Pioneer transcription factors are associated with the modulation of DNA methylation patterns across cancers

Jaenisch R, Bird A. Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat Genet. 2003;33(Suppl):245–54.

CAS  Article  Google Scholar 

Kouzarides T. Chromatin modifications and their function. Cell. 2007;128:693–705.

CAS  Article  Google Scholar 

Sood AJ, Viner C, Hoffman MM. DNAmod: the DNA modification database. J Cheminform. 2019;11:30.

Article  Google Scholar 

Breiling A, Lyko F. Epigenetic regulatory functions of DNA modifications: 5-methylcytosine and beyond. Epigenetics Chromatin. 2015;8:24.

Article  Google Scholar 

Curradi M, Izzo A, Badaracco G, Landsberger N. Molecular mechanisms of gene silencing mediated by DNA methylation. Mol Cell Biol. 2002;22:3157–73.

CAS  Article  Google Scholar 

Costello JF, Frühwald MC, Smiraglia DJ, Rush LJ, Robertson GP, Gao X, et al. Aberrant CpG-island methylation has non-random and tumour-type–specific patterns. Nat Genet Nat Publ Gr. 2000;24:132–8.

CAS  Article  Google Scholar 

Gebhard C, Benner C, Ehrich M, Schwarzfischer L, Schilling E, Klug M, et al. General transcription factor binding at CpG islands in normal cells correlates with resistance to de novo DNA methylation in cancer cells. Cancer Res. 2010;70:1398–407.

CAS  Article  Google Scholar 

Fleischer T, Tekpli X, Mathelier A, Wang S, Nebdal D, Dhakal HP, et al. DNA methylation at enhancers identifies distinct breast cancer lineages. Nat Commun. 2017;8:1379.

Article  Google Scholar 

Zhu H, Wang G, Qian J. Transcription factors as readers and effectors of DNA methylation. Nat Rev Genet. 2016;17:551–65.

CAS  Article  Google Scholar 

Rasmussen KD, Helin K. Role of TET enzymes in DNA methylation, development, and cancer. Genes Dev. 2016;30:733–50.

CAS  Article  Google Scholar 

Williams K, Christensen J, Pedersen MT, Johansen JV, Cloos PAC, Rappsilber J, et al. TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity. Nature. 2011;473:343–8.

CAS  Article  Google Scholar 

Laisné M, Gupta N, Kirsh O, Pradhan S, Defossez P-A. Mechanisms of DNA methyltransferase recruitment in mammals. Genes. 2018;9(12):617.

Article  Google Scholar 

Ginno PA, Gaidatzis D, Feldmann A, Hoerner L, Imanci D, Burger L, et al. A genome-scale map of DNA methylation turnover identifies site-specific dependencies of DNMT and TET activity. Nat Commun. 2020;11:2680.

CAS  Article  Google Scholar 

Lambert SA, Jolma A, Campitelli LF, Das PK, Yin Y, Albu M, et al. The human transcription factors. Cell. 2018;172:650–65.

CAS  Article  Google Scholar 

Reiter F, Wienerroither S, Stark A. Combinatorial function of transcription factors and cofactors. Curr Opin Genet Dev. 2017;43:73–81.

CAS  Article  Google Scholar 

Zaret KS, Carroll JS. Pioneer transcription factors: establishing competence for gene expression. Genes Dev. 2011;25:2227–41.

CAS  Article  Google Scholar 

Young RA. Control of the embryonic stem cell state. Cell. 2011;144:940–54.

CAS  Article  Google Scholar 

Jozwik KM, Carroll JS. Pioneer factors in hormone-dependent cancers. Nat Rev Cancer. 2012;12:381–5.

CAS  Article  Google Scholar 

Barnett KR, Decato BE, Scott TJ, Hansen TJ, Chen B, Attalla J, et al. ATAC-Me captures prolonged DNA methylation of dynamic chromatin accessibility loci during cell fate transitions. Mol Cell. 2020;77(6):1350–64.

