Multiple, dispersed human U6 small nuclear RNA genes with varied transcriptional efficiencies

Nucleic Acids Research

Volumn 31, Issue 9, 2003, Pages 2344-2352

  Domitrovich, Angela M ^a   Kunkel, Gary R ^a  

^a TEXAS A AND M UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA DIRECTED RNA POLYMERASE III; HISTONE H4; SMALL NUCLEAR RNA; TATA BINDING PROTEIN; HISTONE; SNAPC PROTEIN COMPLEX, HUMAN; TRANSCRIPTION FACTOR; U6 SMALL NUCLEAR RNA;

5' UNTRANSLATED REGION; ACETYLATION; ARTICLE; CONTROLLED STUDY; GENE LOCUS; GENETIC ANALYSIS; GENETIC CONSERVATION; GENETIC IDENTIFICATION; GENETIC TRANSCRIPTION; GENETIC TRANSFECTION; HUMAN; HUMAN CELL; HUMAN CELL CULTURE; HUMAN GENETICS; IN VITRO STUDY; PRIORITY JOURNAL; PROMOTER REGION; PSEUDOGENE; RNA TRANSCRIPTION; SEQUENCE ANALYSIS; CELL LINE; CHROMATIN; CHROMOSOME MAP; GENETICS; GENOME; METABOLISM; MULTIGENE FAMILY; NUCLEOTIDE SEQUENCE; PROTEIN BINDING; SEQUENCE HOMOLOGY;

VERTEBRATA;

ACETYLATION; BASE SEQUENCE; CELL LINE; CHROMATIN; CHROMOSOME MAPPING; GENOME, HUMAN; HISTONES; HUMANS; MULTIGENE FAMILY; PROMOTER REGIONS (GENETICS); PROTEIN BINDING; RNA, SMALL NUCLEAR; SEQUENCE HOMOLOGY, NUCLEIC ACID; TATA-BOX BINDING PROTEIN; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC; TRANSFECTION;

EID: 0038750923     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg331     Document Type: Article

References (52)

