Reviews - 4gzn mentioned but not cited (5)
- On how mammalian transcription factors recognize methylated DNA. Buck-Koehntop BA, Defossez PA. Epigenetics 8 131-137 (2013)
- A Structural Perspective on Readout of Epigenetic Histone and DNA Methylation Marks. Patel DJ. Cold Spring Harb Perspect Biol 8 a018754 (2016)
- Zinc Finger Readers of Methylated DNA. Hudson NO, Buck-Koehntop BA. Molecules 23 E2555 (2018)
- Detecting and interpreting DNA methylation marks. Ren R, Horton JR, Zhang X, Blumenthal RM, Cheng X. Curr Opin Struct Biol 53 88-99 (2018)
- The Mechanisms of Generation, Recognition, and Erasure of DNA 5-Methylcytosine and Thymine Oxidations. Hashimoto H, Zhang X, Vertino PM, Cheng X. J Biol Chem 290 20723-20733 (2015)
Articles - 4gzn mentioned but not cited (8)
- An atomic model of Zfp57 recognition of CpG methylation within a specific DNA sequence. Liu Y, Toh H, Sasaki H, Zhang X, Cheng X. Genes Dev 26 2374-2379 (2012)
- POSA: a user-driven, interactive multiple protein structure alignment server. Li Z, Natarajan P, Ye Y, Hrabe T, Godzik A. Nucleic Acids Res 42 W240-5 (2014)
- A structural approach reveals how neighbouring C2H2 zinc fingers influence DNA binding specificity. Garton M, Najafabadi HS, Schmitges FW, Radovani E, Hughes TR, Kim PM. Nucleic Acids Res 43 9147-9157 (2015)
- DNA recognition of 5-carboxylcytosine by a Zfp57 mutant at an atomic resolution of 0.97 Å. Liu Y, Olanrewaju YO, Zhang X, Cheng X. Biochemistry 52 9310-9317 (2013)
- Flexibility-rigidity index for protein-nucleic acid flexibility and fluctuation analysis. Opron K, Xia K, Burton Z, Wei GW. J Comput Chem 37 1283-1295 (2016)
- Potential Roles of Intrinsic Disorder in Maternal-Effect Proteins Involved in the Maintenance of DNA Methylation. Liu H, Wei Q, Huang C, Zhang Y, Guo Z. Int J Mol Sci 18 E1898 (2017)
- Molecular basis for DNA recognition by the maternal pioneer transcription factor FoxH1. Pluta R, Aragón E, Prescott NA, Ruiz L, Mees RA, Baginski B, Flood JR, Martin-Malpartida P, Massagué J, David Y, Macias MJ. Nat Commun 13 7279 (2022)
- Approximating lattice similarity. Andrews LC, Bernstein HJ, Sauter NK. Acta Crystallogr A Found Adv 79 480-484 (2023)
Reviews citing this publication (19)
- DNA methylation dynamics during epigenetic reprogramming in the germline and preimplantation embryos. Messerschmidt DM, Knowles BB, Solter D. Genes Dev 28 812-828 (2014)
- Transcription factors as readers and effectors of DNA methylation. Zhu H, Wang G, Qian J. Nat Rev Genet 17 551-565 (2016)
- The Role of KRAB-ZFPs in Transposable Element Repression and Mammalian Evolution. Yang P, Wang Y, Macfarlan TS. Trends Genet 33 871-881 (2017)
- Transposable elements as genetic regulatory substrates in early development. Gifford WD, Pfaff SL, Macfarlan TS. Trends Cell Biol 23 218-226 (2013)
- A common mode of recognition for methylated CpG. Liu Y, Zhang X, Blumenthal RM, Cheng X. Trends Biochem Sci 38 177-183 (2013)
- Evolving insights on how cytosine methylation affects protein-DNA binding. Dantas Machado AC, Zhou T, Rao S, Goel P, Rastogi C, Lazarovici A, Bussemaker HJ, Rohs R. Brief Funct Genomics 14 61-73 (2015)
- The specification of imprints in mammals. Hanna CW, Kelsey G. Heredity (Edinb) 113 176-183 (2014)
