On how mammalian transcription factors recognize methylated DNA

References

• Reik W. Stability and flexibility of epigenetic gene regulation in mammalian development. Nature 2007; 447:425 - 32; http://dx.doi.org/10.1038/nature05918; PMID: 17522676
   PubMed Web of Science ®Google Scholar
• Suzuki MM, Bird A. DNA methylation landscapes: provocative insights from epigenomics. Nat Rev Genet 2008; 9:465 - 76; http://dx.doi.org/10.1038/nrg2341; PMID: 18463664
   PubMed Web of Science ®Google Scholar
• Lister R, Ecker JR. Finding the fifth base: genome-wide sequencing of cytosine methylation. Genome Res 2009; 19:959 - 66; http://dx.doi.org/10.1101/gr.083451.108; PMID: 19273618
   PubMed Web of Science ®Google Scholar
• Li E. Chromatin modification and epigenetic reprogramming in mammalian development. Nat Rev Genet 2002; 3:662 - 73; http://dx.doi.org/10.1038/nrg887; PMID: 12209141
   PubMed Web of Science ®Google Scholar
• Stadler MB, Murr R, Burger L, Ivanek R, Lienert F, Schöler A, et al. DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature 2011; 480:490 - 5; PMID: 22170606
   PubMed Web of Science ®Google Scholar
• Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 2009; 462:315 - 22; http://dx.doi.org/10.1038/nature08514; PMID: 19829295
   PubMed Web of Science ®Google Scholar
• Boyle P, Clement K, Gu H, Smith ZD, Ziller M, Fostel JL, et al. Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling. Genome Biol 2012; 13:R92; http://dx.doi.org/10.1186/gb-2012-13-10-r92; PMID: 23034176
   PubMed Web of Science ®Google Scholar
• Irizarry RA, Ladd-Acosta C, Carvalho B, Wu H, Brandenburg SA, Jeddeloh JA, et al. Comprehensive high-throughput arrays for relative methylation (CHARM). Genome Res 2008; 18:780 - 90; http://dx.doi.org/10.1101/gr.7301508; PMID: 18316654
   PubMed Web of Science ®Google Scholar
• Landan G, Cohen NM, Mukamel Z, Bar A, Molchadsky A, Brosh R, et al. Epigenetic polymorphism and the stochastic formation of differentially methylated regions in normal and cancerous tissues. Nat Genet 2012; 44:1207 - 14; http://dx.doi.org/10.1038/ng.2442; PMID: 23064413
   PubMed Web of Science ®Google Scholar
• Jones PA. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet 2012; 13:484 - 92; http://dx.doi.org/10.1038/nrg3230; PMID: 22641018
   PubMed Web of Science ®Google Scholar
• Shukla S, Kavak E, Gregory M, Imashimizu M, Shutinoski B, Kashlev M, et al. CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing. Nature 2011; 479:74 - 9; http://dx.doi.org/10.1038/nature10442; PMID: 21964334
   PubMed Web of Science ®Google Scholar
• Klose RJ, Bird AP. Genomic DNA methylation: the mark and its mediators. Trends Biochem Sci 2006; 31:89 - 97; http://dx.doi.org/10.1016/j.tibs.2005.12.008; PMID: 16403636
   PubMed Web of Science ®Google Scholar
• Lewis JD, Meehan RR, Henzel WJ, Maurer-Fogy I, Jeppesen P, Klein F, et al. Purification, sequence, and cellular localization of a novel chromosomal protein that binds to methylated DNA. Cell 1992; 69:905 - 14; http://dx.doi.org/10.1016/0092-8674(92)90610-O; PMID: 1606614
   PubMed Web of Science ®Google Scholar
• Hendrich B, Bird A. Identification and characterization of a family of mammalian methyl-CpG binding proteins. Mol Cell Biol 1998; 18:6538 - 47; PMID: 9774669
   PubMed Web of Science ®Google Scholar
• Laget S, Joulie M, Le Masson F, Sasai N, Christians E, Pradhan S, et al. The human proteins MBD5 and MBD6 associate with heterochromatin but they do not bind methylated DNA. PLoS One 2010; 5:e11982; http://dx.doi.org/10.1371/journal.pone.0011982; PMID: 20700456
   PubMed Web of Science ®Google Scholar
• Ohki I, Shimotake N, Fujita N, Jee J, Ikegami T, Nakao M, et al. Solution structure of the methyl-CpG binding domain of human MBD1 in complex with methylated DNA. Cell 2001; 105:487 - 97; http://dx.doi.org/10.1016/S0092-8674(01)00324-5; PMID: 11371345
   PubMed Web of Science ®Google Scholar
