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Transcriptome regulation and chromatin occupancy by E2F3 and MYC in mice.

Publication ,  Journal Article
Tang, X; Liu, H; Srivastava, A; Pécot, T; Chen, Z; Wang, Q; Huang, K; Sáenz-Robles, MT; Cantalupo, P; Pipas, J; Leone, G
Published in: Sci Data
February 16, 2016

E2F3 and MYC are transcription factors that control cellular proliferation. To study their mechanism of action in the context of a regenerating tissue, we isolated both proliferating (crypts) and non-dividing (villi) cells from wild-type and Rb depleted small intestines of mice and performed ChIP-exo-seq (chromatin immunoprecipitation combined with lambda exonuclease digestion followed by high-throughput sequencing). The genome-wide chromatin occupancy of E2F3 and MYC was determined by mapping sequence reads to the genome and predicting preferred binding sites (peaks). Binding sites could be accurately identified within small regions of only 24 bp-28 bp long, highlighting the precision to which binding peaks can be identified by ChIP-exo-seq. Forty randomly selected E2F3- and MYC-specific binding sites were validated by ChIP-PCR. In addition, we also presented gene expression data sets from wild type, Rb-, E2f3- and Myc-depleted crypts and villi within this manuscript. These represent comprehensive and validated datasets that can be integrated to identify putative direct targets of E2F3 and MYC involved in the control of cellular proliferation in normal and Rb-deficient small intestines.

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Published In

Sci Data

DOI

EISSN

2052-4463

Publication Date

February 16, 2016

Volume

3

Start / End Page

160008

Location

England

Related Subject Headings

  • Transcriptome
  • Retinoblastoma Protein
  • Proto-Oncogene Proteins c-myc
  • Oligonucleotide Array Sequence Analysis
  • Mice
  • Intestine, Small
  • Genes, myc
  • Genes, Retinoblastoma
  • E2F3 Transcription Factor
  • Chromatin Immunoprecipitation
 

Citation

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Tang, X., Liu, H., Srivastava, A., Pécot, T., Chen, Z., Wang, Q., … Leone, G. (2016). Transcriptome regulation and chromatin occupancy by E2F3 and MYC in mice. Sci Data, 3, 160008. https://doi.org/10.1038/sdata.2016.8
Tang, Xing, Huayang Liu, Arunima Srivastava, Thierry Pécot, Zhong Chen, Qianben Wang, Kun Huang, et al. “Transcriptome regulation and chromatin occupancy by E2F3 and MYC in mice.Sci Data 3 (February 16, 2016): 160008. https://doi.org/10.1038/sdata.2016.8.
Tang X, Liu H, Srivastava A, Pécot T, Chen Z, Wang Q, et al. Transcriptome regulation and chromatin occupancy by E2F3 and MYC in mice. Sci Data. 2016 Feb 16;3:160008.
Tang, Xing, et al. “Transcriptome regulation and chromatin occupancy by E2F3 and MYC in mice.Sci Data, vol. 3, Feb. 2016, p. 160008. Pubmed, doi:10.1038/sdata.2016.8.
Tang X, Liu H, Srivastava A, Pécot T, Chen Z, Wang Q, Huang K, Sáenz-Robles MT, Cantalupo P, Pipas J, Leone G. Transcriptome regulation and chromatin occupancy by E2F3 and MYC in mice. Sci Data. 2016 Feb 16;3:160008.

Published In

Sci Data

DOI

EISSN

2052-4463

Publication Date

February 16, 2016

Volume

3

Start / End Page

160008

Location

England

Related Subject Headings

  • Transcriptome
  • Retinoblastoma Protein
  • Proto-Oncogene Proteins c-myc
  • Oligonucleotide Array Sequence Analysis
  • Mice
  • Intestine, Small
  • Genes, myc
  • Genes, Retinoblastoma
  • E2F3 Transcription Factor
  • Chromatin Immunoprecipitation