- Emerging concept in DNA methylation: role of transcription factors in shaping DNA methylation patterns. Marchal C, Miotto B. J Cell Physiol 230 743-751 (2015)
- Toward a Mechanistic Understanding of DNA Methylation Readout by Transcription Factors. Kribelbauer JF, Lu XJ, Rohs R, Mann RS, Bussemaker HJ. J Mol Biol 432 1801-1815 (2020)
- DNA Base Flipping: A General Mechanism for Writing, Reading, and Erasing DNA Modifications. Hong S, Cheng X. Adv Exp Med Biol 945 321-341 (2016)
- ZFP57 and the Targeted Maintenance of Postfertilization Genomic Imprints. Takahashi N, Gray D, Strogantsev R, Noon A, Delahaye C, Skarnes WC, Tate PH, Ferguson-Smith AC. Cold Spring Harb Symp Quant Biol 80 177-187 (2015)
- DNA methylation in epigenetic inheritance of metabolic diseases through the male germ line. Illum LRH, Bak ST, Lund S, Nielsen AL. J Mol Endocrinol 60 R39-R56 (2018)
- Do social insects support Haig's kin theory for the evolution of genomic imprinting? Pegoraro M, Marshall H, Lonsdale ZN, Mallon EB. Epigenetics 12 725-742 (2017)
- Erase-Maintain-Establish: Natural Reprogramming of the Mammalian Epigenome. Leseva M, Knowles BB, Messerschmidt DM, Solter D. Cold Spring Harb Symp Quant Biol 80 155-163 (2015)
- Maternal regulation of chromosomal imprinting in animals. Singh PB, Shloma VV, Belyakin SN. Chromosoma 128 69-80 (2019)
- Biology and Physics of Heterochromatin-Like Domains/Complexes. Singh PB, Belyakin SN, Laktionov PP. Cells 9 E1881 (2020)
- Heterochromatin and the molecular mechanisms of 'parent-of-origin' effects in animals. Singh PB. J Biosci 41 759-786 (2016)
- Genes, assisted reproductive technology and trans-illumination. Dias RP, Maher ER. Epigenomics 5 331-340 (2013)
- [Structure basis of versatile base recognition of MBD4]. Ariyoshi M, Otani J, Shirakawa M. Yakugaku Zasshi 135 3-9 (2015)
Articles citing this publication (64)
- Reversing DNA methylation: mechanisms, genomics, and biological functions. Wu H, Zhang Y. Cell 156 45-68 (2014)
- DNA methylation presents distinct binding sites for human transcription factors. Hu S, Wan J, Su Y, Song Q, Zeng Y, Nguyen HN, Shin J, Cox E, Rho HS, Woodard C, Xia S, Liu S, Lyu H, Ming GL, Wade H, Song H, Qian J, Zhu H. Elife 2 e00726 (2013)
- KRAB-Zinc Finger Proteins: A Repressor Family Displaying Multiple Biological Functions. Lupo A, Cesaro E, Montano G, Zurlo D, Izzo P, Costanzo P. Curr Genomics 14 268-278 (2013)
- Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA. Hashimoto H, Wang D, Horton JR, Zhang X, Corces VG, Cheng X. Mol Cell 66 711-720.e3 (2017)
- Allele-specific binding of ZFP57 in the epigenetic regulation of imprinted and non-imprinted monoallelic expression. Strogantsev R, Krueger F, Yamazawa K, Shi H, Gould P, Goldman-Roberts M, McEwen K, Sun B, Pedersen R, Ferguson-Smith AC. Genome Biol 16 112 (2015)
- Single-cell DNA-methylation analysis reveals epigenetic chimerism in preimplantation embryos. Lorthongpanich C, Cheow LF, Balu S, Quake SR, Knowles BB, Burkholder WF, Solter D, Messerschmidt DM. Science 341 1110-1112 (2013)
- Wilms tumor protein recognizes 5-carboxylcytosine within a specific DNA sequence. Hashimoto H, Olanrewaju YO, Zheng Y, Wilson GG, Zhang X, Cheng X. Genes Dev 28 2304-2313 (2014)
