Dampening DNA binding: A common mechanism of transcriptional repression for both ncRNAs and protein domains

RNA Biology

Volumn 7, Issue 3, 2010, Pages

  Goodrich, James A ^a   Kugel, Jennifer F ^a  

^a UNIVERSITY OF COLORADO   (United States)

Author keywords

ncRNA; RNA polymerase II; SINE; Transcription

Indexed keywords

EID: 85011941619     PISSN: 15476286     EISSN: 15558584     Source Type: Journal    
DOI: 10.4161/rna.7.3.11910     Document Type: Review

References (35)

1. Goodrich JA, Kugel JF. From bacteria to humans, chromatin to elongation and activation to repression: The expanding roles of noncoding RNAs in regulating transcription. Crit Rev Biochem Mol Biol 2009; 44:3-15.
2. Kapranov P, Willingham AT, Gingeras TR. Genomewide transcription and the implications for genomic organization. Nat Rev Genet 2007; 8:413-23.
3. Pheasant M, Mattick JS. Raising the estimate of functional human sequences. Genome Res 2007; 17:1245-53.
4. Allen TA, Von Kaenel S, Goodrich JA, Kugel JF. The SINE-encoded mouse B2 RNA represses mRNA transcription in response to heat shock. Nat Struct Mol Biol 2004; 11:816-21.
5. Espinoza CA, Allen TA, Hieb AR, Kugel JF, Goodrich JA. B2 RNA binds directly to RNA polymerase II to repress transcript synthesis. Nat Struct Mol Biol 2004; 11:822-9.
6. Mariner PD, Walters RD, Espinoza CA, Drullinger LF, Wagner SD, Kugel JF, Goodrich JA. Human Alu RNA is a modular transacting repressor of mRNA transcription during heat shock. Mol Cell 2008; 29:499-509.
7. Kramerov DA, Vassetzky NS. Short retroposons in eukaryotic genomes. Int Rev Cytol 2005; 247:165-221.
8. Li T, Spearow J, Rubin CM, Schmid CW. Physiological stresses increase mouse short interspersed element (SINE) RNA expression in vivo. Gene 1999; 239:367-72.
9. Liu WM, Chu WM, Choudary PV, Schmid CW. Cell stress and translational inhibitors transiently increase the abundance of mammalian SINE transcripts. Nucl Acids Res 1995; 23:1758-65.
10. Yakovchuk P, Goodrich JA, Kugel JF. B2 RNA and Alu RNA repress transcription by disrupting contacts between RNA polymerase II and promoter DNA within assembled complexes. Proc Natl Acad Sci USA 2009; 106:5569-74.
11. Mittal V, Ma B, Hernandez N. SNAP(c): a core promoter factor with a built-in DNA-binding damper that is deactivated by the Oct-1 POU domain. Genes Dev 1999; 13:1807-21.
12. Hernandez N. Small nuclear RNA genes: a model system to study fundamental mechanisms of transcription. J Biol Chem 2001; 276:26733-6.
13. Mittal V, Cleary MA, Herr W, Hernandez N. The Oct-1 POU-specific domain can stimulate small nuclear RNA gene transcription by stabilizing the basal transcription complex SNAPc. Mol Cell Biol 1996; 16:1955-65.
14. Smale ST, Kadonaga JT. The RNA polymerase II core promoter. Annu Rev Biochem 2003; 72:449-79.
15. Kokubo T, Yamashita S, Horikoshi M, Roeder RG, Nakatani Y. Interaction Between the N-Terminal Domain of the 230-kDa Subunit and the TATA Box-Binding Subunit of TFIID Negatively Regulates TATA-Box Binding. Proc Natl Acad Sci USA 1994; 91:3520-4.
16. Kokubo T, Gong D-W, Yamashita S, Horikoshi M, Roeder RG, Nakatani Y. Drosophila 230-kD TFIID subunit, a functional homolog of the human cell cycle gene product, negatively regulates DNA binding of the TATA box-binding subunit of TFIID. Genes Dev 1993; 7:1033-46.
