Three novel downstream promoter elements regulate MHC class I promoter activity in mammalian cells

PLoS ONE

Volumn 5, Issue 12, 2010, Pages

  Lee, Namhoon ^a,b   Iyer, Shankar S ^a,c   Mu, Jie ^a   Weissman, Jocelyn D ^a   Ohali, Anat ^a   Howcroft, T Kevin ^a   Lewis, Brian A ^a   Singer, Dinah S ^a  

^a NATIONAL CANCER INSTITUTE   (United States)

^b JOHNS HOPKINS UNIVERSITY   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 1; CYTOKINE; HLA ANTIGEN CLASS 1; TATA BINDING PROTEIN ASSOCIATED FACTOR; TATA BINDING PROTEIN ASSOCIATED FACTOR 250 KDA; TATA-BINDING PROTEIN ASSOCIATED FACTOR 250 KDA; TRANSCRIPTION FACTOR IID;

3' UNTRANSLATED REGION; ANTIGEN DETECTION; ANTIGEN EXPRESSION; ANTIGEN FUNCTION; ARTICLE; CONTROLLED STUDY; GENE LOCATION; GENE MUTATION; GENE SEQUENCE; HELA CELL; HUMAN; HUMAN CELL; MAMMAL CELL; PROMOTER REGION; REGULATORY MECHANISM; ANIMAL; BIOLOGICAL MODEL; CRICETULUS; GENE; GENETIC TRANSCRIPTION; GENETICS; HAMSTER; METABOLISM; PLASMID; REGULATORY SEQUENCE; TISSUE DISTRIBUTION;

MAMMALIA;

ANIMALS; CRICETINAE; CRICETULUS; CYTOKINES; GENES, MHC CLASS I; HELA CELLS; HISTOCOMPATIBILITY ANTIGENS CLASS I; HUMANS; MODELS, GENETIC; PLASMIDS; PROMOTER REGIONS, GENETIC; REGULATORY ELEMENTS, TRANSCRIPTIONAL; TATA-BINDING PROTEIN ASSOCIATED FACTORS; TISSUE DISTRIBUTION; TRANSCRIPTION FACTOR TFIID; TRANSCRIPTION, GENETIC;

EID: 78650786671     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0015278     Document Type: Article

References (54)

