Core promoter factor TAF9B regulates neuronal gene expression

eLife

Volumn 2014, Issue 3, 2014, Pages

  Herrera, Francisco J ^a   Yamaguchi, Teppei ^a   Roelink, Henk ^a   Tjian, Robert ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE ACETYLTRANSFERASE PCAF; OLIGODENDROCYTE TRANSCRIPTION FACTOR 2; RNA POLYMERASE II; TATA BINDING PROTEIN ASSOCIATED FACTOR; TATA BINDING PROTEIN ASSOCIATED FACTOR TAF9B; TRANSCRIPTION FACTOR IID; UNCLASSIFIED DRUG;

ANIMAL CELL; ANIMAL TISSUE; APOPTOSIS; ARTICLE; BINDING SITE; CELL CYCLE ASSAY; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; DNA TRANSFECTION; EMBRYO; EMBRYOID BODY; EMBRYONIC STEM CELL; GENE; GENE EXPRESSION REGULATION; GENE INDUCTION; GENETIC TRANSCRIPTION; IMMUNOHISTOCHEMISTRY; MOTONEURON; MOUSE; NERVE CELL DIFFERENTIATION; NEWBORN; NONHUMAN; PROMOTER REGION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA ANALYSIS; RNA ISOLATION; TAF9B GENE; TRANSCRIPTION INITIATION; WESTERN BLOTTING;

EID: 84904044542     PISSN: None     EISSN: 2050084X     Source Type: Journal    
DOI: 10.7554/elife.02559     Document Type: Article

References (43)

