title: Transcriptome regulation and chromatin occupancy by E2F3 and MYC in mice.
abstract: 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.
authors.affiliation: Department of Molecular Virology, Immunology and Medical Genetics, College of Medicine, Columbus, Ohio 43210, USA.|Department of Molecular Genetics, College of Biological Sciences, Columbus, Ohio 43210, USA.|Comprehensive Cancer Center, Columbus, Ohio 43210, USA.
authors.forename: Xing
authors.initials: X
authors.lastname: Tang
authors.affiliation: Department of Molecular Virology, Immunology and Medical Genetics, College of Medicine, Columbus, Ohio 43210, USA.|Department of Molecular Genetics, College of Biological Sciences, Columbus, Ohio 43210, USA.|Comprehensive Cancer Center, Columbus, Ohio 43210, USA.
authors.forename: Huayang
authors.initials: H
authors.lastname: Liu
authors.affiliation: Department of Molecular Virology, Immunology and Medical Genetics, College of Medicine, Columbus, Ohio 43210, USA.|Department of Molecular Genetics, College of Biological Sciences, Columbus, Ohio 43210, USA.|Comprehensive Cancer Center, Columbus, Ohio 43210, USA.
authors.forename: Arunima
authors.initials: A
authors.lastname: Srivastava
authors.affiliation: Department of Molecular Virology, Immunology and Medical Genetics, College of Medicine, Columbus, Ohio 43210, USA.|Department of Molecular Genetics, College of Biological Sciences, Columbus, Ohio 43210, USA.|Comprehensive Cancer Center, Columbus, Ohio 43210, USA.
authors.forename: Thierry
authors.initials: T
authors.lastname: Pécot
authors.affiliation: Department of Molecular and Cellular Biochemistry, Columbus, Ohio 43210, USA.
authors.forename: Zhong
authors.initials: Z
authors.lastname: Chen
authors.affiliation: Department of Molecular and Cellular Biochemistry, Columbus, Ohio 43210, USA.
authors.forename: Qianben
authors.initials: Q
authors.lastname: Wang
authors.affiliation: Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, USA.
authors.forename: Kun
authors.initials: K
authors.lastname: Huang
authors.affiliation: Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA.
authors.forename: Maria Teresa
authors.initials: MT
authors.lastname: Sáenz-Robles
authors.affiliation: Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA.
authors.forename: Paul
authors.initials: P
authors.lastname: Cantalupo
authors.affiliation: Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA.
authors.forename: James
authors.initials: J
authors.lastname: Pipas
authors.affiliation: Department of Molecular Virology, Immunology and Medical Genetics, College of Medicine, Columbus, Ohio 43210, USA.|Department of Molecular Genetics, College of Biological Sciences, Columbus, Ohio 43210, USA.|Comprehensive Cancer Center, Columbus, Ohio 43210, USA.
authors.forename: Gustavo
authors.initials: G
authors.lastname: Leone
mesh_terms: D000818:Animals; D001665:Binding Sites; D049109:Cell Proliferation; D002843:Chromatin / Q000235:genetics* / Q000378:metabolism; D047369:Chromatin Immunoprecipitation; D050699:E2F3 Transcription Factor / Q000235:genetics / Q000378:metabolism; D016161:Genes, Retinoblastoma; D016259:Genes, myc; D007421:Intestine, Small / Q000166:cytology / Q000378:metabolism; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis; D016271:Proto-Oncogene Proteins c-myc / Q000235:genetics / Q000378:metabolism; D016160:Retinoblastoma Protein / Q000235:genetics / Q000378:metabolism; D059467:Transcriptome
chemical_list: D002843:Chromatin; D050699:E2F3 Transcription Factor; C490840:E2f3 protein, mouse; D016271:Proto-Oncogene Proteins c-myc; D016160:Retinoblastoma Protein