Establishment of a cell-type-specific genetic network by the mediator complex component Med1

Molecular and Cellular Biology

Volumn 33, Issue 10, 2013, Pages 1938-1955

  Pope, Nathaniel J ^a   Bresnick, Emery H ^a  

^a University of Wisconsin Health   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GUANOSINE TRIPHOSPHATASE; MEDIATOR COMPLEX; MEDIATOR COMPLEX MED1; TRANSCRIPTION FACTOR GATA 1; UNCLASSIFIED DRUG; ESTRADIOL; GATA1 PROTEIN, MOUSE; MED1 PROTEIN, MOUSE; PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR BINDING PROTEIN; RAS PROTEIN; RRAD PROTEIN, MOUSE; SMALL INTERFERING RNA; TRANSCRIPTOME;

ANIMAL CELL; ARTICLE; CELL DIFFERENTIATION; CELL PROLIFERATION; CELL SURVIVAL; CELL TYPE; CONTROLLED STUDY; ERYTHROCYTE; ERYTHROID CELL; ERYTHROPOIESIS; FIBROBLAST; GENE; HUMAN; HUMAN CELL; LOSS OF FUNCTION MUTATION; MOUSE; NONHUMAN; PRIORITY JOURNAL; RRAD GENE; STEM CELL; ANIMAL; ANTIBODY SPECIFICITY; CHO CELL; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENE SILENCING; GENETIC TRANSCRIPTION; GENETICS; HAMSTER; METABOLISM; PHYSIOLOGY; TUMOR CELL LINE;

ANIMALS; CELL LINE, TUMOR; CELL SURVIVAL; CHO CELLS; CRICETINAE; ERYTHROID CELLS; ESTRADIOL; GATA1 TRANSCRIPTION FACTOR; GENE EXPRESSION REGULATION; GENE KNOCKDOWN TECHNIQUES; GENE REGULATORY NETWORKS; MEDIATOR COMPLEX; MEDIATOR COMPLEX SUBUNIT 1; MICE; ORGAN SPECIFICITY; RAS PROTEINS; RNA, SMALL INTERFERING; TRANSCRIPTION, GENETIC; TRANSCRIPTOME;

MLCS; MLOWN;

EID: 84878966951     PISSN: 02707306     EISSN: 10985549     Source Type: Journal    
DOI: 10.1128/MCB.00141-13     Document Type: Article

References (75)

