Common themes in the function of transcription and splicing enhancers

Current Opinion in Cell Biology

Volumn 9, Issue 3, 1997, Pages 350-357

  Hertel, Klemens J ^a   Lynch, Kristen W ^a   Maniatis, Tom ^a  

^a HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

REGULATOR PROTEIN; RNA POLYMERASE II; TATA BINDING PROTEIN;

CHROMATIN; CONTROLLED STUDY; DNA SEQUENCE; ENHANCER REGION; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN PROTEIN INTERACTION; REVIEW; RNA SEQUENCE; RNA SPLICING; RNA TRANSCRIPTION; TATA BOX; TRANSCRIPTION REGULATION;

EID: 0030912313     PISSN: 09550674     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0955-0674(97)80007-5     Document Type: Article

References (68)

1. Orphanides G, Lagrange T, Reinberg D: The general transcription factors of RNA polymerase II. Genes Dev 1996, 10:2657-2683.
2. Koleske AJ, Young RA: An RNA polymerase II holoenzyme responsive to activators. Nature 1994, 368:466-469.
3. Koleske AJ, Young RA: The RNA polymerase II holoenzyme and its implications for gene regulation. Trends Biochem 1995, 20:113-114.
4. Chao DM, Gadbois EL, Murray PJ, Anderson SF, Sonu MS, Parvin JD, Young RA: A mammalian SRB protein associated with an RNA polymerase II holoenzyme. Nature 1996, 380:82-85. SRB proteins (suppressors of RNA polymerase B) are essential components of the yeast holoenzyme, originally identified by genetic suppression of polll truncation mutations. This paper shows that a mammalian polll holoenzyme containing polll, TFIIE and TFIIH can be isolated using antibodies against SRB7, a human homolog of yeast SRB proteins. Thus, both the yeast and mammalian polll holoenzymes can be identified, and both contain SRB proteins.
5. Maldonado E, Shiekhattar R, Sheldon M, Cho H, Drapkin R, Rickert P, Lees E, Anderson CW, Linn S, Reinberg D: A human RNA polymerase II complex associated with SRB and DNA-repair proteins. Nature 1996, 381:86-89.
6. Maniatis T, Goodbourn S, Fischer JA: Regulation of inducible and tissue-specific gene expression. Science 1987, 236:1237-1245.
7. Tjian R, Maniatis T: Transcriptional activation: a complex puzzle with few easy pieces. Cell 1994, 77:5-8.
8. Hill CS, Treisman R: Transcriptional regulation by extracellular signals: mechanisms and specificity. Cell 1995, 80:199-211. A comprehensive review describing how combinatorial interactions allow for the transcriptional activation of specific genes in response to various external stimuli.
9. Grosschedl R: Higher-order nucleoprotein complexes in transcription: analogies with site-specific recombination. Curr Opin Cell Biol 1995, 7:362-370. An excellent minireview describing the role of architectural proteins and DNA bending in the function of transcriptional enhancers.
10. Thanos D, Maniatis T: Virus induction of human IFN-β gene expression requires the assembly of an enhanceosome. Cell 1995, 83:1091-1100. The authors of this paper demonstrate a role of the architectural protein HMG I(Y) in enhancer function, and show that cooperative binding of transcription activator proteins in vitro and transcriptional synergy in vivo require the precise positioning of transcription factor binding sites on the face of the DNA helix. Thus, at least some enhancers may form higher-order multiprotein complexes termed enhanceosomes.
11. Falvo JV, Thanos D, Maniatis T: Reversal of intrinsic DNA bends in the IFN-β gene enhancer by transcription factors and the architectural protein HMG I(Y). Cell 1995, 83:1101-1111.
12. Ptashne M, Gann A: Transcriptional activation by recruitment in bacteria and yeast. Nature 1997, 386:569-577 A comprehensive and critical review summarizing recent progress in understanding the mechanisms of transcriptional activation.
13. Pugh BF: Mechanisms of transcription complex assembly. Curr Opin Cell Biol 1996, 8:303-311. This review discusses the mechanisms involved in gene activation, including enhancer accessibility, recruitment of TFIID and polll, and transcriptional synergy. These processes are discussed in the context of the stepwise or holoenzyme recruitment models.
