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tRNA DERIVED FRAGMENTS

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https://www.readbyqxmd.com/read/27899625/ym500v3-a-database-for-small-rna-sequencing-in-human-cancer-research
#1
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...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899576/the-nuclear-and-organellar-trna-derived-rna-fragment-population-in-arabidopsis-thaliana-is-highly-dynamic
#2
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...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27892771/a-trna-derived-fragment-competes-with-mrna-for-ribosome-binding-and-regulates-translation-during-stress
#3
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 three 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 to 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/27876680/identification-of-unknown-rna-partners-using-maps
#4
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)...
November 19, 2016: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/27872161/identification-of-urinary-exosomal-non-coding-rnas-as-novel-biomarkers-in-chronic-kidney-disease
#5
Rimpi Khurana, Glory Ranches, Simon Schafferer, Melanie Lukasser, Michael Rudnicki, Gert Mayer, Alexander Hüttenhofer
In chronic kidney disease (CKD), the decline in glomerular filtration rate is associated with increased morbidity and mortality and thus poses a major challenge for healthcare systems. While the contribution of tissue-derived miRNAs and mRNAs to CKD progression has extensively been studied, little is known about the role of urinary exosomes and their association with CKD. Exosomes are small, membrane-derived endocytic vesicles that contribute to cell-to-cell communication and are present in various body fluids, such as blood or urine...
November 21, 2016: RNA
https://www.readbyqxmd.com/read/27681945/genome-wide-identification-and-characterization-of-trna-derived-rna-fragments-in-land-plants
#6
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...
September 28, 2016: 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
#7
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/27444405/the-mitochondrial-genome-map-of-nelumbo-nucifera-reveals-ancient-evolutionary-features
#8
Songtao Gui, Zhihua Wu, Hongyuan Zhang, Yinzhen Zheng, Zhixuan Zhu, Dequan Liang, Yi Ding
Nelumbo nucifera is an evolutionary relic from the Late Cretaceous period. Sequencing the N. nucifera mitochondrial genome is important for elucidating the evolutionary characteristics of basal eudicots. Here, the N. nucifera mitochondrial genome was sequenced using single molecule real-time sequencing technology (SMRT), and the mitochondrial genome map was constructed after de novo assembly and annotation. The results showed that the 524,797-bp N. nucifera mitochondrial genome has a total of 63 genes, including 40 protein-coding genes, three rRNA genes and 20 tRNA genes...
2016: Scientific Reports
https://www.readbyqxmd.com/read/27179031/trf2cancer-a-web-server-to-detect-trna-derived-small-rna-fragments-trfs-and-their-expression-in-multiple-cancers
#9
Ling-Ling Zheng, Wei-Lin Xu, Shun Liu, Wen-Ju Sun, Jun-Hao Li, Jie Wu, Jian-Hua Yang, Liang-Hu Qu
tRNA-derived small RNA fragments (tRFs) are one class of small non-coding RNAs derived from transfer RNAs (tRNAs). tRFs play important roles in cellular processes and are involved in multiple cancers. High-throughput small RNA (sRNA) sequencing experiments can detect all the cellular expressed sRNAs, including tRFs. However, distinguishing genuine tRFs from RNA fragments generated by random degradation remains a major challenge. In this study, we developed an integrated web-based computing system, tRF2Cancer, to accurately identify tRFs from sRNA deep-sequencing data and evaluate their expression in multiple cancers...
July 8, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27073879/transfer-rna-bound-to-mnmh-protein-is-enriched-with-geranylated-trna-a-possible-intermediate-in-its-selenation
#10
Gunilla Jäger, Peng Chen, Glenn R Björk
The wobble nucleoside 5-methylaminomethyl-2-thio-uridine (mnm5s2U) is present in bacterial tRNAs specific for Lys and Glu and 5-carboxymethylaminomethyl-2-thio-uridine (cmnm5s2U) in tRNA specific for Gln. The sulfur of (c)mnm5s2U may be exchanged by selenium (Se)-a reaction catalyzed by the selenophosphate-dependent tRNA 2-selenouridine synthase encoded by the mnmH (ybbB, selU, sufY) gene. The MnmH protein has a rhodanese domain containing one catalytic Cys (C97) and a P-loop domain containing a Walker A motif, which is a potential nucleotide binding site...
