Identification of critical base pairs required for CTCF binding in motif M1 and M2

References

[1] BainDL, YangQ, ConnaghanKD, RobbleeJP, MiuraMT, DegalaGD, LambertJR, MalufNK (2012) Glucocorticoid receptor-DNA interactions: binding energetics are the primary determinant of sequence-specific transcriptional activity. J Mol Biol422: 18–32

[2] FilippovaGN, QiCF, UlmerJE, MooreJM, WardMD, HuYJ, LoukinovDI, PugachevaEM, KlenovaEM, GrundyPE(2002) Tumor-associated zinc finger mutations in the CTCF transcription factor selectively alter tts DNA-binding specificity. Cancer Res62:48–52

[3] KandothC, SchultzN, CherniackAD, AkbaniR, LiuY, ShenH, RobertsonAG, PashtanI, ShenR, BenzCC(2013) Integrated genomic characterization of endometrial carcinoma. Nature497:67–73

[4] KimTH, AbdullaevZK, SmithAD, ChingKA, LoukinovDI, GreenRD, ZhangMQ, LobanenkovVV, RenB (2007) Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell128:1231–1245

[5] LobanenkovVV, NicolasRH, AdlerVV, PatersonH, KlenovaEM, PolotskajaAV, GoodwinGH (1990) A novel sequence-specific DNA binding protein which interacts with three regularly spaced direct repeats of the CCCTC-motif in the 5’-flanking sequence of the chicken c-myc gene. Oncogene5:1743–1753

[6] MullighanCG, ZhangJ, KasperLH, LerachS, Payne-TurnerD, PhillipsLA, HeatleySL, HolmfeldtL, Collins-UnderwoodJR, MaJ (2011) CREBBP mutations in relapsed acute lymphoblastic leukaemia. Nature471:235–239

[7] OhlssonR, RenkawitzR, LobanenkovV (2001) CTCF is a uniquely versatile transcription regulator linked to epigenetics and disease. Trends Genet17:520–527

[8] PersikovAV, SinghM (2014) De novo prediction of DNA-binding specificities for Cys2His2 zinc finger proteins. Nucleic Acids Res42:97–108

[9] PhillipsJE, CorcesVG (2009) CTCF: master weaver of the genome. Cell137:1194–1211

[10] RaskoJE, KlenovaEM, LeonJ, FilippovaGN, LoukinovDI, VatolinS, RobinsonAF, HuYJ, UlmerJ, WardMD (2001) Cell growth inhibition by the multifunctional multivalent zinc-finger factor CTCF. Cancer Res61:6002–6007

[11] RendaM, BaglivoI, Burgess-BeusseB, EspositoS, FattorussoR, FelsenfeldG, PedonePV (2007) Critical DNA binding interactions of the insulator protein CTCF: a small number of zinc fingers mediate strong binding, and a single finger-DNA interaction controls binding at imprinted loci. J Biol Chem282:33336–33345

[12] SchmidtD, SchwaliePC, WilsonMD, BallesterB, GoncalvesA, KutterC, BrownGD, MarshallA, FlicekP, OdomDT (2012) Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages. Cell148:335–348

[13] TangZ, LuoOJ, LiX, ZhengM, ZhuJJ, SzalajP, TrzaskomaP, MagalskaA, WlodarczykJ, RuszczyckiB (2015) CTCFmediated human 3D genome architecture reveals chromatin topology for transcription. Cell163:1611–1627

[14] XiaoT, WongtrakoongateP, TrainorC, FelsenfeldG (2015) CTCF recruits centromeric protein CENP-E to the pericentromeric/centromeric regions of chromosomes through unusual CTCF-binding sites. Cell Rep12:1704–1714

[15] YaoH, BrickK, EvrardY, XiaoT, Camerini-OteroRD, FelsenfeldG (2010) Mediation of CTCF transcriptional insulation by DEAD-box RNA-binding protein p68 and steroid receptor RNA activator SRA. Genes Dev24:2543–2555

RIGHTS & PERMISSIONS

2017 The Author(s) 2017. This article is published with open access at Springerlink.com and journal.hep.com.cn