A conserved GA element in Tata-Less RNA polymerase II promoters

PLoS ONE

Volumn 6, Issue 11, 2011, Pages

  Seizl, Martin ^a   Hartmann, Holger ^a   Hoeg, Friederike ^a   Kurth, Fabian ^a,b   Martin, Dietmar E ^a   Söding, Johannes ^a   Cramer, Patrick ^a  

^a UNIVERSITY OF MUNICH   (Germany)

^b UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

RNA POLYMERASE II; TATA BINDING PROTEIN; FUNGAL DNA;

ARTICLE; COMPLEX FORMATION; CONTROLLED STUDY; DNA STRUCTURE; FUNGAL GENE; GA ELEMENT; GENE FUNCTION; GENE MUTATION; GENE STRUCTURE; GENETIC ASSOCIATION; GENETIC CONSERVATION; IN VITRO STUDY; IN VIVO STUDY; NONHUMAN; PROMOTER REGION; PROTEIN DEPLETION; SEQUENCE ANALYSIS; STRUCTURAL BIOINFORMATICS; TNT1 GENE; TRANSCRIPTION INITIATION SITE; YEAST; BIOLOGY; ENZYMOLOGY; GENETIC TRANSCRIPTION; GENETICS; METABOLISM; NUCLEOTIDE SEQUENCE; REPORTER GENE; SACCHAROMYCES CEREVISIAE; TATA BOX;

SACCHAROMYCES CEREVISIAE;

BASE SEQUENCE; COMPUTATIONAL BIOLOGY; CONSERVED SEQUENCE; DNA, FUNGAL; GENES, REPORTER; PROMOTER REGIONS, GENETIC; RNA POLYMERASE II; SACCHAROMYCES CEREVISIAE; TATA BOX; TATA-BOX BINDING PROTEIN; TRANSCRIPTION, GENETIC;

EID: 81155137514     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0027595     Document Type: Article

References (35)

