Co-occupancy by multiple cardiac transcription factors identifies transcriptional enhancers active in heart

Proceedings of the National Academy of Sciences of the United States of America

Volumn 108, Issue 14, 2011, Pages 5632-5637

  He, Aibin ^a,b   Kong, Sek Won ^a,b   Ma, Qing ^a,b   Pu, William T ^a,b  

^a BOSTON CHILDREN S HOSPITAL   (United States)

^b HARVARD STEM CELL INSTITUTE   (United States)

Author keywords

Gene regulation; In vivo biotinylation; Motif enrichment analysis; TEA domain family member 1

Indexed keywords

MYOCYTE ENHANCER FACTOR 2; PROTEIN P300; SERUM RESPONSE FACTOR; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR GATA 4; TRANSCRIPTION FACTOR NKX2.5; TRANSCRIPTION FACTOR SMARCD3; TRANSCRIPTION FACTOR TBX5; UNCLASSIFIED DRUG;

ANIMAL EXPERIMENT; CHROMATIN; CONFERENCE PAPER; CONTROLLED STUDY; EMBRYO; ENHANCER REGION; GENE CONTROL; GENE EXPRESSION; GENE IDENTIFICATION; GENE LOCATION; GENE LOCUS; GENE SEQUENCE; HEART; HEART DEVELOPMENT; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING;

EID: 79955027617     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1016959108     Document Type: Article

References (38)

