Histone-like transcription factors in eukaryotes

Current Opinion in Structural Biology

Volumn 7, Issue 1, 1997, Pages 94-102

  Burley, Stephen K ^a   Xie, Xiaoling ^b   Clark, Kirk L ^c   Shu, Fong ^a  

^a ROCKEFELLER UNIVERSITY   (United States)

^b VERTEX PHARMACEUTICALS   (United States)

^c NOVARTIS PHARMA AG   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE; TRANSCRIPTION FACTOR;

ARCHITECTURE; BACTERIOPHAGE; COMPREHENSION; DNA BINDING; EUKARYOTE; EVOLUTION; GENE DUPLICATION; GENE EXPRESSION REGULATION; GENETIC PROCEDURES; MASS SPECTROMETRY; NONHUMAN; PRIORITY JOURNAL; REVIEW; THREE DIMENSIONAL IMAGING; TRANSCRIPTION INITIATION;

EUKARYOTA;

EID: 0031049523     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(97)80012-7     Document Type: Article

References (47)

1. Kornberg RD, Thomas JO. Chromatin structure: oligomers of the histones. Science. 184:1974;865-868.
2. Kornberg RD. Chromatin structure: a repeating unit of histones and DNA. Science. 184:1974;868-871.
3. Klug A, Rhodes D, Smith J, Finch JT, Thomas JO. A low resolution structure for the histone core of the nucleosome. Nature. 287:1980;509-516.
4. Bentley GA, Lewit-Bentley A, Finch JT, Podjarny AD, Roth M. Crystal structure of the nucleosome core particle at 16 Å resolution. J Mol Biol. 176:1984;55-75.
5. Richmond TJ, Finch JT, Rushton B, Rhodes D, Klug A. Structure of the nucleosome core particle at 7Å resolution. Nature. 311:1984;532-537.
6. Arents G, Burlingame RW, Wang B-C, Love WE, Moudrianakis EN. The nucleosomal core histone octamer at 3.1 Å resolution: a tripartite protein assembly and a left-handed superhelix. Proc Natl Acad Sci USA. 88:1991;10148-10152.
7. Finch JT, Klug A. Solenoidal model for superstructure in chromatin. Proc Natl Acad Sci USA. 73:1976;1897-1901.
8. Thoma F, Losa R, Klug A. Involvement of histone H1 in the organization of the nucleosome and of the salt dependent superstructures of chromatin. J Cell Biol. 83:1979;403-427.
9. Graziano V, Gerchman SE, Schneider DK, Ramakrishnan V. Histone H1 is located in the interior of the chromatin 30 nm filament. Nature. 368:1994;351-354.
10. Ramakrishnan V, Finch J, Graziano V, Sweet R. Crystal structure of the globular domain of histone H5 and its implications for nucleosome binding. Nature. 362:1993;219-223.
11. D'Anna JA, Isenberg I. A histone cross-complexing pattern. Biochemistry. 13:1974;4992-4997.
12. Arents G, Moudrianakis E. The histone fold: a ubiquitous architectural motif utilized in DNA compaction and protein dimerization. of outstanding interest Proc Natl Acad Sci USA. 92:1995;11170-11174 This paper reports the first detailed characterization of the histone fold at high resolution.
13. Xie X, Kokubo T, Cohen SL, Hoffmann A, Chait BT, Roeder RG, Nakatani Y, Burley SK. Structural similarity between TAFs and the heterotetrameric core of the histone octamer. of outstanding interest Nature. 380:1996;316-322 The first high-resolution X-ray crystal structures of TBP-associated factors and proof of their structural similarity to core histone proteins H3 and H4 are presented.
14. Starich MR, Sandman K, Reeve JN, Summers MF. NMR structure of HMfB from the hyperthermophile, methanothermus fervidus, confirms that this archael protein is a histone. of special interest J Mol Biol. 255:1996;187-203 This paper presents the first NMR study of an archael histone protein, and proof of its structural similarity to core histone proteins.
15. Arents G, Moudrianakis E. Topography of the histone octamer surface: repeating structural motifs utilized in the docking of nucleosomal DNA. Proc Natl Acad Sci USA. 90:1993;10489-10493.
16. 2 heterotetramer are reported.
17. Kaufman PD, Kobayashi R, Kessler N, Stillman B. The p150 and p60 subunits of chromatin assembly factor 1: a molecular link between newly synthesized histones and DNA replication. Cell. 81:1995;1105-1114.
18. Drew H, Travers A. DNA bending and its relation to nucleosome positioning. J Mol Biol. 186:1985;773-790.
19. Satchwell S, Drew H, Travers A. Sequence periodicities in chicken nucleosomal core DNA. J Mol Biol. 191:1986;659-679.
20. Burley SK, Roeder RG. Biochemistry and structural biology of transcription factor IID. of special interest Annu Rev Biochem. 65:1996;769-799 A comprehensive review on the structure and function of transcription factor IID.
21. Kingston RE, Bunker CA, Imbalzano AN. Repression and activation by multiprotein complexes that alter chromatin structure. of special interest Genes Dev. 10:1996;905-920 A useful review on the interplay between transcription and DNA packaging.
22. Workman JL, Roeder RG. Binding of transcription factor TFIID to the major late promoter during in vitro nucleosome assembly potentiates subsequent initiation by RNA polymerase II. Cell. 51:1987;613-622.
23. Meisterernst M, Horikoshi M, Roeder RG. Recombinant yeast TFIID, a general transcription factor, mediates activation by the gene-specific factor USF in a chromatin assembly assay. Proc Natl Acad Sci USA. 87:1990;9153-9157.
24. Kokubo T, Gong D-W, Wootton J, Horikoshi M, Roeder R, Nakatani Y. Molecular cloning of Drosophila TFIID subunits. Nature. 367:1994;484-487.
