keyword
MENU ▼
Read by QxMD icon Read
search

trna-derived

keyword
https://www.readbyqxmd.com/read/29748504/trna-derived-small-rna-a-novel-regulatory-small-non-coding-rna
#1
REVIEW
Siqi Li, Zhengping Xu, Jinghao Sheng
Deep analysis of next-generation sequencing data unveils numerous small non-coding RNAs with distinct functions. Recently, fragments derived from tRNA, named as tRNA-derived small RNA (tsRNA), have attracted broad attention. There are mainly two types of tsRNAs, including tRNA-derived stress-induced RNA (tiRNA) and tRNA-derived fragment (tRF), which differ in the cleavage position of the precursor or mature tRNA transcript. Emerging evidence has shown that tsRNAs are not merely tRNA degradation debris but have been recognized to play regulatory roles in many specific physiological and pathological processes...
May 10, 2018: Genes
https://www.readbyqxmd.com/read/29743091/the-dysregulation-of-trnas-and-trna-derivatives-in-cancer
#2
REVIEW
Shi-Qiong Huang, Bao Sun, Zong-Ping Xiong, Yan Shu, Hong-Hao Zhou, Wei Zhang, Jing Xiong, Qing Li
Transfer RNAs (tRNAs), traditionally considered to participate in protein translation, were interspersed in the entire genome. Recent studies suggested that dysregulation was observed in not only tRNAs, but also tRNA derivatives generated by the specific cleavage of pre- and mature tRNAs in the progression of cancer. Accumulating evidence had identified that certain tRNAs and tRNA derivatives were involved in proliferation, metastasis and invasiveness of cancer cell, as well as tumor growth and angiogenesis in several malignant human tumors...
May 9, 2018: Journal of Experimental & Clinical Cancer Research: CR
https://www.readbyqxmd.com/read/29730207/sports1-0-a-tool-for-annotating-and-profiling-non-coding-rnas-optimized-for-rrna-and-trna-derived-small-rnas
#3
Junchao Shi, Eun-A Ko, Kenton M Sanders, Qi Chen, Tong Zhou
High-throughput RNA-seq has revolutionized the process of small RNA (sRNA) discovery, leading to a rapid expansion of sRNA categories. In addition to the previously well-characterized sRNAs such as microRNAs (miRNAs), piwi-interacting RNAs (piRNAs), and small nucleolar RNA (snoRNAs), recent emerging studies have spotlighted on tRNA-derived sRNAs (tsRNAs) and rRNA-derived sRNAs (rsRNAs) as new categories of sRNAs that bear versatile functions. Since existing software and pipelines for sRNA annotation are mostly focused on analyzing miRNAs or piRNAs, here we developed the sRNA annotation pipeline optimized for rRNA- and tRNA- derived sRNAs (SPORTS1...
May 3, 2018: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29703750/identification-of-substrates-of-the-small-rna-methyltransferase-hen1-in-mouse-spermatogonial-stem-cells-and-analysis-of-its-methyl-transfer-domain
#4
Ling Peng, Fengjuan Zhang, Renfu Shang, Xueyan Wang, Jiayi Chen, James J Chou, Jinbiao Ma, Ligang Wu, Ying Huang
Small noncoding RNAs (sncRNAs) regulate many genes in eukaryotic cells. Hua enhancer 1 (Hen1) is a 2'-O-methyltransferase that adds a methyl group to the 2'-OH of 3'-terminal nucleotide of sncRNAs. The types and properties of sncRNAs may vary among different species, and the domain composition, structure, and function of Hen1 proteins differ accordingly. In mammals, Hen1 specifically methylates sncRNAs called p-element-induced wimpy testis (PIWI)-interacting RNAs (piRNAs). However, other types of sncRNAs that are methylated by Hen1 have not yet been reported, and the structures and the substrates of mammalian Hen1 remain unknown...
April 27, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29702004/human-trna-derived-small-rnas-modulate-host-oral-microbial-interactions
#5
X He, F Li, B Bor, K Koyano, L Cen, X Xiao, W Shi, D T W Wong
Coevolution of the human host and its associated microbiota has led to sophisticated interactions to maintain a delicate homeostasis. Emerging evidence suggests that in addition to small molecules, peptides, and proteins, small regulatory noncoding RNAs (sRNAs) might play an important role in cross-domain interactions. In this study, we revealed the presence of diverse host transfer RNA-derived small RNAs (tsRNAs) among human salivary sRNAs. We selected 2 tsRNAs (tsRNA-000794 and tsRNA-020498) for further study based on their high sequence similarity to specific tRNAs from a group of Gram-negative oral bacteria, including Fusobacterium nucleatum, a key oral commensal and opportunistic pathogen...
