Journal
GENOMICS
Volume 98, Issue 5, Pages 337-342Publisher
ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.ygeno.2011.07.001
Keywords
Nonsense-mediated decay; Whole-genome sequencing; RNA-Seq; Premature termination codons
Funding
- NIAID Center for HIV/AIDS Vaccine Immunology [UO1AI067854]
- Bill & Melinda Gates Foundation
- NIMH [RC2MH089915]
- NINDS [RC2NS070344]
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We sequenced the genomes of ten unrelated individuals and identified heterozygous stop codon-gain variants in protein-coding genes: we then sequenced their transcriptomes and assessed the expression levels of the stop codon-gain alleles. An ANOVA showed statistically significant differences between their expression levels (p = 4 x 10(-16)). This difference was almost entirely accounted for by whether the stop codon-gain variant had a second, non-protein-truncating function in or near an alternate transcript: stop codon-gains without alternate functions were generally not found in the cDNA (p = 3 x 10(-5)). Additionally, stop colon-gain variants in two intronless genes were not expressed, an unexpected outcome given previous studies. In this study, stop codon-gain variants were either well expressed in all individuals or were never expressed. Our finding that stop codon-gain variants were generally expressed only when they had an alternate function suggests that most naturally occurring stop codon-gain variants in protein-coding genes are either not transcribed or have their transcripts destroyed. (C) 2011 Elsevier Inc. All rights reserved.
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