1. Tsai FY, Keller G, Kuo FC, Weiss M, Chen J, Rosenblatt M, Alt FW, Orkin SH. 1994. An early haematopoietic defect in mice lacking the transcription factor GATA-2. Nature 371:221-226.
2. - mouse embryonic stem cells. Nat. Genet. 1:92-98.
3. Pevny L, Simon MC, Robertson E, Klein WH, Tsai SF, D'Agati V, Orkin SH, Costantini F. 1991. Erythroid differentiation in chimaeric mice blocked by a targeted mutation in the gene for transcription factor GATA-1. Nature 349:257-260.
4. Joulin V, Bories D, Eleouet JF, Labastie MC, Chretien S, Mattei MG, Romeo PH. 1991. A T-cell specific TCR DNA binding protein is a member of the human GATA family. EMBO J. 10:1809 -1816.
5. Pandolfi PP, Roth ME, Karis A, Leonard MW, Dzierzak E, Grosveld FG, Engel JD, Lindenbaum MH. 1995. Targeted disruption of the GATA3 gene causes severe abnormalities in the nervous system and in fetal liver haematopoiesis. Nat. Genet. 11:40-44.
6. Evans T, Felsenfeld G. 1989. The erythroid-specific transcription factor Eryf1: a new finger protein. Cell 58:877-885.
7. Tsai SF, Martin DI, Zon LI, D'Andrea AD, Wong GG, Orkin SH. 1989. Cloning of cDNA for the major DNA-binding protein of the erythroid lineage through expression in mammalian cells. Nature 339:446-451.
8. Molkentin JD, Lin Q, Duncan SA, Olson EN. 1997. Requirement of the transcription factor GATA4 for heart tube formation and ventral morphogenesis. Genes Dev. 11:1061-1072.
9. Kuo CT, Morrisey EE, Anandappa R, Sigrist K, Lu MM, Parmacek MS, Soudais C, Leiden JM. 1997. GATA4 transcription factor is required for ventral morphogenesis and heart tube formation. Genes Dev. 11:1048-1060.
10. Morrisey EE, Ip HS, Tang Z, Lu MM, Parmacek MS. 1997. GATA-5: a transcriptional activator expressed in a novel temporally and spatiallyrestricted pattern during embryonic development. Dev. Biol. 183:21-36.
11. Morrisey EE, Tang Z, Sigrist K, Lu MM, Jiang F, Ip HS, Parmacek MS. 1998. GATA6 regulates HNF4 and is required for differentiation of visceral endoderm in the mouse embryo. Genes Dev. 12:3579 -3590.
12. Weiss MJ, Orkin SH. 1995. GATA transcription factors: key regulators of hematopoiesis. Exp. Hematol. 23:99 -107.
13. Kim SI, Bresnick EH. 2007. Transcriptional control of erythropoiesis: emerging mechanisms and principles. Oncogene 26:6777-6794.
14. Fujiwara Y, Browne CP, Cunniff K, Goff SC, Orkin SH. 1996. Arrested development of embryonic red cell precursors in mouse embryos lacking transcription factor GATA-1. Proc. Natl. Acad. Sci. U. S. A. 93:12355-12358.
15. Crispino JD. 2005. GATA-1 in normal and malignant hematopoiesis. Semin. Cell Dev. Biol. 16:137-147.
16. Bresnick EH, Katsumura KR, Lee HY, Johnson KD, Perkins AS. 2012. Master regulatory GATA transcription factors: mechanistic principles and emerging links to hematologic malignancies. Nucleic Acids Res. 40:5819-5831.
17. Martin DI, Orkin SH. 1990. Transcriptional activation and DNA binding by the erythroid factor GF-1/NF-E1/Eryf 1. Genes Dev. 4:1886 -1898. 18. Ko LJ, Engel JD. 1993. DNA-binding specificities of the GATA transcription factor family. Mol. Cell. Biol. 13:4011-4022.
18. Ko LJ, Engel JD. 1993. DNA-binding specificities of the GATA transcription factor family. Mol. Cell. Biol. 13:4011-4022.
19. Merika M, Orkin SH. 1993. DNA-binding specificity of GATA family transcription factors. Mol. Cell. Biol. 13:3999-4010.
20. Fujiwara T, O'Geen H, Keles S, Blahnik K, Linnemann AK, Kang YA, Choi K, Farnham PJ, Bresnick EH. 2009. Discovering hematopoietic mechanisms through genome-wide analysis of GATA factor chromatin occupancy. Mol. Cell 36:667-681.
