Functional elements demarcated by histone modifications in breast cancer cells

Moon Kyung Choe, Chang Pyo Hong, Jihwan Park, Seong Hye Seo, Tae Young Roh

Research output: Contribution to journalArticlepeer-review

26 Scopus citations


Histone modifications are regarded as one of markers to identify regulatory elements which are DNA segments modulating gene transcription. Aberrant changes of histone modification levels are frequently observed in cancer. We have employed ChIP-Seq to identify regulatory elements in human breast cancer cell line, MCF-7 by comparing histone modification patterns of H3K4me1, H3K4me3, and H3K9/14ac to those in normal mammary epithelial cell line, MCF-10A. The genome-wide analysis shows that H3K4me3 and H3K9/14ac are highly enriched at promoter regions and H3K4me1 has a relatively broad distribution over proximity of TSSs as well as other genomic regions. We identified that many differentially expressed genes in MCF-7 have divergent histone modification patterns. To understand the functional roles of distinctively histone-modified regions, we selected 35 genomic regions marked by at least one histone modification and located from 3 to 10. kb upstream of TSS in both MCF-7 and MCF-10A and assessed their transcriptional activities. About 66% and 60% of selected regions in MCF-7 and MCF-10A, respectively, enhanced the transcriptional activity. Interestingly, most regions marked by H3K4me1 exhibited an enhancer activity. Regions with two or more kinds of histone modifications did show varying activities. In conclusion, our data reflects that comprehensive analysis of histone modification profiles under cell type-specific chromatin environment should provide a better chance for defining functional regulatory elements in the genome.

Original languageEnglish
Pages (from-to)475-482
Number of pages8
JournalBiochemical and Biophysical Research Communications
Issue number3
StatePublished - 17 Feb 2012

Bibliographical note

Funding Information:
We thank members of Lab. of System Genomics, POSTECH, for active discussion and Dr. Y.K. Shin, Seoul National University for kindly providing MCF-7. This work was supported by National Research Foundation (KRF-2008-313- C00665 , 2010-0023412, and 2010-0026759), Korea Healthcare technology R&D Project , MHWFA (A084519), and the World Class University program , NRF, MEST (R31-10105), Republic of Korea.


  • Breast cancer
  • Enhancer
  • Epigenome
  • Histone modification
  • Regulatory elements


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