Cofactor-Mediated Restriction of GATA-1 Chromatin Occupancy Coordinates Lineage-Specific Gene Expression

Molecular Cell

Volumn 47, Issue 4, 2012, Pages 608-621

  Chlon, Timothy M ^a   Doré, Louis C ^a   Crispino, John D ^a  

^a NORTHWESTERN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR FOG 1; TRANSCRIPTION FACTOR GATA 1; UNCLASSIFIED DRUG;

ANIMAL CELL; ARTICLE; BINDING SITE; CELL LINEAGE; CHROMATIN; CONTROLLED STUDY; DNA BINDING MOTIF; DNA MICROARRAY; DOWN REGULATION; GENE EXPRESSION; GENE IDENTIFICATION; GENOME ANALYSIS; HEMATOPOIETIC CELL; MAST CELL; MEGAKARYOCYTE; MOLECULAR INTERACTION; MOLECULAR MECHANICS; MOUSE; NONHUMAN;

AMINO ACID MOTIFS; ANIMALS; BINDING SITES; CELLS, CULTURED; CHROMATIN; DOWN-REGULATION; GATA1 TRANSCRIPTION FACTOR; GENE EXPRESSION REGULATION; MAST CELLS; MICE; MICE, INBRED C57BL; MUTATION; NUCLEAR PROTEINS; PROTEIN BINDING; PROTO-ONCOGENE PROTEIN C-FLI-1; TRANSCRIPTION FACTORS; UBIQUITIN-PROTEIN LIGASES;

EID: 84865353203     PISSN: 10972765     EISSN: 10974164     Source Type: Journal    
DOI: 10.1016/j.molcel.2012.05.051     Document Type: Article

References (50)

