Subnuclear segregation of genes and core promoter factors in myogenesis

Genes and Development

Volumn 25, Issue 6, 2011, Pages 569-580

  Yao, Jie ^a,b   Fetter, Richard D ^a   Hu, Ping ^b   Betzig, Eric ^a   Tjian, Robert ^a,b  

^a HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Core promoter factors; MyoD; Nucleus; Superresolution microscopy; Transcription

Indexed keywords

PROTEIN SUBUNIT; PROTEIN TAF3; TRANSCRIPTION FACTOR IID; UNCLASSIFIED DRUG;

ANIMAL CELL; ANIMAL TISSUE; ARTICLE; CELL DIFFERENTIATION; CONTROLLED STUDY; GENE; GENE SEGREGATION; GENETIC TRANSCRIPTION; MOUSE; MUSCLE DEVELOPMENT; MYOBLAST; MYOD GENE; MYOTUBE; NEWBORN; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN LOCALIZATION;

ANIMALS; CELL DIFFERENTIATION; CELL LINE; CELL NUCLEUS; CELLS, CULTURED; HOMEODOMAIN PROTEINS; MICE; MUSCLE DEVELOPMENT; MYOD PROTEIN; MYOGENIN; PROMOTER REGIONS, GENETIC; PROTEIN TRANSPORT; TRANSCRIPTION FACTORS;

EID: 79952597171     PISSN: 08909369     EISSN: 15495477     Source Type: Journal    
DOI: 10.1101/gad.2021411     Document Type: Article

References (61)