1. Wong C, Rougier-Chapman EM, Frederick JP, Datto MB, Liberati NT, et al. (1999) Smad3-Smad4 and AP-1 complexes synergize in transcriptional activation of the c-Jun promoter by transforming growth factor beta. Mol Cell Biol 19: 1821-1830.
2. Berk AJ (1999) Activation of RNA polymerase II transcription. Curr Opin Cell Biol 11: 330-335.
3. Chen JL, Attardi LD, Verrijzer CP, Yokomori K, Tjian R (1994) Assembly of recombinant TFIID reveals differential coactivator requirements for distinct transcriptional activators. Cell 79: 93-105.
4. Gill G (2001) Regulation of the initiation of eukaryotic transcription. Essays Biochem 37: 33-43.
5. Kadonaga JT (2004) Regulation of RNA polymerase II transcription by sequence-specific DNA binding factors. Cell 116: 247-257.
6. Roeder RG (1996) The role of general initiation factors in transcription by RNA polymerase II. Trends Biochem Sci 21: 327-335.
7. Struhl K (2001) Gene regulation. A paradigm for precision. Science 293: 1054-1055.
8. Burke TW, Kadonaga JT (1997) The downstream core promoter element, DPE, is conserved from Drosophila to humans and is recognized by TAFII60 of Drosophila. Genes Dev 11: 3020-3031.
9. Kutach AK, Kadonaga JT (2000) The downstream promoter element DPE appears to be as widely used as the TATA box in Drosophila core promoters. Mol Cell Biol 20: 4754-4764.
10. Lagrange T, Kapanidis AN, Tang H, Reinberg D, Ebright RH (1998) New core promoter element in RNA polymerase II-dependent transcription: sequencespecific DNA binding by transcription factor IIB. Genes Dev 12: 34-44.
11. Lee DH, Gershenzon N, Gupta M, Ioshikhes IP, Reinberg D, et al. (2005) Functional characterization of core promoter elements: the downstream core element is recognized by TAF1. Mol Cell Biol 25: 9674-9686.
12. Smale ST, Baltimore D (1989) The ''initiator'' as a transcription control element. Cell 57: 103-113.
13. Willy PJ, Kobayashi R, Kadonaga JT (2000) A basal transcription factor that activates or represses transcription. Science 290: 982-985.
14. Butler JE, Kadonaga JT (2002) The RNA polymerase II core promoter: a key component in the regulation of gene expression. Genes Dev 16: 2583-2592.
15. Smale ST, Kadonaga JT (2003) The RNA polymerase II core promoter. Annu Rev Biochem 72: 449-479.
16. Burke TW, Kadonaga JT (1996) Drosophila TFIID binds to a conserved downstream basal promoter element that is present in many TATA-boxdeficient promoters. Genes Dev 10: 711-724.
17. Lewis BA, Kim TK, Orkin SH (2000) A downstream element in the human beta-globin promoter: evidence of extended sequence-specific transcription factor IID contacts. Proc Natl Acad Sci U S A 97: 7172-7177.
18. Tokusumi Y, Ma Y, Song X, Jacobson RH, Takada S (2007) The new core promoter element XCPE1 (X Core Promoter Element 1) directs activator-, mediator-, and TATA-binding protein-dependent but TFIID-independent RNA polymerase II transcription from TATA-less promoters. Mol Cell Biol 27: 1844-1858.
19. Anish R, Hossain MB, Jacobson RH, Takada S (2009) Characterization of transcription from TATA-less promoters: identification of a new core promoter element XCPE2 and analysis of factor requirements. PLoS One 4: e5103.
20. Lim CY, Santoso B, Boulay T, Dong E, Ohler U, et al. (2004) The MTE, a new core promoter element for transcription by RNA polymerase II. Genes Dev 18: 1606-1617.
21. Shao H, Revach M, Moshonov S, Tzuman Y, Gazit K, et al. (2005) Core promoter binding by histone-like TAF complexes. Mol Cell Biol 25: 206-219.
22. Wright KJ, Marr MT, 2nd, Tjian R (2006) TAF4 nucleates a core subcomplex of TFIID and mediates activated transcription from a TATA-less promoter. Proc Natl Acad Sci U S A 103: 12347-12352.
23. Lewis BA, Sims RJ, 3rd, Lane WS, Reinberg D (2005) Functional characterization of core promoter elements: DPE-specific transcription requires the protein kinase CK2 and the PC4 coactivator. Mol Cell 18: 471-481.
24. Hampsey M (1998) Molecular genetics of the RNA polymerase II general transcriptional machinery. Microbiol Mol Biol Rev 62: 465-503.
25. Reinberg D, Orphanides G, Ebright R, Akoulitchev S, Carcamo J, et al. (1998) The RNA polymerase II general transcription factors: past, present, and future. Cold Spring Harb Symp Quant Biol 63: 83-103.
26. Smale ST (2001) Core promoters: active contributors to combinatorial gene regulation. Genes Dev 15: 2503-2508.
27. Girdlestone J (1996) Transcriptional regulation of MHC class I genes. Eur J Immunogenet 23: 395-413.