• Scarsdale JN, Webb HD, Ginder GD, Williams DC Jr.. Solution structure and dynamic analysis of chicken MBD2 methyl binding domain bound to a target-methylated DNA sequence. Nucleic Acids Res 2011; 39:6741 - 52; http://dx.doi.org/10.1093/nar/gkr262; PMID: 21531701
   PubMed Web of Science ®Google Scholar
• Ho KL, McNae IW, Schmiedeberg L, Klose RJ, Bird AP, Walkinshaw MD. MeCP2 binding to DNA depends upon hydration at methyl-CpG. Mol Cell 2008; 29:525 - 31; http://dx.doi.org/10.1016/j.molcel.2007.12.028; PMID: 18313390
   PubMed Web of Science ®Google Scholar
• Klose RJ, Sarraf SA, Schmiedeberg L, McDermott SM, Stancheva I, Bird AP. DNA binding selectivity of MeCP2 due to a requirement for A/T sequences adjacent to methyl-CpG. Mol Cell 2005; 19:667 - 78; http://dx.doi.org/10.1016/j.molcel.2005.07.021; PMID: 16137622
   PubMed Web of Science ®Google Scholar
• Clouaire T, de Las Heras JI, Merusi C, Stancheva I. Recruitment of MBD1 to target genes requires sequence-specific interaction of the MBD domain with methylated DNA. Nucleic Acids Res 2010; 38:4620 - 34; http://dx.doi.org/10.1093/nar/gkq228; PMID: 20378711
   PubMed Web of Science ®Google Scholar
• Unoki M, Nishidate T, Nakamura Y. ICBP90, an E2F-1 target, recruits HDAC1 and binds to methyl-CpG through its SRA domain. Oncogene 2004; 23:7601 - 10; http://dx.doi.org/10.1038/sj.onc.1208053; PMID: 15361834
   PubMed Web of Science ®Google Scholar
• Bostick M, Kim JK, Estève PO, Clark A, Pradhan S, Jacobsen SE. UHRF1 plays a role in maintaining DNA methylation in mammalian cells. Science 2007; 317:1760 - 4; http://dx.doi.org/10.1126/science.1147939; PMID: 17673620
   PubMed Web of Science ®Google Scholar
• Sharif J, Muto M, Takebayashi S, Suetake I, Iwamatsu A, Endo TA, et al. The SRA protein Np95 mediates epigenetic inheritance by recruiting Dnmt1 to methylated DNA. Nature 2007; 450:908 - 12; http://dx.doi.org/10.1038/nature06397; PMID: 17994007
   PubMed Web of Science ®Google Scholar
• Arita K, Ariyoshi M, Tochio H, Nakamura Y, Shirakawa M. Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism. Nature 2008; 455:818 - 21; http://dx.doi.org/10.1038/nature07249; PMID: 18772891
   PubMed Web of Science ®Google Scholar
• Avvakumov GV, Walker JR, Xue S, Li Y, Duan S, Bronner C, et al. Structural basis for recognition of hemi-methylated DNA by the SRA domain of human UHRF1. Nature 2008; 455:822 - 5; http://dx.doi.org/10.1038/nature07273; PMID: 18772889
   PubMed Web of Science ®Google Scholar
• Hashimoto H, Horton JR, Zhang X, Bostick M, Jacobsen SE, Cheng X. The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix. Nature 2008; 455:826 - 9; http://dx.doi.org/10.1038/nature07280; PMID: 18772888
   PubMed Web of Science ®Google Scholar
• Song J, Teplova M, Ishibe-Murakami S, Patel DJ. Structure-based mechanistic insights into DNMT1-mediated maintenance DNA methylation. Science 2012; 335:709 - 12; http://dx.doi.org/10.1126/science.1214453; PMID: 22323818
   PubMed Web of Science ®Google Scholar
• Prokhortchouk A, Hendrich B, Jørgensen H, Ruzov A, Wilm M, Georgiev G, et al. The p120 catenin partner Kaiso is a DNA methylation-dependent transcriptional repressor. Genes Dev 2001; 15:1613 - 8; http://dx.doi.org/10.1101/gad.198501; PMID: 11445535
   PubMed Web of Science ®Google Scholar
• Daniel JM, Spring CM, Crawford HC, Reynolds AB, Baig A. The p120(ctn)-binding partner Kaiso is a bi-modal DNA-binding protein that recognizes both a sequence-specific consensus and methylated CpG dinucleotides. Nucleic Acids Res 2002; 30:2911 - 9; http://dx.doi.org/10.1093/nar/gkf398; PMID: 12087177
   PubMed Web of Science ®Google Scholar
• Sasai N, Defossez PA. Many paths to one goal? The proteins that recognize methylated DNA in eukaryotes. Int J Dev Biol 2009; 53:323 - 34; http://dx.doi.org/10.1387/ijdb.082652ns; PMID: 19412889
   PubMed Web of Science ®Google Scholar
• Filion GJ, Zhenilo S, Salozhin S, Yamada D, Prokhortchouk E, Defossez PA. A family of human zinc finger proteins that bind methylated DNA and repress transcription. Mol Cell Biol 2006; 26:169 - 81; http://dx.doi.org/10.1128/MCB.26.1.169-181.2006; PMID: 16354688