April 1, 2018: Journal of Dental Research
https://www.readbyqxmd.com/read/29695786/dnmt2-mediates-intergenerational-transmission-of-paternally-acquired-metabolic-disorders-through-sperm-small-non-coding-rnas
#6
Yunfang Zhang, Xudong Zhang, Junchao Shi, Francesca Tuorto, Xin Li, Yusheng Liu, Reinhard Liebers, Liwen Zhang, Yongcun Qu, Jingjing Qian, Maya Pahima, Ying Liu, Menghong Yan, Zhonghong Cao, Xiaohua Lei, Yujing Cao, Hongying Peng, Shichao Liu, Yue Wang, Huili Zheng, Rebekah Woolsey, David Quilici, Qiwei Zhai, Lei Li, Tong Zhou, Wei Yan, Frank Lyko, Ying Zhang, Qi Zhou, Enkui Duan, Qi Chen
The discovery of RNAs (for example, messenger RNAs, non-coding RNAs) in sperm has opened the possibility that sperm may function by delivering additional paternal information aside from solely providing the DNA 1 . Increasing evidence now suggests that sperm small non-coding RNAs (sncRNAs) can mediate intergenerational transmission of paternally acquired phenotypes, including mental stress2,3 and metabolic disorders4-6 . How sperm sncRNAs encode paternal information remains unclear, but the mechanism may involve RNA modifications...
May 2018: Nature Cell Biology
https://www.readbyqxmd.com/read/29685897/characterization-of-human-salivary-extracellular-rna-by-next-generation-sequencing
#7
Feng Li, Karolina Elżbieta Kaczor-Urbanowicz, Jie Sun, Blanca Majem, Hsien-Chun Lo, Yong Kim, Kikuye Koyano, Shannon Liu Rao, So Young Kang, Su Mi Kim, Kyoung-Mee Kim, Sung Kim, David Chia, David Elashoff, Tristan R Grogan, Xinshu Xiao, David T W Wong
BACKGROUND: It was recently discovered that abundant and stable extracellular RNA (exRNA) species exist in bodily fluids. Saliva is an emerging biofluid for biomarker development for noninvasive detection and screening of local and systemic diseases. Use of RNA-Sequencing (RNA-Seq) to profile exRNA is rapidly growing; however, no single preparation and analysis protocol can be used for all biofluids. Specifically, RNA-Seq of saliva is particularly challenging owing to high abundance of bacterial contents and low abundance of salivary exRNA...
April 23, 2018: Clinical Chemistry
https://www.readbyqxmd.com/read/29628141/pseudouridylation-of-trna-derived-fragments-steers-translational-control-in-stem-cells
#8
Nicola Guzzi, Maciej Cieśla, Phuong Cao Thi Ngoc, Stefan Lang, Sonali Arora, Marios Dimitriou, Kristyna Pimková, Mikael N E Sommarin, Roberto Munita, Michal Lubas, Yiting Lim, Kazuki Okuyama, Shamit Soneji, Göran Karlsson, Jenny Hansson, Göran Jönsson, Anders H Lund, Mikael Sigvardsson, Eva Hellström-Lindberg, Andrew C Hsieh, Cristian Bellodi
Pseudouridylation (Ψ) is the most abundant and widespread type of RNA epigenetic modification in living organisms; however, the biological role of Ψ remains poorly understood. Here, we show that a Ψ-driven posttranscriptional program steers translation control to impact stem cell commitment during early embryogenesis. Mechanistically, the Ψ "writer" PUS7 modifies and activates a novel network of tRNA-derived small fragments (tRFs) targeting the translation initiation complex. PUS7 inactivation in embryonic stem cells impairs tRF-mediated translation regulation, leading to increased protein biosynthesis and defective germ layer specification...
April 4, 2018: Cell
https://www.readbyqxmd.com/read/29593348/profiles-of-mirna-isoforms-and-trna-fragments-in-prostate-cancer
#9
Rogan G Magee, Aristeidis G Telonis, Phillipe Loher, Eric Londin, Isidore Rigoutsos
MicroRNA (miRNA) isoforms ("isomiRs") and tRNA-derived fragments ("tRFs") are powerful regulatory non-coding RNAs (ncRNAs). In human tissues, both types of molecules are abundant, with expression patterns that depend on a person's race, sex and population origin. Here, we present our analyses of the Prostate Cancer (PRAD) datasets of The Cancer Genome Atlas (TCGA) from the standpoint of isomiRs and tRFs. This study represents the first simultaneous examination of isomiRs and tRFs in a large cohort of PRAD patients...