1. Bailey T.L. DREME: motif discovery in transcription factor ChIP-seq data. Bioinformatics 2011, 27:1653-1659.
2. Bailey T.L., Boden M., Buske F.A., Frith M., Grant C.E., Clementi L., Ren J., Li W.W., Noble W.S. MEME Suite: tools for motif discovery and searching. Nucleic Acids Res. 2009, 37:W202-W208.
3. Blahnik K.R., Dou L., O'Geen H., McPhillips T., Xu X., Cao A.R., Iyengar S., Nicolet C.M., Ludascher B., Korf I., et al. Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data. Nucleic Acids Res. 2010, 38:e13. 10.1093/nar/gkp1012.
4. Cantor A.B., Katz S.G., Orkin S.H. Distinct domains of the GATA-1 cofactor FOG-1 differentially influence erythroid versus megakaryocytic maturation. Mol. Cell. Biol. 2002, 22:4268-4279.
5. Cantor A.B., Iwasaki H., Arinobu Y., Moran T.B., Shigematsu H., Sullivan M.R., Akashi K., Orkin S.H. Antagonism of FOG-1 and GATA factors in fate choice for the mast cell lineage. J. Exp. Med. 2008, 205:611-624.
6. Chang A.N., Cantor A.B., Fujiwara Y., Lodish M.B., Droho S., Crispino J.D., Orkin S.H. GATA-factor dependence of the multitype zinc-finger protein FOG-1 for its essential role in megakaryopoiesis. Proc. Natl. Acad. Sci. USA 2002, 99:9237-9242.
7. Ciovacco W.A., Raskind W.H., Kacena M.A. Human phenotypes associated with GATA-1 mutations. Gene 2008, 427:1-6.
8. Crispino J.D. GATA1 in normal and malignant hematopoiesis. Semin. Cell Dev. Biol. 2005, 16:137-147.
9. Crispino J.D., Lodish M.B., MacKay J.P., Orkin S.H. Use of altered specificity mutants to probe a specific protein-protein interaction in differentiation: the GATA-1:FOG complex. Molecular Cell 1999, 3:219-228.
10. de Hoon M.J.L., Imoto S., Nolan J., Miyano S. Open source clustering software. Bioinformatics 2004, 20:1453-1454.
11. Deveaux S., Filipe A., Lemarchandel V., Ghysdael J., Romeo P., Mignotte V. Analysis of the thrombopoietin receptor (MPL) promoter implicates GATA and Ets proteins in the coregulation of megakaryocyte-specific genes. Blood 1996, 87:4678-4685.
12. Dore L.C., Crispino J.D. Transcription factor networks in erythroid cell and megakaryocyte development. Blood 2011, 118:231-239.
13. Dore L.C., Chlon T.M., Brown C.D., White K.P., Crispino J.D. Chromatin occupancy analysis reveals genome-wide GATA factor switching during hematopoiesis. Blood 2012, 119:3724-3733.
14. Eisbacher M., Holmes M.L., Newton A., Hogg P.J., Khachigian L.M., Crossley M., Chong B.H. Protein-protein interaction between Fli-1 and GATA-1 mediates synergistic expression of megakaryocyte-specific genes through cooperative DNA binding. Mol. Cell. Biol. 2003, 23:3427-3441.
15. Ferreira R., Ohneda K., Yamamoto M., Philipsen S. GATA1 function, a paradigm for transcription factors in hematopoiesis. Mol. Cell. Biol. 2005, 25:1215-1227.
16. Forsberg E.C., Downs K.M., Bresnick E.H. Direct interaction of NF-E2 with hypersensitive site 2 of the β-globin locus control region in living cells. Blood 2000, 96:334-339.
17. Fox A.H., Liew C., Holmes M., Kowalski K., Mackay J., Crossley M. Transcriptional cofactors of the FOG family interact with GATA proteins by means of multiple zinc fingers. EMBO J. 1999, 18:2812-2822.
18. Gao Z., Huang Z., Olivey H.E., Gurbuxani S., Crispino J.D., Svensson E.C. FOG-1-mediated recruitment of NuRD is required for cell lineage re-enforcement during haematopoiesis. EMBO J. 2010, 29:457-468.
19. Grass J.A., Boyer M.E., Pal S., Wu J., Weiss M.J., Bresnick E.H. GATA-1-dependent transcriptional repression of GATA-2 via disruption of positive autoregulation and domain-wide chromatin remodeling. Proc. Natl. Acad. Sci. USA 2003, 100:8811-8816.
20. Gregory G.D., Miccio A., Bersenev A., Wang Y., Hong W., Zhang Z., Poncz M., Tong W., Blobel G.A. FOG1 requires NuRD to promote hematopoiesis and maintain lineage fidelity within the megakaryocytic-erythroid compartment. Blood 2010, 115:2156-2166.
21. Guccione E., Martinato F., Finocchiaro G., Luzi L., Tizzoni L., Dall'Olio V., Zardo G., Nervi C., Bernard L., Amati B. Myc-binding-site recognition in the human genome is determined by chromatin context. Nat. Cell Biol. 2006, 8:764-770.
22. Heinz S., Benner C., Spann N., Bertolino E., Lin Y.C., Laslo P., Cheng J.X., Murre C., Singh H., Glass C.K. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 2010, 38:576-589.
23. Hong W., Nakazawa M., Chen Y.-Y., Kori R., Vakoc C.R., Rakowski C., Blobel G.A. FOG-1 recruits the NuRD repressor complex to mediate transcriptional repression by GATA-1. EMBO J. 2005, 24:2367-2378.
24. Huang H., Yu M., Akie T.E., Moran T.B., Woo A.J., Tu N., Waldon Z., Lin Y.Y., Steen H., Cantor A.B. Differentiation-dependent interactions between RUNX-1 and FLI-1 during megakaryocyte development. Mol. Cell. Biol. 2009, 29:4103-4115.
25. Johnson D.S., Mortazavi A., Myers R.M., Wold B. Genome-wide mapping of in vivo protein-DNA interactions. Science 2007, 316:1497-1502.
26. Letting D.L., Chen Y.-Y., Rakowski C., Reedy S., Blobel G.A. Context-dependent regulation of GATA-1 by friend of GATA-1. Proc. Natl. Acad. Sci. USA 2004, 101:476-481.