- Structural basis for Klf4 recognition of methylated DNA. Liu Y, Olanrewaju YO, Zheng Y, Hashimoto H, Blumenthal RM, Zhang X, Cheng X. Nucleic Acids Res 42 4859-4867 (2014)
- DNA methylation: old dog, new tricks? Spruijt CG, Vermeulen M. Nat Struct Mol Biol 21 949-954 (2014)
- MAX is an epigenetic sensor of 5-carboxylcytosine and is altered in multiple myeloma. Wang D, Hashimoto H, Zhang X, Barwick BG, Lonial S, Boise LH, Vertino PM, Cheng X. Nucleic Acids Res 45 2396-2407 (2017)
- Measuring quantitative effects of methylation on transcription factor-DNA binding affinity. Zuo Z, Roy B, Chang YK, Granas D, Stormo GD. Sci Adv 3 eaao1799 (2017)
- High grade glioblastoma is associated with aberrant expression of ZFP57, a protein involved in gene imprinting, and of CPT1A and CPT1C that regulate fatty acid metabolism. Cirillo A, Di Salle A, Petillo O, Melone MA, Grimaldi G, Bellotti A, Torelli G, De' Santi MS, Cantatore G, Marinelli A, Galderisi U, Peluso G. Cancer Biol Ther 15 735-741 (2014)
- G9a/GLP Complex Maintains Imprinted DNA Methylation in Embryonic Stem Cells. Zhang T, Termanis A, Özkan B, Bao XX, Culley J, de Lima Alves F, Rappsilber J, Ramsahoye B, Stancheva I. Cell Rep 15 77-85 (2016)
- ZFP57 maintains the parent-of-origin-specific expression of the imprinted genes and differentially affects non-imprinted targets in mouse embryonic stem cells. Riso V, Cammisa M, Kukreja H, Anvar Z, Verde G, Sparago A, Acurzio B, Lad S, Lonardo E, Sankar A, Helin K, Feil R, Fico A, Angelini C, Grimaldi G, Riccio A. Nucleic Acids Res 44 8165-8178 (2016)
- ZFP57 recognizes multiple and closely spaced sequence motif variants to maintain repressive epigenetic marks in mouse embryonic stem cells. Anvar Z, Cammisa M, Riso V, Baglivo I, Kukreja H, Sparago A, Girardot M, Lad S, De Feis I, Cerrato F, Angelini C, Feil R, Pedone PV, Grimaldi G, Riccio A. Nucleic Acids Res 44 1118-1132 (2016)
- Genetic variation influencing DNA methylation provides insights into molecular mechanisms regulating genomic function. Hawe JS, Wilson R, Schmid KT, Zhou L, Lakshmanan LN, Lehne BC, Kühnel B, Scott WR, Wielscher M, Yew YW, Baumbach C, Lee DP, Marouli E, Bernard M, Pfeiffer L, Matías-García PR, Autio MI, Bourgeois S, Herder C, Karhunen V, Meitinger T, Prokisch H, Rathmann W, Roden M, Sebert S, Shin J, Strauch K, Zhang W, Tan WLW, Hauck SM, Merl-Pham J, Grallert H, Barbosa EGV, MuTHER Consortium, Illig T, Peters A, Paus T, Pausova Z, Deloukas P, Foo RSY, Jarvelin MR, Kooner JS, Loh M, Heinig M, Gieger C, Waldenberger M, Chambers JC. Nat Genet 54 18-29 (2022)
- Methyl-dependent and spatial-specific DNA recognition by the orthologous transcription factors human AP-1 and Epstein-Barr virus Zta. Hong S, Wang D, Horton JR, Zhang X, Speck SH, Blumenthal RM, Cheng X. Nucleic Acids Res 45 2503-2515 (2017)
- Synthetic epigenetics-towards intelligent control of epigenetic states and cell identity. Jurkowski TP, Ravichandran M, Stepper P. Clin Epigenetics 7 18 (2015)
- Structural impact of complete CpG methylation within target DNA on specific complex formation of the inducible transcription factor Egr-1. Zandarashvili L, White MA, Esadze A, Iwahara J. FEBS Lett 589 1748-1753 (2015)
