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Research Paper

Analysis of KLF4 regulated genes in cancer cells reveals a role of DNA methylation in promoter- enhancer interactions

, , , , , , , , , & ORCID Icon show all
Pages 751-768 | Received 27 Feb 2018, Accepted 16 Jul 2018, Published online: 25 Aug 2018

References

  • Vogelstein B, Papadopoulos N, Velculescu VE, et al. Cancer genome landscapes. Science. 2013;339:1546–1558.
  • Quick A, Patel D, Hadziahmetovic M, et al. Current therapeutic paradigms in glioblastoma. Rev Recent Clin Trials. 2010;5:14–27.
  • Bird A. DNA methylation patterns and epigenetic memory. Genes Dev. 2002;16:6–21.
  • Jones PA. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet. 2012;13:484–492.
  • Nan X, Cross S, Bird A. Gene silencing by methyl-CpG-binding proteins. Novartis Found Symp. 1998;214:6–16. discussion 16–21, 46–50.
  • Filion GJ, Zhenilo S, Salozhin S, et al. A family of human zinc finger proteins that bind methylated DNA and repress transcription. Mol Cell Biol. 2006;26:169–181.
  • Mann IK, Chatterjee R, Zhao J, et al. CG methylated microarrays identify a novel methylated sequence bound by the CEBPB|ATF4 heterodimer that is active in vivo. Genome Res. 2013;23:988–997.
  • Spruijt CG, Gnerlich F, Smits AH, et al. Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives. Cell. 2013;152:1146–1159.
  • Yin Y, Morgunova E, Jolma A, et al. Impact of cytosine methylation on DNA binding specificities of human transcription factors. Science. 2017;356.
  • Hu S, Wan J, Su Y, et al. DNA methylation presents distinct binding sites for human transcription factors. Elife. 2013;2:e00726.
  • Wan J, Su Y, Song Q, et al. Methylated cis-regulatory elements mediate KLF4-dependent gene transactivation and cell migration. Elife. 2017;6.
  • Dymecki SM, Niederhuber JE. Desiderio SV Specific expression of a tyrosine kinase gene, blk, in B lymphoid cells. Science. 1990;247:332–336.
  • Wu YY, Georg I, Diaz-Barreiro A, et al. Concordance of increased B1 cell subset and lupus phenotypes in mice and humans is dependent on BLK expression levels. J Immunol. 2015;194:5692–5702.
  • Bartolome RA, Diaz-Martinez M, Colo GP, et al. A Blk-p190RhoGAP signaling module downstream of activated Galpha13 functionally opposes CXCL12-stimulated RhoA activation and cell invasion. Cell Signal. 2014;26:2551–2561.
  • Goodwin CR, Lal B, Ho S, et al. PTEN reconstitution alters glioma responses to c-Met pathway inhibition. Anticancer Drugs. 2011;22:905–912.
  • Li Y, Fan X, Goodwin CR, et al. Hepatocyte growth factor enhances death receptor-induced apoptosis by up-regulating DR5. BMC Cancer. 2008;8:325.
  • Herbrich SM, Cole RN, West KP Jr., et al. Statistical inference from multiple iTRAQ experiments without using common reference standards. J Proteome Res. 2013;12:594–604.
  • Kammers K, Cole RN, Tiengwe C, et al. Detecting Significant Changes in Protein Abundance. EuPA Open Proteom. 2015;7:11–19.
  • Smyth GK. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol. 2004;3:Article3.
  • Ying M, Sang Y, Li Y, et al. Kruppel-like family of transcription factor 9, a differentiation-associated transcription factor, suppresses Notch1 signaling and inhibits glioblastoma-initiating stem cells. Stem Cells. 2011;29:20–31.
  • Woodard CL, Goodwin CR, Wan J, et al. Profiling the dynamics of a human phosphorylome reveals new components in HGF/c-Met signaling. PLoS One. 2013;8:e72671.
  • Wu Y, Richard JP, Wang SD, et al. Regulation of glioblastoma multiforme stem-like cells by inhibitor of DNA binding proteins and oligodendroglial lineage-associated transcription factors. Cancer Sci. 2012;103:1028–1037.
  • Sun P, Xia S, Lal B, et al. Lipid metabolism enzyme ACSVL3 supports glioblastoma stem cell maintenance and tumorigenicity. BMC Cancer. 2014;14:401.
  • Splinter E, De Wit E, Van De Werken HJ, et al. Determining long-range chromatin interactions for selected genomic sites using 4C-seq technology: from fixation to computation. Methods. 2012;58:221–230.
  • Xia S, Lal B, Tung B, et al. Tumor microenvironment tenascin-C promotes glioblastoma invasion and negatively regulates tumor proliferation. Neuro Oncol. 2016; 18:507-517
  • Christman JK. 5-Azacytidine and 5-aza-2ʹ-deoxycytidine as inhibitors of DNA methylation: mechanistic studies and their implications for cancer therapy. Oncogene. 2002;21:5483–5495.
  • Charlet J, Duymich CE, Lay FD, et al. Bivalent Regions of Cytosine Methylation and H3K27 Acetylation Suggest an Active Role for DNA Methylation at Enhancers. Mol Cell. 2016;62:422–431.
  • Rishi V, Bhattacharya P, Chatterjee R, et al. CpG methylation of half-CRE sequences creates C/EBPalpha binding sites that activate some tissue-specific genes. Proc Natl Acad Sci U S A. 2010;107:20311–20316.
  • Sasai N, Nakao M. Defossez PA Sequence-specific recognition of methylated DNA by human zinc-finger proteins. Nucleic Acids Res. 2010;38:5015–5022.
  • Serra RW, Fang MG, Park SM, et al. A KRAS-directed transcriptional silencing pathway that mediates the CpG island methylator phenotype. Elife. 2014;3.
  • Spruijt CG. Vermeulen M DNA methylation: old dog. New Tricks? Nat Struct Mol Biol. 2014;21:949–954.
  • Gao T, He B, Liu S, et al. EnhancerAtlas: a resource for enhancer annotation and analysis in 105 human cell/tissue types. Bioinformatics. 2016;32:3543–3551.
  • Li YQ, Li A, Glas M, et al. c-Met signaling induces a reprogramming network and supports the glioblastoma stem-like phenotype. Proc Natl Acad Sci USA. 2011;108:9951–9956.
  • Esteller M. Epigenetic gene silencing in cancer: the DNA hypermethylome. Hum Mol Genet. 2007;16(Spec No 1):R50–59.
  • Martinez R. Esteller M The DNA methylome of glioblastoma multiforme. Neurobiol Dis. 2010;39:40–46.
  • Waha A, Guntner S, Huang TH, et al. Epigenetic silencing of the protocadherin family member PCDH-gamma-A11 in astrocytomas. Neoplasia. 2005;7:193–199.
  • Hu Q, Guo C, Li Y, et al. LMO7 mediates cell-specific activation of the Rho-myocardin-related transcription factor-serum response factor pathway and plays an important role in breast cancer cell migration. Mol Cell Biol. 2011;31:3223–3240.
  • Liu Y, Olanrewaju YO, Zheng Y, et al. Structural basis for Klf4 recognition of methylated DNA. Nucleic Acids Res. 2014;42:4859–4867.
  • Shields JM. Yang VW Identification of the DNA sequence that interacts with the gut-enriched Kruppel-like factor. Nucleic Acids Res. 1998;26:796–802.
  • Evans PM. and Liu C Roles of Krupel-like factor 4 in normal homeostasis, cancer and stem cells. Acta Biochim Biophys Sin (Shanghai). 2008;40:554–564.

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