1. Akhtar A, Gasser SM. 2007. The nuclear envelope and transcriptional control. Nat Rev Genet 8: 507-517. (Pubitemid 46955211)
2. Andrulis ED, Neiman AM, Zappulla DC, Sternglanz R. 1998. Perinuclear localization of chromatin facilitates transcriptional silencing. Nature 394: 592-595. (Pubitemid 28366836)
3. Bancaud A, Huet S, Daigle N, Mozziconacci J, Beaudouin J, Ellenberg J. 2009. Molecular crowding affects diffusion and binding of nuclear proteins in heterochromatin and reveals the fractal organization of chromatin. EMBO J 28: 3785-3798.
4. Bates M, Huang B, Dempsey GT, Zhuang X. 2007. Multicolor super-resolution imaging with photo-switchable fluorescent probes. Science 317: 1749-1753. (Pubitemid 47461839)
5. Betzig E, Patterson GH, Sougrat R, Lindwasser OW, Olenych S, Bonifacino JS, Davidson MW, Lippincott-Schwartz J, Hess HF. 2006. Imaging intracellular fluorescent proteins at nanometer resolution. Science 313: 1642-1645.
6. Brown TA, Fetter RD, Tkachuk AN, Clayton DA. 2010. Approaches toward super-resolution fluorescence imaging of mitochondrial proteins using PALM. Methods 51: 458-463.
7. Chuang CH, Carpenter AE, Fuchsova B, Johnson T, de Lanerolle P, Belmont AS. 2006. Long-range directional movement of an interphase chromosome site. Curr Biol 16: 825-831.
8. Cremer T, Cremer C. 2001. Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat Rev Genet 2: 292-301. (Pubitemid 33674777)
9. D'Alessio JA, Wright KJ, Tjian R. 2009. Shifting players and paradigms in cell-specific transcription. Mol Cell 36: 924-931.
10. Darzacq X, Yao J, Larson DR, Causse SZ, Bosanac L, de Turris V, Ruda VM, Lionnet T, Zenklusen D, Guglielmi B, et al. 2009. Imaging transcription in living cells. Annu Rev Biophys 38: 173-196.
11. Davies HG. 1967. Fine structure of heterochromatin in certain cell nuclei. Nature 214: 208-210.
12. Deato MD, Tjian R. 2007. Switching of the core transcription machinery during myogenesis. Genes Dev 21: 2137-2149. (Pubitemid 47360836)
13. 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.
14. de Graaf P, Mousson F, Geverts B, Scheer E, Tora L, Houtsmuller AB, Timmers HT. 2010. Chromatin interaction of TATA-binding protein is dynamically regulated in human cells. J Cell Sci 123: 2663-2671.
15. Edmondson DG, Olson EN. 1989. A gene with homology to the myc similarity region of MyoD1 is expressed during myogenesis and is sufficient to activate the muscle differentiation program. Genes Dev 3: 628-640.
16. Fakhouri TH, Stevenson J, Chisholm AD, Mango SE. 2010. Dynamic chromatin organization during foregut development mediated by the organ selector gene PHA-4/FoxA. PLoS Genet 6: e1001060. doi: 10.1371/journal.pgen.1001060.
17. Farnham PJ. 2009. Insights from genomic profiling of transcription factors. Nat Rev Genet 10: 605-616.
18. Finlan LE, Sproul D, Thomson I, Boyle S, Kerr E, Perry P, Ylstra B, Chubb JR, Bickmore WA. 2008. Recruitment to the nuclear periphery can alter expression of genes in human cells. PLoS Genet 4: e1000039. doi: 10.1371/journal.pgen.1000039.
19. Gangloff YG, Pointud JC, Thuault S, Carre L, Romier C, Muratoglu S, Brand M, Tora L, Couderc JL, Davidson I. 2001. The TFIID components human TAF(II)140 and Drosophila BIP2 (TAF(II)155) are novel metazoan homologues of yeast TAF(II)47 containing a histone fold and a PHD finger. Mol Cell Biol 21: 5109-5121. (Pubitemid 32656407)
20. Giglia-Mari G, Theil AF, Mari PO, Mourgues S, Nonnekens J, Andrieux LO, de Wit J, Miquel C, Wijgers N, Maas A, et al. 2009. Differentiation driven changes in the dynamic organization of Basal transcription initiation. PLoS Biol 7: e1000220. doi: 10.1371/journal.pbio.1000220.
21. Goodrich JA, Tjian R. 2010. Unexpected roles for core promoter recognition factors in cell-type-specific transcription and gene regulation. Nat Rev Genet 11: 549-558.
22. Gould TJ, Verkhusha VV, Hess ST. 2009. Imaging biological structures with fluorescence photoactivation localization microscopy. Nat Protoc 4: 291-308.
23. Guertin MJ, Lis JT. 2010. Chromatin landscape dictates HSF binding to target DNA elements. PLoS Genet 6: e1001114. doi: 10.1371/journal.pgen.1001114.
24. Hager GL, McNally JG, Misteli T. 2009. Transcription dynamics. Mol Cell 35: 741-753.
25. Heessen S, Fornerod M. 2007. The inner nuclear envelope as a transcription factor resting place. EMBO Rep 8: 914-919. (Pubitemid 47500473)
26. Hu P, Geles KG, Paik JH, DePinho RA, Tjian R. 2008. Codependent activators direct myoblast-specific MyoD transcription. Dev Cell 15: 534-546.
27. Iwase S, Lan F, Bayliss P, de la Torre-Ubieta L, Huarte M, Qi HH, Whetstine JR, Bonni A, Roberts TM, Shi Y. 2007. The X-linked mental retardation gene SMCX/JARID1C defines a family of histone H3 lysine 4 demethylases. Cell 128: 1077-1088. (Pubitemid 46437259)
28. Jenuwein T, Allis CD. 2001. Translating the histone code. Science 293: 1074-1080. (Pubitemid 32758077)
29. Ji N, Shroff H, Zhong H, Betzig E. 2008. Advances in the speed and resolution of light microscopy. Curr Opin Neurobiol 18: 605-616.
30. Johnson CV, Singer RH, Lawrence JB. 1991. Fluorescent detection of nuclear RNA and DNA: implications for genome organization. Methods Cell Biol 35: 73-99.
31. Joshi R, Passner JM, Rohs R, Jain R, Sosinsky A, Crickmore MA, Jacob V, Aggarwal AK, Honig B, Mann RS. 2007. Functional specificity of a Hox protein mediated by the recognition of minor groove structure. Cell 131: 530-543. (Pubitemid 350007697)
32. Kumaran RI, Spector DL. 2008. A genetic locus targeted to the nuclear periphery in living cells maintains its transcriptional competence. J Cell Biol 180: 51-65.
