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PtRFdb: a database for plant transfer RNA-derived fragments

Nikita Gupta, Ajeet Singh, Shafaque Zahra, Shailesh Kumar
2018 Database: The Journal of Biological Databases and Curation  
., Singh,A., Zahra,S. et al. PtRFdb: a database for plant transfer RNA-derived fragments.  ...  Abstract Transfer RNA-derived fragments (tRFs) represent a novel class of small RNAs (sRNAs) generated through endonucleolytic cleavage of both mature and precursor transfer RNAs (tRNAs).  ...  Funding This work was supported by core research grant from National Institute of Plant Genome Research (NIPGR), India, an autonomous institute of Department of Biotechnology (DBT), India.  ... 
doi:10.1093/database/bay063 pmid:29939244 pmcid:PMC6016605 fatcat:r3keav4vvnhtbjd63xbxzj652m

Action mechanisms and research methods of tRNA-derived small RNAs

Yaoyao Xie, Lipeng Yao, Xiuchong Yu, Yao Ruan, Zhe Li, Junming Guo
2020 Signal Transduction and Targeted Therapy  
tRNA-derived small RNAs (tsRNAs), including tRNA-derived fragments (tRFs) and tRNA halves (tiRNAs), are small regulatory RNAs processed from mature tRNAs or precursor tRNAs. tRFs and tiRNAs play biological  ...  This paper summarizes the classification, action mechanisms, and roles of tRFs and tiRNAs in human diseases and the related signal transduction pathways, targeted therapies, databases, and research methods  ...  PtRFdb, developed by Gupta et al., is a database for plant tRFs. 87 Users of PtRFdb can quite conveniently verify and gain understanding of the characteristics of plants.  ... 
doi:10.1038/s41392-020-00217-4 pmid:32606362 fatcat:djqytg3yqnh4dfxfv25owlv44q

Transfer RNA-Derived Small Non-Coding RNA: Dual Regulator of Protein Synthesis

Hak Kyun Kim
2019 Molecules and Cells  
Transfer RNA-derived small RNAs (tsRNAs) play a role in various cellular processes.  ...  RNAs by repressing or activating protein synthesis with distinct mechanisms.  ...  Recently, they were identified as functional non-coding RNAs and were called tsRNAs (tRNA-derived small RNAs), tRFs (tRNA-derived RNA fragments), or tiRNAs (tRNA-derived stress-induced RNAs) (Haussecker  ... 
doi:10.14348/molcells.2019.0214 pmid:31656062 pmcid:PMC6821453 fatcat:eoeeuppkjrbedm2cksyaufmm4e

Transfer RNA-derived non-coding RNAs (tncRNAs): Uncovering hidden regulators of transcriptional regulatory circuits in plants [article]

Shafaque Zahra, Ajeet Singh, Nikita Poddar, Shailesh Kumar
2021 bioRxiv   pre-print
Among them, the existence of transfer RNA (tRNA)-derived non-coding RNAs (tncRNAs) demands their exploration in the plant kingdom.  ...  Here, we have designed a methodology to uncover the bigger picture of tncRNAome in plants.  ...  Gupta, A. Singh, S. Zahra, and S. Kumar, "PtRFdb: a database for plant transfer Biochemistry, vol. 49, no. 24. American Chemical Society, Jun. 22, ] B. El Yacoubi, M. Bailly, and V.  ... 
doi:10.1101/2021.04.08.438949 fatcat:qmyza7qgcfhjfn6zvamisdexg4

Biogenesis, Functions, Interactions, and Resources of Non-Coding RNAs in Plants

Haoyu Chao, Yueming Hu, Liang Zhao, Saige Xin, Qingyang Ni, Peijing Zhang, Ming Chen
2022 International Journal of Molecular Sciences  
Then, we systematically summarize tools for analysis and prediction of plant ncRNAs, as well as databases.  ...  Plant transcriptomes encompass a large number of functional non-coding RNAs (ncRNAs), only some of which have protein-coding capacity.  ...  Abbreviations: tRNA, transfer RNA; rRNA, ribosomal RNA; snRNA, small nuclear RNA; snoRNA, small nucleolar RNA; miRNA, micro RNA; siRNA, small interfering RNA; tsRNA, tRNA-derived small RNA; circRNA, circular  ... 
doi:10.3390/ijms23073695 pmid:35409060 pmcid:PMC8998614 fatcat:yo7c23hus5bu5dyrdpj6hlhuya

