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Structural insights into how 5-hydroxymethylation influences transcription factor binding.

Lercher L, McDonough MA, El-Sagheer AH, Thalhammer A, Kriaucionis S, Brown T, Schofield CJ
Chem Commun (Camb) 50 1794-6 (2014)
Related entries: 4c63, 4c64

Cited: 33 times
EuropePMC logo PMID: 24287551

Abstract

Transcription factor binding and high resolution crystallographic studies (1.3 Å) of Dickerson-Drew duplexes with cytosine, methylcytosine and hydroxymethylcytosine bases provide evidence that C-5 cytosine modifications could regulate transcription by context dependent effects on DNA transcription factor interactions.

Reviews - 4c5x mentioned but not cited (1)

  1. Making the bend: DNA tertiary structure and protein-DNA interactions. Harteis S, Schneider S. Int J Mol Sci 15 12335-12363 (2014)

Articles - 4c5x mentioned but not cited (1)

  1. Enriched Conformational Sampling of DNA and Proteins with a Hybrid Hamiltonian Derived from the Protein Data Bank. Peter EK, Cerny J. Int J Mol Sci 19 E3405 (2018)


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  2. Functional Consequences of Mutations in Myeloproliferative Neoplasms. Constantinescu SN, Vainchenker W, Levy G, Papadopoulos N. Hemasphere 5 e578 (2021)
  3. Epigenetic Modifications of Cytosine: Biophysical Properties, Regulation, and Function in Mammalian DNA. Hardwick JS, Lane AN, Brown T. Bioessays 40 (2018)
  4. Beyond the double helix: DNA structural diversity and the PDB. Neidle S. J Biol Chem 296 100553 (2021)
  5. Advances in understanding the initiation of HIV-1 reverse transcription. Krupkin M, Jackson LN, Ha B, Puglisi EV. Curr Opin Struct Biol 65 175-183 (2020)
  6. Exploring links between 2-oxoglutarate-dependent oxygenases and Alzheimer's disease. Liu H, Xie Y, Wang X, Abboud MI, Ma C, Ge W, Schofield CJ. Alzheimers Dement 18 2637-2668 (2022)
  7. TALEored Epigenetics: A DNA-Binding Scaffold for Programmable Epigenome Editing and Analysis. Kubik G, Summerer D. Chembiochem 17 975-980 (2016)
  8. Recognition of Oxidized 5-Methylcytosine Derivatives in DNA by Natural and Engineered Protein Scaffolds. Muñoz-López Á, Summerer D. Chem Rec 18 105-116 (2018)

