Oct-1, to go or not to go? That is the PolII question

Biochimica et Biophysica Acta - Gene Regulatory Mechanisms

Volumn 1859, Issue 6, 2016, Pages 820-824

  Pance, Alena ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

Oct transcription factors; Oct 1 POU2f1; PolII pausing; RNA PolII; transcriptional regulation mechanisms

Indexed keywords

CYCLIN DEPENDENT KINASE 7; CYCLIN DEPENDENT KINASE 9; CYCLIN T; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; INDUCIBLE NITRIC OXIDE SYNTHASE; OCTAMER TRANSCRIPTION FACTOR 1; OCTAMER TRANSCRIPTION FACTOR 2; OCTAMER TRANSCRIPTION FACTOR 4; RNA POLYMERASE II; TATA BINDING PROTEIN; CHROMATIN; HISTONE DEACETYLASE; HISTONE DEMETHYLASE; KDM3A PROTEIN, HUMAN; POU2F1 PROTEIN, HUMAN; PROTEIN BINDING;

ARTICLE; CARBOXY TERMINAL SEQUENCE; GENE CONTROL; HOMEOSTASIS; HUMAN; MOLECULAR INTERACTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN PHOSPHORYLATION; REGULATORY MECHANISM; TRANSCRIPTION ELONGATION; TRANSCRIPTION REGULATION; ANIMAL; CHEMISTRY; CHROMATIN; CHROMATIN ASSEMBLY AND DISASSEMBLY; CYTOLOGY; EUKARYOTIC CELL; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; METABOLISM; SIGNAL TRANSDUCTION;

ANIMALS; CHROMATIN; CHROMATIN ASSEMBLY AND DISASSEMBLY; EUKARYOTIC CELLS; GENE EXPRESSION REGULATION; HUMANS; JUMONJI DOMAIN-CONTAINING HISTONE DEMETHYLASES; MI-2 NUCLEOSOME REMODELING AND DEACETYLASE COMPLEX; OCTAMER TRANSCRIPTION FACTOR-1; PROTEIN BINDING; RNA POLYMERASE II; SIGNAL TRANSDUCTION; TRANSCRIPTION, GENETIC;

EID: 84982860445     PISSN: 18749399     EISSN: 18764320     Source Type: Journal    
DOI: 10.1016/j.bbagrm.2016.04.003     Document Type: Article

References (74)

