translation
#10
Simon P Keam, Andrew Sobala, Sara Ten Have, Gyorgy Hutvagner
The functionality of small RNAs from abundant species of "housekeeping" noncoding RNAs (e.g., rRNA, tRNA, snRNA, snoRNA, etc.) remains a highly studied topic. The current state of research on short RNAs derived from transfer RNA (tRNA), called tRNA-derived fragments (tRFs), has been restricted largely to expression studies and limited functional studies. 5' tRFs are known translational inhibitors in mammalian cells, yet little is known about their functionality. Here we report on the first experimental evidence of the tRF protein interactome, identifying the mammalian multisynthetase complex as the primary interactor of the 5' tRF Gln19...
December 12, 2016: Journal of Proteome Research
https://www.readbyqxmd.com/read/27901112/depletion-of-trna-halves-enables-effective-small-rna-sequencing-of-low-input-murine-serum-samples
#11
Alan Van Goethem, Nurten Yigit, Celine Everaert, Myrthala Moreno-Smith, Liselot M Mus, Eveline Barbieri, Frank Speleman, Pieter Mestdagh, Jason Shohet, Tom Van Maerken, Jo Vandesompele
The ongoing ascent of sequencing technologies has enabled researchers to gain unprecedented insights into the RNA content of biological samples. MiRNAs, a class of small non-coding RNAs, play a pivotal role in regulating gene expression. The discovery that miRNAs are stably present in circulation has spiked interest in their potential use as minimally-invasive biomarkers. However, sequencing of blood-derived samples (serum, plasma) is challenging due to the often low RNA concentration, poor RNA quality and the presence of highly abundant RNAs that dominate sequencing libraries...
November 30, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27899625/ym500v3-a-database-for-small-rna-sequencing-in-human-cancer-research
#12
I-Fang Chung, Shing-Jyh Chang, Chen-Yang Chen, Shu-Hsuan Liu, Chia-Yang Li, Chia-Hao Chan, Chuan-Chi Shih, Wei-Chung Cheng
We previously presented the YM500 database, which contains >8000 small RNA sequencing (smRNA-seq) data sets and integrated analysis results for various cancer miRNome studies. In the updated YM500v3 database (http://ngs.ym.edu.tw/ym500/) presented herein, we not only focus on miRNAs but also on other functional small non-coding RNAs (sncRNAs), such as PIWI-interacting RNAs (piRNAs), tRNA-derived fragments (tRFs), small nuclear RNAs (snRNAs) and small nucleolar RNAs (snoRNAs). There is growing knowledge of the role of sncRNAs in gene regulation and tumorigenesis...
January 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899576/the-nuclear-and-organellar-trna-derived-rna-fragment-population-in-arabidopsis-thaliana-is-highly-dynamic
#13
Valérie Cognat, Geoffrey Morelle, Cyrille Megel, Stéphanie Lalande, Jean Molinier, Timothée Vincent, Ian Small, Anne-Marie Duchêne, Laurence Maréchal-Drouard
In the expanding repertoire of small noncoding RNAs (ncRNAs), tRNA-derived RNA fragments (tRFs) have been identified in all domains of life. Their existence in plants has been already proven but no detailed analysis has been performed. Here, short tRFs of 19-26 nucleotides were retrieved from Arabidopsis thaliana small RNA libraries obtained from various tissues, plants submitted to abiotic stress or fractions immunoprecipitated with ARGONAUTE 1 (AGO1). Large differences in the tRF populations of each extract were observed...
April 7, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27892771/a-trna-derived-fragment-competes-with-mrna-for-ribosome-binding-and-regulates-translation-during-stress
#14
Jennifer Gebetsberger, Leander Wyss, Anna M Mleczko, Julia Reuther, Norbert Polacek
Posttranscriptional processing of RNA molecules is a common strategy to enlarge the structural and functional repertoire of RNomes observed in all 3 domains of life. Fragmentation of RNA molecules of basically all functional classes has been reported to yield smaller non-protein coding RNAs (ncRNAs) that typically possess different roles compared with their parental transcripts. Here we show that a valine tRNA-derived fragment (Val-tRF) that is produced under certain stress conditions in the halophilic archaeon Haloferax volcanii is capable of binding to the small ribosomal subunit...
November 28, 2016: RNA Biology
https://www.readbyqxmd.com/read/27882181/angiogenin-is-upregulated-during-the-alloreactive-immune-response-and-has-no-effect-on-the-t-cell-expansion-phase-whereas-it-affects-the-contraction-phase-by-inhibiting-cd4-t-cell-apoptosis
#15
Theodoros Eleftheriadis, Georgios Pissas, Maria Sounidaki, Nikolaos Antoniadis, Georgia Antoniadi, Vassilios Liakopoulos, Ioannis Stefanidis
Under growth conditions, angiogenin is translocated into the nucleus, where it enhances ribosomal RNA transcription, facilitating increased protein synthesis and cellular proliferation. During stress conditions, angiogenin is sequestered in the cytoplasm, where it cleaves transfer RNA (tRNA) to produce tRNA-derived, stress-induced small RNAs (tiRNAs) that inhibit global protein synthesis, but increase the translation of anti-apoptotic factors. In the present study, the role of angiogenin in the human alloreactive immune response was evaluated using mixed lymphocyte reactions (MLRs) and neamine, an inhibitor of angiogenin nuclear translocation...