2016: PloS One
https://www.readbyqxmd.com/read/27015120/a-comprehensive-repertoire-of-trna-derived-fragments-in-prostate-cancer
#11
Michael Olvedy, Mauro Scaravilli, Youri Hoogstrate, Tapio Visakorpi, Guido Jenster, Elena S Martens-Uzunova
Prostate cancer (PCa) is the most common cancer among men in developed countries. Although its genetic background is thoroughly investigated, rather little is known about the role of small non-coding RNAs (sncRNA) in this disease. tRNA-derived fragments (tRFs) represent a new class of sncRNAs, which are present in a broad range of species and have been reported to play a role in several cellular processes. Here, we analyzed the expression of tRFs in fresh frozen patient samples derived from normal adjacent prostate and different stages of PCa by RNA-sequencing...
April 26, 2016: Oncotarget
https://www.readbyqxmd.com/read/26865839/small-non-coding-transfer-rna-derived-rna-fragments-trfs-their-biogenesis-function-and-implication-in-human-diseases
#12
REVIEW
Yu Fu, Inhan Lee, Yong Sun Lee, Xiaoyong Bao
tRNA-derived RNA fragments (tRFs) are an emerging class of non-coding RNAs (ncRNAs). A growing number of reports have shown that tRFs are not random degradation products but are functional ncRNAs made of specific tRNA cleavage. They play regulatory roles in several biological contexts such as cancer, innate immunity, stress responses, and neurological disorders. In this review, we summarize the biogenesis and functions of tRFs.
December 2015: Genomics & Informatics
https://www.readbyqxmd.com/read/26865164/trna-derived-small-non-coding-rnas-in-response-to-ischemia-inhibit-angiogenesis
#13
Qing Li, Bin Hu, Guo-Wen Hu, Chun-Yuan Chen, Xin Niu, Juan Liu, Shu-Min Zhou, Chang-Qing Zhang, Yang Wang, Zhi-Feng Deng
Ischemic injuries will lead to necrotic tissue damage, and post-ischemia angiogenesis plays critical roles in blood flow restoration and tissue recovery. Recently, several types of small RNAs have been reported to be involved in this process. In this study, we first generated a rat brain ischemic model to investigate the involvement of new types of small RNAs in ischemia. We utilized deep sequencing and bioinformatics analyses to demonstrate that the level of small RNA fragments derived from tRNAs strikingly increased in the ischemic rat brain...
2016: Scientific Reports
https://www.readbyqxmd.com/read/26843810/beyond-the-ribosome-extra-translational-functions-of-trna-fragments
#14
REVIEW
Kevin W Diebel, Kun Zhou, Aaron B Clarke, Lynne T Bemis
High-throughput sequencing studies of small RNAs reveal a complex milieu of noncoding RNAs in biological samples. Early data analysis was often limited to microRNAs due to their regulatory nature and potential as biomarkers; however, many more classes of noncoding RNAs are now being recognized. A class of fragments initially excluded from analysis were those derived from transfer RNAs (tRNAs) because they were thought to be degradation products. More recently, critical cellular function has been attributed to tRNA fragments (tRFs), and their conservation across all domains of life has propelled them into an emerging area of scientific study...
2016: Biomarker Insights
https://www.readbyqxmd.com/read/26828742/biological-processes-discovered-by-high-throughput-sequencing
#15
REVIEW
Brian J Reon, Anindya Dutta
Advances in DNA and RNA sequencing technologies have completely transformed the field of genomics. High-throughput sequencing (HTS) is now a widely used and accessible technology that allows scientists to sequence an entire transcriptome or genome in a timely and cost-effective manner. Application of HTS techniques has led to many key discoveries, including the identification of long noncoding RNAs, microDNAs, a family of small extrachromosomal circular DNA species, and tRNA-derived fragments, which are a group of small non-miRNAs that are derived from tRNAs...