1. [1] Kuras, L., Struhl, K., Binding of TBP to promoters in vivo is stimulated by activators and requires Pol II holoenzyme. Nature 399:6736 (1999), 609–613.
2. [2] Kim, T.H., Barrera, L.O., Zheng, M., et al. A high-resolution map of active promoters in the human genome. Nature 436:7052 (2005), 876–880.
3. [3] Guenther, M.G., Levine, S.S., Boyer, L.A., Jaenisch, R., Young, R.A., A chromatin landmark and transcription initiation at most promoters in human cells. Cell 130:1 (2007), 77–88.
4. [4] Core, L.J., Waterfall, J.J., Lis, J.T., Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322:5909 (2008), 1845–1848.
5. [5] Muse, G.W., Gilchrist, D.A., Nechaev, S., et al. RNA polymerase is poised for activation across the genome. Nat. Genet. 39:12 (2007), 1507–1511.
6. [6] Zeitlinger, J., Stark, A., Kellis, M., et al. RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo. Nat. Genet. 39:12 (2007), 1512–1516.
7. [7] Rougvie, A.E., Lis, J.T., The RNA polymerase II molecule at the 5′ end of the uninduced hsp70 gene of D. melanogaster is transcriptionally engaged. Cell 54:6 (1988), 795–804.
8. [8] Adelman, K., Kennedy, M.A., Nechaev, S., et al. Immediate mediators of the inflammatory response are poised for gene activation through RNA polymerase II stalling. Proc. Natl. Acad. Sci. U. S. A. 106:43 (2009), 18207–18212.
9. [9] Bunch, H., Zheng, X., Burkholder, A., et al. TRIM28 regulates RNA polymerase II promoter-proximal pausing and pause release. Nat. Struct. Mol. Biol. 21:10 (2014), 876–883.
10. [10] Gilchrist, D.A., Dos Santos, G., Fargo, D.C., et al. Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation. Cell 143:4 (2010), 540–551.
11. [11] Tantin, D., Oct transcription factors in development and stem cells: insights and mechanisms. Development 140:14 (2013), 2857–2866.
12. [12] Theodorou, E., Dalembert, G., Heffelfinger, C., et al. A high throughput embryonic stem cell screen identifies Oct-2 as a bifunctional regulator of neuronal differentiation. Genes Dev. 23:5 (2009), 575–588.
13. [13] Staudt, L.M., Singh, H., Sen, R., Wirth, T., Sharp, P.A., Baltimore, D., A lymphoid-specific protein binding to the octamer motif of immunoglobulin genes. Nature 323:6089 (1986), 640–643.
14. [14] Tokuzawa, Y., Maruyama, M., Yamanaka, S., Utilization of digital differential display to identify novel targets of Oct3/4. Methods Mol. Biol. 329 (2006), 223–231.
15. [15] Ferraris, L., Stewart, A.P., Kang, J., et al. Combinatorial binding of transcription factors in the pluripotency control regions of the genome. Genome Res. 21:7 (2011), 1055–1064.
16. [16] Myers, L.C., Kornberg, R.D., Mediator of transcriptional regulation. Annu. Rev. Biochem. 69 (2000), 729–749.
17. [17] Komarnitsky, P., Cho, E.J., Buratowski, S., Different phosphorylated forms of RNA polymerase II and associated mRNA processing factors during transcription. Genes Dev. 14:19 (2000), 2452–2460.
18. [18] Krumm, A., Meulia, T., Brunvand, M., Groudine, M., The block to transcriptional elongation within the human c-myc gene is determined in the promoter-proximal region. Genes Dev. 6:11 (1992), 2201–2213.
19. [19] Narita, T., Yamaguchi, Y., Yano, K., et al. Human transcription elongation factor NELF: identification of novel subunits and reconstitution of the functionally active complex. Mol. Cell. Biol. 23:6 (2003), 1863–1873.
20. [20] Gilchrist, D.A., Nechaev, S., Lee, C., et al. NELF-mediated stalling of Pol II can enhance gene expression by blocking promoter-proximal nucleosome assembly. Genes Dev. 22:14 (2008), 1921–1933.
21. [21] Yamaguchi, Y., Takagi, T., Wada, T., et al. NELF, a multisubunit complex containing RD, cooperates with DSIF to repress RNA polymerase II elongation. Cell 97:1 (1999), 41–51.
22. [22] Yamaguchi, Y., Inukai, N., Narita, T., Wada, T., Handa, H., Evidence that negative elongation factor represses transcription elongation through binding to a DRB sensitivity-inducing factor/RNA polymerase II complex and RNA. Mol. Cell. Biol. 22:9 (2002), 2918–2927.
23. [23] Cheng, B., Price, D.H., Properties of RNA polymerase II elongation complexes before and after the P-TEFb-mediated transition into productive elongation. J. Biol. Chem. 282:30 (2007), 21901–21912.
24. [24] Cheng, B., Li, T., Rahl, P.B., et al. Functional association of Gdown1 with RNA polymerase II poised on human genes. Mol. Cell 45:1 (2012), 38–50.
25. [25] Peterlin, B.M., Price, D.H., Controlling the elongation phase of transcription with P-TEFb. Mol. Cell 23:3 (2006), 297–305.
26. [26] Odawara, J., Harada, A., Yoshimi, T., et al. The classification of mRNA expression levels by the phosphorylation state of RNAPII CTD based on a combined genome-wide approach. BMC Genomics, 12, 2011, 516.
