Exome-based Variant Detection in Core Promoters

Yeong C. Kim, Jian Cui, Jiangtao Luo, Fengxia Xiao, Bradley Downs, San Ming Wang

Research output: Contribution to journalArticle

Abstract

Core promoter controls the initiation of transcription. Core promoter sequence change can disrupt transcriptional regulation, lead to impairment of gene expression and ultimately diseases. Therefore, comprehensive characterization of core promoters is essential to understand normal and abnormal gene expression in biomedical studies. Here we report the development of EVDC (Exome-based Variant Detection in Core promoters) method for genome-scale analysis of core-promoter sequence variation. This method is based on the fact that exome sequences contain the sequences not only from coding exons but also from non-coding region including core promoters generated by random fragmentation in exome sequencing process. Using exome data from three cell types of CD4+ T cells, CD19+ B cells and neutrophils of a single individual, we characterized the features of core promoter-mapped exome sequences, and analysed core-promoter variation in this individual genome. We also compared the core promoters between YRI (Yoruba in Ibadan, Nigeria) and the CEU (Utah residents of European decedent) populations using the exome data generated by the 1000 Genome project, and observed much higher variation in YRI population than in CEU population. Our study demonstrates that the EVDC method provides a simple but powerful means for genome-wile de novo characterization of core promoter sequence variation.

Original languageEnglish (US)
Article number30716
JournalScientific reports
Volume6
DOIs
StatePublished - Jul 28 2016

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Exome
Genome
Population
Gene Expression
Nigeria
Exons
Neutrophils
B-Lymphocytes
T-Lymphocytes

ASJC Scopus subject areas

  • General

Cite this

Kim, Y. C., Cui, J., Luo, J., Xiao, F., Downs, B., & Wang, S. M. (2016). Exome-based Variant Detection in Core Promoters. Scientific reports, 6, [30716]. https://doi.org/10.1038/srep30716

Exome-based Variant Detection in Core Promoters. / Kim, Yeong C.; Cui, Jian; Luo, Jiangtao; Xiao, Fengxia; Downs, Bradley; Wang, San Ming.

In: Scientific reports, Vol. 6, 30716, 28.07.2016.

Research output: Contribution to journalArticle

Kim, YC, Cui, J, Luo, J, Xiao, F, Downs, B & Wang, SM 2016, 'Exome-based Variant Detection in Core Promoters', Scientific reports, vol. 6, 30716. https://doi.org/10.1038/srep30716
Kim YC, Cui J, Luo J, Xiao F, Downs B, Wang SM. Exome-based Variant Detection in Core Promoters. Scientific reports. 2016 Jul 28;6. 30716. https://doi.org/10.1038/srep30716
Kim, Yeong C. ; Cui, Jian ; Luo, Jiangtao ; Xiao, Fengxia ; Downs, Bradley ; Wang, San Ming. / Exome-based Variant Detection in Core Promoters. In: Scientific reports. 2016 ; Vol. 6.
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