April 2016: American Journal of Pathology
https://www.readbyqxmd.com/read/26820526/arabidopsis-trna-ligase-completes-the-cytoplasmic-splicing-of-bzip60-mrna-in-the-unfolded-protein-response
#16
Yukihiro Nagashima, Yuji Iwata, Kei-ichiro Mishiba, Nozomu Koizumi
Arabidopsis bZIP60 is a major transcription factor that activates the unfolded protein response and is regulated by cytoplasmic splicing. Two Arabidopsis inositol-requiring 1s (IRE1A and IRE1B) cleave bZIP60 mRNA; however, the ligase that connects the two half-molecules of the split bZIP60 mRNA has not yet been identified. We aimed to determine whether the Arabidopsis tRNA ligase RLG1 catalyzes the ligation of cleaved bZIP60 mRNA. Recombinant IRE1B containing the ribonuclease domain correctly cleaved synthetic RNA covering the cleaved site of bZIP60 in vitro...
February 19, 2016: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/26740583/trna-is-a-new-target-for-cleavage-by-a-mazf-toxin
#17
Jason M Schifano, Jonathan W Cruz, Irina O Vvedenskaya, Regina Edifor, Ming Ouyang, Robert N Husson, Bryce E Nickels, Nancy A Woychik
Toxin-antitoxin (TA) systems play key roles in bacterial persistence, biofilm formation and stress responses. The MazF toxin from the Escherichia coli mazEF TA system is a sequence- and single-strand-specific endoribonuclease, and many studies have led to the proposal that MazF family members exclusively target mRNA. However, recent data indicate some MazF toxins can cleave specific sites within rRNA in concert with mRNA. In this report, we identified the repertoire of RNAs cleaved by Mycobacterium tuberculosis toxin MazF-mt9 using an RNA-seq-based approach...
February 18, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/26703738/trna-derived-fragments-trfs-emerging-new-roles-for-an-ancient-rna-in-the-regulation-of-gene-expression
#18
REVIEW
Simon P Keam, Gyorgy Hutvagner
This review will summarise the recent discoveries and current state of research on short noncoding RNAs derived from tRNAs-known as tRNA-derived fragments (tRFs). It will describe the features of the known subtypes of these RNAs; including sequence characteristics, protein interactors, expression characteristics, biogenesis, and similarity to canonical miRNA pathways. Also their role in regulating gene expression; including mediating translational suppression, will be discussed. We also highlight their potential use as biomarkers, functions in gene regulation and links to disease...
2015: Life
https://www.readbyqxmd.com/read/26694924/conserved-and-highly-expressed-trna-derived-fragments-in-zebrafish
#19
Ana Raquel Soares, Noémia Fernandes, Marisa Reverendo, Hugo Rafael Araújo, José Luís Oliveira, Gabriela M R Moura, Manuel A S Santos
BACKGROUND: Small non-coding RNAs (sncRNAs) are a class of transcripts implicated in several eukaryotic regulatory mechanisms, namely gene silencing and chromatin regulation. Despite significant progress in their identification by next generation sequencing (NGS) we are still far from understanding their full diversity and functional repertoire. RESULTS: Here we report the identification of tRNA derived fragments (tRFs) by NGS of the sncRNA fraction of zebrafish...
2015: BMC Molecular Biology
https://www.readbyqxmd.com/read/26606401/immuno-northern-blotting-detection-of-rna-modifications-by-using-antibodies-against-modified-nucleosides
#20
Eikan Mishima, Daisuke Jinno, Yasutoshi Akiyama, Kunihiko Itoh, Shinnosuke Nankumo, Hisato Shima, Koichi Kikuchi, Yoichi Takeuchi, Alaa Elkordy, Takehiro Suzuki, Kuniyasu Niizuma, Sadayoshi Ito, Yoshihisa Tomioka, Takaaki Abe
The biological roles of RNA modifications are still largely not understood. Thus, developing a method for detecting RNA modifications is important for further clarification. We developed a method for detecting RNA modifications called immuno-northern blotting (INB) analysis and herein introduce its various capabilities. This method involves the separation of RNAs using either polyacrylamide or agarose gel electrophoresis, followed by transfer onto a nylon membrane and subsequent immunoblotting using antibodies against modified nucleosides for the detection of specific modifications...
2015: PloS One
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