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tRNA DERIVED FRAGMENTS

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https://www.readbyqxmd.com/read/29145635/trex-a-web-portal-for-exploration-of-trna-derived-fragments-in-arabidopsis-thaliana
#1
Agnieszka Thompson, Andrzej Zielezinski, Patrycja Plewka, Maciej Szymanski, Przemyslaw Nuc, Zofia Szweykowska-Kulinska, Artur Jarmolowski, Wojciech M Karlowski
tRNA-derived fragments (tRFs) constitute a new class of short regulatory RNAs that are a product of nascent or mature tRNA processing. tRF sequences have been identified in all domains of life; however, most published research pertains to human, yeast and some bacterial organisms. Despite growing interest in plant tRFs and accumulating evidence of their function in plant development and stress responses, no public, web-based repository dedicated to these molecules is currently available. Here, we introduce tRex (http://combio...
November 14, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/29107107/roles-of-trna-derived-fragments-in-human-cancers
#2
Chunxiao Sun, Ziyi Fu, Siwei Wang, Jun Li, Yongfei Li, Yanhong Zhang, Fan Yang, Jiahui Chu, Hao Wu, Xiang Huang, Wei Li, Yongmei Yin
Transfer RNAs (tRNAs) were traditionally considered to participate in protein translation. Recent studies have identified a novel class of small non-coding RNAs (sncRNAs), produced by the specific cleavage of pre- and mature tRNAs, which have been named tRNA-derived fragments. tRNA-derived fragments are classified into diverse subtypes based on the different cleavage positions of the pre- and mature tRNAs. Recently, accumulated evidence has shown that these tRNA-derived fragments are frequently dysregulated in several cancers...
October 26, 2017: Cancer Letters
https://www.readbyqxmd.com/read/29089639/placental-trophoblast-debris-mediated-feto-maternal-signalling-via-small-rna-delivery-implications-for-preeclampsia
#3
Jia Wei, Cherie Blenkiron, Peter Tsai, Joanna L James, Qi Chen, Peter R Stone, Lawrence W Chamley
To profile the small RNA cargo carried by trophoblast debris derived from the placenta during normal and preeclamptic pregnancies and to determine whether trophoblast debris can deliver its small RNAs to endothelial cells with functional consequences. We confirmed that trophoblast debris can deliver its small RNAs contents to recipient endothelial cells during the co-culture. Next generation sequencing was employed to profile the small RNA contents in both normotensive and preeclamptic trophoblast debris. We identified 1278 mature miRNAs and 2646 non-miRNA small RNA fragments contained...
October 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29074968/coding-and-noncoding-landscape-of-extracellular-rna-released-by-human-glioma-stem-cells
#4
Zhiyun Wei, Arsen O Batagov, Sergio Schinelli, Jintu Wang, Yang Wang, Rachid El Fatimy, Rosalia Rabinovsky, Leonora Balaj, Clark C Chen, Fred Hochberg, Bob Carter, Xandra O Breakefield, Anna M Krichevsky
Tumor-released RNA may mediate intercellular communication and serve as biomarkers. Here we develop a protocol enabling quantitative, minimally biased analysis of extracellular RNAs (exRNAs) associated with microvesicles, exosomes (collectively called EVs), and ribonucleoproteins (RNPs). The exRNA complexes isolated from patient-derived glioma stem-like cultures exhibit distinct compositions, with microvesicles most closely reflecting cellular transcriptome. exRNA is enriched in small ncRNAs, such as miRNAs in exosomes, and precisely processed tRNA and Y RNA fragments in EVs and exRNPs...
October 26, 2017: Nature Communications
https://www.readbyqxmd.com/read/29066746/identification-of-functional-tetramolecular-rna-g-quadruplexes-derived-from-transfer-rnas
#5
Shawn M Lyons, Dorota Gudanis, Stephen M Coyne, Zofia Gdaniec, Pavel Ivanov
RNA G-quadruplex (RG4) structures are involved in multiple biological processes. Recent genome-wide analyses of human mRNA transcriptome identified thousands of putative intramolecular RG4s that readily assemble in vitro but shown to be unfolded in vivo. Previously, we have shown that mature cytoplasmic tRNAs are cleaved during stress response to produce tRNA fragments that function to repress translation in vivo. Here we report that these bioactive tRNA fragments assemble into intermolecular RG4s. We provide evidence for the formation of uniquely stable tetramolecular RG4 structures consisting of five tetrad layers formed by 5'-terminal oligoguanine motifs of an individual tRNA fragment...
