Characterization of Chromatin Structure-associated Histone Modifications in Breast Cancer Cells

Division of Molecular and Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea.
Genomics & informatics 09/2012; 10(3):145-52. DOI: 10.5808/GI.2012.10.3.145
Source: PubMed

ABSTRACT Chromatin structure and dynamics that are influenced by epigenetic marks, such as histone modification and DNA methylation, play a crucial role in modulating gene transcription. To understand the relationship between histone modifications and regulatory elements in breast cancer cells, we compared our chromatin immunoprecipitation sequencing (ChIP-Seq) histone modification patterns for histone H3K4me1, H3K4me3, H3K9/16ac, and H3K27me3 in MCF-7 cells with publicly available formaldehyde-assisted isolation of regulatory elements (FAIRE)-chip signals in human chromosomes 8, 11, and 12, identified by a method called FAIRE. Active regulatory elements defined by FAIRE were highly associated with active histone modifications, like H3K4me3 and H3K9/16ac, especially near transcription start sites. The H3K9/16ac-enriched genes that overlapped with FAIRE signals (FAIRE-H3K9/14ac) were moderately correlated with gene expression levels. We also identified functional sequence motifs at H3K4me1-enriched FAIRE sites upstream of putative promoters, suggesting that regulatory elements could be associated with H3K4me1 to be regarded as distal regulatory elements. Our results might provide an insight into epigenetic regulatory mechanisms explaining the association of histone modifications with open chromatin structure in breast cancer cells.

Download full-text


Available from: Tae-Young Roh, May 28, 2014
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Macrophages as phagocytes and professional antigen presenting cells play critical roles in both innate and adaptive immunity. Main transcription factors acting during their differentiation and function are known, but the behavior and co-operation of these factors still remained unexplored. We introduce a new approach to map nucleosome-free regions using exclusively active enhancer and core promoter marking histone modification ChIP-seq data. We could detect approximately 56,000 potential active enhancers/promoters showing different lengths and histone modification shapes. Beside the highly enriched PU.1 and C/EBP sites, we could also detect binding sites for RUNX and AP-1, as well as for the MiT (MITF-TFE) family and MEF2 proteins. The PU.1 and C/EBP transcription factors are known for transforming cells into macrophages. The other transcription factors found in this study can play a role in macrophages as well, since it is known that the MiT family proteins are responsible for phagocytic activity and the MEF2 proteins specify monocytic differentiation over the granulocyte direction. Our results imply that this method can provide novel information about transcription factor organization at enhancers and core promoters as well as about the histone modifications surrounding regulatory regions in any immune or other cell types.
    Immunobiology 07/2013; DOI:10.1016/j.imbio.2013.07.006 · 3.18 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The transcriptional silencing of human immunodeficiency virus type 1 (HIV-1) provirus in latently infected cells is a major hurdle on the pathway to HIV-1 elimination. The epigenetic mechanisms established by histone modifications may affect the transcriptional silencing of HIV-1 and viral latency. A systematic epigenome profiling could be applicable to develop new epigenetic diagnostic markers for detecting HIV-1 latency. The HIV-1 latency cell lines (NCHA1, NCHA2, and ACH2) were compared to CD4 T cell line (A3.01). The histone modification profiles obtained from chromatin immunoprecipiation followed by sequencing (ChIP-Seq) for histone H3K4me3 and H3K9ac were systematically examined and differential gene expression patterns along with levels of histone modifications were used for network analysis. The HIV-1 latency gave rise to down-regulation of histone H3K4me3 and H3K9ac levels in 387 and 493 regions and up-regulation in 451 and 962 sites, respectively. By network analysis, 5 gene clusters were associated with down-regulated histone modifications and 6 gene clusters came up with up-regulated histone modifications. Integration of gene expression with epigenetic information revealed that the cell cycle regulatory genes such as CDKN1A (p21) and cyclin D2 (CCND2) identified by differentially modified histones might be an important role in maintaining the HIV-1 latency. The transcriptional regulation by epigenetic memory should play a key role in the evolution and maintenance of HIV-1 latency accompanied by modulation of signaling molecules in the host cells.
    AIDS (London, England) 04/2014; 28(12). DOI:10.1097/QAD.0000000000000309 · 6.56 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Stable introduction of a functional gene in hematopoietic progenitor cells (HPCs) has appeared to be an alternative approach to correct genetically linked blood diseases. However, it is still unclear whether lentiviral vector (LV) is subjected to gene silencing in HPCs. Here, we show that LV carrying green fluorescent protein (GFP) reporter gene driven by cytomegalovirus (CMV) promoter was subjected to transgene silencing after transduction into HPCs. This phenomenon was not due to the deletion of proviral copy number. Study using DNA demethylating agent and histone deacetylase (HDAC) inhibitor showed that the drugs could either prevent or reverse the silencing effect. Using sodium bisulfite sequencing and chromatin immunoprecipitation (ChIP) assay, we demonstrated that DNA methylation occurred soon after LV transduction. At the highest level of gene expression, CMV promoter was acetylated and was in a euchromatin state, while GFP reporter gene was acetylated but was strangely in a heterochromatin state. When the expression declined, CMV promoter underwent transition from acetylated and euchromatic state to a heterochromatic state, while the GFP reporter gene was in deacetylated and heterochromatic state. With these, we verify that DNA methylation and dynamic histone modifications lead to transgene silencing in HPCs transduced with LV.
    01/2015; 2015:1-11. DOI:10.1155/2015/346134