25. Hisatake K, Ohta T, Takada R, Guermah M, Horikoshi M, Nakatani Y, Roeder R. Evolutionary conservation of human TBP-associated factors TAF31 and TAF80 and interactions of TAF80 with other TAFs and with general transcription factors. Proc Natl Acad Sci USA. 92:1995;8195-8199.
26. Hoffmann A, Chiang C-M, Oelgeschlager T, Xie X, Burley SK, Nakatani Y, Roeder RG. A histone octamer-like structure within TFIID. of outstanding interest Nature. 380:1996;356-359 This paper presents results of biochemical studies that complement the X-ray crystallographic work described in reference [13] and provides further evidence of a histone octamer-like structure within transcription factor IID.
27. Mengus G, May M, Jacq X, Staub A, Tora L, Chambon P, Davidson I. Cloning and characterization of hTAFII18, hTAF1120 and hTAFII28: Three subunits of the human transcription factor TFIID. EMBO J. 14:1995;1520-1531.
28. Baxevanis A, Arents G, Moudrianakis E, Landsman D. A variety of DNA-binding and multimeric proteins contain the histone fold motif. Nucleic Acids Res. 23:1995;2685-2691.
29. Janin J. Elusive affinities. Proteins. 21:1995;30-39.
30. Sawadogo M, Roeder RG. Interaction of a gene-specific transcription factor with the adenovirus major late promoter upstream of the TATA box region. Cell. 43:1985;165-175.
31. Oelgeschlager T, Chiang C-M, Roeder RG. Topology and reorganization of a human TFIID-promoter complex. of outstanding interest Nature. 382:1996;735-738 The authors report the results of DNA - protein photocrosslinking studies of transcription factor IID and provide the first evidence for negative super-coiling of closed circular DNA by transcription factor IID under standard nucleosome assembly conditions.
32. Kim JL, Burley SK. 1.9 Å resolution refined structure of TBP recognizing the minor groove of TATAAAAG. Nat Struct Biol. 1:1994;638-653.
33. Meisterernst M, Roeder RG. Family of proteins that interact with TFIID and regulate promoter activity. Cell. 67:1991;557-567.
34. Inostroza JA, Mermelstein FH, Ha I, Lane WS, Reinberg D. Dr1, a TATA-binding protein-associated phosphoprotein and inhibitor of class II gene transcription. Cell. 70:1992;477-489.
35. Goppelt A, Stelzer G, Lottspeich F, Meisterernst M. A mechanism for repression of class II gene transcription through specific binding of NC2 to TBP-promoter complexes via heterodimeric histone fold domains. of special interest EMBO J. 15:1996;3105-3116 The authors report their discovery that NC2, a negative regulator of RNA polymerase II transcription initiation, is an H2A/H2B-like heterodimer. Similar findings are reported in [36].
36. Mermelstein F, Yeung K, Cao J, Inostroza JA, Erdjument-Bromage H, Eagelson K, Landsman D, Levitt P, Tempst P, Reinberg D. Requirement for a corepressor for Dr1-mediated repression of transcription. of special interest Genes Dev. 10:1996;1033-1048 See annotation [35].
37. Patikoglou G, Burley SK. Eukaryotic transcription factor-DNA complexes. of special interest Annu Rev Biophys Biomolec Struct. 26:1997; A useful, comprehensive review of all high-resolution X-ray crystallographic and NMR structures of eukaryotic transcription factor/DNA complexes published before August 1996.
38. Schultz SC, Shields GC, Steitz TA. Crystal structure of a CAP - DNA complex: the DNA is bent by 90° Science. 253:1991;1001-1007.
39. Clark KL, Halay ED, Lai E, Burley SK. Co-crystal structure of the HNF-3/fork head DNA-recognition motif resembles histone H5. Nature. 364:1993;412-420.
40. Lai E, Clark KL, Burley S, James E, Darnell J. Hepatocyte nuclear factor 3/fork head or 'winged helix' proteins: a family of transcription factors of diverse biological function. Proc Natl Acad Sci USA. 90:1993;10421-10423.
41. Wilson KP, Shewchuk LM, Brennan RG, Otsuka AJ, Matthews BW. E. coli biotin holoenzyme synthetase/bio repressor crystal structure delineates the biotin-and DNA-binding domains. Proc Natl Acad Sci USA. 89:1992;9257-9261.
42. Sander C, Schneider R. Database of homology-derived protein structures and structural meaning of sequence alignment. Proteins. 9:1991;56-68.
43. Goytisolo FA, Gerchman S-E, Yu X, Rees C, Graziano V, Ramakrishnan V, Thomas JO. Identification of two DNA-binding sites on the globular domain of histone H5. of special interest EMBO J. 15:1996;3421-3429 This paper reports further characterization of the DNA-binding properties of the linker histone H5, which builds on earlier work in [10].
44. Liu J-K, DiPersio CM, Zaret KS. Extracellular signals that regulate liver transcription factors during hepatic differentiation in vitro. Mol Cell Biol. 11:1991;773-784.
45. McPherson C, Shin E-Y, Friedman D, Zaret K. An active tissue-specific enhancer and bound transcription factors existing in a precisely position nucleosomal array. Cell. 75:1993;387-398.
46. McPherson CE, Horowitz R, Woodcock CL, Jiang C, Zaret KS. Nucleosome positioning properties of the albumin transcriptional enhancer. of special interest Nucleic Acids Res. 24:1996;397-404 The authors report further characterization of the nucleosome-phasing properties of the linker histone-like transcription factor HNF-3α, which builds on earlier work in [45].
47. Kraulis PJ. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J Appl Cryst. 24:1991;946-950.