17. Kokubo T, Swanson MJ, Nishikawa JI, Hinnebusch AG, Nakatani Y. The yeast TAF145 inhibitory domain and TFIIA competitively bind to TATA-binding protein. Mol Cell Biol 1998; 18:1003-12.
18. Ozer J, Mitsouras K, Zerby D, Carey M, Lieberman PM. Transcription factor IIA derepresses TATA-binding protein (TBP)-associated factor inhibition of TBP-DNA binding. J Biol Chem 1998; 273:14293-300.
19. Lively TN, Ferguson HA, Galasinski SK, Seto AG, Goodrich JA. c-Jun binds the N terminus of human TAF(II)250 to derepress RNA polymerase II transcription in vitro. J Biol Chem 2001; 276:25582-8.
20. Lively TN, Nguyen TN, Galasinski SK, Goodrich JA. The basic leucine zipper domain of c-Jun functions in transcriptional activation through interaction with the N terminus of human TATA-binding protein-associated factor-1 (human TAF(II)250). J Biol Chem 2004; 279:26257-65.
21. Kotani T, Banno K, Ikura M, Hinnebusch AG, Nakatani Y, Kawaichi M, Kokubo T. A role of transcriptional activators as antirepressors for the autoinhibitory activity of TATA box binding of transcription factor IID. Proc Natl Acad Sci USA 2000; 97:7178-83.
22. Liu D, Ishima R, Tong KI, Bagby S, Kokubo T, Muhandiram DR, et al. Solution structure of a TBPTAF(II)230 complex: protein mimicry of the minor groove surface of the TATA box unwound by TBP. Cell 1998; 94:573-83.
23. Kettenberger H, Eisenfuhr A, Brueckner F, Theis M, Famulok M, Cramer P. Structure of an RNA polymerase II-RNA inhibitor complex elucidates transcription regulation by noncoding RNAs. Nat Struct Mol Biol 2006; 13:44-8.
24. Espinoza CA, Goodrich JA, Kugel JF. Characterization of the structure, function and mechanism of B2 RNA, an ncRNA repressor of RNA polymerase II transcription. RNA 2007; 13:583-96.
25. Coleman RA, Pugh BF. Evidence for the functional binding and stable sliding of the TATA binding protein on nonspecific DNA. J Biol Chem 1995; 270:13850-9.
26. Mooney RA, Darst SA, Landick R. Sigma and RNA polymerase: an on-again, off-again relationship? Mol Cell 2005; 20:335-45.
27. Gruber TM, Gross CA. Multiple sigma subunits and the partitioning of bacterial transcription space. Annu Rev Microbiol 2003; 57:441-66.
28. Wassarman KM, Storz G. 6S RNA regulates E. coli RNA polymerase activity. Cell 2000; 101:613-23.
29. Gildehaus N, Neusser T, Wurm R, Wagner R. Studies on the function of the riboregulator 6S RNA from E. coli: RNA polymerase binding, inhibition of in vitro transcription and synthesis of RNA-directed de novo transcripts. Nucleic Acids Res 2007; 35:1885-96.
30. Wassarman KM, Saecker RM. Synthesis-mediated release of a small RNA inhibitor of RNA polymerase. Science 2006; 314:1601-3.
31. Barrick JE, Sudarsan N, Weinberg Z, Ruzzo WL, Breaker RR. 6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter. RNA 2005; 11:774-84.
32. Trotochaud AE, Wassarman KM. A highly conserved 6S RNA structure is required for regulation of transcription. Nat Struct Mol Biol 2005; 12:313-9.
33. Cavanagh AT, Klocko AD, Liu X, Wassarman KM. Promoter specificity for 6S RNA regulation of transcription is determined by core promoter sequences and competition for region 4.2 of sigma70. Mol Microbiol 2008; 67:1242-56.
34. Klocko AD, Wassarman KM. 6S RNA binding to Esigma(70) requires a positively charged surface of sigma(70) region 4.2. Mol Microbiol 2009; 73:152-64.
35. Lehmann E, Brueckner F, Cramer P. Molecular basis of RNA-dependent RNA polymerase II activity. Nature 2007; 450:445-9.