Genome-wide analysis of 5-hydroxymethylcytosine distribution reveals its dual function in transcriptional regulation in mouse embryonic stem cells

Genes and Development

Volumn 25, Issue 7, 2011, Pages 679-684

  Wu, Hao ^a,b,g,h   D'Alessio, Ana C ^c,d   Ito, Shinsuke ^c,d   Wang, Zhibin ^e   Cui, Kairong ^f   Zhao, Keji ^f   Sun, Yi Eve ^a,b   Zhang, Yi ^c,d  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF NORTH CAROLINA   (United States)

^d UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

^e JOHNS HOPKINS BLOOMBERG SCHOOL OF PUBLIC HEALTH   (United States)

^f NATIONAL HEART LUNG AND BLOOD INSTITUTE   (United States)

^g MASSACHUSETTS GENERAL HOSPITAL   (United States)

^h Harvard University   (United States)

Author keywords

5 hydroxymethylcytosine (5hmC); 5 methylcytosine (5mC); Genome wide 5hmC distribution; Mouse embryonic stem cells; Polycomb repression; Tet1

Indexed keywords

5 HYDROXYMETHYLCYTOSINE; POLYCOMB GROUP PROTEIN; TEN ELEVEN TRANSLOCATION 1 PROTEIN; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG;

ANIMAL CELL; ARTICLE; CONTROLLED STUDY; DEVELOPMENTAL GENE; EMBRYO; EMBRYONIC STEM CELL; GENE ACTIVATION; GENE EXPRESSION PROFILING; GENE FUNCTION; GENE LOCATION; GENE REPRESSION; GENETIC TRANSCRIPTION; GENOME ANALYSIS; MOUSE; NONHUMAN; PLURIPOTENT STEM CELL; PRIORITY JOURNAL; PROMOTER REGION; TRANSCRIPTION REGULATION; WILD TYPE;

ANIMALS; CELL LINE; CHROMATIN; CYTOSINE; DNA-BINDING PROTEINS; EMBRYONIC STEM CELLS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENOME-WIDE ASSOCIATION STUDY; MICE; PROTO-ONCOGENE PROTEINS; TRANSCRIPTION FACTORS;

EID: 79954457998     PISSN: 08909369     EISSN: 15495477     Source Type: Journal    
DOI: 10.1101/gad.2036011     Document Type: Article

References (32)