CAS  Article  Google Scholar 

Di Croce L, Raker VA, Corsaro M, Fazi F, Fanelli M, Faretta M, et al. Methyltransferase recruitment and DNA hypermethylation of target promoters by an oncogenic transcription factor. Science. 2002;295:1079–82.

Article  Google Scholar 

de la Rica L, Rodríguez-Ubreva J, García M, Islam AB, Urquiza JM, Hernando H, et al. PU.1 target genes undergo Tet2-coupled demethylation and DNMT3b-mediated methylation in monocyte-to-osteoclast differentiation. Genome Biol. 2013;14:99.

Article  Google Scholar 

Suzuki T, Shimizu Y, Furuhata E, Maeda S, Kishima M, Nishimura H, et al. RUNX1 regulates site specificity of DNA demethylation by recruitment of DNA demethylation machineries in hematopoietic cells. Blood Adv. 2017;1:1699–711.

CAS  Article  Google Scholar 

Yang YA, Zhao JC, Fong K-W, Kim J, Li S, Song C, et al. FOXA1 potentiates lineage-specific enhancer activation through modulating TET1 expression and function. Nucleic Acids Res. 2016;44:8153–64.

CAS  Article  Google Scholar 

Suzuki T, Maeda S, Furuhata E, Shimizu Y, Nishimura H, Kishima M, et al. A screening system to identify transcription factors that induce binding site-directed DNA demethylation. Epigenetics Chromatin. 2017;10:60.

Article  Google Scholar 

Vanzan L, Soldati H, Ythier V, Anand S, Braun SMG, Francis N, et al. High throughput screening identifies SOX2 as a super pioneer factor that inhibits DNA methylation maintenance at its binding sites. Nat Commun. 2021;12:3337.

CAS  Article  Google Scholar 

Yao L, Shen H, Laird PW, Farnham PJ, Berman BP. Inferring regulatory element landscapes and transcription factor networks from cancer methylomes. Genome Biol. 2015;16:105.

Article  Google Scholar 

Rhie SK, Guo Y, Tak YG, Yao L, Shen H, Coetzee GA, et al. Identification of activated enhancers and linked transcription factors in breast, prostate, and kidney tumors by tracing enhancer networks using epigenetic traits. Epigenetics Chromatin. 2016;9:50.

Article  Google Scholar 

Cancer Genome Atlas Research Network, Weinstein JN, Collisson EA, Mills GB, Shaw KRM, Ozenberger BA, et al. The cancer genome Atlas Pan-Cancer analysis project. Nat Genet. 2013;45:1113–20.

Article  Google Scholar 

Gheorghe M, Sandve GK, Khan A, Chèneby J, Ballester B, Mathelier A. A map of direct TF-DNA interactions in the human genome. Nucleic Acids Res. 2019;4:e21.

Article  Google Scholar 

Sandoval J, Heyn H, Moran S, Serra-Musach J, Pujana MA, Bibikova M, et al. Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome. Epigenetics. 2011;6:692–702.

CAS  Article  Google Scholar 

Puig RR, Boddie P, Khan A, Castro-Mondragon JA, Mathelier A. UniBind: maps of high-confidence direct TF-DNA interactions across nine species. BMC Genomics. 2021;22:482.

CAS  Article  Google Scholar 

Jones PA, Baylin SB. The epigenomics of cancer. Cell. 2007;128:683–92.

CAS  Article  Google Scholar 

Iwafuchi-Doi M, Zaret KS. Pioneer transcription factors in cell reprogramming. Genes Dev. 2014;28:2679–92.

Article  Google Scholar 

Dobersch S, Rubio K, Barreto G. Pioneer factors and architectural proteins mediating embryonic expression signatures in cancer. Trends Mol Med. 2019;25:287–302.

CAS  Article  Google Scholar 

Vernimmen D, Bickmore WA. The hierarchy of transcriptional activation: from enhancer to promoter. Trends Genet. 2015;31:696–708.

