Large-scale evidence for conservation of NMD candidature across mammals.

PloS One
David A de Lima Morais, Paul M Harrison

Abstract

Alternatively-spliced (AS) forms can vary protein function, intracellular localization and post-translational modifications. AS coupled with mRNA nonsense-mediated decay (NMD) can also control the transcript abundance. Here, we have investigated the genome-scale conservation of alternatively-spliced NMD candidates (AS-NMD candidates), in mammals. We mapped>12 million cDNA/EST library transcripts, comprising pooled data from both older and next-generation sequencing techniques, against genomic sequences to annotate AS-NMD candidates generated by in-frame premature termination codons (PTCs), in the human, mouse, rat and cow genomes. In these genomes, we found populations of genes that harbour AS-NMD candidates, varying in number from approximately 149 to 2,051 genes. We discovered that a highly-significant proportion (27%-35%) of AS-NMD candidate genes in mouse, rat and cow, also have human orthologs targeted for NMD. Intron retention was the most abundant type of AS-NMD, ranging from 43% to 67% of genes harbouring an AS-NMD candidate. Groupings of AS-NMD candidate genes either with or without intron retentions also have highly significant AS-NMD conservation, indicating that the trend is not due primarily to conservation of intr...Continue Reading

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Jan 8, 2013·Nucleic Acids Research·Svetlana A ShabalinaAnna Kashina
Feb 25, 2015·International Journal of Molecular Sciences·Florent Hubé, Claire Francastel
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Nov 11, 2017·G3 : Genes - Genomes - Genetics·Virginia S MuirPhilip Anderson
Aug 1, 2020·Frontiers in Genetics·Jian-Tao ZhengHong-Dong Li
May 3, 2018·Journal of Experimental Botany·Ravi P SanyalAjay Saini
May 28, 2019·Wiley Interdisciplinary Reviews. RNA·Aparna KishorJ Robert Hogg
May 28, 2021·Nature Communications·Evi GoulielmakiGeorge A Garinis

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Methods Mentioned

BETA
GTPase
EST sequencing

Software Mentioned

ECR browser
BioCarta
FatiGO
NMD
AS
Ensembl
GMAP
Exonerate
Perl
BLASTx

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