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MNase and HpaII sensitivity assays in MCF7 breast cancer cells

ABSTRACT: DNA are packaged into nucleosomes and chromatin. We performed incomplete MNase digestion of chromatin to identify nucleosome-free regions that may indicate active promoters and regulatory regions. Additionally, HpaII digestion was performed which cleaves CCGG sites when the internal C remains unmodified. The hypomethylation state and nuclease sensitivity of the chromatin are indicators of transcription regulatory regions.

INSTRUMENT(S): 454 GS 20, Illumina HiSeq 2000

ORGANISM(S): Homo sapiens

SUBMITTER: Ming-Ta Hsu

PROVIDER: E-MTAB-1958 | 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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