CAS  Article  Google Scholar 

Fuglerud BM, Lemma RB, Wanichawan P, Sundaram AYM, Eskeland R, Gabrielsen OS. A c-Myb mutant causes deregulated differentiation due to impaired histone binding and abrogated pioneer factor function. Nucleic Acids Res. 2017;45:7681–96.

CAS  Article  Google Scholar 

Hoogenkamp M, Lichtinger M, Krysinska H, Lancrin C, Clarke D, Williamson A, et al. Early chromatin unfolding by RUNX1: a molecular explanation for differential requirements during specification versus maintenance of the hematopoietic gene expression program. Blood. 2009;114:299–309.

CAS  Article  Google Scholar 

Wang D, Diao H, Getzler AJ, Rogal W, Frederick MA, Milner J, et al. The transcription factor Runx3 establishes chromatin accessibility of cis-regulatory landscapes that drive memory cytotoxic T lymphocyte formation. Immunity. 2018;48:659-74 e6.

CAS  Article  Google Scholar 

Lee J-W, Kim D-M, Jang J-W, Park T-G, Song S-H, Lee Y-S, et al. RUNX3 regulates cell cycle-dependent chromatin dynamics by functioning as a pioneer factor of the restriction-point. Nat Commun. 2019;10:1897.

Article  Google Scholar 

Riggi N, Knoechel B, Gillespie SM, Rheinbay E, Boulay G, Suvà ML, et al. EWS-FLI1 utilizes divergent chromatin remodeling mechanisms to directly activate or repress enhancer elements in Ewing sarcoma. Cancer Cell. 2014;26:668–81.

CAS  Article  Google Scholar 

Pang Z-Y, Wei Y-T, Shang M-Y, Li S, Li Y, Jin Q-X, et al. Leptin-elicited PBX3 confers letrozole resistance in breast cancer. Endocr Relat Cancer. 2021;28(3):173–89.

CAS  Article  Google Scholar 

Plachetka A, Chayka O, Wilczek C, Melnik S, Bonifer C, Klempnauer K-H. C/EBPbeta induces chromatin opening at a cell- type-specific enhancer. Mol Cell Biol. 2008;28:2102–12.

CAS  Article  Google Scholar 

Corces MR, Granja JM, Shams S, Louie BH, Seoane JA, Zhou W, et al. The chromatin accessibility landscape of primary human cancers. Science. 2018;362(6413):eaav1898.

Article  Google Scholar 

Baek S, Goldstein I, Hager GL. Bivariate genomic footprinting detects changes in transcription factor activity. Cell Rep. 2017;19:1710–22.

CAS  Article  Google Scholar 

Brandeis M, Frank D, Keshet I, Siegfried Z, Mendelsohn M, Names A, et al. Spl elements protect a CpG island from de novo methylation. Nature. 1994;371:435–8.

CAS  Article  Google Scholar 

Macleod D, Charlton J, Mullins J, Bird AP. Sp1 sites in the mouse aprt gene promoter are required to prevent methylation of the CpG island. Genes Dev. 1994;8:2282–92.

CAS  Article  Google Scholar 

Pant V, Mariano P, Kanduri C, Mattsson A. The nucleotides responsible for the direct physical contact between the chromatin insulator protein CTCF and the H19 imprinting control region manifest parent of origin-specific long-distance insulation and methylation-free domains. Genes Dev. 2003;17(5):586–90.

CAS  Article  Google Scholar 

Schmidt F, Marx A, Baumgarten N, Hebel M, Wegner M, Kaulich M, et al. Integrative analysis of epigenetics data identifies gene-specific regulatory elements. Nucleic Acids Res. 2021;49:10397–418.

CAS  Article  Google Scholar 

Liberzon A, Birger C, Thorvaldsdóttir H, Ghandi M, Mesirov JP, Tamayo P. The molecular signatures database (MSigDB) hallmark gene set collection. Cell Syst. 2015;1:417–25.

CAS  Article  Google Scholar 

Iwafuchi-Doi M, Zaret KS. Cell fate control by pioneer transcription factors. Development. 2016;143:1833–7.

CAS  Article 

留言 (0)

沒有登入
gif