1. Bu P, Evrard YA, Lozano G, Dent SYR. 2007. Loss of Gcn5 acetyltransferase activity leads to neural tube closure defects and exencephaly in mouse embryos. Molecular and Cellular Biology 27:3405-3416. doi: 10.1128/ MCB.00066-07.
2. Chen X, Hiller M, Sancak Y, Fuller MT. 2005. Tissue-specific TAFs counteract Polycomb to turn on terminal differentiation. Science 310:869-872. doi: 10.1126/science.1118101.
3. Chen Z, Manley JL. 2003. In vivo functional analysis of the histone 3-like TAF9 and a TAF9-related factor, TAF9L. Journal of Biological Chemistry 278:35172-35183. doi: 10.1074/jbc.M304241200.
4. Cheng Y, Buffone MG, Kouadio M, Goodheart M, Page DC, Gerton GL, Davidson I, Wang PJ. 2007. Abnormal sperm in mice lacking the Taf7l gene. Molecular and Cellular Biology 27:2582-2589. doi: 10.1128/ MCB.01722-06.
5. Crawford TQ, Roelink H. 2007. The notch response inhibitor DAPT enhances neuronal differentiation in embryonic stem cell-derived embryoid bodies independently of sonic hedgehog signaling. Developmental Dynamics 236:886-892. doi: 10.1002/dvdy.21083.
6. D'Alessio JA, Ng R, Willenbring H, Tjian R. 2011. Core promoter recognition complex changes accompany liver development. Proceedings of the National Academy of Sciences of the United States of America 108:3906-3911. doi: 10.1073/pnas.1100640108.
7. D'Alessio JA, Wright KJ, Tjian R. 2009. Shifting players and paradigms in cell-specific transcription. Molecular Cell 36:924-931. doi: 10.1016/j.molcel.2009.12.011.
8. Deato MDE, Tjian R. 2007. Switching of the core transcription machinery during myogenesis. Genes & Development 21:2137-2149. doi: 10.1101/gad.1583407.
9. di Sanguinetto SADT, Dasen JS, Arber S. 2008. Transcriptional mechanisms controlling motor neuron diversity and connectivity. Current Opinion in Neurobiology 18:36-43. doi: 10.1016/j.conb.2008.04.002.
10. Falender AE. 2005. Maintenance of spermatogenesis requires TAF4b, a gonad-specific subunit of TFIID. Genes & Development 19:794-803. doi: 10.1101/gad.1290105.
11. Freiman RN, Albright SR, Zheng S, Sha WC, Hammer RE, Tjian R. 2001. Requirement of tissue-selective TBP-associated factor TAFII105 in ovarian development. Science 293:2084-2087. doi: 10.1126/science.1061935.
12. Frontini M, Soutoglou E, Argentini M, Bole-Feysot C, Jost B, Scheer E, Tora L. 2005. TAF9b (Formerly TAF9L) is a bona fide TAF that has unique and overlapping roles with TAF9. Molecular and Cellular Biology 25:4638-4649. doi: 10.1128/MCB.25.11.4638-4649.2005.
13. Graf T. 2011. Historical origins of transdifferentiation and reprogramming. Cell Stem Cell 9:504-516. doi: 10.1016/j. stem.2011.11.012.
14. Goodrich JA, Tjian R. 2010. Unexpected roles for core promoter recognition factors in cell-type-specific transcription and gene regulation. Nature Reviews Genetics 11:549-558. doi: 10.1038/nrg2847.
15. Guermah M, Ge K, Chiang C-M, Roeder RG. 2003. The TBN protein, which is essential for early embryonic mouse development, is an inducible TAFII implicated in adipogenesis. Molecular Cell 12:991-1001. doi: 10.1016/ S1097-2765(03)00396-4.
16. Hiller M, Chen X, Pringle MJ, Suchorolski M, Sancak Y, Viswanathan S, Bolival B, Lin T-Y, Marino S, Fuller MT. 2004. Testis-specific TAF homologs collaborate to control a tissue-specific transcription program. Development 131:5297-5308. doi: 10.1242/dev.01314.
17. Huang DW, Sherman BT, Lempicki RA. 2009. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protocols 4:44-57. doi: 10.1038/nprot.2008.211.
18. Jessell TM. 2000. Neuronal specification in the spinal cord: inductive signals and transcriptional codes. Nature Reviews Genetics 1:20-29. doi: 10.1038/35049541.
19. Kanning KC, Kaplan A, Henderson CE. 2010. Motor neuron diversity in development and disease. Annual Review of Neuroscience 33:409-440. doi: 10.1146/annurev.neuro.051508.135722.
20. Knight ZA, Tan K, Birsoy K, Schmidt S, Garrison JL, Wysocki RW, Emiliano A, Ekstrand MI, Friedman JM. 2012. Molecular profiling of activated neurons by phosphorylated ribosome capture. Cell 151:1126-1137. doi: 10.1016/j. cell.2012.10.039.
21. Koutelou E, Hirsch CL, Dent SYR. 2010. Multiple faces of the SAGA complex. Current Opinion in Cell Biology 22:374-382. doi: 10.1016/j.ceb.2010.03.005.
