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https://www.readbyqxmd.com/read/29229607/race-disparities-in-the-contribution-of-mirna-isoforms-and-trna-derived-fragments-to-triple-negative-breast-cancer
#1
Aristeidis G Telonis, Isidore Rigoutsos
Triple-Negative Breast Cancer (TNBC) is a breast cancer subtype characterized by marked differences between White and Black/African-American women. We performed a systems-level analysis on datasets from The Cancer Genome Atlas (TCGA) to elucidate how the expression patterns of messenger RNAs (mRNAs) are shaped by regulatory non-coding RNAs (ncRNAs). Specifically, we studied isomiRs, i.e. isoforms of microRNAs (miRNAs), and tRNA-derived fragments (tRFs). In normal breast tissue, we observed a marked cohesiveness in both the ncRNA and mRNA layers and the associations between them...
December 11, 2017: Cancer Research
https://www.readbyqxmd.com/read/29222070/regulation-of-trna-biogenesis-in-plants-and-its-link-to-plant-growth-and-response-to-pathogens
#2
REVIEW
Adriana Santos Soprano, Juliana Helena Costa Smetana, Celso Eduardo Benedetti
The field of tRNA biology, encompassing the functional and structural complexity of tRNAs, has fascinated scientists over the years and is continuously growing. Besides their fundamental role in protein translation, new evidence indicates that tRNA-derived molecules also regulate gene expression and protein synthesis in all domains of life. This review highlights some of the recent findings linking tRNA transcription and modification with plant cell growth and response to pathogens. In fact, mutations in proteins directly involved in tRNA synthesis and modification most often lead to pleiotropic effects on plant growth and immunity...
December 6, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29201533/trnas-as-primers-and-inhibitors-of-retrotransposons
#3
REVIEW
German Martinez
The functional relationship between tRNAs and retrotransposons have been known for more than 35 years. tRNAs are used as primer molecules to guide the reverse transcription of retrotransposons. Recently, tRNAs have also emerge as important players in the postranscriptional regulation of retrotransposons by means of tRNA-derived small RNAs. This surprisingly new layer of regulation indicates that tRNAs are used both in the promotion and the suppression of the reverse transcription of retrotransposons indicating their primary role in the life cycle of LTR retrotransposons...
2017: Mobile Genetic Elements
https://www.readbyqxmd.com/read/29186503/mintbase-v2-0-a-comprehensive-database-for-trna-derived-fragments-that-includes-nuclear-and-mitochondrial-fragments-from-all-the-cancer-genome-atlas-projects
#4
Venetia Pliatsika, Phillipe Loher, Rogan Magee, Aristeidis G Telonis, Eric Londin, Megumi Shigematsu, Yohei Kirino, Isidore Rigoutsos
MINTbase is a repository that comprises nuclear and mitochondrial tRNA-derived fragments ('tRFs') found in multiple human tissues. The original version of MINTbase comprised tRFs obtained from 768 transcriptomic datasets. We used our deterministic and exhaustive tRF mining pipeline to process all of The Cancer Genome Atlas datasets (TCGA). We identified 23 413 tRFs with abundance of ≥ 1.0 reads-per-million (RPM). To facilitate further studies of tRFs by the community, we just released version 2.0 of MINTbase that contains information about 26 531 distinct human tRFs from 11 719 human datasets as of October 2017...
November 23, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29186115/a-transfer-rna-derived-small-rna-regulates-ribosome-biogenesis
#5
Hak Kyun Kim, Gabriele Fuchs, Shengchun Wang, Wei Wei, Yue Zhang, Hyesuk Park, Biswajoy Roy-Chaudhuri, Pan Li, Jianpeng Xu, Kirk Chu, Feijie Zhang, Mei-Sze Chua, Samuel So, Qiangfeng Cliff Zhang, Peter Sarnow, Mark A Kay
Transfer-RNA-derived small RNAs (tsRNAs; also called tRNA-derived fragments) are an abundant class of small non-coding RNAs whose biological roles are not well understood. Here we show that inhibition of a specific tsRNA, LeuCAG3'tsRNA, induces apoptosis in rapidly dividing cells in vitro and in a patient-derived orthotopic hepatocellular carcinoma model in mice. This tsRNA binds at least two ribosomal protein mRNAs (RPS28 and RPS15) to enhance their translation. A decrease in translation of RPS28 mRNA blocks pre-18S ribosomal RNA processing, resulting in a reduction in the number of 40S ribosomal subunits...
