PMID- 30058478 OWN - NLM STAT- MEDLINE DCOM- 20190308 LR - 20211204 IS - 1559-2308 (Electronic) IS - 1559-2294 (Print) IS - 1559-2294 (Linking) VI - 13 IP - 7 DP - 2018 TI - Analysis of KLF4 regulated genes in cancer cells reveals a role of DNA methylation in promoter- enhancer interactions. PG - 751-768 LID - 10.1080/15592294.2018.1504592 [doi] AB - Recent studies have revealed an unexpected role of DNA methylation at promoter regions in transcription activation. However, whether DNA methylation at enhancer regions activates gene expression and influences cellular functions remains to be determined. In this study, by employing the transcription factor krUppel-like factor 4 (KLF4) that binds to methylated CpGs (mCpGs), we investigated the molecular outcomes of the recruitment of KLF4 to mCpGs at enhancer regions in human glioblastoma cells. First, by integrating KLF4 ChIP-seq, whole-genome bisulfite sequence, and H3K27ac ChIP-seq datasets, we found 1,299 highly methylated (beta >0.5) KLF4 binding sites, three-quarters of which were located at putative enhancer regions, including gene bodies and intergenic regions. In the meantime, by proteomics, we identified 16 proteins as putative targets upregulated by KLF4-mCpG binding at enhancer regions. By chromosome conformation capture (3C) analysis, we demonstrated that KLF4 bound to methylated CpGs at the enhancer regions of the B-cell lymphocyte kinase (BLK) and Lim domain only protein 7 (LMO7) genes, and activated their expression via 3D chromatin loop formation with their promoter regions. Expression of mutant KLF4, which lacks KLF4 ability to bind methylated DNA, or removal of DNA methylation in enhancer regions by a DNA methyltransferase inhibitor abolished chromatin loop formation and gene expression, suggesting the essential role of DNA methylation in enhancer-promoter interactions. Finally, we performed functional assays and showed that BLK was involved in glioblastoma cell migration. Together, our study established the concept that DNA methylation at enhancer regions interacts with transcription factors to activate gene expression and influence cellular functions. FAU - Oyinlade, Olutobi AU - Oyinlade O AD - a Hugo W. Moser Research Institute at Kennedy Krieger , Baltimore , Maryland , USA. AD - b Department of Pharmacology and Molecular Sciences , Johns Hopkins School of Medicine, Johns Hopkins University , Baltimore , Maryland , USA. FAU - Wei, Shuang AU - Wei S AD - a Hugo W. Moser Research Institute at Kennedy Krieger , Baltimore , Maryland , USA. AD - c Department of Neurology , Johns Hopkins School of Medicine, Johns Hopkins University , Baltimore , Maryland , USA. AD - g Department of Respiratory and Critical Care Medicine, Tongji Hospital , Tongji Medical College Huazhong University of Science and Technology , Wuhan , China. FAU - Kammers, Kai AU - Kammers K AD - d Division of Biostatistics and Bioinformatics,Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine , Johns Hopkins University , Baltimore , Maryland , USA. FAU - Liu, Sheng AU - Liu S AD - i Department of Medical and Molecular Genetics , Indiana University School of Medicine , Indianapolis , IN , USA. FAU - Wang, Shuyan AU - Wang S AD - a Hugo W. Moser Research Institute at Kennedy Krieger , Baltimore , Maryland , USA. AD - c Department of Neurology , Johns Hopkins School of Medicine, Johns Hopkins University , Baltimore , Maryland , USA. FAU - Ma, Ding AU - Ma D AD - a Hugo W. Moser Research Institute at Kennedy Krieger , Baltimore , Maryland , USA. AD - c Department of Neurology , Johns Hopkins School of Medicine, Johns Hopkins University , Baltimore , Maryland , USA. FAU - Huang, Zhi-Yong AU - Huang ZY AD - h Department of General Surgery, Tongji Hospital , Tongji Medical College Huazhong University of Science and Technology , Wuhan , China. FAU - Qian, Jiang AU - Qian J AD - e Wilmer Eye Institute,Johns Hopkins School of Medicine , Johns Hopkins University , Baltimore , Maryland , USA. FAU - Zhu, Heng AU - Zhu H AD - b Department of Pharmacology and Molecular Sciences , Johns Hopkins School of Medicine, Johns Hopkins University , Baltimore , Maryland , USA. AD - f Center for High Throughput Biology, Johns Hopkins School of Medicine , Johns Hopkins University , Baltimore , Maryland , USA. FAU - Wan, Jun AU - Wan J AD - i Department of Medical and Molecular Genetics , Indiana University School of Medicine , Indianapolis , IN , USA. AD - j Center for Computational Biology and Bioinformatics , Indiana University School of Medicine , Indianapolis , IN , USA. FAU - Xia, Shuli AU - Xia S AUID- ORCID: 0000-0001-5849-6967 AD - a Hugo W. Moser Research Institute at Kennedy Krieger , Baltimore , Maryland , USA. AD - c Department of Neurology , Johns Hopkins School of Medicine, Johns Hopkins University , Baltimore , Maryland , USA. LA - eng GR - R33 CA186790/CA/NCI NIH HHS/United States GR - U54 HG006434/HG/NHGRI NIH HHS/United States GR - R01 NS091165/NS/NINDS NIH HHS/United States GR - U24 CA160036/CA/NCI NIH HHS/United States GR - T32 GM007445/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20180825 PL - United States TA - Epigenetics JT - Epigenetics JID - 101265293 RN - 0 (KLF4 protein, human) RN - 0 (Kruppel-Like Factor 4) RN - 0 (Kruppel-Like Transcription Factors) RN - 0 (LIM Domain Proteins) RN - 0 (LMO7 protein, human) RN - 0 (Transcription Factors) RN - EC 2.7.10.2 (BLK protein, human) RN - EC 2.7.10.2 (src-Family Kinases) SB - IM MH - Cell Movement MH - CpG Islands MH - *DNA Methylation MH - *Enhancer Elements, Genetic MH - *Gene Expression Regulation, Neoplastic MH - Glioblastoma/genetics/metabolism/*pathology MH - Humans MH - Kruppel-Like Factor 4 MH - Kruppel-Like Transcription Factors/genetics/*metabolism MH - LIM Domain Proteins/genetics/metabolism MH - Promoter Regions, Genetic MH - Transcription Factors/genetics/metabolism MH - Tumor Cells, Cultured MH - src-Family Kinases/genetics/metabolism PMC - PMC6224223 OTO - NOTNLM OT - B-cell lymphocyte kinase OT - Chromosome conformation capture OT - KrUppel-like factor 4 (KLF4) OT - enhancer OT - methylated DNA EDAT- 2018/07/31 06:00 MHDA- 2019/03/09 06:00 PMCR- 2019/08/25 CRDT- 2018/07/31 06:00 PHST- 2018/07/31 06:00 [pubmed] PHST- 2019/03/09 06:00 [medline] PHST- 2018/07/31 06:00 [entrez] PHST- 2019/08/25 00:00 [pmc-release] AID - 1504592 [pii] AID - 10.1080/15592294.2018.1504592 [doi] PST - ppublish SO - Epigenetics. 2018;13(7):751-768. doi: 10.1080/15592294.2018.1504592. Epub 2018 Aug 25.