14. Barberis A, Pearlberg J, Simkovich N, Farrell S, Reinagel P, Bamdad C, Sigal G, Ptashne M: Contact with a component of the polymerase II holoenzyme suffices for gene activation. Cell 1995, 81:359-368. The Gal11 protein is a component of the yeast holoenzyme. This paper shows that a fortuitous interaction between a mutant of the Gal11 protein and a fragment of the transcriptional activator protein Gal4 suffices for transcriptional activation. Thus, a single contact between a DNA-bound protein and the holoenzyme is sufficient for transcriptional activation, supporting the view that the primary function of activators is to recruit the holoenzyme to the promoter.
15. Ranish JA, Hahn S: Transcription: basal factors and activations. Curr Opin Genet Dev 1996, 6:151-158.
16. Chatterjee S, Struhl K: Connecting a promoter-bound protein to TBP bypasses the need for a transcriptional activation domain. Nature 1995, 374:820-822. This paper shows that the requirement for an activation domain can be bypassed by covalently joining a DNA-binding domain and a component of the transcription machinery (i.e. TBP). In addition, the results show that recruitment of TBP to the promoter can be a rate-limiting step for transcription in vivo.
17. Farrell S, Simkovich N, Wu Y, Barberis A, Ptashne M: Gene activation by recruitment of the RNA polymerase II holoenzyme. Genes Dev 1996, 10:2359-2367.
18. Wu Y, Reece RJ, Ptashne M: Quantitation of putative activator target affinities predicts transcriptional activating potentials. EMBO J 1996, 15:3951-3963. Deletion and point mutation variants of a yeast transcriptional activation domain are tested for their affinities to TBP and TFIIB and for their transcriptional activities in vivo. A remarkable correlation between affinity and activity was observed, providing strong evidence that TBP and TFIIB are activator targets.
19. Bentley DL: Regulation of transcriptional elongation by RNA polymerase II. Curr Opin Genet Dev 1995, 5:210-216.
20. Blau J, Xiao H, McCracken S, O'Hare P, Greenblatt J, Bentley D: Three functional classes of transcriptional activation domains. Mol Cell Biol 1996, 16:2044-2055. This paper shows that distinct activator domains can function at different stages of transcription in vivo, some at the level of initiation, others at the level of elongation. Thus, transcriptional synergy could result, at least in part, by stimulating different steps of transcription.
21. Kingston RE, Bunker CA, Imbalzano AN: Repression and activation by multiprotein complexes that alter chromatin structure. Genes Dev 1996, 10:905-920.
22. Brownell JE, Allis CD: Special HATs for special occasions: linking histone acetylation to chromatin assembly and gene activation. Curr Opin Genet Dev 1996, 6:176-184.
23. Bannister AJ, Kouzarides T: The CBP co-activator is a histone acetyl-transferase. Nature 1996, 384:641-643. CBP (CREB-binding protein) is a protein that was originally found to specifically associate with activated CREB (cAMP response element binding protein) proteins, but which was subsequently found to associate with, and stimulate the activities of, several transcriptional activator proteins. CBP was also associated with a histone acetylase, P/CAF (p300/CBP-associated protein). The authors of this paper show that CBP has intrinsic histone acetylase activity. Thus, one function of activator proteins is to recruit histone acetylases to the promoter, resulting in a weakening of histone-DNA interactions.
24. Cote J, Quinn J, Workman JL, Peterson CL: Stimulation of GAL4 derivative binding to nucleosomal DNA by the yeast SWI/SNF complex. Science 1994, 265:53-60.
25. Tsukiyama T, Wu C: Purification and properties of an ATP-dependent nucleosome remodeling factor. Cell 1995, 83:1011-1020.
26. Wilson CJ, Chao DM, Imbalzano AN, Schnitzler GR, Kingston RE, Young RA: RNA polymerase II holoenzyme contains SWI/SNF regulators involved in chromatin remodeling. Cell 1996, 84:235-244. The authors of this paper show that components of the yeast Swi/Snf chromatin-remodeling complex are present in the yeast holoenzyme. Thus, one function of transcriptional activators is to recruit chromatin-remodeling machinery to specific promoters.