1. Visel A, et al. (2009) ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 457:854-858.
2. Heintzman ND, et al. (2007) Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet 39:311-318. (Pubitemid 46328487)
3. Olson EN (2006) Gene regulatory networks in the evolution and development of the heart. Science 313:1922-1927. (Pubitemid 44497993)
4. Oka T, Xu J, Molkentin JD (2007) Re-employment of developmental transcription factors in adult heart disease. Semin Cell Dev Biol 18:117-131. (Pubitemid 46330840)
5. Naya FJ, et al. (2002) Mitochondrial deficiency and cardiac sudden death in mice lacking the MEF2A transcription factor. Nat Med 8:1303-1309. (Pubitemid 35373564)
6. Nemer G, Nemer M (2001) Regulation of heart development and function through combinatorial interactions of transcription factors. Ann Med 33:604-610. (Pubitemid 34081498)
7. Durocher D, Charron F, Warren R, Schwartz RJ, Nemer M (1997) The cardiac transcription factors Nkx2-5 and GATA-4 are mutual cofactors. EMBO J 16:5687-5696. (Pubitemid 27399860)
8. Sepulveda JL, et al. (1998) GATA-4 and Nkx-2.5 coactivate Nkx-2 DNA binding targets: Role for regulating early cardiac gene expression. Mol Cell Biol 18:3405-3415. (Pubitemid 28240513)
9. Garg V, et al. (2003) GATA4 mutations cause human congenital heart defects and reveal an interaction with TBX5. Nature 424:443-447. (Pubitemid 36917494)
10. Morin S, Charron F, Robitaille L, Nemer M (2000) GATA-dependent recruitment of MEF2 proteins to target promoters. EMBO J 19:2046-2055. (Pubitemid 30237580)
11. Kim J, Chu J, Shen X, Wang J, Orkin SH (2008) An extended transcriptional network for pluripotency of embryonic stem cells. Cell 132:1049-1061. (Pubitemid 351381745)
12. de Boer E, et al. (2003) Efficient biotinylation and single-step purification of tagged transcription factors in mammalian cells and transgenic mice. Proc Natl Acad Sci USA 100:7480-7485. (Pubitemid 36759995)
13. Rodriguez P, et al. (2006) Isolation of transcription factor complexes by in vivo biotinylation tagging and direct binding to streptavidin beads. Methods Mol Biol 338:305-323.
14. Yu C, et al. (2002) Targeted deletion of a high-affinity GATA-binding site in the GATA-1 promoter leads to selective loss of the eosinophil lineage in vivo. J Exp Med 195:1387-1395. (Pubitemid 34602816)
15. Lausen J, et al. (2010) Targets of the Tal1 transcription factor in erythrocytes: E2 ubiquitin conjugase regulation by Tal1. J Biol Chem 285:5338-5346.
16. Claycomb WC, et al. (1998) HL-1 cells: A cardiac muscle cell line that contracts and retains phenotypic characteristics of the adult cardiomyocyte. Proc Natl Acad Sci USA 95:2979-2984. (Pubitemid 28135840)
17. Blow MJ, et al. (2010) ChIP-Seq identification of weakly conserved heart enhancers. Nat Genet 42:806-810.
18. Blahnik KR, et al. (2010) Sole-Search: An integrated analysis program for peak detection and functional annotation using ChIP-seq data. Nucleic Acids Res 38:e13.
19. Portales-Casamar E, et al. (2010) JASPAR 2010: The greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Res 38(Database issue):D105-D110.
20. Newburger DE, Bulyk ML (2009) UniPROBE: An online database of protein binding microarray data on protein-DNA interactions. Nucleic Acids Res 37(Database issue):D77-D82.
21. Mori AD, et al. (2006) Tbx5-dependent rheostatic control of cardiac gene expression and morphogenesis. Dev Biol 297:566-586. (Pubitemid 44354936)
22. Andrés V, Cervera M, Mahdavi V (1995) Determination of the consensus binding site for MEF2 expressed in muscle and brain reveals tissue-specific sequence constraints. J Biol Chem 270:23246-23249.
23. Pavesi G, Mauri G, Pesole G (2001) An algorithm for finding signals of unknown length in DNA sequences. Bioinformatics 17 (Suppl 1):S207-S214. (Pubitemid 33793512)
24. Bailey TL, Williams N, Misleh C, Li WW (2006) MEME: Discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res 34(Web Server issue):W369-W373. (Pubitemid 44529795)
25. Kuo H, et al. (1999) Control of segmental expression of the cardiac-restricted ankyrin repeat protein gene by distinct regulatory pathways in murine cardiogenesis. Development 126:4223-4234. (Pubitemid 29509338)
26. Zhao Y, Samal E, Srivastava D (2005) Serum response factor regulates a muscle-specific microRNA that targets Hand2 during cardiogenesis. Nature 436:214-220. (Pubitemid 41021266)
27. Lee Y, et al. (1998) The cardiac tissue-restricted homeobox protein Csx/Nkx2.5 physically associates with the zinc finger protein GATA4 and cooperatively activates atrial natriuretic factor gene expression. Mol Cell Biol 18:3120-3129. (Pubitemid 28240485)
28. Yoshida T (2008) MCAT elements and the TEF-1 family of transcription factors in muscle development and disease. Arterioscler Thromb Vasc Biol 28:8-17.
29. Gupta M, et al. (2001) Physical interaction between the MADS box of serum response factor and the TEA/ATTS DNA-binding domain of transcription enhancer factor-1. J Biol Chem 276:10413-10422.
30. Sucharov CC, Dockstader K, McKinsey TA (2008) YY1 protects cardiac myocytes from pathologic hypertrophy by interacting with HDAC5. Mol Biol Cell 19:4141-4153.
31. Lickert H, et al. (2004) Baf60c is essential for function of BAF chromatin remodelling complexes in heart development. Nature 432:107-112. (Pubitemid 39490836)
32. Takeuchi JK, Bruneau BG (2009) Directed transdifferentiation of mouse mesoderm to heart tissue by defined factors. Nature 459:708-711.
33. Searcy RD, Vincent EB, Liberatore CM, Yutzey KE (1998) A GATA-dependent nkx-2.5 regulatory element activates early cardiac gene expression in transgenic mice. Development 125:4461-4470. (Pubitemid 28564290)
34. Rojas A, et al. (2005) Gata4 expression in lateral mesoderm is downstream of BMP4 and is activated directly by Forkhead and GATA transcription factors through a distal enhancer element. Development 132:3405-3417. (Pubitemid 41246116)
35. Xi H, et al. (2007) Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome. PLoS Genet 3:e136.
36. Dai YS, Markham BE (2001) p300 Functions as a coactivator of transcription factor GATA-4. J Biol Chem 276:37178-37185.
37. Farnham PJ (2009) Insights from genomic profiling of transcription factors. Nat Rev Genet 10:605-616.
38. Zhao R, et al. (2008) Loss of both GATA4 and GATA6 blocks cardiac myocyte differentiation and results in acardia in mice. Dev Biol 317:614-619.