1. Bannister AJ, Zegerman P, Partridge JF, Miska EA, Thomas JO, Allshire RC, Kouzarides T. 2001. Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature 410: 120-124.
2. Cleary J, Sitwala KV, Khodadoust MS, Kwok RP, Mor-Vaknin N, Cebrat M, Cole PA, Markovitz DM. 2005. p300/CBP-associated factor drives DEK into interchromatin granule clusters. J Biol Chem 280: 31760-31767.
3. Eskeland R, Eberharter A, Imhof A. 2007. HP1 binding to chromatin methylated at H3K9 is enhanced by auxiliary factors. Mol Cell Biol 27: 453-465.
4. Faulkner NE, Hilfinger JM, Markovitz DM. 2001. Protein phosphatase 2A activates the HIV-2 promoter through enhancer elements that include the pets site. J Biol Chem 276: 25804-25812.
5. Gamble MJ, Fisher RP. 2007. SET and PARP1 remove DEK from chromatin to permit access by the transcription machinery. Nat Struct Mol Biol 14: 548-555.
6. Grewal SI, Jia S. 2007. Heterochromatin revisited. Nat Rev Genet 8: 35-46.
7. Hediger F, Gasser SM. 2006. Heterochromatin protein 1: don't judge the book by its cover! Curr Opin Genet Dev 16: 143-150.
8. Hollenbach AD, McPherson CJ, Mientjes EJ, Iyengar R, Grosveld G. 2002. Daxx and histone deacetylase II associate with chromatin through an interaction with core histones and the chromatin-associated protein Dek. J Cell Sci 115: 3319-3330.
9. Kappes F, Burger K, Baack M, Fackelmayer FO, Gruss C. 2001. Subcellular localization of the human proto-oncogene protein DEK. J Biol Chem 276: 26317-26323.
10. Kappes F, Damoc C, Knippers R, Przybylski M, Pinna LA, Gruss C. 2004a. Phosphorylation by protein kinase CK2 changes the DNA binding properties of the human chromatin protein DEK. Mol Cell Biol 24: 6011-6020.
11. Kappes F, Scholten I, Richter N, Gruss C, Waldmann T. 2004b. Functional domains of the ubiquitous chromatin protein DEK. Mol Cell Biol 24: 6000-6010.
12. Kappes F, Fahrer J, Khodadoust MS, Tabbert A, Strasser C, Mor-Vaknin N, Moreno-Villanueva M, Burkle A, Markovitz DM, Ferrando-May E. 2008. DEK is a poly(ADP-ribose) acceptor in apoptosis and mediates resistance to genotoxic stress. Mol Cell Biol 28: 3245-3257.
13. Khodadoust MS, Verhaegen M, Kappes F, Riveiro-Falkenbach E, Cigudosa JC, Kim DSL, Chinnaiyan AM, Markovitz DM, Soengas MS. 2009. Melanoma proliferation and chemoresistance controlled by the DEK oncogene. Cancer Res 69: 6405-6413.
14. Ko SI, Lee IS, Kim JY, Kim SM, Kim DW, Lee KS, Woo KM, Baek JH, Choo JK, Seo SB. 2006. Regulation of histone acetyltransferase activity of p300 and PCAF by proto-oncogene protein DEK. FEBS Lett 580: 3217-3222.
15. Lachner M, O'Carroll D, Rea S, Mechtler K, Jenuwein T. 2001. Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature 410: 116-120.
16. Lomberk G, Wallrath L, Urrutia R. 2006. The heterochromatin protein 1 family. Genome Biol 7: 228. doi: 10.1186/gb-2006-7-7-228.
17. Lusser A, Kadonaga JT. 2004. Strategies for the reconstitution of chromatin. Nat Methods 1: 19-26.
18. Maison C, Almouzni G. 2004. HP1 and the dynamics of heterochromatin maintenance. Nat Rev Mol Cell Biol 5: 296-304.
19. Mor-Vaknin N, Punturieri A, Sitwala K, Faulkner N, Legendre M, Khodadoust MS, Kappes F, Ruth JH, Koch A, Glass D, et al 2006. The DEK nuclear autoantigen is a secreted chemotactic factor. Mol Cell Biol 26: 9484-9496.
20. Mor-Vaknin N, Kappes F, Dick AE, Legendre M, Damoc C, Teitz-Tennenbaum S, Kwok R, Ferrando-May E, Adams BS, Markovitz DM. 2011. DEK in the synovium of JIA patients: characterization of DEK antibodies and posttranslational modification of the DEK autoantigen. Arthritis Rheum 63: 556-567.
21. Muchardt C, Guilleme M, Seeler JS, Trouche D, Dejean A, Yaniv M. 2002. Coordinated methyl and RNA binding is required for heterochromatin localization of mammalian HP1a. EMBO Rep 3: 975-981.
22. Riveiro-Falkenbach E, Soengas MS. 2010. Control of tumorigenesis and chemoresistance by the DEK oncogene. Clin Cancer Res 16: 2932-2938.
23. Sawatsubashi S, Murata T, Lim J, Fujiki R, Ito S, Suzuki E, Tanabe M, Zhao Y, Kimura S, Fujiyama S, et al. 2010. A histone chaperone, DEK, transcriptionally coactivates a nuclear receptor. Genes Dev 24: 159-170.
24. Sitwala KV, Mor-Vaknin N, Markovitz DM. 2003. Minireview: DEK and gene regulation, oncogenesis and AIDS. Anticancer Res 23: 2155-2158.
25. Soares LM, Zanier K, Mackereth C, Sattler M, Valcarcel J. 2006. Intron removal requires proofreading of U2AF/39 splice site recognition by DEK. Science 312: 1961-1965.
26. Tartof KD, Hobbs C, Jones M. 1984. A structural basis for variegating position effects. Cell 37: 869-878.
27. von Lindern M, Fornerod M, van Baal S, Jaegle M, de Wit T, Buijs A, Grosveld G. 1992. The translocation (6;9), associated with a specific subtype of acute myeloid leukemia, results in the fusion of two genes, dek and can, and the expression of a chimeric, leukemia-specific dekcan mRNA. Mol Cell Biol 12: 1687-1697.
28. Waldmann T, Eckerich C, Baack M, Gruss C. 2002. The ubiquitous chromatin protein DEK alters the structure of DNA by introducing positive supercoils. J Biol Chem 277: 24988-24994.
29. Waldmann T, Scholten I, Kappes F, Hu HG, Knippers R. 2004. The DEK protein-an abundant and ubiquitous constituent of mammalian chromatin. Gene 343: 1-9.
30. Wise-Draper TM, Allen HV, Jones EE, Habash KB, Matsuo H, Wells SI. 2006. Apoptosis inhibition by the human DEK oncoprotein involves interference with p53 functions. Mol Cell Biol 26: 7506-7519.
31. Wise-Draper TM, Mintz-Cole RA, Morris TA, Simpson DS, Wikenheiser-Brokamp KA, Currier MA, Cripe TP, Grosveld GC, Wells SI. 2009a. Overexpression of the cellular DEK protein promotes epithelial transformation in vitro and in vivo. Cancer Res 69: 1792-1799.
32. Wise-Draper TM, Morreale RJ, Morris TA, Mintz-Cole RA, Hoskins EE, Balsitis SJ, Husseinzadeh N, Witte DP, Wikenheiser-Brokamp KA, Lambert PF, et al. 2009b. DEK proto-oncogene expression interferes with the normal epithelial differentiation program. Am J Pathol 174: 71-81.