27. Gaudreau L, Schmid A, Blaschke D, Ptashne M, Horz W: RNA polymerase II holoenzyme recruitment is sufficient to remodel chromatin at the yeast PHO5 promoter. Cell 1997, 89:63-72.
28. Lin YS, Carey M, Ptashne M, Green MR: How different eukaryotic transcriptional activators can cooperate promiscuously. Nature 1990, 345:359-361.
29. Carey M, Lin YS, Green MR, Ptashne M: A mechanism for synergistic activation of a mammalian gene by Gal4 derivatives. Nature 1990, 345:361-364.
30. Chi T, Lieberman P, Ellwood K, Carey M: A general mechanism for transcriptional synergy by eukaryotic activators. Nature 1995, 377:254-257. This paper shows that the synergistic interactions of transcriptional activators in vitro correlate with the assembly of a TFIID-TFIIA complex on the promoter, thus supporting the view that activators recruit GTFs to the promoter and stabilize their interactions with DNA.
31. Sauer F, Hansen SK, Tjian R: Multiple TAFIIs directing synergistic activation of transcription. Science 1995, 270:1783-1787. This paper shows that interactions between multiple activators and different TBP-associated factors (TAFs) can result in transcriptional synergy in vitro.
32. Giniger E, Ptashne M: Cooperative DNA binding of the yeast transcriptional activator GAL4. Proc Natl Acad Sci USA 1988, 85:382-386.
33. Xiao H, Perisic O, Lis JT: Cooperative binding of Drosophila heat shock factor to arrays of a conserved 5 bp unit Cell 1991, 64:585-593.
34. Ohashi Y, Brickman JM, Furman E, Middleton B, Carey M: Modulating the potency of an activator in a yeast in vitro transcription system. Mol Cell Biol 1994, 14:2731-2739.
35. Choy B, Green MR: Eukaryotic activators function during multiple steps of preinitiation complex assembly. Nature 1993, 366:531-536.
36. Herschlag D, Johnson FB: Synergism in transcriptional activation: a kinetic view. Genes Dev 1993, 7:173-179.
37. Krämer A: The structure and function of proteins involved in mammalian pre-mRNA splicing. Annu Rev Biochem 1996, 65:367-409.
38. Reed R, Palandjian L: Spliceosome assembly. In Eukaryotic mRNA Processing. Edited by Krainer AR. Oxford, England: IRL Press; 1997:103-129.
39. Reed R, Maniatis T: A role for exon sequences and splice site proximity in splice site selection. Cell 1986, 46:681-690.
40. Reed R: Initial splice-site recognition and pairing during pre-mRNA splicing. Curr Opin Genet Dev 1996, 6:215-220. This minireview discusses a model for initial splice-site recognition that involves multiple weak interactions. In this model, a network of cross-exon protein-protein interactions bridges the splice sites on either side of the exon and recruits U2snRNP to the branchsite.
41. Watakabe A, Tanaka K, Shimura Y: The role of exon sequences in splice site selection. Genes Dev 1993, 7:407-418.
42. Tian M, Maniatis T: Positive control of pre-mRNA splicing in vitro. Science 1992, 256:237-240.
43. Chabot B: Directing alternative splicing: cast and scenarios. Trends Gene 1996, 12:172-177.
44. Fu XD: The superfamily of arginine/serine-rich splicing factors. RNA 1995, 1:663-680.
45. Manley JL, Tacke R: SR proteins and splicing control. Genes Dev 1996, 10:1569-1579.
46. Wu JY, Maniatis T: Specific interactions between proteins implicated in splice site selection and regulated alternative splicing. Cell 1993, 75:1061-1070.
47. Kohtz JD, Jamison SF, Will CL, Zuo P, Liihrmann R, Garcia-Blanco M, Manley JL: Protein-protein interactions and 5′-splice site recognition in mammalian mRNA precursors. Nature 1994, 368:119-124.
48. Valcarcel J, Singh R, Zamore PD, Green MR: The protein Sex-lethal antagonizes the splicing factor U2AF to regulate alternative splicing of transformer pre-mRNA. Nature 1993, 362:171-175.
49. 35 may be the primary target for recruitment by the enhancer complex.
50. Zahler AM, Roth MB: Distinct functions of SR proteins in recruitment of U1 small nuclear ribonucleoprotein to alternative 5′ splice sites. Proc Natl Acad Sci USA 1995, 92:2642-2646.
51. Chiara MD, Reed R: A two-step mechanism for 5′ and 3′ splice site pairing. Nature 1995, 375:510-513. RNAs can be spliced in trans if the 3′ splice site is associated with an exonic enhancer or a downstream 5′ splice site. As the selection of 5′ splice sites was shown to occur after U2snRNP is assembled on the 3′ splice-site, it is suggested that splice-site pairing can occur after initial spice-site recognition.
