Quantitative analysis of ChIP-seq data uncovers dynamic and sustained H3K4me3 and H3K27me3 modulation in cancer cells under hypoxia.
A comprehensive assessment of the epigenetic dynamics in cancer cells is the key to understanding the molecular mechanisms underlying cancer and to improving cancer diagnostics, prognostics and treatment. By combining genome-wide ChIP-seq epigenomics and microarray transcriptomics, we studied the effects of oxygen deprivation and subsequent reoxygenation on histone 3 trimethylation of lysine 4 (H3K4me3) and lysine 27 (H3K27me3) in a breast cancer cell line, serving as a model for abnormal oxygenation in solid tumors. A priori, epigenetic markings and gene expression levels not only are expected to vary greatly between hypoxic and normoxic conditions, but also display a large degree of heterogeneity across the cell population. Where traditionally ChIP-seq data are often treated as dichotomous data, the model and experiment here necessitate a quantitative, data-driven analysis of both datasets.



We first identified genomic regions with sustained epigenetic markings, which provided a sample-specific reference enabling quantitative ChIP-seq data analysis. Sustained H3K27me3 marking was located around centromeres and intergenic regions, while sustained H3K4me3 marking is associated with genes involved in RNA binding, translation and protein transport and localization. Dynamic marking with both H3K4me3 and H3K27me3 (hypoxia-induced bivalency) was found in CpG-rich regions at loci encoding factors that control developmental processes, congruent with observations in embryonic stem cells.



In silico-identified epigenetically sustained and dynamic genomic regions were confirmed through ChIP-PCR in vitro, and obtained results are corroborated by published data and current insights regarding epigenetic regulation.
Maastricht Centre for Systems Biology - MaCSBio, Maastricht University, Maastricht, The Netherlands.|Department of Bioinformatics - BiGCaT, Maastricht University, Maastricht, The Netherlands.
Michiel E
0000-0002-4472-7119
ME
Adriaens
Department of Molecular Genetics, Maastricht University, Maastricht, The Netherlands.
Peggy
P
Prickaerts
Departments of Informatics and Bio-computing, University Health Network, Toronto, ON Canada.|Heart Centre Biobank, The Hospital for Sick Children, Toronto, ON Canada.
Michelle
M
Chan-Seng-Yue
Princess Margaret Cancer Centre and Campbell Family Institute for Cancer Research, University Health Network, Toronto, ON Canada.|Department of Radiation Oncology, University of Toronto, Toronto, ON Canada.|Maastricht Radiation Oncology (MaastRO) Laboratory, Maastricht University, Maastricht, The Netherlands.
Twan
T
van den Beucken
Department of Molecular Genetics, Maastricht University, Maastricht, The Netherlands.
Vivian E H
VEH
Dahlmans
Department of Bioinformatics - BiGCaT, Maastricht University, Maastricht, The Netherlands.
Lars M
LM
Eijssen
Departments of Informatics and Bio-computing, University Health Network, Toronto, ON Canada.|Human Longevity Inc., San Diego, CA USA.
Timothy
T
Beck
Princess Margaret Cancer Centre and Campbell Family Institute for Cancer Research, University Health Network, Toronto, ON Canada.|Department of Radiation Oncology, University of Toronto, Toronto, ON Canada.|Maastricht Radiation Oncology (MaastRO) Laboratory, Maastricht University, Maastricht, The Netherlands.
Bradly G
BG
Wouters
Department of Molecular Genetics, Maastricht University, Maastricht, The Netherlands.
Jan Willem
JW
Voncken
Department of Bioinformatics - BiGCaT, Maastricht University, Maastricht, The Netherlands.
Chris T A
CTA
Evelo
D015687:Cell Hypoxia; D045744:Cell Line, Tumor; D047369:Chromatin Immunoprecipitation; D018899:CpG Islands; D056751:Cyclin A2 / Q000235:genetics / Q000378:metabolism; D057890:Epigenomics; D059014:High-Throughput Nucleotide Sequencing; D006657:Histones / Q000235:genetics / Q000378:metabolism*; D006801:Humans; D061986:MCF-7 Cells; D008745:Methylation; D020411:Oligonucleotide Array Sequence Analysis; D053498:Sarcoplasmic Reticulum Calcium-Transporting ATPases / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA
C503721:CCNA2 protein, human; D056751:Cyclin A2; D006657:Histones; D053498:Sarcoplasmic Reticulum Calcium-Transporting ATPases; C506949:ATP2A3 protein, human
ChIP-sequencing; Data normalization; Epigenomics; H3K27me3; H3K4me3; Hypoxia; MCF7; Transcriptomics