33. Kumaran RI, Thakar R, Spector DL. 2008. Chromatin dynamics and gene positioning. Cell 132: 929-934. (Pubitemid 351381750)
34. Lan F, Collins RE, De Cegli R, Alpatov R, Horton JR, Shi X, Gozani O, Cheng X, Shi Y. 2007. Recognition of unmethylated histone H3 lysine 4 links BHC80 to LSD1-mediated gene repression. Nature 448: 718-722. (Pubitemid 47236862)
35. Lee H, Quinn JC, Prasanth KV, Swiss VA, Economides KD, Camacho MM, Spector DL, Abate-Shen C. 2006. PIAS1 confers DNA-binding specificity on the Msx1 homeoprotein. Genes Dev 20: 784-794.
36. Liu WL, Coleman RA, Grob P, King DS, Florens L, Washburn MP, Geles KG, Yang JL, Ramey V, Nogales E, et al. 2008. Structural changes in TAF4b-TFIID correlate with promoter selectivity. Mol Cell 29: 81-91.
37. Liu WL, Coleman RA, Ma E, Grob P, Yang JL, Zhang Y, Dailey G, Nogales E, Tjian R. 2009. Structures of three distinct activator-TFIID complexes. Genes Dev 23: 1510-1521.
38. Lusk CP, Blobel G, King MC. 2007. Highway to the inner nuclear membrane: rules for the road. Nat Rev Mol Cell Biol 8: 414-420. (Pubitemid 46643242)
39. Malhas AN, Lee CF, Vaux DJ. 2009. Lamin B1 controls oxidative stress responses via Oct-1. J Cell Biol 184: 45-55.
40. Marr MT II, Isogai Y, Wright KJ, Tjian R. 2006. Coactivator cross-talk specifies transcriptional output. Genes Dev 20: 1458-1469. (Pubitemid 43830653)
41. Meister P, Towbin BD, Pike BL, Ponti A, Gasser SM. 2010. The spatial dynamics of tissue-specific promoters during C. elegans development. Genes Dev 24: 766-782.
42. Misteli T. 2007. Beyond the sequence: cellular organization of genome function. Cell 128: 787-800. (Pubitemid 46273571)
43. Moen PT Jr, Johnson CV, Byron M, Shopland LS, de la Serna IL, Imbalzano AN, Lawrence JB. 2004. Repositioning of muscle-specific genes relative to the periphery of SC-35 domains during skeletal myogenesis. Mol Biol Cell 15: 197-206. (Pubitemid 38044956)
44. Muller F, Zaucker A, Tora L. 2010. Developmental regulation of transcription initiation: more than just changing the actors. Curr Opin Genet Dev 20: 533-540.
45. Naar AM, Lemon BD, Tjian R. 2001. Transcriptional coactivator complexes. Annu Rev Biochem 70: 475-501. (Pubitemid 32662218)
46. Peric-Hupkes D, Meuleman W, Pagie L, Bruggeman SW, Solovei I, Brugman W, Graf S, Flicek P, Kerkhoven RM, van Lohuizen M, et al. 2010. Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation. Mol Cell 38: 603-613.
47. Reddy KL, Zullo JM, Bertolino E, Singh H. 2008. Transcriptional repression mediated by repositioning of genes to the nuclear lamina. Nature 452: 243-247. (Pubitemid 351380248)
48. Schermelleh L, Carlton PM, Haase S, Shao L, Winoto L, Kner P, Burke B, Cardoso MC, Agard DA, Gustafsson MG, et al. 2008. Subdiffraction multicolor imaging of the nuclear periphery with 3D structured illumination microscopy. Science 320: 1332-1336. (Pubitemid 351929468)
49. Schmid M, Arib G, Laemmli C, Nishikawa J, Durussel T, Laemmli UK. 2006. Nup-PI: the nucleopore-promoter interaction of genes in yeast. Mol Cell 21: 379-391. (Pubitemid 43163533)
50. Segura-Totten M, Wilson KL. 2004. BAF: roles in chromatin, nuclear structure and retrovirus integration. Trends Cell Biol 14: 261-266. (Pubitemid 38591330)
51. Shimi T, Pfleghaar K, Kojima S, Pack CG, Solovei I, Goldman AE, Adam SA, Shumaker DK, Kinjo M, Cremer T, et al. 2008. The A- and B-type nuclear lamin networks: microdomains involved in chromatin organization and transcription. Genes Dev 22: 3409-3421.
52. Shroff H, Galbraith CG, Galbraith JA, White H, Gillette J, Olenych S, Davidson MW, Betzig E. 2007. Dual-color superresolution imaging of genetically expressed probes within individual adhesion complexes. Proc Natl Acad Sci 104: 20308-20313.
53. Sinclair P, Bian Q, Plutz M, Heard E, Belmont AS. 2010. Dynamic plasticity of large-scale chromatin structure revealed by self-assembly of engineered chromosome regions. J Cell Biol 190: 761-776.
54. Spector DL. 2003. The dynamics of chromosome organization and gene regulation. Annu Rev Biochem 72: 573-608. (Pubitemid 36930454)
55. Tapscott SJ, Davis RL, Thayer MJ, Cheng PF, Weintraub H, Lassar AB. 1988. MyoD1: a nuclear phosphoprotein requiring a Myc homology region to convert fibroblasts to myoblasts. Science 242: 405-411.
56. Toomre D, Bewersdorf J. 2010. A new wave of cellular imaging. Annu Rev Cell Dev Biol 26: 285-314.
57. van Ingen H, van Schaik FM, Wienk H, Ballering J, Rehmann H, Dechesne AC, Kruijzer JA, Liskamp RM, Timmers HT, Boelens R. 2008. Structural insight into the recognition of the H3K4me3 mark by the TFIID subunit TAF3. Structure 16: 1245-1256.
58. Vermeulen M, Mulder KW, Denissov S, Pijnappel WW, van Schaik FM, Varier RA, Baltissen MP, Stunnenberg HG, Mann M, Timmers HT. 2007. Selective anchoring of TFIID to nucleosomes by trimethylation of histone H3 lysine 4. Cell 131: 58-69. (Pubitemid 47498531)
59. Wright KJ, Marr MT II, Tjian R. 2006. TAF4 nucleates a core subcomplex of TFIID and mediates activated transcription from a TATA-less promoter. Proc Natl Acad Sci 103: 12347-12352. (Pubitemid 44267262)
60. Yao J, Ardehali MB, Fecko CJ, Webb WW, Lis JT. 2007. Intranuclear distribution and local dynamics of RNA polymerase II during transcription activation. Mol Cell 28: 978-990. (Pubitemid 350297022)
61. Zhai W, Jeong H, Cui L, Krainc D, Tjian R. 2005. In vitro analysis of huntingtin-mediated transcriptional repression reveals multiple transcription factor targets. Cell 123: 1241-1253.