High-resolution human core-promoter prediction with CoreBoost-HM

Xiaowo Wang, Zhenyu Xuan, Xiaoyue Zhao, Yanda Li, Michael Q. Zhang

Research output: Contribution to journalArticlepeer-review

88 Scopus citations


Correctly locating the gene transcription start site and the core-promoter is important for understanding transcriptional regulation mechanism. Here we have integrated specific genome-wide histone modification and DNA sequence features together to predict RNA polymerase II core-promoters in the human genome. Our new predictor CoreBoost-HM outperforms existing promoter prediction algorithms by providing significantly higher sensitivity and specificity at high resolution. We demonstrated that even though the histone modification data used in this study are from a specific cell type (CD4+ T-cell), our method can be used to identify both active and repressed promoters. We have applied it to search the upstream regions of microRNA genes, and show that CoreBoost-HM can accurately identify the known promoters of the intergenic microRNAs. We also identified a few intronic microRNAs that may have their own promoters. This result suggests that our new method can help to identify and characterize the core-promoters of both coding and noncoding genes.

Original languageEnglish (US)
Pages (from-to)266-275
Number of pages10
JournalGenome Research
Issue number2
StatePublished - Feb 2009
Externally publishedYes

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)


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