21. Tsang AP, Visvader JE, Turner CA, Fujiwara Y, Yu C, Weiss MJ, Crossley M, Orkin SH. 1997. FOG, a multitype zinc finger protein, acts as a cofactor for transcription factor GATA-1 in erythroid and megakaryocytic differentiation. Cell 90:109 -119.
22. Tsang AP, Fujiwara Y, Hom DB, Orkin SH. 1998. Failure of megakaryopoiesis and arrested erythropoiesis in mice lacking the GATA-1 transcriptional cofactor FOG. Genes Dev. 12:1176 -1188.
23. Crispino JD, Lodish MB, MacKay JP, Orkin SH. 1999. Use of altered specificity mutants to probe a specific protein-protein interaction in differentiation: the GATA-1:FOG complex. Mol. Cell 3:219 -228.
24. Blobel GA, Nakajima T, Eckner R, Montminy M, Orkin SH. 1998. CREB-binding protein cooperates with transcription factor GATA-1 and is required for erythroid differentiation. Proc. Natl. Acad. Sci. U. S. A. 95:2061-2066.
25. Stumpf M, Waskow C, Krotschel M, van Essen D, Rodriguez P, Zhang X, Guyot B, Roeder RG, Borggrefe T. 2006. The mediator complex functions as a coactivator for GATA-1 in erythropoiesis via subunit Med1/ TRAP220. Proc. Natl. Acad. Sci. U. S. A. 103:18504 -18509.
26. Kornberg RD. 2005. Mediator and the mechanism of transcriptional activation. Trends Biochem. Sci. 30:235-239.
27. Conaway RC, Sato S, Tomomori-Sato C, Yao T, Conaway JW. 2005. The mammalian mediator complex and its role in transcriptional regulation. Trends Biochem. Sci. 30:250 -255.
28. Johnson KD, Boyer ME, Kang JA, Wickrema A, Cantor AB, Bresnick EH. 2007. Friend of GATA-1-independent transcriptional repression: a novel mode of GATA-1 function. Blood 109:5230 -5233.
29. Lee HY, Johnson KD, Fujiwara T, Boyer ME, Kim SI, Bresnick EH. 2009. Controlling hematopoiesis through sumoylation-dependent regulation of a GATA factor. Mol. Cell 36:984 -995.
30. Lee HY, Johnson KD, Boyer ME, Bresnick EH. 2011. Relocalizing genetic loci into specific subnuclear neighborhoods. J. Biol. Chem. 286: 18834-18844.
31. Chen W, Roeder RG. 2011. Mediator-dependent nuclear receptor function. Semin. Cell Dev. Biol. 22:749 -758.
32. Belakavadi M, Fondell JD. 2006. Role of the mediator complex in nuclear hormone receptor signaling. Rev. Physiol. Biochem. Pharmacol. 156: 23-43.
33. Zhu Y, Qi C, Jia Y, Nye JS, Rao MS, Reddy JK. 2000. Deletion of PBP/PPARBP, the gene for nuclear receptor coactivator peroxisome proliferator-activated receptor-binding protein, results in embryonic lethality. J. Biol. Chem. 275:14779 -14782.
34. Crawford SE, Qi C, Misra P, Stellmach V, Rao MS, Engel JD, Zhu Y, Reddy JK. 2002. Defects of the heart, eye, and megakaryocytes in peroxisome proliferator activator receptor-binding protein (PBP) null embryos implicate GATA family of transcription factors. J. Biol. Chem. 277:3585-3592.
35. Landles C, Chalk S, Steel JH, Rosewell I, Spencer-Dene B, Lalani E-N, Parker MG. 2003. The thyroid hormone receptor-associated protein TRAP220 is required at distinct embryonic stages in placental, cardiac, and hepatic development. Mol. Endocrinol. 17:2418 -2435.
36. Ito M, Yuan CX, Okano HJ, Darnell RB, Roeder RG. 2000. Involvement of the TRAP220 component of the TRAP/SMCC coactivator complex in embryonic development and thyroid hormone action. Mol. Cell 5:683-693.
37. Stumpf M, Yue X, Schmitz S, Luche H, Reddy JK, Borggrefe T. 2010. Specific erythroid-lineage defect in mice conditionally deficient for Mediator subunit Med1. Proc. Natl. Acad. Sci. U. S. A. 107:21541-21546.
38. Ting CN, Olson MC, Barton KP, Leiden JM. 1996. Transcription factor GATA-3 is required for development of the T-cell lineage. Nature 384: 474-478.