27. [27] Kwak, H., Fuda, N.J., Core, L.J., Lis, J.T., Precise maps of RNA polymerase reveal how promoters direct initiation and pausing. Science 339:6122 (2013), 950–953.
28. [28] Ansari, S.A., He, Q., Morse, R.H., Mediator complex association with constitutively transcribed genes in yeast. Proc. Natl. Acad. Sci. U. S. A. 106:39 (2009), 16734–16739.
29. [29] Takagi, Y., Kornberg, R.D., Mediator as a general transcription factor. J. Biol. Chem. 281:1 (2006), 80–89.
30. [30] Taatjes, D.J., Tjian, R., Structure and function of CRSP/Med2; a promoter-selective transcriptional coactivator complex. Mol. Cell 14:5 (2004), 675–683.
31. [31] Meyer, K.D., Lin, S.C., Bernecky, C., Gao, Y., Taatjes, D.J., p53 activates transcription by directing structural shifts in mediator. Nat. Struct. Mol. Biol. 17:6 (2010), 753–760.
32. [32] Wang, Y., Liu, F., Wang, W., Dynamic mechanism for the transcription apparatus orchestrating reliable responses to activators. Sci. Report., 2, 2012, 422.
33. [33] Kim, Y.J., Bjorklund, S., Li, Y., Sayre, M.H., Kornberg, R.D., A multiprotein mediator of transcriptional activation and its interaction with the C-terminal repeat domain of RNA polymerase II. Cell 77:4 (1994), 599–608.
34. [34] Jiang, Y.W., Veschambre, P., Erdjument-Bromage, H., et al. Mammalian mediator of transcriptional regulation and its possible role as an end-point of signal transduction pathways. Proc. Natl. Acad. Sci. U. S. A. 95:15 (1998), 8538–8543.
35. [35] Sogaard, T.M., Svejstrup, J.Q., Hyperphosphorylation of the C-terminal repeat domain of RNA polymerase II facilitates dissociation of its complex with mediator. J. Biol. Chem. 282:19 (2007), 14113–14120.
36. [36] Park, J.M., Werner, J., Kim, J.M., Lis, J.T., Kim, Y.J., Mediator, not holoenzyme, is directly recruited to the heat shock promoter by HSF upon heat shock. Mol. Cell 8:1 (2001), 9–19.
37. [37] Poss, Z.C., Ebmeier, C.C., Taatjes, D.J., The Mediator complex and transcription regulation. Crit. Rev. Biochem. Mol. Biol. 48:6 (2013), 575–608.
38. [38] Cartwright, P., McLean, C., Sheppard, A., Rivett, D., Jones, K., Dalton, S., LIF/STAT3 controls ES cell self-renewal and pluripotency by a Myc-dependent mechanism. Development 132:5 (2005), 885–896.
39. [39] Rahl, P.B., Lin, C.Y., Seila, A.C., et al. c-Myc regulates transcriptional pause release. Cell 141:3 (2010), 432–445.
40. [40] Hendrix, D.A., Hong, J.W., Zeitlinger, J., Rokhsar, D.S., Levine, M.S., Promoter elements associated with RNA Pol II stalling in the Drosophila embryo. Proc. Natl. Acad. Sci. U. S. A. 105:22 (2008), 7762–7767.
41. [41] Jonkers, I., Lis, J.T., Getting up to speed with transcription elongation by RNA polymerase II. Nat. Rev. Mol. Cell Biol. 16:3 (2015), 167–177.
42. [42] Blau, J., Xiao, H., McCracken, S., O'Hare, P., Greenblatt, J., Bentley, D., Three functional classes of transcriptional activation domain. Mol. Cell. Biol. 16:5 (1996), 2044–2055.
43. [43] Remenyi, A., Tomilin, A., Pohl, E., et al. Differential dimer activities of the transcription factor Oct-1 by DNA-induced interface swapping. Mol. Cell 8:3 (2001), 569–580.
44. [44] Takahashi, K., Yamanaka, S., Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126:4 (2006), 663–676.
45. [45] Latchman, D.S., POU family transcription factors in the nervous system. J. Cell. Physiol. 179:2 (1999), 126–133.
46. [46] Reveneau, S., Petrakis, T.G., Goldring, C.E., Chantome, A., Jeannin, J.F., Pance, A., Oct-1 cooperates with the TATA binding initiation complex to control rapid transcription of human iNOS. Cell. Mol. Life Sci. 69:15 (2012), 2609–2619.
47. [47] Latchman, D.S., Activation and repression of gene expression by POU family transcription factors. Philos. Trans. R. Soc. Lond. Ser. B Biol. Sci. 351:1339 (1996), 511–515.
48. [48] Lillycrop, K.A., Latchman, D.S., Alternative splicing of the Oct-2 transcription factor RNA is differentially regulated in neuronal cells and B cells and results in protein isoforms with opposite effects on the activity of octamer/TAATGARAT-containing promoters. J. Biol. Chem. 267:35 (1992), 24960–24965.
49. [49] Kim, Y.M., Ko, C.B., Park, Y.P., Kim, Y.J., Paik, S.G., Octamer motif is required for the NF-kappaB-mediated induction of the inducible nitric oxide synthase gene expression in RAW 264.7 macrophages. Mol. Cell 9:1 (1999), 99–109.
50. [50] Shakya, A., Kang, J., Chumley, J., Williams, M.A., Tantin, D., Oct1 is a switchable, bipotential stabilizer of repressed and inducible transcriptional states. J. Biol. Chem. 286:1 (2011), 450–459.
51. [51] Kim, M.H., Peterson, D.O., Stimulation of basal transcription from the mouse mammary tumor virus promoter by Oct proteins. J. Virol. 69:8 (1995), 4717–4726.
