Literature DB >> 33581077

High-resolution quantitative profiling of tRNA abundance and modification status in eukaryotes by mim-tRNAseq.

Andrew Behrens1, Geraldine Rodschinka1, Danny D Nedialkova2.   

Abstract

Measurements of cellular tRNA abundance are hampered by pervasive blocks to cDNA synthesis at modified nucleosides and the extensive similarity among tRNA genes. We overcome these limitations with modification-induced misincorporation tRNA sequencing (mim-tRNAseq), which combines a workflow for full-length cDNA library construction from endogenously modified tRNA with a comprehensive and user-friendly computational analysis toolkit. Our method accurately captures tRNA abundance and modification status in yeast, fly, and human cells and is applicable to any organism with a known genome. We applied mim-tRNAseq to discover a dramatic heterogeneity of tRNA isodecoder pools among diverse human cell lines and a surprising interdependence of modifications at distinct sites within the same tRNA transcript.
Copyright © 2021 The Author(s). Published by Elsevier Inc. All rights reserved.

Entities:  

Keywords:  RNA modification; tRNA quantitation; transfer RNA; translation regulation

Year:  2021        PMID： 33581077     DOI： 10.1016/j.molcel.2021.01.028

Source DB:  PubMed          Journal:  Mol Cell        ISSN： 1097-2765            Impact factor:   17.970


  23 in total

Review 1.  tRNA modification dynamics from individual organisms to metaepitranscriptomics of microbiomes.

Authors:  Wen Zhang; Marcus Foo; A Murat Eren; Tao Pan
Journal:  Mol Cell       Date:  2022-01-14       Impact factor: 17.970

2.  TGIRT-seq Protocol for the Comprehensive Profiling of Coding and Non-coding RNA Biotypes in Cellular, Extracellular Vesicle, and Plasma RNAs.

Authors:  Hengyi Xu; Ryan M Nottingham; Alan M Lambowitz
Journal:  Bio Protoc       Date:  2021-12-05

3.  Immunoprecipation Assay to Quantify the Amount of tRNAs associated with Their Interacting Proteins in Tissue and Cell Culture.

Authors:  Sarada Das; Amila Zuko; Robin Thompson; Erik Storkebaum; Zoya Ignatova
Journal:  Bio Protoc       Date:  2022-02-20

4.  Experimental and computational workflow for the analysis of tRNA pools from eukaryotic cells by mim-tRNAseq.

Authors:  Andrew Behrens; Danny D Nedialkova
Journal:  STAR Protoc       Date:  2022-07-31

5.  Genome-wide analysis of the in vivo tRNA structurome reveals RNA structural and modification dynamics under heat stress.

Authors:  Ryota Yamagami; Jacob P Sieg; Sarah M Assmann; Philip C Bevilacqua
Journal:  Proc Natl Acad Sci U S A       Date:  2022-06-13       Impact factor: 12.779

Review 6.  Codon-Reduced Protein Synthesis With Manipulating tRNA Components in Cell-Free System.

Authors:  Jiaojiao Li; Mengtong Tang; Hao Qi
Journal:  Front Bioeng Biotechnol       Date:  2022-05-13

7.  Reactivity-dependent profiling of RNA 5-methylcytidine dioxygenases.

Authors:  A Emilia Arguello; Ang Li; Xuemeng Sun; Tanner W Eggert; Elisabeth Mairhofer; Ralph E Kleiner
Journal:  Nat Commun       Date:  2022-07-19       Impact factor: 17.694

8.  AAV-delivered suppressor tRNA overcomes a nonsense mutation in mice.

Authors:  Jiaming Wang; Yue Zhang; Craig A Mendonca; Onur Yukselen; Khaja Muneeruddin; Lingzhi Ren; Jialing Liang; Chen Zhou; Jun Xie; Jia Li; Zhong Jiang; Alper Kucukural; Scott A Shaffer; Guangping Gao; Dan Wang
Journal:  Nature       Date:  2022-03-23       Impact factor: 69.504

Review 9.  Transfer RNA-Derived Fragments, the Underappreciated Regulatory Small RNAs in Microbial Pathogenesis.

Authors:  Zhongyou Li; Bruce A Stanton
Journal:  Front Microbiol       Date:  2021-05-17       Impact factor: 5.640

10.  Changes of the tRNA Modification Pattern during the Development of Dictyostelium discoideum.

Authors:  Anne Hoffmann; Lieselotte Erber; Heike Betat; Peter F Stadler; Mario Mörl; Jörg Fallmann
Journal:  Noncoding RNA       Date:  2021-05-28
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