Cryptic sequence features in the active postmortem transcriptome

BMC Genomics
Peter A Noble, Alexander E Pozhitkov

Abstract

Our previous study found that more than 500 transcripts significantly increased in abundance in the zebrafish and mouse several hours to days postmortem relative to live controls. The current literature suggests that most mRNAs are post-transcriptionally regulated in stressful conditions. We rationalized that the postmortem transcripts must contain sequence features (3- to 9- mers) that are unique from those in the rest of the transcriptome and that these features putatively serve as binding sites for proteins and/or non-coding RNAs involved in post-transcriptional regulation. We identified 5117 and 2245 over-represented sequence features in the mouse and zebrafish, respectively, which represents less than 1.5% of all possible features. Some of these features were disproportionately distributed along the transcripts with high densities in the 3' untranslated regions of the zebrafish (0.3 mers/nt) and the open reading frames of the mouse (0.6 mers/nt). Yet, the highest density (2.3 mers/nt) occurred in the open reading frames of 11 mouse transcripts that lacked 3' or 5' untranslated regions. These results suggest the transcripts with high density of features might serve as 'molecular sponges' that sequester RNA binding proteins ...Continue Reading

References

Apr 25, 1990·Nucleic Acids Research·H J Jeffrey
May 20, 1998·Electrophoresis·P A NobleO A Ogunseitan
May 2, 2001·Bioinformatics·J S AlmeidaM Fletcher
Dec 6, 2001·Nature Reviews. Genetics·S R Eddy
Mar 19, 2002·Genome Biology·Flavio MignoneGraziano Pesole
Sep 10, 2005·International Journal of Cancer. Journal International Du Cancer·Josefin FernebroMef Nilbert
Jan 5, 2006·Nucleic Acids Research·Carine BarreauH Beverley Osborne
Nov 10, 2007·The Journal of Biological Chemistry·Lisa B FrankelAnders H Lund
Oct 28, 2008·Current Opinion in Chemical Biology·J Robert Hogg, Kathleen Collins
Jul 3, 2009·Genes & Development·Jeremy E WiluszDavid L Spector
May 29, 2010·Genome Research·Anders JacobsenAnders Krogh
Aug 2, 2011·Cell·Leonardo SalmenaPier Paolo Pandolfi
Jul 13, 2013·Nature·Debashish RayTimothy R Hughes
Oct 21, 2014·Wiley Interdisciplinary Reviews. RNA·Sandrine CastellaJean-Christophe Larcher
Nov 5, 2014·Nature Reviews. Genetics·Stefanie GerstbergerThomas Tuschl
Oct 8, 2016·Biochimica Et Biophysica Acta·Anna ŁabnoAndrzej Dziembowski
Oct 18, 2016·Wiley Interdisciplinary Reviews. RNA·John G Conboy
Jan 27, 2017·Open Biology·Alex E PozhitkovPeter A Noble
Mar 11, 2017·Molecular Cancer·Jing LiuAili He
May 23, 2017·Genomics, Proteomics & Bioinformatics·Iain M Dykes, Costanza Emanueli
Jul 16, 2017·Biochemical Society Transactions·Robert HarveyAnne E Willis
Jul 20, 2017·Tumour Biology : the Journal of the International Society for Oncodevelopmental Biology and Medicine·Yunfei ZhaoHuai Yang
Aug 7, 2017·Wiley Interdisciplinary Reviews. RNA·Richard J MaraiaMaria R Conte
Sep 19, 2017·Communicative & Integrative Biology·Alexander E Pozhitkov, Peter A Noble
Oct 11, 2017·Nature Cell Biology·David GilotMarie-Dominique Galibert
Nov 1, 2017·Nature Cell Biology·Maria S Soengas, Eva Hernando
Feb 15, 2018·Nature Communications·Pedro G FerreiraRoderic Guigó

Citations

Methods Mentioned

BETA
random draws
immunoprecipitation

Related Concepts

Metazoa
DNA Sequence
Livor Mortis
RNA Processing, Post-Transcriptional
Poly(A) Tail
Metabolic Stress Response
Zebrafish
Unassigned Reading Frames
RNA-Binding Proteins
5' Untranslated Regions

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