- The effects of cytosine methylation on general transcription factors. Jin J, Lian T, Gu C, Yu K, Gao YQ, Su XD. Sci Rep 6 29119 (2016)
- New insights into DNA recognition by zinc fingers revealed by structural analysis of the oncoprotein ZNF217. Vandevenne M, Jacques DA, Artuz C, Nguyen CD, Kwan AH, Segal DJ, Matthews JM, Crossley M, Guss JM, Mackay JP. J Biol Chem 288 10616-10627 (2013)
- Genes and Conditions Controlling Mammalian Pre- and Post-implantation Embryo Development. Anifandis G, Messini CI, Dafopoulos K, Messinis IE. Curr Genomics 16 32-46 (2015)
- Characterization of How DNA Modifications Affect DNA Binding by C2H2 Zinc Finger Proteins. Patel A, Hashimoto H, Zhang X, Cheng X. Methods Enzymol 573 387-401 (2016)
- DNA Conformation Induces Adaptable Binding by Tandem Zinc Finger Proteins. Patel A, Yang P, Tinkham M, Pradhan M, Sun MA, Wang Y, Hoang D, Wolf G, Horton JR, Zhang X, Macfarlan T, Cheng X. Cell 173 221-233.e12 (2018)
- Human and mouse ZFP57 proteins are functionally interchangeable in maintaining genomic imprinting at multiple imprinted regions in mouse ES cells. Takikawa S, Wang X, Ray C, Vakulenko M, Bell FT, Li X. Epigenetics 8 1268-1279 (2013)
- Genetic and epigenetic mutations affect the DNA binding capability of human ZFP57 in transient neonatal diabetes type 1. Baglivo I, Esposito S, De Cesare L, Sparago A, Anvar Z, Riso V, Cammisa M, Fattorusso R, Grimaldi G, Riccio A, Pedone PV. FEBS Lett 587 1474-1481 (2013)
- The KRAB-zinc-finger protein ZFP708 mediates epigenetic repression at RMER19B retrotransposons. Seah MKY, Wang Y, Goy PA, Loh HM, Peh WJ, Low DHP, Han BY, Wong E, Leong EL, Wolf G, Mzoughi S, Wollmann H, Macfarlan TS, Guccione E, Messerschmidt DM. Development 146 dev170266 (2019)
- Carboxylation of cytosine (5caC) in the CG dinucleotide in the E-box motif (CGCAG|GTG) increases binding of the Tcf3|Ascl1 helix-loop-helix heterodimer 10-fold. Golla JP, Zhao J, Mann IK, Sayeed SK, Mandal A, Rose RB, Vinson C. Biochem Biophys Res Commun 449 248-255 (2014)
- Structural basis for effects of CpA modifications on C/EBPβ binding of DNA. Yang J, Horton JR, Wang D, Ren R, Li J, Sun D, Huang Y, Zhang X, Blumenthal RM, Cheng X. Nucleic Acids Res 47 1774-1785 (2019)
- A randomized controlled trial of folic acid intervention in pregnancy highlights a putative methylation-regulated control element at ZFP57. Irwin RE, Thursby SJ, Ondičová M, Pentieva K, McNulty H, Richmond RC, Caffrey A, Lees-Murdock DJ, McLaughlin M, Cassidy T, Suderman M, Relton CL, Walsh CP. Clin Epigenetics 11 31 (2019)
- Distinctive Klf4 mutants determine preference for DNA methylation status. Hashimoto H, Wang D, Steves AN, Jin P, Blumenthal RM, Zhang X, Cheng X. Nucleic Acids Res 44 10177-10185 (2016)
- CH···O Hydrogen Bonds Mediate Highly Specific Recognition of Methylated CpG Sites by the Zinc Finger Protein Kaiso. Nikolova EN, Stanfield RL, Dyson HJ, Wright PE. Biochemistry 57 2109-2120 (2018)
- Structural basis of the methylation specificity of R.DpnI. Mierzejewska K, Siwek W, Czapinska H, Kaus-Drobek M, Radlinska M, Skowronek K, Bujnicki JM, Dadlez M, Bochtler M. Nucleic Acids Res 42 8745-8754 (2014)
- Structural insights into methylated DNA recognition by the C-terminal zinc fingers of the DNA reader protein ZBTB38. Hudson NO, Whitby FG, Buck-Koehntop BA. J Biol Chem 293 19835-19843 (2018)