22. Kurooka H, Honjo T. 2000. Functional interaction between the mouse notch1 intracellular region and histone acetyltransferases PCAF and GCN5. The Journal of Biological Chemistry 275:17211-17220. doi: 10.1074/jbc. M000909200.
23. Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25. doi: 10.1186/gb-2009-10-3-r25.
24. Lessard J, Wu JI, Ranish JA, Wan M, Winslow MM, Staahl BT, Wu H, Aebersold R, Graef IA, Crabtree GR. 2007. An essential switch in subunit composition of a chromatin remodeling complex during neural development. Neuron 55:201-215. doi: 10.1016/j.neuron.2007.06.019.
25. Liu Z, Scannell DR, Eisen MB, Tjian R. 2011. Control of embryonic stem cell lineage commitment by core promoter factor, TAF3. Cell 146:720-731. doi: 10.1016/j.cell.2011.08.005.
26. Louvi A, Artavanis-Tsakonas S. 2006. Notch signalling in vertebrate neural development. Nature Reviews Neuroscience 7:93-102. doi: 10.1038/nrn1847.
27. Mazzoni EO, Mahony S, Iacovino M, Morrison CA, Mountoufaris G, Closser M, Whyte WA, Young RA, Kyba M, Gifford DK, Wichterle H. 2011. Embryonic stem cell-based mapping of developmental transcriptional programs. Nature Methods 8:1056-1058. doi: 10.1038/nmeth.1775.
28. Müller F, Zaucker A, Tora L. 2010. Developmental regulation of transcription initiation: more than just changing the actors. Current Opinion in Genetics & Development 20:533-540. doi: 10.1016/j.gde.2010.06.004.
29. McLean CY, Bristor D, Hiller M, Clarke SL, Schaar BT, Lowe CB, Wenger AM, Bejerano G. 2010. GREAT improves functional interpretation of cis-regulatory regions. Nature Biotechnology 28:495-501. doi: 10.1038/ nbt.1630.
30. Olave I, Wang W, Xue Y, Kuo A, Crabtree GR. 2002. Identification of a polymorphic, neuron-specific chromatin remodeling complex. Genes & Development 16:2509-2517. doi: 10.1101/gad.992102.
31. Pijnappel WWMP, Esch D, Baltissen MPA, Wu G, Mischerikow N, Bergsma AJ, van der Wal E, Han DW, Bruch HV, Moritz S, Lijnzaad P, Altelaar AF, Sameith K, Zaehres H, Heck AJ, Holstege FC, Schöler HR, Timmers HT. 2013. A central role for TFIID in the pluripotent transcription circuitry. Nature 495:516-519. doi: 10.1038/nature11970.
32. Pugh BF. 1995. Preparation of HeLa nuclear extracts. Methods in Molecular Biology 37:349-357. doi: 10.1385/0- 89603-288-4:349.
33. Robberecht W, Philips T. 2013. The changing scene of amyotrophic lateral sclerosis. Nature Reviews Neuroscience 14:248-264. doi: 10.1038/nrn3430.
34. Spedale G, Timmers HTM, Pijnappel WWMP. 2012. ATAC-king the complexity of SAGA during evolution. Genes & Development 26:527-541. doi: 10.1101/gad.184705.111.
35. Trapnell C, Pachter L, Salzberg SL. 2009. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25:1105-1111. doi: 10.1093/bioinformatics/btp120.
36. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. 2010. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnology 28:511-515. doi: 10.1038/nbt.1621.
37. Wallberg AE, Pedersen K, Lendahl U, Roeder RG. 2002. p300 and PCAF act cooperatively to mediate transcriptional activation from chromatin templates by notch intracellular domains in vitro. Molecular and Cellular Biology 22:7812-7819. doi: 10.1128/MCB.22.22.7812-7819.2002.
38. Weake VM, Workman JL. 2012. SAGA function in tissue-specific gene expression. Trends in Cell Biology 22:177-184. doi: 10.1016/j.tcb.2011.11.005.
39. Weake VM, Lee KK, Guelman S, Lin C-H, Seidel C, Abmayr SM, Workman JL. 2008. SAGA-mediated H2B deubiquitination controls the development of neuronal connectivity in the Drosophila visual system. The EMBO Journal 27:394-405. doi: 10.1038/sj.emboj.7601966.
40. Wichterle H, Lieberam I, Porter JA, Jessell TM. 2002. Directed differentiation of embryonic stem cells into motor neurons. Cell 110:385-397. doi: 10.1016/S0092-8674(02)00835-8.
41. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. 2008. Model-based analysis of ChIP-Seq (MACS). Genome Biology 9:R137. doi: 10.1186/gb-2008-9-9-r137.
42. Zhou H, Grubisic I, Zheng K, He Y, Wang PJ, Kaplan T, Tjian R. 2013a. Taf7l cooperates with Trf2 to regulate spermiogenesis. Proceedings of the National Academy of Sciences of the United States of America 110:16886-16891. doi: 10.1073/pnas.1317034110.
43. Zhou H, Kaplan T, Li Y, Grubisic I, Zhang Z, Wang PJ, Eisen MB, Tjian R. 2013b. Dual functions of TAF7L in adipocyte differentiation. eLife 2:e00170. doi: 10.7554/eLife.00170.