Dissecting tRNA-derived fragment complexities using personalized transcriptomes reveals novel fragment classes and unexpected dependencies

Oncotarget
Aristeidis G TelonisIsidore Rigoutsos

Abstract

We analyzed transcriptomic data from 452 healthy men and women representing five different human populations and two races, and, 311 breast cancer samples from The Cancer Genome Atlas. Our studies revealed numerous constitutive, distinct fragments with overlapping sequences and quantized lengths that persist across dozens of individuals and arise from the genomic loci of all nuclear and mitochondrial human transfer RNAs (tRNAs). Surprisingly, we discovered that the tRNA fragments' length, starting and ending points, and relative abundance depend on gender, population, race and also on amino acid identity, anticodon, genomic locus, tissue, disease, and disease subtype. Moreover, the length distribution of mitochondrially-encoded tRNAs differs from that of nuclearly-encoded tRNAs, and the specifics of these distributions depend on tissue. Notably, tRNA fragments from the same anticodon do not have correlated abundances. We also report on a novel category of tRNA fragments that significantly contribute to the differences we observe across tissues, genders, populations, and races: these fragments, referred to as i-tRFs, are abundant in human tissues, wholly internal to the respective mature tRNA, and can straddle the anticodon. HIT...Continue Reading

References

Sep 30, 1998·Cell·D R Green
Apr 20, 2001·Proceedings of the National Academy of Sciences of the United States of America·V G TusherG Chu
Feb 16, 2002·Methods : a Companion to Methods in Enzymology·K J Livak, T D Schmittgen
Nov 14, 2003·Nature·Katrin Henze, William Martin
Nov 8, 2005·The Journal of Biological Chemistry·Suzanne R Lee, Kathleen Collins
Apr 26, 2006·Proceedings of the National Academy of Sciences of the United States of America·Isidore RigoutsosDaniel Platt
Jul 25, 2006·Current Biology : CB·Heidi M McBrideSylwia Wasiak
Mar 10, 2007·Science·Daniel C PregibonPatrick S Doyle
Dec 18, 2007·Nucleic Acids Research·Henry J HaiserMarie A Elliot
Apr 12, 2008·BMC Genomics·Hideya KawajiYoshihide Hayashizaki
Oct 11, 2008·Journal of Cellular Biochemistry·Carolyn M Klinge
Nov 6, 2008·Nucleic Acids Research·Patricia P Chan, Todd M Lowe
Dec 31, 2008·FEBS Letters·Hanjiang FuXiaofei Zheng
Apr 1, 2009·The Journal of Cell Biology·Satoshi YamasakiPaul Anderson
Apr 1, 2009·The Journal of Cell Biology·Debrah M Thompson, Roy Parker
Jul 28, 2009·Cell·Debrah M Thompson, Roy Parker
Sep 29, 2009·Nucleic Acids Research·Mariana Pavon-EternodTao Pan
Nov 26, 2009·Genes & Development·Yong Sun LeeAnindya Dutta
Feb 5, 2010·The Journal of Biological Chemistry·Mohamed M EmaraPaul Anderson
Mar 17, 2010·Molecular Cell·Yide MeiXiaolu Yang
Feb 26, 2011·Angewandte Chemie·Stephen C ChapinPatrick S Doyle
Aug 23, 2011·Cell·Tim R MercerJohn S Mattick
Aug 23, 2011·Molecular Cell·Pavel IvanovPaul Anderson
Oct 7, 2011·Wiley Interdisciplinary Reviews. RNA·Andrew Sobala, Gyorgy Hutvagner
Sep 25, 2012·Nature·UNKNOWN Cancer Genome Atlas Network
Oct 23, 2012·The Journal of Biological Chemistry·Mridusmita SaikiaMaria Hatzoglou
Nov 28, 2012·Molecular Therapy : the Journal of the American Society of Gene Therapy·Qingrong WangXiaoyong Bao
Jan 9, 2013·Proceedings of the National Academy of Sciences of the United States of America·Roy L MauteRiccardo Dalla-Favera
Sep 17, 2013·Nature·Tuuli LappalainenEmmanouil T Dermitzakis
Sep 17, 2013·Nature Biotechnology·Peter A C 't HoenTuuli Lappalainen
Nov 8, 2013·Nucleic Acids Research·Carsten A RaabeTimofey S Rozhdestvensky
Dec 20, 2013·RNA Biology·Jennifer Gebetsberger, Norbert Polacek