- Letter Structural insights into the recognition of γ-globin gene promoter by BCL11A. Yang Y, Xu Z, He C, Zhang B, Shi Y, Li F. Cell Res 29 960-963 (2019)
- Structural basis of human PR/SET domain 9 (PRDM9) allele C-specific recognition of its cognate DNA sequence. Patel A, Zhang X, Blumenthal RM, Cheng X. J Biol Chem 292 15994-16002 (2017)
- ZFP57 dictates allelic expression switch of target imprinted genes. Jiang W, Shi J, Zhao J, Wang Q, Cong D, Chen F, Zhang Y, Liu Y, Zhao J, Chen Q, Gu L, Zhou W, Wang C, Fang Z, Geng S, Xie W, Chen LN, Yang Y, Bai Y, Lin H, Li X. Proc Natl Acad Sci U S A 118 e2005377118 (2021)
- DNA binding of the p21 repressor ZBTB2 is inhibited by cytosine hydroxymethylation. Lafaye C, Barbier E, Miscioscia A, Saint-Pierre C, Kraut A, Couté Y, Plo I, Gasparutto D, Ravanat JL, Breton J. Biochem Biophys Res Commun 446 341-346 (2014)
- Epigenome editing reveals core DNA methylation for imprinting control in the Dlk1-Dio3 imprinted domain. Kojima S, Shiochi N, Sato K, Yamaura M, Ito T, Yamamura N, Goto N, Odamoto M, Kobayashi S, Kimura T, Sekita Y. Nucleic Acids Res 50 5080-5094 (2022)
- Insights from multidimensional analyses of the pan-cancer DNA methylome heterogeneity and the uncanonical CpG-gene associations. Liu Y, Huang R, Liu Y, Song W, Wang Y, Yang Y, Dong S, Yang X. Int J Cancer 143 2814-2827 (2018)
- On the role of steric clashes in methylation control of restriction endonuclease activity. Mierzejewska K, Bochtler M, Czapinska H. Nucleic Acids Res 44 485-495 (2016)
- Synthetic DNA fragments bearing ICR cis elements become differentially methylated and recapitulate genomic imprinting in transgenic mice. Matsuzaki H, Okamura E, Kuramochi D, Ushiki A, Hirakawa K, Fukamizu A, Tanimoto K. Epigenetics Chromatin 11 36 (2018)
- A Conformational Switch in the Zinc Finger Protein Kaiso Mediates Differential Readout of Specific and Methylated DNA Sequences. Nikolova EN, Stanfield RL, Dyson HJ, Wright PE. Biochemistry 59 1909-1926 (2020)
- DNA sequence and chromatin modifiers cooperate to confer epigenetic bistability at imprinting control regions. Butz S, Schmolka N, Karemaker ID, Villaseñor R, Schwarz I, Domcke S, Uijttewaal ECH, Jude J, Lienert F, Krebs AR, de Wagenaar NP, Bao X, Zuber J, Elling U, Schübeler D, Baubec T. Nat Genet 54 1702-1710 (2022)
- Engineering nicking enzymes that preferentially nick 5-methylcytosine-modified DNA. Gutjahr A, Xu SY. Nucleic Acids Res 42 e77 (2014)
- Structural basis of DNA methylation-dependent site selectivity of the Epstein-Barr virus lytic switch protein ZEBRA/Zta/BZLF1. Bernaudat F, Gustems M, Günther J, Oliva MF, Buschle A, Göbel C, Pagniez P, Lupo J, Signor L, Müller CW, Morand P, Sattler M, Hammerschmidt W, Petosa C. Nucleic Acids Res 50 490-511 (2022)
- MBD2 and EZH2 regulate the expression of SFRP1 without affecting its methylation status in a colorectal cancer cell line. Yu J, Xie Y, Liu Y, Wang F, Li M, Qi J. Exp Ther Med 20 242 (2020)
- Crystal structure of the EcoKMcrA N-terminal domain (NEco): recognition of modified cytosine bases without flipping. Slyvka A, Zagorskaitė E, Czapinska H, Sasnauskas G, Bochtler M. Nucleic Acids Res 47 11943-11955 (2019)