52. [52] Xie, Q., A novel lipopolysaccharide-response element contributes to induction of nitric oxide synthase. J. Biol. Chem. 272:23 (1997), 14867–14872.
53. [53] Kang, H.B., Fan, J., Lin, R., et al. Metabolic rewiring by oncogenic BRAF V600E links ketogenesis pathway to BRAF-MEK1 signaling. Mol. Cell 59:3 (2015), 345–358.
54. [54] Murayama A, Sakura K, Nakama M, et al. A specific CpG site demethylation in the human interleukin 2 gene promoter is an epigenetic memory. EMBO J. 2006;25(5):1081-1092.
55. [55] Bertolino, E., Singh, H., POU/TBP cooperativity: a mechanism for enhancer action from a distance. Mol. Cell 10:2 (2002), 397–407.
56. [56] Zwilling, S., Annweiler, A., Wirth, T., The POU domains of the Oct1 and Oct2 transcription factors mediate specific interaction with TBP. Nucleic Acids Res. 22:9 (1994), 1655–1662.
57. [57] Kim, M.H., Peterson, D.O., Oct-1 protein promotes functional transcription complex assembly on the mouse mammary tumor virus promoter. J. Biol. Chem. 270:46 (1995), 27823–27828.
58. [58] Nakshatri, H., Nakshatri, P., Currie, R.A., Interaction of Oct-1 with TFIIB. Implications for a novel response elicited through the proximal octamer site of the lipoprotein lipase promoter. J. Biol. Chem. 270:33 (1995), 19613–19623.
59. [59] Schild-Poulter, C., Shih, A., Tantin, D., et al. DNA-PK phosphorylation sites on Oct-1 promote cell survival following DNA damage. Oncogene 26:27 (2007), 3980–3988.
60. [60] Ansari, K.I., Ogawa, D., Rooj, A.K., et al. Glucose-based regulation of miR-451/AMPK signaling depends on the OCT1 transcription factor. Cell Rep. 11:6 (2015), 902–909.
61. [61] James Faresse, N., Canella, D., Praz, V., Michaud, J., Romascano, D., Hernandez, N., Genomic study of RNA polymerase II and III SNAPc-bound promoters reveals a gene transcribed by both enzymes and a broad use of common activators. PLoS Genet., 8(11), 2012, e1003028.
62. [62] Bentrari, F., Chantome, A., Knights, A., Jeannin, J.F., Pance, A., Oct-2 forms a complex with Oct-1 on the iNOS promoter and represses transcription by interfering with recruitment of RNA PolII by Oct-1. Nucleic Acids Res. 43:20 (2015), 9757–9765.
63. [63] Inamoto, S., Segil, N., Pan, Z.Q., Kimura, M., Roeder, R.G., The cyclin-dependent kinase-activating kinase (CAK) assembly factor, MAT1, targets and enhances CAK activity on the POU domains of octamer transcription factors. J. Biol. Chem. 272:47 (1997), 29852–29858.
64. [64] Darville, M.I., Terryn, S., Eizirik, D.L., An octamer motif is required for activation of the inducible nitric oxide synthase promoter in pancreatic beta-cells. Endocrinology 145:3 (2004), 1130–1136.
65. [65] Goldring, C.E., Reveneau, S., Algarte, M., Jeannin, J.F., In vivo footprinting of the mouse inducible nitric oxide synthase gene: inducible protein occupation of numerous sites including Oct and NF-IL6. Nucleic Acids Res. 24:9 (1996), 1682–1687.
66. [66] Raschke, E.E., Albert, T., Eick, D., Transcriptional regulation of the Ig kappa gene by promoter-proximal pausing of RNA polymerase II. J. Immunol. 163:8 (1999), 4375–4382.
67. [67] Barboric, M., Nissen, R.M., Kanazawa, S., Jabrane-Ferrat, N., Peterlin, B.M., NF-kappaB binds P-TEFb to stimulate transcriptional elongation by RNA polymerase II. Mol. Cell 8:2 (2001), 327–337.
68. [68] Diamant, G., Dikstein, R., Transcriptional control by NF-kappaB: elongation in focus. Biochim. Biophys. Acta 1829:9 (2013), 937–945.
69. [69] Taylor, B.S., de Vera, M.E., Ganster, R.W., et al. Multiple NF-kappaB enhancer elements regulate cytokine induction of the human inducible nitric oxide synthase gene. J. Biol. Chem. 273:24 (1998), 15148–15156.
70. [70] Luecke, H.F., Yamamoto, K.R., The glucocorticoid receptor blocks P-TEFb recruitment by NFkappaB to effect promoter-specific transcriptional repression. Genes Dev. 19:9 (2005), 1116–1127.
71. [71] van Heel, D.A., Udalova, I.A., De Silva, A.P., et al. Inflammatory bowel disease is associated with a TNF polymorphism that affects an interaction between the OCT1 and NF(-kappa)B transcription factors. Hum. Mol. Genet. 11:11 (2002), 1281–1289.
72. [72] dela Paz, N.G., Simeonidis, S., Leo, C., Rose, D.W., Collins, T., Regulation of NF-kappaB-dependent gene expression by the POU domain transcription factor Oct-1. J. Biol. Chem. 282:11 (2007), 8424–8434.
73. [73] Shakya, A., Goren, A., Shalek, A., et al. Oct1 and OCA-B are selectively required for CD4 memory T cell function. J. Exp. Med. 212:12 (2015), 2115–2131.
74. [74] Donner, A.L., Episkopou, V., Maas, R.L., Sox2 and Pou2f1 interact to control lens and olfactory placode development. Dev. Biol. 303:2 (2007), 784–799.