March 28, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29472946/heavy-chronic-intermittent-ethanol-exposure-alters-small-noncoding-rnas-in-mouse-sperm-and-epididymosomes
#10
Gregory R Rompala, Anais Mounier, Cody M Wolfe, Qishan Lin, Iliya Lefterov, Gregg E Homanics
While the risks of maternal alcohol abuse during pregnancy are well-established, several preclinical studies suggest that chronic preconception alcohol consumption by either parent may also have significance consequences for offspring health and development. Notably, since isogenic male mice used in these studies are not involved in gestation or rearing of offspring, the cross-generational effects of paternal alcohol exposure suggest a germline-based epigenetic mechanism. Many recent studies have demonstrated that the effects of paternal environmental exposures such as stress or malnutrition can be transmitted to the next generation via alterations to small noncoding RNAs in sperm...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29431851/stress-induced-trna-cleavage-and-tirna-generation-in-rat-neuronal-pc12-cells
#11
Alaa Elkordy, Eikan Mishima, Kuniyasu Niizuma, Yasutoshi Akiyama, Miki Fujimura, Teiji Tominaga, Takaaki Abe
Transfer RNA (tRNA) plays a role in stress response programs involved in various pathological conditions including neurological diseases. Under cell stress conditions, intracellular tRNA is cleaved by a specific ribonuclease, angiogenin, generating tRNA-derived fragments or tRNA-derived stress-induced RNA (tiRNA). Generated tiRNA contributes to the cell stress response and has potential cell protective effects. However, tiRNA generation under stress conditions in neuronal cells has not been fully elucidated...
February 12, 2018: Journal of Neurochemistry
https://www.readbyqxmd.com/read/29419808/fine-tuning-of-gene-expression-by-trna-derived-fragments-during-abiotic-stress-signal-transduction
#12
Eun Joo Park, Tae-Houn Kim
When plants are subjected to unfavorable environmental conditions, overall gene expression in stressed cells is altered from a programmed pattern for normal development to an adaptive pattern for survival. Rapid changes in plant gene expression include production of stress responsive proteins for protection as well as reduction of irrelevant proteins to minimize energy consumption during growth. In addition to the many established mechanisms known to modulate gene expression in eukaryotes, a novel strategy involving tRNA-derived fragments (tRFs) was recently reported to control gene expression...
February 8, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29343745/malaria-infected-red-blood-cells-release-small-regulatory-rnas-through-extracellular-vesicles
#13
Kehinde Adebayo Babatunde, Smart Mbagwu, María Andrea Hernández-Castañeda, Swamy R Adapa, Michael Walch, Luis Filgueira, Laurent Falquet, Rays H Y Jiang, Ionita Ghiran, Pierre-Yves Mantel
The parasite Plasmodium falciparum causes the most severe form of malaria. Cell communication between parasites is an important mechanism to control population density and differentiation. The infected red blood cells (iRBCs) release small extracellular vesicles (EVs) that transfer cargoes between cells. The EVs synchronize the differentiation of the asexual parasites into gametocytes to initiate the transmission to the mosquito. Beside their role in parasite communication, EVs regulate vascular function. So far, the exact cargoes responsible for cellular communication remain unknown...
January 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29337107/trna-derived-small-non-coding-rnas-in-human-disease
#14
Lei Zhu, Xuesha Liu, Wenchen Pu, Yong Peng
Besides attending protein synthesis, transfer RNA (tRNA) is an important regulatory non-coding RNA (ncRNA) that participates in various cellular processes, including cellular metabolism and cell death. Fragments generated from pre- or mature tRNAs by specific endonucleases cleavage (tRNA-derived small non-coding RNA [tsncRNAs]), rather than random degradation products, are newly defined functional small non-coding RNAs (sncRNAs). They can be regulated in bacteria, yeast, plants and animals to respond to stress conditions, resulting in regulation of gene expressions at both transcriptional and post-transcriptional level...
April 10, 2018: Cancer Letters
https://www.readbyqxmd.com/read/29334896/global-analysis-of-prokaryotic-trna-derived-cyclodipeptide-biosynthesis
#15
Michael A Skinnider, Chad W Johnston, Nishanth J Merwin, Chris A Dejong, Nathan A Magarvey
BACKGROUND: Among naturally occurring small molecules, tRNA-derived cyclodipeptides are a class that have attracted attention for their diverse and desirable biological activities. However, no tools are available to link cyclodipeptide synthases identified within prokaryotic genome sequences to their chemical products. Consequently, it is unclear how many genetically encoded cyclodipeptides represent novel products, and which producing organisms should be targeted for discovery. RESULTS: We developed a pipeline for identification and classification of cyclodipeptide biosynthetic gene clusters and prediction of aminoacyl-tRNA substrates and complete chemical structures...
January 15, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29229607/race-disparities-in-the-contribution-of-mirna-isoforms-and-trna-derived-fragments-to-triple-negative-breast-cancer
#16
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
#17
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
#18
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
#19
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...
January 4, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29186115/a-transfer-rna-derived-small-rna-regulates-ribosome-biogenesis
#20
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
keyword
keyword
77879
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"