❮ Previous
Next ❯

Citations

Jun 14, 2017·Wiley Interdisciplinary Reviews. RNA·Ana Raquel Soares, Manuel Santos
Nov 21, 2017·Nucleic Acids Research·Amadís PagèsEduardo Eyras
Jul 10, 2019·Pigment Cell & Melanoma Research·Eric LondinIsidore Rigoutsos
Sep 19, 2019·Acta Physiologica·Chunsheng ZhuZheng Zhou
Sep 6, 2020·Nucleic Acids Research·Rogan Magee, Isidore Rigoutsos
Aug 16, 2016·Human Mutation·Dario VenezianoCarlo M Croce
Dec 3, 2016·Nucleic Acids Research·Valérie CognatLaurence Maréchal-Drouard
Jun 17, 2016·Molecular & Cellular Oncology·Shozo Honda, Yohei Kirino
Jul 12, 2019·F1000Research·Lorena PantanoShannan Ho Sui
Nov 19, 2019·Database : the Journal of Biological Databases and Curation·Alessandro La FerlitaAlfredo Pulvirenti
May 20, 2020·International Journal of Cancer. Journal International Du Cancer·Tianyu ZengYongmei Yin
Aug 14, 2020·International Journal of Molecular Sciences·Panagiotis BalaskasMandy J Peffers
Mar 26, 2016·Oncotarget·Michael OlvedyElena S Martens-Uzunova
Jan 22, 2017·Nucleic Acids Research·Megumi ShigematsuYohei Kirino
Jun 25, 2017·Nucleic Acids Research·Shozo HondaYohei Kirino
Mar 31, 2016·Life·Hsiao-Yun Huang, Anita K Hopper
Feb 6, 2019·Non-coding RNA·Marine LambertPatrick Provost
Oct 23, 2018·International Journal of Rheumatic Diseases·Yan ZhangXiaodong Liu
Oct 16, 2019·RNA Biology·Lingyu GuanAndrey Grigoriev
Oct 1, 2020·Cancers·Joonhyeong ParkSuhwan Chang
Mar 11, 2016·BMC Bioinformatics·Aristeidis G TelonisIsidore Rigoutsos
Feb 5, 2016·Biomarker Insights·Kevin W DiebelLynne T Bemis
Mar 30, 2018·Scientific Reports·Rogan G MageeIsidore Rigoutsos
Dec 13, 2018·Frontiers in Genetics·Megumi ShigematsuYohei Kirino
Apr 21, 2016·Cellular and Molecular Life Sciences : CMLS·Markus DuechlerBarbara Nawrot
Jul 3, 2018·Oncotarget·Ezequiel LacunzaMagalí Pellon-Maison
Jan 4, 2017·Non-coding RNA·Wei-Lin XuLing-Ling Zheng
Mar 19, 2020·RNA Biology·Domenico RosaceSandra Blanco
May 28, 2020·Frontiers in Genetics·Ruaidhri CappaAmy J McKnight
Oct 13, 2020·Frontiers in Pharmacology·Jun CaoDa-Zhi Wang

❮ Previous
Next ❯

Methods Mentioned

BETA
RNA-seq
PCR
PCA
HITS-CLIP
Assay
CLIP-seq
HITS-CLIP-seq
electrophoreses

Software Mentioned

SAM
dendextend
Firefly BioWorks
Argonaute
FirePlex
samr
PLS
Ago
AlaACG
R

Related Concepts

Related Feeds

Cancer Genomics (Keystone)

Cancer genomics approaches employ high-throughput technologies to identify the complete catalog of somatic alterations that characterize the genome, transcriptome and epigenome of cohorts of tumor samples. Discover the latest research using such technologies in this feed.

Cancer -Omics

A variety of different high-throughput technologies can be used to identify the complete catalog of changes that characterize the molecular profile of cohorts of tumor samples. Discover the latest insights gained from cancer 'omics' in this feed.