Transcriptome regulation and chromatin occupancy by E2F3 and MYC in mice
Transcriptome regulation and chromatin occupancy by E2F3 and MYC in mice
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DOI：
10.1038/sdata.2016.8
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发表时间：
2016-02-16
期刊：
影响因子：
9.8
通讯作者：
Leone, Gustavo
中科院分区：
文献类型：
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作者：
Tang, Xing;Liu, Huayang;Leone, Gustavo
E2F3 和 MYC 是控制细胞增殖的转录因子。为了研究它们在再生组织中的作用机制，我们从野生型和 Rb 耗尽的小鼠小肠中分离了增殖（隐窝）和非分裂（绒毛）细胞，并进行 ChIP-exo-seq（染色质免疫沉淀结合 lambda 核酸外切酶消化，然后进行高通量测序）。 E2F3 和 MYC 的全基因组染色质占用率是通过将序列读取映射到基因组并预测首选结合位点（峰）来确定的。可以在长度仅为 24 bp-28 bp 的小区域内准确识别结合位点，凸显了 ChIP-exo-seq 识别结合峰的精确度。通过 ChIP-PCR 验证了 40 个随机选择的 E2F3 和 MYC 特异性结合位点。此外，我们还在本手稿中提供了来自野生型、Rb、E2f3 和 Myc 耗尽的隐窝和绒毛的基因表达数据集。这些代表了全面且经过验证的数据集，可以整合这些数据集来识别 E2F3 和 MYC 的推定直接靶点，这些靶点参与控制正常和 Rb 缺乏的小肠中的细胞增殖。
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.