Genome-wide ChIP-seq analysis of human TOP2B occupancy in MCF7 breast cancer epithelial cells

We report the whole genome ChIP seq for human TOP2B from MCF7 cells. Using three different peak calling methods, regions of binding were identified in the presence or absence of the nuclear hormone estradiol, as TOP2B has been reported to play a role in ligand-induced transcription. TOP2B peaks were...

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Bibliographic Details
Published in:Biology open 2015-10, Vol.4 (11), p.1436-1447
Main Authors: Manville, Catriona M, Smith, Kayleigh, Sondka, Zbyslaw, Rance, Holly, Cockell, Simon, Cowell, Ian G, Lee, Ka Cheong, Morris, Nicholas J, Padget, Kay, Jackson, Graham H, Austin, Caroline A
Format: Article
Language:English
Subjects:
17β-Estradiol
Axon guidance
Axonogenesis
Biosynthesis
Breast cancer
ChIP seq
Danio rerio
Deoxyribonucleic acid
DNA
Enrichment
Epigenetics
Epithelial cells
Epithelium
ESR1 protein
Gene sequencing
Genomes
Glycosaminoglycans
Heparin
KLF4 protein
Nucleotide sequence
Ontology
Promoters
Sex hormones
Sulfates
TOP2B
Topoisomerase II
Zebrafish
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Summary:We report the whole genome ChIP seq for human TOP2B from MCF7 cells. Using three different peak calling methods, regions of binding were identified in the presence or absence of the nuclear hormone estradiol, as TOP2B has been reported to play a role in ligand-induced transcription. TOP2B peaks were found across the whole genome, 50% of the peaks fell either within a gene or within 5 kb of a transcription start site. TOP2B peaks coincident with gene promoters were less frequently associated with epigenetic features marking active promoters in estradiol treated than in untreated cells. Significantly enriched transcription factor motifs within the DNA sequences underlying the peaks were identified. These included SP1, KLF4, TFAP2A, MYF, REST, CTCF, ESR1 and ESR2. Gene ontology analysis of genes associated with TOP2B peaks found neuronal development terms including axonogenesis and axon guidance were significantly enriched. In the absence of functional TOP2B there are errors in axon guidance in the zebrafish eye. Specific heparin sulphate structures are involved in retinal axon targeting. The glycosaminoglycan biosynthesis-heparin sulphate/heparin pathway is significantly enriched in the TOP2B gene ontology analysis, suggesting changes in this pathway in the absence of TOP2B may cause the axon guidance faults.
ISSN:2046-6390
2046-6390
DOI:10.1242/bio.014308