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ChIP-chip of H3K4Me1, H3K4Me3, H3K4Ac, H3K9Ac, H3K9Me2, H3K27Me3, CTCF and HP1a in MCF7 breast cancer cells

ABSTRACT: We report the high-throughput profiling of histone modifications, CTCF and HP1a binding sites in MCF7 breast cancer cells. ChIP-chip experiments were performed using the Agilent Human Genome CGH Microarray 1x1M. Regulatory markers H3K4Me1, H3K4Me3, H3K4Ac, H3K9Ac, CTCF are known to be positively correlated with gene expression, and H3K9Me2, H3K27Me3 and HP1a are negative markers. Together with MCF7 methylation data, we showed hypomethylated promoters are significantly enriched with positive regulatory elements, and lacks repressive markers.

ORGANISM(S): Homo sapiens

SUBMITTER: Ming-Ta Hsu

PROVIDER: E-MTAB-1935 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Hierarchical clustering of breast cancer methylomes revealed differentially methylated and expressed breast cancer genes.

Lin I-Hsuan IH Chen Dow-Tien DT Chang Yi-Feng YF Lee Yu-Ling YL Su Chia-Hsin CH Cheng Ching C Tsai Yi-Chien YC Ng Swee-Chuan SC Chen Hsiao-Tan HT Lee Mei-Chen MC Chen Hong-Wei HW Suen Shih-Hui SH Chen Yu-Cheng YC Liu Tze-Tze TT Chang Chuan-Hsiung CH Hsu Ming-Ta MT

PloS one 20150223 2

Oncogenic transformation of normal cells often involves epigenetic alterations, including histone modification and DNA methylation. We conducted whole-genome bisulfite sequencing to determine the DNA methylomes of normal breast, fibroadenoma, invasive ductal carcinomas and MCF7. The emergence, disappearance, expansion and contraction of kilobase-sized hypomethylated regions (HMRs) and the hypomethylation of the megabase-sized partially methylated domains (PMDs) are the major forms of methylation ...[more]

PMID: 25706888

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Drosophila HP1a IP-MS - The composition and organization of Drosophila heterochromatin are heterogeneous and dynamic

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2016-08-18 | PXD003780 | Pride

Various modes of HP1a interactions with the euchromatic chromosome arms in Drosophila ovarian somatic cells

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HP1a recruitment to promoters is independent of H3K9 methylation in Drosophila melanogaster

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Heterochromatic 3D genome organization is directed by HP1a and H3K9-dependent and independent mechanisms [RNA-seq]

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RNA expression in Drosophila melanogaster mutants lacking HP1a

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Heterochromatic 3D genome organization is directed by HP1a and H3K9-dependent and independent mechanisms[CUT&RUN]

Project description:Whether and how histone post-translational modifications and the proteins that bind them drive 3D genome organization remains unanswered. Here, we evaluate the contribution of H3K9-methylated constitutive heterochromatin to 3D genome organization in Drosophila tissues. We find that the predominant organizational feature of wildtype tissues is segregation of euchromatic chromosome arms from heterochromatic pericentromeres. Reciprocal perturbation of HP1a•H3K9me binding, using a point mutation in the HP1a chromodomain or replacement of the replication-dependent histone H3 with H3K9R mutant histones, revealed that HP1a binding to methylated H3K9 in constitutive heterochromatin is required to limit contact frequency between pericentromeres and chromosome arms and regulate the distance between arm and pericentromeric regions. Surprisingly, self-association of pericentromeric regions is largely preserved despite loss of H3K9 methylation and HP1a occupancy. Thus, the HP1a•H3K9 interaction contributes to, but does not solely drive, segregation of euchromatin and heterochromatin inside the nucleus.

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