28. Le Bouteiller P (1994) HLA class I chromosomal region, genes, and products: facts and questions. Crit Rev Immunol 14: 89-129.
29. Singer DS, Maguire JE (1990) Regulation of the expression of class I MHC genes. Crit Rev Immunol 10: 235-257.
30. David-Watine B, Israel A, Kourilsky P (1990) The regulation and expression of MHC class I genes. Immunol Today 11: 286-292.
31. Girdlestone J (1995) Regulation of HLA class I loci by interferons. Immunobiology 193: 229-237.
32. Singer DS, Mozes E, Kirshner S, Kohn LD (1997) Role of MHC class I molecules in autoimmune disease. Crit Rev Immunol 17: 463-468.
33. Gobin SJ, Peijnenburg A, Keijsers V, van den Elsen PJ (1997) Site alpha is crucial for two routes of IFN gamma-induced MHC class I transactivation: the ISRE-mediated route and a novel pathway involving CIITA. Immunity 6: 601-611.
34. Ishiguro N, Brown GD, Meruelo D (1997) Activation transcription factor 1 involvement in the regulation of murine H-2Dd expression. J Biol Chem 272: 15993-16001.
35. Nagarajan UM, Peijnenburg A, Gobin SJ, Boss JM, van den elsen PJ (2000) Novel mutations within the RFX-B gene and partial rescue of MHC and related genes through exogenous class II transactivator in RFX-B-deficient cells. J Immunol 164: 3666-3674.
36. Howcroft TK, Singer DS (2003) Expression of nonclassical MHC class Ib genes: comparison of regulatory elements. Immunol Res 27: 1-30.
37. Martin BK, Chin KC, Olsen JC, Skinner CA, Dey A, et al. (1997) Induction of MHC class I expression by the MHC class II transactivator CIITA. Immunity 6: 591-600.
38. Raval A, Howcroft TK, Weissman JD, Kirshner S, Zhu XS, et al. (2001) Transcriptional coactivator, CIITA, is an acetyltransferase that bypasses a promoter requirement for TAF(II)250. Mol Cell 7: 105-115.
39. Iyer V, Struhl K (1995) Mechanism of differential utilization of the his3 TR and TC TATA elements. Mol Cell Biol 15: 7059-7066.
40. Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa K, et al. (2006) Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet 38: 626-635.
41. Lee MP, Howcroft K, Kotekar A, Yang HH, Buetow KH, et al. (2005) ATG deserts define a novel core promoter subclass. Genome Res 15: 1189-1197.
42. Singer DS, Ehrlich R (1988) Identification of regulatory elements associated with a class I MHC gene. Curr Top Microbiol Immunol 137: 148-154.
43. Raval A, Weissman JD, Howcroft TK, Singer DS (2003) The GTP-binding domain of class II transactivator regulates its nuclear export. J Immunol 170: 922-930.
44. Howcroft TK, Raval A, Weissman JD, Gegonne A, Singer DS (2003) Distinct transcriptional pathways regulate basal and activated major histocompatibility complex class I expression. Mol Cell Biol 23: 3377-3391.
45. Weissman JD, Howcroft TK, Singer DS (2000) TAF(II)250-independent transcription can be conferred on a TAF(II)250-dependent basal promoter by upstream activators. J Biol Chem 275: 10160-10167.
46. Howcroft TK, Murphy C, Weissman JD, Huber SJ, Sawadogo M, et al. (1999) Upstream stimulatory factor regulates major histocompatibility complex class I gene expression: the U2DeltaE4 splice variant abrogates E-box activity. Mol Cell Biol 19: 4788-4797.
47. Maguire JE, Frels WI, Richardson JC, Weissman JD, Singer DS (1992) In vivo function of regulatory DNA sequence elements of a major histocompatibility complex class I gene. Mol Cell Biol 12: 3078-3086.
48. Kaufmann J, Verrijzer CP, Shao J, Smale ST (1996) CIF, an essential cofactor for TFIID-dependent initiator function. Genes Dev 10: 873-886.
49. Butler JE, Kadonaga JT (2001) Enhancer-promoter specificity mediated by DPE or TATA core promoter motifs. Genes Dev 15: 2515-2519.
50. Ohtsuki S, Levine M, Cai HN (1998) Different core promoters possess distinct regulatory activities in the Drosophila embryo. Genes Dev 12: 547-556.
51. Frels WI, Bluestone JA, Hodes RJ, Capecchi MR, Singer DS (1985) Expression of a microinjected porcine class I major histocompatibility complex gene in transgenic mice. Science 228: 577-580.
52. Singer DS, Camerini-Otero RD, Satz ML, Osborne B, Sachs D, et al. (1982) Characterization of a porcine genomic clone encoding a major histocompatibility antigen: expression in mouse L cells. Proc Natl Acad Sci U S A 79: 1403-1407.
53. Howcroft TK, Richardson JC, Singer DS (1993) MHC class I gene expression is negatively regulated by the proto-oncogene, c-jun. EMBO J 12: 3163-3169.
54. Howcroft TK, Palmer LA, Brown J, Rellahan B, Kashanchi F, et al. (1995) HIV Tat represses transcription through Sp1-like elements in the basal promoter. Immunity 3: 127-138.