Plant tRNA‐derived fragments: biogenesis and functions

Xuan Ma, Chunyan Liu, Xiaofeng Cao
2021 Journal of Integrative Plant Biology  
Processing of mature tRNAs produces complex populations of tRNA-derived fragments (tRFs). Emerging evidence shows that tRFs have important functions in bacteria, animals, and plants.  ...  Finally, we discuss future directions for plant tRF research, which will expand our knowledge of plant non-coding RNAs. This article is protected by copyright. All rights reserved.  ...  Hackenberg et al. (2013) investigated the sRNA transfer RNA-derived fragments (tRFs) have versatile biological functions (A) In plants, tRFs are involved in diverse stress responses, but how these stresses  ... 
doi:10.1111/jipb.13143 pmid:34114725 fatcat:jbnw7vbcqbd7rflbvarqpxd5xi

tRNA-derived fragments from wheat are potentially involved in susceptibility to Fusarium head blight

Zhengxi Sun, Yi Hu, Yilei Zhou, Ning Jiang, Sijia Hu, Lei Li, Tao Li
2022 BMC Plant Biology  
The mechanism underlying F. graminearum-wheat interaction remains largely unknown. tRNA-derived fragments (tRFs) are RNase-dependent small RNAs derived from tRNAs, and they have not been reported in wheat  ...  Background Fusarium head blight (FHB) caused by Fusarium graminearum is a devastating fungal disease of wheat.  ...  YH and YZ collected the samples for sRNA-sequencing and RNA-sequencing. ZS and LL performed data analysis. YH, SH and NJ performed qRT-PCR validation. ZS and TL wrote the manuscript.  ... 
doi:10.1186/s12870-021-03393-9 pmid:34979923 pmcid:PMC8722339 fatcat:ycap7uic7zgqhmqcdg7czkteyy

Transfer RNA-derived small RNA: an emerging small non-coding RNA with key roles in cancer

Xinliang Gu, Yu Zhang, Xinyue Qin, Shuo Ma, Yuejiao Huang, Shaoqing Ju
2022 Experimental Hematology & Oncology  
RNAs (tsRNAs) are derived fragments of tRNAs that are cleaved explicitly under certain conditions.  ...  AbstractTransfer RNAs (tRNAs) promote protein translation by binding to the corresponding amino acids and transporting them to the ribosome, which is essential in protein translation. tRNA-derived small  ...  PtRFdb includes various information about tRFs in plants, facilitating the study of tRFs in plants [109] . tRex is a database of tRFs in plants Arabidopsis thaliana and summarizes information about the  ... 
doi:10.1186/s40164-022-00290-1 pmid:35658952 pmcid:PMC9164556 fatcat:2xcmfumkijhrdhpmvqywdegncm

Sorghum's Whole-Plant Transcriptome and Proteome Responses to Drought Stress: A Review

Rudo Ngara, Tatenda Goche, Dirk Z. H. Swanevelder, Stephen Chivasa
2021 Life  
These stress tolerances also present a useful scientific resource for studying the molecular basis for environmental resilience.  ...  Sorghum is a cereal crop with key agronomic traits of drought and heat stress tolerance, making it an ideal food and industrial commodity for hotter and more arid climates.  ...  Plant stress-specific transcriptome data [44] psRNATarget http://plantgrn.noble.org/psRNATarget/ Potential miRNA sorghum target predictions [45] PtRFdb http://www.nipgr.ac.in Plant transfer RNA-derived  ... 
doi:10.3390/life11070704 fatcat:yuczmfd7unc5ffv4ckpxocc7qa

Advances in Non-Coding RNA Sequencing

Julia Micheel, Aram Safrastyan, Damian Wollny
2021
Non-coding RNAs (ncRNAs) comprise a set of abundant and functionally diverse RNA molecules.  ...  Moreover, RNA sequencing revealed crucial roles of many ncRNAs in human health and disease.  ...  Acknowledgments: We apologize to all authors whose work could not be included and thank the anonymous reviewers for their contribution to improve this manuscript.  ... 
doi:10.3390/ncrna7040070 pmid:34842804 pmcid:PMC8628893 fatcat:trztplu7t5f5vep7ft5qwxg3qe