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

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.

Keywords: ChIP-Seq; breast neoplasms; epigenetic regulation; formaldehyde-assisted isolation of regulatory elements (FAIRE); histone modification.

Fig. 1

Chromatin structure in genomic regions defined by formaldehyde-assisted isolation of regulatory elements (FAIRE) in MCF7. (A) Profile of FAIRE and histone modifications (H3K4me1, H3K4me3, H3K9/14ac, and H3K27me3) on a chromosome scale (chromosome 8, 11, and 12). The peaks denoted by spots were plotted by k-clustering using seqMiner program. (B) Histone modification peak profiles were analyzed, centered on FAIRE signals. The Y axis represents the normalized sum of peak counts, multiplied by 10,000. (C) The overlapping of each FAIRE-histone modification was estimated. (D) FAIRE-histone modifications ranging from -5 kb to 5 kb of transcription start sites (TSSs) were plotted. (E) Chromatin state at CCND1 locus. The box indicates ±3 kb region from TSS.

Fig. 2

Formaldehyde-assisted isolation of regulatory elements (FAIRE)-histone modifications and gene expression profile. (A) Gene expression level and histone modification enrichment. Inserts are Pearson correlation coefficients (r). (B) Gene expression level and histone H3K4me3 enrichment. (C) Gene expression level and histone H3K9/14ac enrichment. (D) Gene ontology (GO) analysis for top 30% ranked expressed genes in H3K9/14ac enrichment. (E) Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis for top 30% ranked expressed genes in H3K9/14ac enrichment. MAPK, mitogen-activated protein kinase.

Fig. 3

Motif analysis for formaldehyde-assisted isolation of regulatory elements (FAIRE)-related genomic regions marked by H3K4me1, H3K4me3, and H3K9/14ac. (A) Motif analysis for FAIRE marked by H3K4me3 and H3K9/14ac. (B) Motif analysis for FAIRE marked by H3K4me1. (C) Genomic distribution of motifs identified from FAIRE-H3K4me1. (D) Genomic distribution of motifs identified from FAIRE-H3K4me3. (E) Genomic distribution of motifs identified from FAIRE-H3K9/14ac. N.D., not determined. ^aUpstream regions from transcription start sites.