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  1. C/EBPβ (CEBPB) protein binding to the C/EBP|CRE DNA 8-mer TTGC|GTCA is inhibited by 5hmC and enhanced by 5mC, 5fC, and 5caC in the CG dinucleotide. Sayeed SK, Zhao J, Sathyanarayana BK, Golla JP, Vinson C. Biochim Biophys Acta 1849 583-589 (2015)
  2. 5-Formylcytosine does not change the global structure of DNA. Hardwick JS, Ptchelkine D, El-Sagheer AH, Tear I, Singleton D, Phillips SEV, Lane AN, Brown T. Nat Struct Mol Biol 24 544-552 (2017)
  3. Selective recognition of N4-methylcytosine in DNA by engineered transcription-activator-like effectors. Rathi P, Maurer S, Summerer D. Philos Trans R Soc Lond B Biol Sci 373 20170078 (2018)
  4. Cytosine base modifications regulate DNA duplex stability and metabolism. Rausch C, Zhang P, Casas-Delucchi CS, Daiß JL, Engel C, Coster G, Hastert FD, Weber P, Cardoso MC. Nucleic Acids Res 49 12870-12894 (2021)
  5. Polymerase synthesis of photocaged DNA resistant against cleavage by restriction endonucleases. Vaníková Z, Hocek M. Angew Chem Int Ed Engl 53 6734-6737 (2014)
  6. Oxidized Derivatives of 5-Methylcytosine Alter the Stability and Dehybridization Dynamics of Duplex DNA. Sanstead PJ, Ashwood B, Dai Q, He C, Tokmakoff A. J Phys Chem B 124 1160-1174 (2020)
  7. Adaptive resolution simulation of oligonucleotides. Netz PA, Potestio R, Kremer K. J Chem Phys 145 234101 (2016)
  8. Combined Effects of Methylated Cytosine and Molecular Crowding on the Thermodynamic Stability of DNA Duplexes. Tsuruta M, Sugitani Y, Sugimoto N, Miyoshi D. Int J Mol Sci 22 947 (2021)
  9. Modeling Functional Motions of Biological Systems by Customized Natural Moves. Demharter S, Knapp B, Deane CM, Minary P. Biophys J 111 710-721 (2016)
  10. DNA methylation and hydroxymethylation characterize the identity of D1 and D2 striatal projection neurons. Marion-Poll L, Roussarie JP, Taing L, Dard-Dascot C, Servant N, Jaszczyszyn Y, Jordi E, Mulugeta E, Hervé D, Bourc'his D, Greengard P, Thermes C, Girault JA. Commun Biol 5 1321 (2022)
  11. Dicationic styryl dyes for colorimetric and fluorescent detection of nucleic acids. Supabowornsathit K, Faikhruea K, Ditmangklo B, Jaroenchuensiri T, Wongsuwan S, Junpra-Ob S, Choopara I, Palaga T, Aonbangkhen C, Somboonna N, Taechalertpaisarn J, Vilaivan T. Sci Rep 12 14250 (2022)
  12. Published Erratum Correction to differential stabilities and sequence-dependent base pair opening dynamics of watson-crick base pairs with 5-hydroxymethylcytosine, 5-formylcytosine, or 5-carboxylcytosine. Szulik MW, Pallan PS, Nocek B, Voehler M, Banerjee S, Brooks S, Joachimiak A, Egli M, Eichman BF, Stone MP. Biochemistry 54 2550 (2015)
  13. Machine learning shows torsion angle preferences in left-handed and right-handed quadruplex DNAs. Li K, Yatsunyk LA, Neidle S. Biophys J 121 4874-4881 (2022)
  14. Peroxoniobium inhibits leukemia cell growth. Pereira-Maia EC, Souza IP, Nunes KJRC, Castro AA, Ramalho TC, Steffler F, Duarte HA, Pacheli A, Chagas P, Oliveira LCA. RSC Adv 8 10310-10313 (2018)
  15. Toward a base-resolution panorama of the in vivo impact of cytosine methylation on transcription factor binding. Hernandez-Corchado A, Najafabadi HS. Genome Biol 23 151 (2022)
  16. Water-bridged hydrogen bond formation between 5-hydroxylmethylcytosine (5-hmC) and its 3'-neighbouring bases in A- and B-form DNA duplexes. Wang R, Ranganathan SV, Valsangkar VA, Magliocco SM, Shen F, Chen A, Sheng J. Chem Commun (Camb) 51 16389-16392 (2015)
  17. Whole-Genome Differentially Hydroxymethylated DNA Regions among Twins Discordant for Cardiovascular Death. Dai J, Leung M, Guan W, Guo HT, Krasnow RE, Wang TJ, El-Rifai W, Zhao Z, Reed T. Genes (Basel) 12 1183 (2021)
  18. Developmental exposures to common environmental contaminants, DEHP and lead, alter adult brain and blood hydroxymethylation in mice. Petroff RL, Cavalcante RG, Colacino JA, Goodrich JM, Jones TR, Lalancette C, Morgan RK, Neier K, Perera BPU, Rygiel CA, Svoboda LK, Wang K, Sartor MA, Dolinoy DC. Front Cell Dev Biol 11 1198148 (2023)
  19. Homologues of epigenetic pyrimidines: 5-alkyl-, 5-hydroxyalkyl and 5-acyluracil and -cytosine nucleotides: synthesis, enzymatic incorporation into DNA and effect on transcription with bacterial RNA polymerase. Gracias F, Ruiz-Larrabeiti O, Vaňková Hausnerová V, Pohl R, Klepetářová B, Sýkorová V, Krásný L, Hocek M. RSC Chem Biol 3 1069-1075 (2022)
  20. In silico structural modeling of multiple epigenetic marks on DNA. Krawczyk K, Demharter S, Knapp B, Deane CM, Minary P. Bioinformatics 34 41-48 (2018)
  21. 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)
  22. Predicting accurate ab initio DNA electron densities with equivariant neural networks. Lee AJ, Rackers JA, Bricker WP. Biophys J 121 3883-3895 (2022)
  23. Supercoiling-dependent DNA binding: quantitative modeling and applications to bulk and single-molecule experiments. Kolbeck PJ, Tišma M, Analikwu BT, Vanderlinden W, Dekker C, Lipfert J. Nucleic Acids Res 52 59-72 (2024)


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