1. Sikorski TW, Buratowski S, (2009) The basal initiation machinery: beyond the general transcription factors. Current Opinion in Cell Biology 21: 344-351.
2. Roeder RG, (1996) The role of general initiation factors in transcription by RNA polymerase II. Trends in Biochemical Sciences 21: 327-335.
3. Koleske AJ, Young RA, (1994) An RNA polymerase-II holoenzyme responsive to activators. Nature 368: 466-469.
4. Ranish JA, Yudkovsky N, Hahn S, (1999) Intermediates in formation and activity of the RNA polymerase II preinitiation complex: holoenzyme recruitment and a postrecruitment role for the TATA box and TFIIB. Genes & Development 13: 49-63.
5. Basehoar AD, Zanton SJ, Pugh BF, (2004) Identification and distinct regulation of yeast TATA box-containing genes. Cell 116: 699-709.
6. Yang CH, Bolotin E, Jiang T, Sladek FM, Martinez E, (2007) Prevalence of the initiator over the TATA box in human and yeast genes and identification of DNA motifs enriched in human TATA-less core promoters. Gene 389: 52-65.
7. Cormack BP, Struhl K, (1992) The TATA-binding protein is required for transcription by all 3 nuclear-RNA polymerases in yeast-cells. Cell 69: 685-696.
8. Burley SK, (1996) The TATA box binding protein. Current Opinion in Structural Biology 6: 69-75.
9. Pugh BF, Tjian R, (1991) Transcription from a TATA-less promoter requires a multisubunit TFIID complex. Genes & Development 5: 1935-1945.
10. Hahn S, Buratowski S, Sharp PA, Guarente L, (1989) Yeast TATA-binding protein TFIID binds to TATA elements with both consensus and nonconsensus DNA-sequences. Proceedings of the National Academy of Sciences of the United States of America 86: 5718-5722.
11. Smale ST, (1996) Transcription initiation from TATA-less promoters within eukaryotic protein-coding genes. Biochimica et Biophysica Acta 1351: 73-88.
12. Chalkley GE, Verrijzer CP, (1999) DNA binding site selection by RNA polymerase II TAFs: a TAF(II)250-TAF(II)150 complex recognizes the Initiator. Embo Journal 18: 4835-4845.
13. Juven-Gershon T, Hsu JY, Theisen JWM, Kadonaga JT, (2008) The RNA polymerase II core promoter- the gateway to transcription. Current Opinion in Cell Biology 20: 253-259.
14. Singer VL, Wobbe CR, Struhl K, (1990) A wide variety of DNA-sequences can functionally replace a yeast TATA element for transcriptional activation. Genes & Development 4: 636-645.
15. Sugihara F, Kasahara K, Kokubo T, (2011) Highly redundant function of multiple AT-rich sequences as core promoter elements in the TATA-less RPS5 promoter of Saccharomyces cerevisiae. Nucleic Acids Research 39: 59-75.
16. Kuehner JN, Brow DA, (2006) Quantitative analysis of in vivo initiator selection by yeast RNA polymerase II supports a scanning model. Journal of Biological Chemistry 281: 14119-14128.
17. Auble DT, Hansen KE, Mueller CGF, Lane WS, Thorner J, et al. (1994) Mot1, a global repressor of RNA-polyermase-II transcription, inhibits TBP binding to DNA by an ATP-dependent mechanism. Genes & Development 8: 1920-1934.
18. Muldrow TA, Campbell AM, Weil PA, Auble DT, (1999) MOT1 can activate basal transcription in vitro by regulating the distribution of TATA binding protein between promoter and nonpromoter sites. Molecular and Cellular Biology 19: 2835-2845.
19. Lariviere L, Seizl M, van Wageningen S, Rother S, van de Pasch L, et al. (2008) Structure-system correlation identifies a gene regulatory Mediator submodule. Genes & Development 22: 872-877.
20. Struhl K, (1985) Naturally-occuring poly(dA-dT) sequences are upstream promoter elements for constitutive transcription in yeast. Proceedings of the National Academy of Sciences of the United States of America 82: 8419-8423.
21. Iyer V, Struhl K, (1995) Poly(dA-dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA-structure. Embo Journal 14: 2570-2579.
22. Kuras L, Struhl K, (1999) Binding of TBP to promoters in vivo is stimulated by activators and requires Pol II holoenzyme. Nature 399: 609-613.
23. Muller F, Demeny MA, Tora L, (2007) New problems in RNA polymerase II transcription initiation: Matching the diversity of core promoters with a variety of promoter recognition factors. Journal of Biological Chemistry 282: 14685-14689.
24. Faiger H, Ivanchenko M, Cohen I, Haran TE, (2006) TBP flanking sequences: asymmetry of binding, long-range effects and consensus sequences. Nucleic Acids Research 34: 104-119.
25. Huisinga KL, Pugh BF, (2004) A genome-wide housekeeping role for TFIID and a highly regulated stress-related role for SAGA in Saccharomyces cerevisiae. Molecular Cell 13: 573-585.
26. Tsukihashi Y, Miyake T, Kawaichi M, Kokubo T, (2000) Impaired core promoter recognition caused by novel yeast TAF145 mutations can be restored by creating a canonical TATA element within the promoter region of the TUB2 gene. Molecular and Cellular Biology 20: 2385-2399.
27. Thiryblaise LM, Loppes R, (1990) Deletion analysis of the ARG4 promoter of Saccharomyces cerevisiae- a poly(dA-dT) stretch involved in gene-transcription. Molecular & General Genetics 223: 474-480.
28. Moreira JMA, Horz W, Holmberg S, (2002) Neither Reb1p nor Poly(dA-dT) elements are responsible for the highly specific chromatin organization at the ILV1 promoter. Journal of Biological Chemistry 277: 3202-3209.
29. Graham IR, Chambers A, (1994) A Reb1p-binding site is required for efficient activation of the yeast RAP1 gene, but multiple binding-sites for Rap1p are not essential. Molecular Microbiology 12: 931-940.
30. Wu R, Li H, (2010) Positioned and G/C-capped poly(dA:dT) tracts associate with the centers of nucleosome-free regions in yeast promoters. Genome Research 20: 473-484.
31. Miura F, Kawaguchi N, Sese J, Toyoda A, Hattori M, et al. (2006) A large-scale full-length cDNA analysis to explore the budding yeast transcriptome. Proceedings of the National Academy of Sciences of the United States of America 103: 17846-17851.
32. Zhang ZH, Dietrich FS, (2005) Mapping of transcription start sites in Saccharomyces cerevisiae using 5 ' SAGE. Nucleic Acids Research 33: 2838-2851.
33. Seizl M, Lariviere L, Pfaffeneder T, Wenzeck L, Cramer P, (2011) Mediator head subcomplex Med11/22 contains a common helix bundle building block with a specific function in transcription initiation complex stabilization. Nucleic Acids Research 39: 6291-6304.
34. Auble DT, Hahn S, (1993) An ATP-dependent inhibitor of TBP binding to DNA. Genes & Development 7: 844-856.
35. Kostrewa D, Zeller ME, Armache KJ, Seizl M, Leike K, et al. (2009) RNA polymerase II-TFIIB structure and mechanism of transcription initiation. Nature 462: 323-330.