December 7, 2017: Nature
https://www.readbyqxmd.com/read/29156628/-differentially-expressed-trna-derived-small-rnas-co-sediment-primarily-with-non-polysomal-fractions-in-drosophila
#6
Çağdaş Göktaş, Hatice Yiğit, Mehmet İlyas Coşacak, Bünyamin Akgül
Recent studies point to the existence of poorly characterized small regulatory RNAs generated from mRNAs, rRNAs and tRNAs. To explore the subcellular location of tRNA-derived small RNAs, 0-1 and 7-8 h Drosophila embryos were fractionated on sucrose density gradients. Analysis of 12,553,921 deep-sequencing reads from unfractionated and fractionated Drosophila embryos has revealed that tRFs, which are detected mainly from the 5'ends of tRNAs, co-sediment with the non-polysomal fractions. Interestingly, the expression levels of a subset of tRFs change temporally following the maternal-to-zygotic transition in embryos...
November 20, 2017: Genes
https://www.readbyqxmd.com/read/29145635/trex-a-web-portal-for-exploration-of-trna-derived-fragments-in-arabidopsis-thaliana
#7
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/29120263/trna-derived-small-rnas-new-players-in-genome-protection-against-retrotransposons
#8
German Martinez
Previously believed to be mere random degradation products, tRNA-derived small RNAs have been lately connected to a series of functions that include, surprisingly, genome protection against retrotransposons. tRNAs have been known for a long time to be involved in the replication cycle of retroviruses, pararetroviruses and retrotransposons as primers of their reverse transcription. tRNA-derived small RNAs, as functional small RNAs or as mere tRNA degradation products, have emerged as important players in the regulation of genic transcription...
November 9, 2017: RNA Biology
https://www.readbyqxmd.com/read/29107107/roles-of-trna-derived-fragments-in-human-cancers
#9
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/29030853/accurate-profiling-and-quantification-of-trna-fragments-from-rna-seq-data-a-vade-mecum-for-mintmap
#10
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/28882222/role-of-the-trna-derived-small-rnas-in-cancer-new-potential-biomarkers-and-target-for-therapy
#11
Veronica Balatti, Yuri Pekarsky, Carlo M Croce
Noncoding RNAs are untranslated RNA molecules that can be divided into two main types: infrastructural, including transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs), and regulatory, including long ncRNAs (lncRNAs) and small ncRNAs (sRNA). Among small ncRNA, the role of microRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs) in cancer is well documented. Recently, other small ncRNAs have been described. In particular, tRNA-derived small RNAs (tsRNA) have been found to be frequently dysregulated in cancer. Since tsRNAs can be considered unique sequences and are able to bind both Argonaute proteins (like miRNAs) and Piwi proteins (like piRNAs), their dysregulation could play a critical role in cancer by interfering with gene expression regulation at different levels...
2017: Advances in Cancer Research
https://www.readbyqxmd.com/read/28840860/tsrnas-new-players-in-mammalian-retrotransposon-control
#12
Yunfang Zhang, Junchao Shi, Qi Chen
A recent study led by Professor Rob Martienssen in Cell showed that 3'-tRNA-derived small RNAs can suppress long terminal repeat retrotransposon activity in mammalian cells by mechanisms independent of DNA-associated epigenetic marks, suggesting how the genome may defend itself from retrotransposon invasion during epigenetic reprogramming.
