Abstract
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 language | English (US) |
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Pages (from-to) | 266-275 |
Number of pages | 10 |
Journal | Genome Research |
Volume | 19 |
Issue number | 2 |
DOIs | |
State | Published - Feb 2009 |
Externally published | Yes |
ASJC Scopus subject areas
- Genetics
- Genetics(clinical)