- Structural basis for glucocorticoid receptor recognition of both unmodified and methylated binding sites, precursors of a modern recognition element. Liu X, Weikum ER, Tilo D, Vinson C, Ortlund EA. Nucleic Acids Res 49 8923-8933 (2021)
- DNA methyltransferases are complementary in maintaining DNA methylation in embryonic stem cells. Liu Y, Xu Z, Shi J, Zhang Y, Yang S, Chen Q, Song C, Geng S, Li Q, Li J, Xu GL, Xie W, Lin H, Li X. iScience 25 105003 (2022)
- Letter Is there a telltale RH fingerprint in zinc fingers that recognizes methylated CpG dinucleotides? Mackay JP, Segal DJ, Crossley M. Trends Biochem Sci 38 421-422 (2013)
- Transient neonatal diabetes mellitus in a Turkish patient with three novel homozygous variants in the ZFP57 gene. Boyraz M, Ulucan K, Taşkın N, Akçay T, Flanagan SE, Mackay DJ. J Clin Res Pediatr Endocrinol 5 125-128 (2013)
- Methylation-targeted specificity of the DNA binding proteins R.DpnI and MeCP2 studied by molecular dynamics simulations. Shanak S, Ulucan O, Helms V. J Mol Model 23 152 (2017)
- Letter Response to mackay et Al. Cheng X, Blumenthal RM. Trends Biochem Sci 38 423 (2013)
- Structural basis for transcription factor ZBTB7A recognition of DNA and effects of ZBTB7A somatic mutations that occur in human acute myeloid leukemia. Ren R, Horton JR, Chen Q, Yang J, Liu B, Huang Y, Blumenthal RM, Zhang X, Cheng X. J Biol Chem 299 102885 (2023)
- Structural insights into the recognition of telomeric variant repeat TTGGGG by broad-complex, tramtrack and bric-à-brac - zinc finger protein ZBTB10. Wang S, Xu Z, Li M, Lv M, Shen S, Shi Y, Li F. J Biol Chem 299 102918 (2023)
- Zfp57 Exerts Maternal and Sexually Dimorphic Effects on Genomic Imprinting. Xu Z, Shi J, Zhang Y, Liu Y, Zhao J, Chen Q, Song C, Geng S, Xie W, Wu F, Bai Y, Yang Y, Li X. Front Cell Dev Biol 10 784128 (2022)
- Characterization of H3K9me3 and DNA methylation co-marked CpG-rich regions during mouse development. Yang H, Wang Y, Zhang Y. BMC Genomics 24 663 (2023)
- DNA Methylation: Genomewide Distribution, Regulatory Mechanism and Therapy Target. Kaplun DS, Kaluzhny DN, Prokhortchouk EB, Zhenilo SV. Acta Naturae 14 4-19 (2022)
- Exploration of the regulatory relationship between KRAB-Zfp clusters and their target transposable elements via a gene editing strategy at the cluster specific linker-associated sequences by CRISPR-Cas9. Zhang Y, He F, Zhang Y, Dai Q, Li Q, Nan J, Miao R, Cheng B. Mob DNA 13 25 (2022)
- MBD4 loss results in global reactivation of promoters and retroelements with low methylated CpG density. Papin C, Ibrahim A, Sabir JSM, Le Gras S, Stoll I, Albiheyri RS, Zari AT, Bahieldin A, Bellacosa A, Bronner C, Hamiche A. J Exp Clin Cancer Res 42 301 (2023)
- Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet. Viner C, Ishak CA, Johnson J, Walker NJ, Shi H, Sjöberg-Herrera MK, Shen SY, Lardo SM, Adams DJ, Ferguson-Smith AC, De Carvalho DD, Hainer SJ, Bailey TL, Hoffman MM. Genome Biol 25 11 (2024)
- Proteins That Read DNA Methylation. Liu K, Shimbo T, Song X, Wade PA, Min J. Adv Exp Med Biol 1389 269-293 (2022)
- Recent Advances on DNA Base Flipping: A General Mechanism for Writing, Reading, and Erasing DNA Modifications. Ren R, Horton JR, Hong S, Cheng X. Adv Exp Med Biol 1389 295-315 (2022)