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Relation between expression and DNA methylation amongst the four lineages, the
Relation involving expression and DNA methylation amongst the four lineages, the DMVs were clustered to group II. Around the contrary, if we observed a good correlation between expression and DNA methylation, these DMVs were clustered to group III.Acknowledgements We thank Dr. Bing Ren for sharing the WT, Eed -/- (l7Rn5-3354SB) mESC lines and Dr. Xiaohua Shen for sharing the Ezh2 -/- mESC line. We are grateful to Drs. Yanhui Xu, Chengran Xu, Anna-Pavlina Haramis, and Pastor-Paraja JC for their help or advice for many experiments. We thank the members on the Xie lab for helpful discussions and comments in the course of the preparation with the manuscript. We are grateful for the sequencing core facility and Biocomputing facility at Tsinghua University. Funding This perform was supported by the National Natural Science Foundation of China (31471211, 31725018 to W.X. and 61773230 and 61721003 to X.W.), the National Essential R D System of China (2016YFC0900301 to W.X.), the National Fundamental Research Program of China (2015CB856201 to W.X.), plus the Tsinghua University-Peking IFN-beta Protein Purity & Documentation University (THU-PKU) Center for Life Sciences (W.X.). W.X. is really a Howard Hughes Medical Institute (HHMI) International Analysis Scholar. Availability of data and supplies All information happen to be deposited for the Gene Expression Omnibus (GEO) beneath accession number [GEO:GSE102753], offered at geo/query/acc.cgisirtuininhibitoracc=GSE102753 [84]. Authors’ contributions YL, HZ, and WX conceived the project. YL and HZ performed a lot of the experiments and bioinformatics analyses. QW MIF Protein Biological Activity helped create the Tet TKO mESCs. CZ, LW, XL, WZ, YZ, and ZD helped with many experiments or bioinformatics analyses. XW and WX supervised the project. YL, HZ, and WX wrote the manuscript. All authors study and approved the final manuscript. Ethics approval and consent to participate Not applicable. Consent for publication Not applicable. Competing interests The authors declare that they’ve no competing interests.Publisher’s NoteSpringer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Author details 1 Center for Stem Cell Biology and Regenerative Medicine, MOE Crucial Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, College of Life Sciences, Tsinghua University, Beijing 100084, China. 2Bioinformatics Division, TNLIST/MOE Essential Laboratory of Bioinformatics, Center for Synthetic and Program Biology, Department of Automation, Tsinghua University, Beijing 100084, China. Received: 13 November 2017 Accepted: 10 JanuaryAdditional filesAdditional file 1: Figure S1. A international survey of DMVs in mouse somatic tissues. Figure S2. DMVs are hotspots of transcription aspect binding web sites and show low levels of deamination mutation rates. Figure S3. Identification of 3 groups of DMVs. Figure S4. Polycomb is required for upkeep of hypomethylation in DMVs. Figure S5. DMVs show a compact self-interacting structure. Figure S6. Polycomb regulates DMV hypomethylation probably by way of TETs. (PDF 3380 kb) Extra file 2: Table S1. Summary of DMVs and related genes for each mouse tissue and early developmental stage. (XLSX 666 kb) Added file three: Table S2. List of orthologous DMV genes in human, mouse, and zebrafish. (XLS 26 kb)Abbreviations 4C: Circular chromosome conformation capture; ChIP: Chromatin immunoprecipitation; DMV: DNA methylation valley; DNMT: DNA methyltransferase; Eed: Embryonic ectoderm improvement; Ezh2: Enhancer.