   PubMed Web of Science ®Google Scholar
• Sasai N, Nakao M, Defossez PA. Sequence-specific recognition of methylated DNA by human zinc-finger proteins. Nucleic Acids Res 2010; 38:5015 - 22; http://dx.doi.org/10.1093/nar/gkq280; PMID: 20403812
   PubMed Web of Science ®Google Scholar
• Quenneville S, Verde G, Corsinotti A, Kapopoulou A, Jakobsson J, Offner S, et al. In embryonic stem cells, ZFP57/KAP1 recognize a methylated hexanucleotide to affect chromatin and DNA methylation of imprinting control regions. Mol Cell 2011; 44:361 - 72; http://dx.doi.org/10.1016/j.molcel.2011.08.032; PMID: 22055183
   PubMed Web of Science ®Google Scholar
• Liu Y, Toh H, Sasaki H, Zhang X, Cheng X. An atomic model of Zfp57 recognition of CpG methylation within a specific DNA sequence. Genes Dev 2012; 26:2374 - 9; http://dx.doi.org/10.1101/gad.202200.112; PMID: 23059534
   PubMed Web of Science ®Google Scholar
• Buck-Koehntop BA, Stanfield RL, Ekiert DC, Martinez-Yamout MA, Dyson HJ, Wilson IA, et al. Molecular basis for recognition of methylated and specific DNA sequences by the zinc finger protein Kaiso. Proc Natl Acad Sci U S A 2012; 109:15229 - 34; http://dx.doi.org/10.1073/pnas.1213726109; PMID: 22949637
   PubMed Web of Science ®Google Scholar
• Vaquerizas JM, Kummerfeld SK, Teichmann SA, Luscombe NM. A census of human transcription factors: function, expression and evolution. Nat Rev Genet 2009; 10:252 - 63; http://dx.doi.org/10.1038/nrg2538; PMID: 19274049
   PubMed Web of Science ®Google Scholar
• Emerson RO, Thomas JH. Adaptive evolution in zinc finger transcription factors. PLoS Genet 2009; 5:e1000325; http://dx.doi.org/10.1371/journal.pgen.1000325; PMID: 19119423
   PubMed Web of Science ®Google Scholar
• Bartels SJ, Spruijt CG, Brinkman AB, Jansen PW, Vermeulen M, Stunnenberg HG. A SILAC-based screen for Methyl-CpG binding proteins identifies RBP-J as a DNA methylation and sequence-specific binding protein. PLoS One 2011; 6:e25884; http://dx.doi.org/10.1371/journal.pone.0025884; PMID: 21991380
   PubMedGoogle Scholar
• Isalan M, Choo Y. Engineered zinc finger proteins that respond to DNA modification by HaeIII and HhaI methyltransferase enzymes. J Mol Biol 2000; 295:471 - 7; http://dx.doi.org/10.1006/jmbi.1999.3366; PMID: 10623539
   PubMed Web of Science ®Google Scholar
• Brinkman AB, Gu H, Bartels SJ, Zhang Y, Matarese F, Simmer F, et al. Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk. Genome Res 2012; 22:1128 - 38; http://dx.doi.org/10.1101/gr.133728.111; PMID: 22466170
   PubMed Web of Science ®Google Scholar
• Prokhortchouk A, Sansom O, Selfridge J, Caballero IM, Salozhin S, Aithozhina D, et al. Kaiso-deficient mice show resistance to intestinal cancer. Mol Cell Biol 2006; 26:199 - 208; http://dx.doi.org/10.1128/MCB.26.1.199-208.2006; PMID: 16354691
   PubMed Web of Science ®Google Scholar
• Li X, Ito M, Zhou F, Youngson N, Zuo X, Leder P, et al. A maternal-zygotic effect gene, Zfp57, maintains both maternal and paternal imprints. Dev Cell 2008; 15:547 - 57; http://dx.doi.org/10.1016/j.devcel.2008.08.014; PMID: 18854139
   PubMed Web of Science ®Google Scholar
• Wu SC, Zhang Y. Active DNA demethylation: many roads lead to Rome. Nat Rev Mol Cell Biol 2010; 11:607 - 20; http://dx.doi.org/10.1038/nrm2950; PMID: 20683471
   PubMed Web of Science ®Google Scholar
• Frauer C, Hoffmann T, Bultmann S, Casa V, Cardoso MC, Antes I, et al. Recognition of 5-hydroxymethylcytosine by the Uhrf1 SRA domain. PLoS One 2011; 6:e21306; http://dx.doi.org/10.1371/journal.pone.0021306; PMID: 21731699
   PubMed Web of Science ®Google Scholar
• Valinluck V, Tsai HH, Rogstad DK, Burdzy A, Bird A, Sowers LC. Oxidative damage to methyl-CpG sequences inhibits the binding of the methyl-CpG binding domain (MBD) of methyl-CpG binding protein 2 (MeCP2). Nucleic Acids Res 2004; 32:4100 - 8; http://dx.doi.org/10.1093/nar/gkh739; PMID: 15302911
   PubMed Web of Science ®Google Scholar