27. Li B., Carey M., Workman J.L. The role of chromatin during transcription. Cell 2007, 128:707-719.
28. Lowry J.A., Mackay J.P. GATA-1: one protein, many partners. Int. J. Biochem. Cell Biol. 2006, 38:6-11.
29. Maeda K., Nishiyama C., Tokura T., Nakano H., Kanada S., Nishiyama M., Okumura K., Ogawa H. FOG-1 represses GATA-1-dependent FcepsilonRI beta-chain transcription: transcriptional mechanism of mast-cell-specific gene expression in mice. Blood 2006, 108:262-269.
30. Miccio A., Wang Y., Hong W., Gregory G.D., Wang H., Yu X., Choi J.K., Shelat S., Tong W., Poncz M., et al. NuRD mediates activating and repressive functions of GATA-1 and FOG-1 during blood development. EMBO J. 2010, 29:442-456.
31. Nakajima T., Matsumoto K., Suto H., Tanaka K., Ebisawa M., Tomita H., Yuki K., Katsunuma T., Akasawa A., Hashida R., et al. Gene expression screening of human mast cells and eosinophils using high-density oligonucleotide probe arrays: abundant expression of major basic protein in mast cells. Blood 2001, 98:1127-1134.
32. Nichols K.E., Crispino J.D., Poncz M., White J.G., Orkin S.H., Maris J.M., Weiss M.J. Familial dyserythropoietic anaemia and thrombocytopenia due to an inherited mutation in GATA1. Nat. Genet. 2000, 24:266-270.
33. Orkin S.H., Zon L.I. Hematopoiesis: an evolving paradigm for stem cell biology. Cell 2008, 132:631-644.
34. Pal S., Cantor A.B., Johnson K.D., Moran T.B., Boyer M.E., Orkin S.H., Bresnick E.H. Coregulator-dependent facilitation of chromatin occupancy by GATA-1. Proc. Natl. Acad. Sci. USA 2004, 101:980-985.
35. Pang L., Xue H.-H., Szalai G., Wang X., Wang Y., Watson D.K., Leonard W.J., Blobel G.A., Poncz M. Maturation stage-specific regulation of megakaryopoiesis by pointed-domain Ets proteins. Blood 2006, 108:2198-2206.
36. Querfurth E., Schuster M., Kulessa H., Crispino J.D., Doderlein G., Orkin S.H., Graf T., Nerlov C. Antagonism between C/EBPE and FOG in eosinophil lineage commitment of multipotent hematopoietic progenitors. Genes Dev. 2000, 14:2515-2525.
37. Saldanha A.J. Java Treeview-extensible visualization of microarray data. Bioinformatics 2004, 20:3246-3248.
38. Stachura D.L., Chou S.T., Weiss M.J. Early block to erythromegakaryocytic development conferred by loss of transcription factor GATA-1. Blood 2006, 107:87-97.
39. Stathopoulos A., Levine M. Genomic regulatory networks and animal development. Dev. Cell 2005, 9:449-462.
40. Sugiyama D., Tanaka M., Kitajima K., Zheng J., Yen H., Murotani T., Yamatodani A., Nakano T. Differential context-dependent effects of friend of GATA-1 (FOG-1) on mast-cell development and differentiation. Blood 2008, 111:1924-1932.
41. Tijssen M.R., Cvejic A., Joshi A., Hannah R.L., Ferreira R., Forrai A., Bellissimo D.C., Oram S.H., Smethurst P.A., Wilson N.K., et al. Genome-wide analysis of simultaneous GATA1/2, RUNX1, FLI1, and SCL binding in megakaryocytes identifies hematopoietic regulators. Dev. Cell 2011, 20:597-609.
42. Tripic T., Deng W., Cheng Y., Zhang Y., Vakoc C.R., Gregory G.D., Hardison R.C., Blobel G.A. SCL and associated proteins distinguish active from repressive GATA transcription factor complexes. Blood 2009, 113:2191-2201.
43. Tsang A.P., Visvader J.E., Turner C.A., Fujiwara Y., Yu C., Weiss M.J., Crossley M., Orkin S.H. FOG, a multitype zinc finger protein, acts as a cofactor for transcription factor GATA-1 in erythroid and megakaryocytic differentiation. Cell 1997, 90:109-119.
44. Tsang A.P., Fujiwara Y., Hom D.B., Orkin S.H. Failure of megakaryopoiesis and arrested erythropoiesis in mice lacking the GATA-1 transcriptional cofactor FOG. Genes Dev. 1998, 12:1176-1188.
45. Vakoc C.R., Letting D.L., Gheldof N., Sawado T., Bender M.A., Groudine M., Weiss M.J., Dekker J., Blobel G.A. Proximity among distant regulatory elements at the [beta]-globin locus requires GATA-1 and FOG-1. Mol. Cell 2005, 17:453-462.
46. Wang X., Crispino J.D., Letting D.L., Nakazawa M., Poncz M., Blobel G.A. Control of megakaryocyte-specific gene expression by GATA-1 and FOG-1: role of Ets transcription factors. EMBO J. 2002, 21:5225-5234.
47. Woo A.J., Moran T.B., Schindler Y.L., Choe S.-K., Langer N.B., Sullivan M.R., Fujiwara Y., Paw B.H., Cantor A.B. Identification of ZBP-89 as a novel GATA-1-associated transcription factor involved in megakaryocytic and erythroid development. Mol. Cell. Biol. 2008, 28:2675-2689.
48. Wozniak R.J., Boyer M.E., Grass J.A., Lee Y., Bresnick E.H. Context-dependent GATA factor function. J. Biol. Chem. 2007, 282:14665-14674.
49. Wu W., Cheng Y., Keller C.A., Ernst J., Kumar S.A., Mishra T., Morrissey C., Dorman C.M., Chen K.-B., Drautz D., et al. Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration. Genome Res. 2011, 21:1659-1671.
50. Zhang Y., Liu T., Meyer C.A., Eeckhoute J., Johnson D.S., Bernstein B.E., Nusbaum C., Myers R.M., Brown M., Li W., Liu X.S. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008, 9:R137. 10.1186/gb-2008-9-9-r137.