39. Pope NJ, Bresnick EH. 2010. Differential coregulator requirements for function of the hematopoietic transcription factor GATA-1 at endogenous loci. Nucleic Acids Res. 38:2190 -2200.
40. Weiss MJ, Yu C, Orkin SH. 1997. Erythroid-cell-specific properties of transcription factor GATA-1 revealed by phenotypic rescue of a genetargeted cell line. Mol. Cell. Biol. 17:1642-1651.
41. Gregory T, Yu C, Ma A, Orkin SH, Blobel GA, Weiss MJ. 1999. GATA-1 and erythropoietin cooperate to promote erythroid cell survival by regulating bcl-xL expression. Blood 94:87-96.
42. Welch JJ, Watts JA, Vakoc CR, Yao Y, Wang H, Hardison RC, Blobel GA, Chodosh LA, Weiss MJ. 2004. Global regulation of erythroid gene expression by transcription factor GATA-1. Blood 104:3136 -3147.
43. Zhu J, Reynet C, Caldwell JS, Kahn CR. 1995. Characterization of Rad, a new member of Ras/GTPase superfamily, and its regulation by a unique GTPase-activating protein (GAP)-like activity. J. Biol. Chem. 270:4805-4812.
44. Chang L, Zhang J, Tseng YH, Xie CQ, Ilany J, Bruning JC, Sun Z, Zhu X, Cui T, Youker KA, Yang Q, Day SM, Kahn CR, Chen YE. 2007. Rad GTPase deficiency leads to cardiac hypertrophy. Circulation 116:2976-2983.
45. Zhang J, Chang L, Chen C, Zhang M, Luo Y, Hamblin M, Villacorta L, Xiong JW, Chen YE, Zhang J, Zhu X. 2011. Rad GTPase inhibits cardiac fibrosis through connective tissue growth factor. Cardiovasc. Res. 91:90 -98.
46. Fu M, Zhang J, Tseng YH, Cui T, Zhu X, Xiao Y, Mou Y, De Leon H, Chang MM, Hamamori Y, Kahn CR, Chen YE. 2005. Rad GTPase attenuates vascular lesion formation by inhibition of vascular smooth muscle cell migration. Circulation 111:1071-1077.
47. Ilany J, Bilan PJ, Kapur S, Caldwell JS, Patti ME, Marette A, Kahn CR. 2006. Overexpression of Rad in muscle worsens diet-induced insulin resistance and glucose intolerance and lowers plasma triglyceride level. Proc. Natl. Acad. Sci. U. S. A. 103:4481-4486.
48. Grass JA, Boyer ME, Pal S, Wu J, Weiss MJ, Bresnick EH. 2003. GATA-1-dependent transcriptional repression of GATA-2 via disruption of positive autoregulation and domain-wide chromatin remodeling. Proc. Natl. Acad. Sci. U. S. A. 100:8811-8816.
49. Nudel U, Salmon JE, Terada M, Bank A, Rifkind RA, Marks PA. 1977. Differential effects of chemical inducers on expression of beta globin genes in murine erythroleukemia cells. Proc. Natl. Acad. Sci. U. S. A. 74:1100-1104.
50. Forsberg EC, Downs KM, Christensen HM, Im H, Nuzzi PA, Bresnick EH. 2000. Developmentally dynamic histone acetylation pattern of a tissue-specific chromatin domain. Proc. Natl. Acad. Sci. U. S. A. 97:14494-14499.
51. Cantor AB, Katz SG, Orkin SH. 2002. Distinct domains of the GATA-1 cofactor FOG-1 differentially influence erythroid versus megakaryocytic maturation. Mol. Cell. Biol. 22:4268-4279.
52. Grass JA, Jing H, Kim SI, Martowicz ML, Pal S, Blobel GA, Bresnick EH. 2006. Distinct functions of dispersed GATA factor complexes at an endogenous gene locus. Mol. Cell. Biol. 26:7056 -7067.
53. Johnson KD, Hsu AP, Ryu MJ, Wang J, Gao X, Boyer ME, Liu Y, Lee Y, Calvo KR, Keles S, Zhang J, Holland SM, Bresnick EH. 2012. Cis-element mutated in GATA2-dependent immunodeficiency governs hematopoiesis and vascular integrity. J. Clin. Invest. 122:3692-3704.
54. Vollrath AL, Smith AA, Craven M, Bradfield CA. 2009. EDGE3: a web-based solution for management and analysis of Agilent two color microarray experiments. BMC Bioinformatics 10:280. doi:10.1186/1471-2105-10-280.
