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Evidence that alternative transcriptional initiation is largely nonadaptive

Title
Evidence that alternative transcriptional initiation is largely nonadaptive
Authors
Park, Joong-KiZhang, JianzhiXu, Chuan
Ewha Authors
박중기
SCOPUS Author ID
박중기scopus
Issue Date
2019
Journal Title
PLOS BIOLOGY
ISSN
1544-9173JCR Link

1545-7885JCR Link
Citation
PLOS BIOLOGY vol. 17, no. 3
Publisher
PUBLIC LIBRARY SCIENCE
Indexed
SCOPUS WOS
Document Type
Article
Abstract
Alternative transcriptional initiation (ATI) refers to the frequent observation that one gene has multiple transcription start sites (TSSs). Although this phenomenon is thought to be adaptive, the specific advantage is rarely known. Here, we propose that each gene has one optimal TSS and that ATI arises primarily from imprecise transcriptional initiation that could be deleterious. This error hypothesis predicts that (i) the TSS diversity of a gene reduces with its expression level; (ii) the fractional use of the major TSS increases, but that of each minor TSS decreases, with the gene expression level; and (iii) cis-elements for major TSSs are selectively constrained, while those for minor TSSs are not. By contrast, the adaptive hypothesis does not make these predictions a priori. Our analysis of human and mouse transcriptomes confirms each of the three predictions. These and other findings strongly suggest that ATI predominantly results from molecular errors, requiring a major revision of our understanding of the precision and regulation of transcription. Author summary Multiple surveys of transcriptional initiation showed that mammalian genes typically have multiple transcription start sites such that transcription is initiated from any one of these sites. Many researchers believe that this phenomenon is adaptive because it allows production of multiple transcripts, from the same gene, that potentially vary in function or post-transcriptional regulation. Nevertheless, it is also possible that each gene has only one optimal transcription start site and that alternative transcriptional initiation arises primarily from molecular errors that are slightly deleterious. This error hypothesis makes a series of predictions about the amount of transcription start site diversity per gene, relative uses of the various start sites of a gene, among-tissue and across-species differences in start site usage, and the evolutionary conservation of cis-regulatory elements of various start sites, all of which are verified in our analyses of genome-wide transcription start site data from the human and mouse. These findings strongly suggest that alternative transcriptional initiation largely reflects molecular errors instead of molecular adaptations and require a rethink of the precision and regulation of transcription.
DOI
10.1371/journal.pbio.3000197
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일반대학원 > 에코과학부 > Journal papers
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