November 2016: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/27879434/5-terminal-nucleotide-variations-in-human-cytoplasmic-trnahisgug-and-its-5-halves
#16
Megumi Shigematsu, Yohei Kirino
Transfer RNAs (tRNAs) are fundamental adapter components of translational machinery. tRNAs can further serve as a source of tRNA-derived noncoding RNAs that play important roles in various biological processes beyond translation. Among all species of tRNAs, tRNA(HisGUG) has been known to uniquely contain an additional guanosine residue at the -1 position (G-1) of its 5'-end. To analyze this -1 nucleotide in detail, we developed a TaqMan qRT-PCR method that can distinctively quantify human mature cytoplasmic tRNA(HisGUG) containing G-1, U-1, A-1, or C-1 or lacking the -1 nucleotide (starting from G1)...
February 2017: RNA
https://www.readbyqxmd.com/read/27876680/identification-of-unknown-rna-partners-using-maps
#17
David Lalaouna, Karine Prévost, Alex Eyraud, Eric Massé
Recent advances in high-throughput sequencing have led to an explosion in the rate of small regulatory RNAs (sRNAs) discovery among bacteria. However, only a handful of them are functionally characterized. Most of the time, little to no targets are known. In Lalaouna et al. (2015), we proposed a new technology to uncover sRNAs targetome, which is based on the MS2-affinity purification (MAPS). We were able to prove its efficiency by applying it on well-characterized sRNAs of Escherichia coli. Thereafter, we adapted the procedure to other kind of RNA (mRNAs and tRNA-derived RNA fragments) and bacteria (pathogenic or Gram-positive strains)...
March 15, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/27681945/genome-wide-identification-and-characterization-of-trna-derived-rna-fragments-in-land-plants
#18
Cristiane S Alves, Renato Vicentini, Gustavo T Duarte, Vitor F Pinoti, Michel Vincentz, Fabio T S Nogueira
The manuscript by Alves et al. entitled "Genome-wide identification and characterization of tRNA-derived RNA fragments in land plants" describes the identification and characterization of tRNAderived sRNA fragments in plants. By combining bioinformatic analysis and genetic and molecular approaches, we show that tRF biogenesis does not rely on canonical microRNA/siRNA processing machinery (i.e., independent of DICER-LIKE proteins). Moreover, we provide evidences that the Arabidopsis S-like Ribonuclease 1 (RNS1) might be involved in the biogenesis of tRFs...
January 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/27609601/trna-derived-short-rnas-bind-to-saccharomyces-cerevisiae-ribosomes-in-a-stress-dependent-manner-and-inhibit-protein-synthesis-in-vitro
#19
Kamilla Bąkowska-Żywicka, Marta Kasprzyk, Tomasz Twardowski
Recently, a number of ribosome-associated non-coding RNAs (rancRNAs) have been discovered in all three domains of life. In our previous studies, we have described several types of rancRNAs in Saccharomyces cerevisiae, derived from many cellular RNAs, including mRNAs, rRNAs, tRNAs and snoRNAs. Here, we present the evidence that the tRNA fragments from simple eukaryotic organism S. cerevisiae directly bind to the ribosomes. Interestingly, rancRNA-tRFs in yeast are derived from both, 5'- and 3'-part of the tRNAs and both types of tRFs associate with the ribosomes in vitro The location of tRFs within the ribosomes is distinct from classical A- and P-tRNA binding sites...
September 2016: FEMS Yeast Research
https://www.readbyqxmd.com/read/27518564/angiogenin-promotes-hematopoietic-regeneration-by-dichotomously-regulating-quiescence-of-stem-and-progenitor-cells
#20
Kevin A Goncalves, Lev Silberstein, Shuping Li, Nicolas Severe, Miaofen G Hu, Hailing Yang, David T Scadden, Guo-Fu Hu
Regulation of stem and progenitor cell populations is critical in the development, maintenance, and regeneration of tissues. Here, we define a novel mechanism by which a niche-secreted RNase, angiogenin (ANG), distinctively alters the functional characteristics of primitive hematopoietic stem/progenitor cells (HSPCs) compared with lineage-committed myeloid-restricted progenitor (MyePro) cells. Specifically, ANG reduces the proliferative capacity of HSPC while simultaneously increasing proliferation of MyePro cells...
August 11, 2016: Cell
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