55. Im H, Grass JA, Johnson KD, Boyer ME, Wu J, Bresnick EH. 2004. Measurement of protein-DNA interactions in vivo by chromatin immunoprecipitation. Methods Mol. Biol. 284:129 -146.
56. Huang DW, Sherman BT, Lempicki RA. 2009. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4:44 -57.
57. Cheng Y, Wu W, Kumar SA, Yu D, Deng W, Tripic T, King DC, Chen KB, Zhang Y, Drautz D, Giardine B, Schuster SC, Miller W, Chiaromonte F, Zhang Y, Blobel GA, Weiss MJ, Hardison RC. 2009. Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression. Genome Res. 19:2172-2184.
58. Kang YA, Sanalkumar R, O'Geen H, Linnemann AK, Chang CJ, Bouhassira EE, Farnham PJ, Keles S, Bresnick EH. 2012. Autophagy driven by a master regulator of hematopoiesis. Mol. Cell. Biol. 32:226 -239.
59. Merryweather-Clarke AT, Atzberger A, Soneji S, Gray N, Clark K, Waugh C, McGowan SJ, Taylor S, Nandi AK, Wood WG, Roberts DJ, Higgs DR, Buckle VJ, Robson KJ. 2011. Global gene expression analysis of human erythroid progenitors. Blood 117:e96-e108. doi:10.1182/blood-2010-07-290825.
60. Kingsley PD, Greenfest-Allen E, Frame JM, Bushnell TP, Malik J, McGrath KE, Stoeckert CJ, Jr, Palis J. 2013. Ontogeny of erythroid gene expression. Blood 121:e5-e13. doi:10.1182/blood-2012-04-422394.
61. Deato MD, Marr MT, Sottero T, Inouye C, Hu P, Tjian R. 2008. MyoD targets TAF3/TRF3 to activate myogenin transcription. Mol. Cell 32:96-105.
62. Bresnick EH, Johnson KD, Kim SI, Im H. 2006. Establishment and regulation of chromatin domains: mechanistic insights from studies of hemoglobin synthesis. Prog. Nucleic Acid Res. Mol. Biol. 81:435-471.
63. Zhu J, Bilan PJ, Moyers JS, Antonetti DA, Kahn CR. 1996. Rad, a novel Ras-related GTPase, interacts with skeletal muscle beta-tropomyosin. J. Biol. Chem. 271:768 -773.
64. 2+ channels in the heart. Circ. Res. 101:69 -77.
65. Ji P, Lodish HF. 2010. Rac GTPases play multiple roles in erythropoiesis. Haematologica 95:2-4.
66. Ji P, Jayapal SR, Lodish HF. 2008. Enucleation of cultured mouse fetal erythroblasts requires Rac GTPases and mDia2. Nat. Cell Biol. 10:314-321.
67. Kalfa TA, Pushkaran S, Mohandas N, Hartwig JH, Fowler VM, Johnson JF, Joiner CH, Williams DA, Zheng Y. 2006. Rac GTPases regulate the morphology and deformability of the erythrocyte cytoskeleton. Blood 108:3637-3645.
68. Watowich SS, Wu H, Socolovsky M, Klingmuller U, Constantinescu SN, Lodish HF. 1996. Cytokine receptor signal transduction and thecontrol of hematopoietic cell development. Annu. Rev. Cell Dev. Biol. 12:91-128.
69. Hu W, Yuan B, Flygare J, Lodish HF. 2011. Long noncoding RNAmediated anti-apoptotic activity in murine erythroid terminal differentiation. Genes Dev. 25:2573-2578.
70. Vallabhapurapu S, Karin M. 2009. Regulation and function of NF-κB transcription factors in the immune system. Annu. Rev. Immunol. 27: 693-733.
71. Baldwin AS. 2012. Regulation of cell death and autophagy by IKK and NF-κB: critical mechanisms in immune function and cancer. Immunol. Rev. 246:327-345.
72. Chen Z, Guo K, Toh SY, Zhou Z, Li P. 2000. Mitochondria localization and dimerization are required for CIDE-B to induce apoptosis. J. Biol. Chem. 275:22619 -22622.
73. Xu L, Zhou L, Li P. 2012. CIDE proteins and lipid metabolism. Arterioscler. Thromb. Vasc. Biol. 32:1094 -1098.
74. Ye J, Li JZ, Liu Y, Li X, Yang T, Ma X, Li Q, Yao Z, Li P. 2009. Cideb, an ER-and lipid droplet-associated protein, mediates VLDL lipidation and maturation by interacting with apolipoprotein B. Cell Metab. 9:177-190.
75. Wojchowski DM, Sathyanarayana P, Dev A. 2010. Erythropoietin receptor response circuits. Curr. Opin. Hematol. 17:169 -176.