November 2017: Cell Research
https://www.readbyqxmd.com/read/28839491/non-coding-rnas-are-differentially-expressed-by-nocardia-brasiliensis-in-vitro-and-in-experimental-actinomycetoma
#13
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/28791028/trna-derived-smallrnas-smallrnas-repertoire-has-yet-to-be-decoded-in-plants
#14
Gaurav Sablok, Kun Yang, Rui Chen, Xiaopeng Wen
Among several smallRNAs classes, microRNAs play an important role in controlling the post-transcriptional events. Next generation sequencing has played a major role in extending the landscape of miRNAs and revealing their spatio-temporal roles in development and abiotic stress. Lateral evolution of these smallRNAs classes have widely been seen with the recently emerging knowledge on tRNA derived smallRNAs. In the present perspective, we discussed classification, identification and roles of tRNA derived smallRNAs across plants and their potential involvement in abiotic and biotic stresses...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28708049/identification-of-two-novel-functional-trna-derived-fragments-induced-in-response-to-respiratory-syncytial-virus-infection
#15
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/28696308/tsrna-signatures-in-cancer
#16
Veronica Balatti, Giovanni Nigita, Dario Veneziano, Alessandra Drusco, Gary S Stein, Terri L Messier, Nicholas H Farina, Jane B Lian, Luisa Tomasello, Chang-Gong Liu, Alexey Palamarchuk, Jonathan R Hart, Catherine Bell, Mariantonia Carosi, Edoardo Pescarmona, Letizia Perracchio, Maria Diodoro, Andrea Russo, Anna Antenucci, Paolo Visca, Antonio Ciardi, Curtis C Harris, Peter K Vogt, Yuri Pekarsky, Carlo M Croce
Small, noncoding RNAs are short untranslated RNA molecules, some of which have been associated with cancer development. Recently we showed that a class of small RNAs generated during the maturation process of tRNAs (tRNA-derived small RNAs, hereafter "tsRNAs") is dysregulated in cancer. Specifically, we uncovered tsRNA signatures in chronic lymphocytic leukemia and lung cancer and demonstrated that the ts-4521/3676 cluster (now called "ts-101" and "ts-53," respectively), ts-46, and ts-47 are down-regulated in these malignancies...
July 25, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28666125/ltr-retrotransposon-control-by-trna-derived-small-rnas
#17
Andrea J Schorn, Michael J Gutbrod, Chantal LeBlanc, Rob Martienssen
Transposon reactivation is an inherent danger in cells that lose epigenetic silencing during developmental reprogramming. In the mouse, long terminal repeat (LTR)-retrotransposons, or endogenous retroviruses (ERV), account for most novel insertions and are expressed in the absence of histone H3 lysine 9 trimethylation in preimplantation stem cells. We found abundant 18 nt tRNA-derived small RNA (tRF) in these cells and ubiquitously expressed 22 nt tRFs that include the 3' terminal CCA of mature tRNAs and target the tRNA primer binding site (PBS) essential for ERV reverse transcription...
June 29, 2017: Cell
https://www.readbyqxmd.com/read/28645172/the-biogenesis-pathway-of-trna-derived-pirnas-in-bombyx-germ-cells
#18
Shozo Honda, Takuya Kawamura, Phillipe Loher, Keisuke Morichika, Isidore Rigoutsos, Yohei Kirino
Transfer RNAs (tRNAs) function in translational machinery and further serves as a source of short non-coding RNAs (ncRNAs). tRNA-derived ncRNAs show differential expression profiles and play roles in many biological processes beyond translation. Molecular mechanisms that shape and regulate their expression profiles are largely unknown. Here, we report the mechanism of biogenesis for tRNA-derived Piwi-interacting RNAs (td-piRNAs) expressed in Bombyx BmN4 cells. In the cells, two cytoplasmic tRNA species, tRNAAspGUC and tRNAHisGUG, served as major sources for td-piRNAs, which were derived from the 5'-part of the respective tRNAs...
September 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28637169/novel-molecules-lncrnas-trfs-and-circrnas-deciphered-from-next-generation-sequencing-rna-sequencing-computational-databases-and-tools
#19
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
#20
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
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