October 24, 2017: Nature Communications
https://www.readbyqxmd.com/read/29030853/accurate-profiling-and-quantification-of-trna-fragments-from-rna-seq-data-a-vade-mecum-for-mintmap
#6
Phillipe Loher, Aristeidis G Telonis, Isidore Rigoutsos
There is an increasing interest within the scientific community in identifying tRNA-derived fragments (tRFs) and elucidating the roles they play in the cell. Such endeavors can be greatly facilitated by mining the numerous datasets from many cellular contexts that exist publicly. However, the standard mapping tools cannot be used for the purpose. Several factors complicate this endeavor including: the presence of multiple identical or nearly identical isodecoders at various genomic locations; the presence of identical sequence segments that are shared by isodecoders of the same or even different anticodons; the existence of numerous partial tRNA sequences across the genome; the existence of hundreds of "lookalike" sequences that resemble true tRNAs; and others...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28919411/homocysteine-upregulates-interleukin-17a-expression-via-nsun2-mediated-rna-methylation-in-t-lymphocytes
#7
Nan Wang, Hao Tang, Xian Wang, Wengong Wang, Juan Feng
Interleukin-17A (IL-17A) has been proven to participate in the process of various autoimmune diseases. The elevation of plasma homocysteine (Hcy), known as hyperhomocysteinemia (HHcy), is related to various chronic inflammatory diseases. Though HHcy-induced upregulation of IL-17A expression in T lymphocytes has been examined, the way in which IL-17A is regulated remains unclear. In this study, western blotting assays showed that Hcy (100 μM) upregulated NOP2/Sun domain family, member 2 (NSun2) expression in rat T lymphocytes...
November 4, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28839491/non-coding-rnas-are-differentially-expressed-by-nocardia-brasiliensis-in-vitro-and-in-experimental-actinomycetoma
#8
Josué S Cruz-Rabadán, Juan Miranda-Ríos, Guadalupe Espín-Ocampo, Luis J Méndez-Tovar, Héctor Rubén Maya-Pineda, Francisca Hernández-Hernández
INTRODUCTION: Nocardia spp. are common soil-inhabiting bacteria that frequently infect humans through traumatic injuries or inhalation routes and cause infections, such as actinomycetoma and nocardiosis, respectively. Nocardia brasiliensis is the main aetiological agent of actinomycetoma in various countries. Many bacterial non-coding RNAs are regulators of genes associated with virulence factors. OBJECTIVE: The aim of this work was to identify non-coding RNAs (ncRNAs) expressed during infection conditions and in free-living form (in vitro) in Nocardia brasiliensis...
2017: Open Microbiology Journal
https://www.readbyqxmd.com/read/28758722/streptomyces-albus-a-new-cell-factory-for-non-canonical-amino-acids-incorporation-into-ribosomally-synthesized-natural-products
#9
Mariia Lopatniuk, Maksym Myronovskyi, Andriy Luzhetskyy
The incorporation of noncanonical amino acids (ncAAs) with different side chains into a peptide is a promising technique for changing the functional properties of that peptide. Of particular interest is the incorporation of ncAAs into peptide-derived natural products to optimize their biophysical properties for medical and industrial applications. Here, we present the first instance of ncAA incorporation into the natural product cinnamycin in streptomycetes using the orthogonal pyrrolysyl-tRNA synthetase/tRNA(Pyl) pair from Methanosarcina barkeri...
September 15, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28708049/identification-of-two-novel-functional-trna-derived-fragments-induced-in-response-to-respiratory-syncytial-virus-infection
#10
Jiehua Zhou, Shenxuan Liu, Yu Chen, Yu Fu, Alexander J Silver, Mark S Hill, Inhan Lee, Yong Sun Lee, Xiaoyong Bao
Respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract infection (LRTI) in children from infancy up to early childhood. Recently, we demonstrated that RSV infection alters cellular small non-coding RNA (sncRNA) expression, most notably the tRNA-derived RNA fragments (tRFs). However, the functions of the tRFs in virus-host interaction are largely unknown. Herein, we examined the role of three RSV-induced tRFs derived from the 5-end of mature tRNAs decoding GlyCCC, LysCTT and CysGCA (named tRF5-GlyCCC, tRF5-LysCTT and tRF5-CysGCA, respectively) in controlling RSV replication...