52. Bruzik J, Maniatis T: Enhancer dependent interaction between 5′ and 3′ splice sites in trans. Proc Natl Acad Sci USA 1995, 92:7056-7059. Trans-splicing can occur if the 3′ substrate contains an exonic enhancer sequence in addition to the 3′ splice site signals. The trans reaction is mediated by SR proteins interacting with general splicing factors that are bound to the 5′ and 3′ splice sites.
53. Lynch KW, Maniatis T: Synergistic interaction between two distinct elements of a regulated splicing enhancer. Genes Dev 1995, 9:284-293.
54. Tian H, Kole R: Selection of novel exon recognition elements from a pool of random sequences. Mol Cell Biol 1995, 15:6291-6298.
55. Tacke R, Manley JL: The human splicing factors ASF/SF2 and SC35 possess different, functionally significant RNA binding specificities. EMBO J 1995, 14:3540-3551. Using a binding site selection method, the authors identified consensus binding sites for the SR proteins ASF/SF2 and SC35. In the case of ASF/SF2, one of these binding sites could direct ASF/SF2-stimulated splicing in vitro when fused to a weak heterologous intron.
56. Tian M, Maniatis T: A splicing enhancer exhibits both constitutive and regulated activities. Genes Dev 1994, 8:1703-1712.
57. Carey M, Leatherwood J, Ptashne M: A potent GAL4 derivative activates transcription at a distance in vitro. Science 1990, 247:710-712.
58. Lynch KW, Maniatis T: Assembly of specific SR protein complexes on distinct regulatory elements of the Drosophila doublesex splicing enhancer. Genes Dev 1996, 10:2089-2101. Specific heterotrimeric complexes associate with each of the two classes of binding sites within the dsx enhancer. The formation of each of these complexes is dependent on highly cooperative interactions between the three proteins of the specific heterotrimeric complexes, and between the proteins and the RNA.
59. Tian M, Maniatis T: A splicing enhancer complex controls alternative splicing of doublesex pre-mRNA. Cell 1993, 74:105-114.
60. Hedley ML, Maniatis T: Sex-specific splicing and polyadenylation of dsx pre-mRNA requires a sequence that binds specifically to tra-2 protein in vitro. Cell 1991, 65:579-586.
61. Ryner LC, Baker BS: Regulation of doublesex pre-mRNA processing occurs by 3'-splice site activation. Genes Dev 1991, 5:2071-2085.
62. Hoshijima K, Inoue K, Higuchi I, Sakamoto H, Shimura Y: Control of doublesex alternative splicing by transformer and transformer-2 in Drosophila. Science 1991, 252:833-836.
63. Min H, Chan RC, Black DL: The generally expressed hnRNP F is involved in a neural-specific pre-mRNA splicing event Genes Dev 1995, 9:2659-2671. The authors of this paper identified an enhancer complex that binds to an intronic sequence and activates recognition of an upstream exon. Evidence is presented that this complex forms through cooperative interactions between a number of proteins.
64. Yeakley JM, Morfin JP, Rosenfeld MG, Fu XD: A complex of nuclear proteins mediates SR protein binding to a purine-rich splicing enhancer. Proc Natl Acad Sci USA 1996, 93:7582-7587.
65. Berget SM: Exon recognition in vertebrate splicing. J Biol Chem 1995, 270:2411-2414. This review summarizes the evidence for the role of cross-exon interactions in splice-site selection and exon definition.
66. Dreyfuss G, Matunis MJ, Pinol-Roma S, Burd CG: hnRNP proteins and the biogenesis of mRNA. Annu Rev Biochem 1993, 62:289-321.
67. McAfee JG, Soltaninassab SR, Lindsay ME, LeStourgeon WM: Proteins C1 and C2 of heterogeneous nuclear ribonucleoprotein complexes bind RNA in a highly cooperative fashion: support for their contiguous deposition on pre-mRNA during transcription. Biochemistry 1996, 35:1212-1222.
68. Sebillon P, Beldjord C, Kaplan JC, Broody E, Marie J: A T to G mutation in the polypyrimidine tract of the second intron of the human β-globin gene reduces in vitro splicing efficiency: evidence for an increased hnRNP C interaction. Nucleic Acids Res 1995, 23:3419-3425.