Understanding Transcription Factor Regulation by Integrating Gene Expression and DNase i Hypersensitive Sites

Guohua Wang, Fang Wang, Qian Huang, Yu Li, Yunlong Liu, Yadong Wang

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

Transcription factors are proteins that bind to DNA sequences to regulate gene transcription. The transcription factor binding sites are short DNA sequences (5-20 bp long) specifically bound by one or more transcription factors. The identification of transcription factor binding sites and prediction of their function continue to be challenging problems in computational biology. In this study, by integrating the DNase I hypersensitive sites with known position weight matrices in the TRANSFAC database, the transcription factor binding sites in gene regulatory region are identified. Based on the global gene expression patterns in cervical cancer HeLaS3 cell and HelaS3-ifnα4h cell (interferon treatment on HeLaS3 cell for 4 hours), we present a model-based computational approach to predict a set of transcription factors that potentially cause such differential gene expression. Significantly, 6 out 10 predicted functional factors, including IRF, IRF-2, IRF-9, IRF-1 and IRF-3, ICSBP, belong to interferon regulatory factor family and upregulate the gene expression levels responding to the interferon treatment. Another factor, ISGF-3, is also a transcriptional activator induced by interferon alpha. Using the different transcription factor binding sites selected criteria, the prediction result of our model is consistent. Our model demonstrated the potential to computationally identify the functional transcription factors in gene regulation.

Original languageEnglish
Article number757530
JournalBioMed Research International
Volume2015
DOIs
StatePublished - 2015

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Deoxyribonucleases
Gene Expression Regulation
Gene expression
Transcription Factors
Binding Sites
DNA sequences
Gene Expression
Interferons
Position-Specific Scoring Matrices
Genes
Interferon Regulatory Factors
Nucleic Acid Regulatory Sequences
Deoxyribonuclease I
Transcription
Computational Biology
Interferon-alpha
Uterine Cervical Neoplasms
Up-Regulation
Databases

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)

Cite this

Understanding Transcription Factor Regulation by Integrating Gene Expression and DNase i Hypersensitive Sites. / Wang, Guohua; Wang, Fang; Huang, Qian; Li, Yu; Liu, Yunlong; Wang, Yadong.

In: BioMed Research International, Vol. 2015, 757530, 2015.

Research output: Contribution to journalArticle

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