July 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28703578/detection-of-a-subset-of-posttranscriptional-transfer-rna-modifications-in-vivo-with-a-restriction-fragment-length-polymorphism-based-method
#11
Thomas F Wulff, Rafael J Argüello, Marc Molina Jordàn, Helena Roura Frigolé, Glenn Hauquier, Liudmila Filonava, Noelia Camacho, Evelina Gatti, Philippe Pierre, Lluís Ribas de Pouplana, Adrian G Torres
Transfer RNAs (tRNAs) are among the most heavily modified RNA species. Posttranscriptional tRNA modifications (ptRMs) play fundamental roles in modulating tRNA structure and function and are being increasingly linked to human physiology and disease. Detection of ptRMs is often challenging, expensive, and laborious. Restriction fragment length polymorphism (RFLP) analyses study the patterns of DNA cleavage after restriction enzyme treatment and have been used for the qualitative detection of modified bases on mRNAs...
August 8, 2017: Biochemistry
https://www.readbyqxmd.com/read/28637169/novel-molecules-lncrnas-trfs-and-circrnas-deciphered-from-next-generation-sequencing-rna-sequencing-computational-databases-and-tools
#12
A Saleembhasha, Seema Mishra
Powerful next-generation sequencing (NGS) technologies, more specifically RNA sequencing (RNA-seq), have been pivotal toward the detection and analysis and hypotheses generation of novel biomolecules, long noncoding RNAs (lncRNAs), tRNA-derived fragments (tRFs) and circular RNAs (circRNAs). Experimental validation of the occurrence of these biomolecules inside the cell has been reported. Their differential expression and functionally important role in several cancers types as well as other diseases such as Alzheimer's and cardiovascular diseases have garnered interest toward further studies in this research arena...
June 20, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/28608481/discovery-and-function-of-transfer-rna-derived-fragments-and-their-role-in-disease
#13
REVIEW
Ana Raquel Soares, Manuel Santos
Until recently, transfer RNAs (tRNAs) were thought to function in protein translation only. However, recent findings demonstrate that both pre- and mature tRNAs can undergo endonucleolytic cleavage by different ribonucleases originating different types of small non-coding RNAs, known as tRNA-derived fragments (tRFs). tRFs are classified according to their origin and are implicated in various cellular processes, namely apoptosis, protein synthesis control, and RNA interference. Although their functions are still poorly understood, their mechanisms of action vary according to the tRF sub-type...
September 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28449079/small-non-coding-rna-and-cancer
#14
REVIEW
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
#15
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 17-bp 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. Ectopic expression of tRF/miR-1280 reduced cell proliferation and colony formation, whereas its suppression reversed these effects...
June 15, 2017: Cancer Research
https://www.readbyqxmd.com/read/28378898/trf-leu-cag-promotes-cell-proliferation-and-cell-cycle-in-non-small-cell-lung-cancer
#16
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...
November 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
#17
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
#18
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
#19
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/28188878/towards-a-higher-level-ensifera-phylogeny-inferred-from-mitogenome-sequences
#20
Zhijun Zhou, Ling Zhao, Nian Liu, Huifang Guo, Bei Guan, Juanxia Di, Fuming Shi
Although mitogenomes are useful tools for inferring evolutionary history, only a few representative ones can be used for most Ensifera lineages. Thirty-two ensiferan mitogenomes were determined using ABI Sanger sequencing and standard primer walking of 2-3 overlapping Long-PCR fragments, or Illumina® HiSeq2000 for "shotgun" sequenced long-PCR-amplified mitochondrial or total genomic DNA. Six patterns of gene arrangements, including the novel trnR-trnS(AGN)-trnA-trnN-trnG-nad3 in Lipotactes tripyrga (Lipotactinae), were identified from 59 ensiferan mitogenomes...
March 2017: Molecular Phylogenetics and Evolution
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