1. Hernandez,N. (2001) Small nuclear RNA genes: a model system to study fundamental mechanisms of transcription. J. Biol. Chem., 276, 26733-26736.
2. Mattaj,I.W., Dathan,N.A., Parry,H.D., Carbon,P. and Krol,A. (1988) Changing the RNA polymerase specificity of U snRNA gene promoters. Cell, 55, 435-442.
3. Lobo,S.M. and Hernandez,N. (1989) A 7 bp mutation converts a human RNA polymerase II snRNA promoter into an RNA polymerase III promoter. Cell, 58, 55-67.
4. Schaub,M., Myslinski,E., Schuster,C., Krol,A. and Carbon,P. (1997) Staf, a promiscuous activator for enhanced transcription by RNA polymerases II and III. EMBO J., 16, 173-181.
5. Kunkel,G.R., Cheung,T.C., Miyake,J.H., Urso,O., McNamara-Schroeder,K.J. and Stumph,W.E. (1996) Identification of a SPH element in the distal region of a human U6 small nuclear RNA gene promoter and characterization of the SPH binding factor in HeLa cell extracts. Gene Expr., 6, 59-72.
6. Murphy,S., Yon,J.-B., Gerster,T. and Roeder,R.G. (1992) Oct-1 and Oct-2 potentiate functional interactions of a transcription factor with the proximal sequence element of small nuclear RNA genes. Mol. Cell. Biol., 12, 3247-3261.
7. c. Mol. Cell. Biol., 16, 1955-1965.
8. c and DNA. J. Biol. Chem., 272, 16048-16055.
9. Ford,E., Strubin,M. and Hernandez,N. (1998) The Oct-1 POU domain activates snRNA gene transcription by contacting a region in the SNAPc largest subunit that bears sequence similarities to the Oct-1 coactivator OBF-1. Genes Dev., 12, 3528-3540.
10. Hovde,S., Hinkley,C.S., Strong,K., Brooks,A., Gu,L., Henry,R.W. and Geiger,J. (2002) Activator recruitment by the general transcription machinery: X-ray structural analysis of the Oct-1 POU domain/human U1 octamer/SNAP190 peptide ternary complex. Genes Dev., 16, 2772-2777.
11. Stunkel,W., Kober,I. and Seifart,K.H. (1997) A nucleosome positioned in the distal promoter region activates transcription of the human U6 gene. Mol. Cell. Biol., 17, 4397-4405.
12. c by the Oct-1 POU domain. Mol. Cell, 7, 539-549.
13. Murphy,S., Tripodi,M. and Melli,M. (1986) A sequence upstream from the coding region is required for the transcription of the 7SK RNA genes. Nucleic Acids Res., 14, 9243-9260.
14. Das,G., Henning,D., Wright,D. and Reddy,R. (1988) Upstream regulatory elements are necessary and sufficient for transcription of a U6 RNA gene by rRNA polymerase III. EMBO J., 7, 503-512.
15. Kunkel,G.R. and Pederson,T. (1989) Transcription of a human U6 small nuclear RNA gene in vivo withstands deletion of intragenic sequences but not of an upstream TATATA box. Nucleic Acids Res., 17, 7371-7379.
16. Willis,I.M. (1993) RNA polymerase III: genes, factors and transcriptional specificity. Eur. J. Biochem., 212, 1-11.
17. Schramm,L. and Hernandez,N. (2002) Recruitment of RNA polymerase III to its target promoters. Genes Dev., 16, 2593-2620.
18. Brummelkamp,T.R., Bernards,R. and Agami,R. (2002) A system for stable expression of short interfering RNAs in mammalian cells. Science, 296, 550-553.
19. Paddison,P.J., Caudy,A.A., Bernstein,E., Hannon,G.J. and Conklin,D.S. (2002) Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells. Genes Dev., 16, 948-958.
20. Sui,G., Soohoo,C., Affar,E.B., Gay,F., Shi,Y., Forrester,W.C. and Shi,Y. (2002) A DNA vector-based RNAi technology to suppress gene expression in mammalian cells. Proc. Natl Acad. Sci. USA, 99, 5515-5520.
21. Yu,J.-Y., DeRuiter,S.L. and Turner,D.L. (2002) RNA interference by expression of short-interfering RNAs and hairpin RNAs in mammalian cells. Proc. Natl Acad. Sci. USA, 99, 6047-6052.
22. Paul,C.P., Good,P.D., Winer,I. and Engelke,D.R. (2002) Effective expression of small interfering RNA in human cells. Nat. Biotechnol., 20, 505-508.
23. Lund,E. and Dahlberg,J.E. (1984) True genes for human U1 small nuclear RNA. Copy number, polymorphism and methylation. J. Biol. Chem., 259, 2013-2021.
24. van Arsdell,S.W. and Weiner,A.M. (1984) Human genes for U2 small nuclear RNA are tandemly repeated. Mol. Cell. Biol., 4, 492-499.
25. Chong,S.S., Hu,P. and Hernandez,N. (2001) Reconstitution of transcription from the human U6 small nuclear RNA promoter with eight recombinant polypeptides and a partially purified RNA polymerase III complex. J. Biol. Chem., 276, 20727-20734.
26. Ma,B. and Hernandez,N. (2002) Redundant cooperative interactions for assembly of a human U6 transcription initiation complex. Mol. Cell. Biol., 22, 8067-8078.
27. Hayashi,K. (1981) Organization of sequences related to U6 RNA in the human genome. Nucleic Acids Res., 9, 3379-3388.
28. Kent,W.J. (2002) BLAT: the Blast-like alignment tool. Genome Res., 12, 656-664.
29. Kunkel,G.R. and Pederson,T. (1988) Upstream elements required for efficient transcription of a human U6 RNA gene resemble those of U1 and U2 genes even though a different polymerase is used. Genes Dev., 2, 196-204.
30. Goomer,R.S. and Kunkel,G.R. (1992) The transcriptional start site for a human U6 small nuclear RNA gene is dictated by a compound promoter element consisting of the PSE and the TATA box. Nucleic Acids Res., 20, 4903-4912.
31. Mach,C.M., Hargrove,B.W. and Kunkel,G.R. (2002) The small RNA gene activator protein, SphI postoctamer homology-binding factor/selenocysteine tRNA gene transcription activating factor, stimulates transcription of the human interferon regulatory factor-3 gene. J. Biol. Chem., 277, 4853-4858.
32. Henry,R.W., Sadowski,C.L., Kobayashi,R. and Hernandez,N. (1995) A TBP-TAF complex required for transcription of human snRNA genes by RNA polymerases II and III. Nature, 374, 653-656.
33. Kunkel,G.R. and Danzeiser,D.A: (1992) Formation of a template committed complex on the promoter of a gene for the U6 small nuclear RNA from the human requires multiple sequence elements, including the distal region. J. Biol. Chem., 267, 14250-14258.
34. Rincon,J.C., Engler,S.K., Hargrove,B.W. and Kunkel,G.R. (1998) Molecular cloning of a cDNA encoding human SPH-binding factor, a conserved protein that binds to the enhancer-like region of the U6 small nuclear RNA gene promoter. Nucleic Acids Res., 26, 4846-4852.
35. Hernandez,N. (1993) TBP, a universal eukaryotic transcription factor? Genes Dev., 7, 1291-1308.
36. Grunstein,M. (1997) Histone acetylation in chromatin structure and transcription. Nature, 389, 349-352.
37. Struhl,K. (1998) Histone acetylation and transcriptional regulatory mechanisms. Genes Dev., 12, 599-606.
38. Wieben,E.D., Vrabel,A.M., Holicky,E.L., Klisak,I., Sparkes,R.S. and Stanford,D.R. (1991) A U6 snRNA gene with an internal promoter is juxtaposed to an snRNA protein sequence within an intron of a human G protein gene. Nucleic Acids Res., 19, 2869-2874.
39. Tichelaar,J.W., Knerer,B., Vrabel,A. and Wieben,E.D. (1994) Transcription of a variant human U6 small nuclear RNA gene is controlled by a novel, internal RNA polymerase III promoter. Mol. Cell. Biol., 14, 5450-5457.
40. Tichelaar,J.W., Wieben,E.D., Reddy,R., Vrabel,A. and Camacho,P. (1998) In vivo expression of a variant human U6 RNA from a unique, internal promoter. Biochemistry, 37, 12943-12951.
41. Tarn,W.Y. and Steitz,J.A. (1996) Highly diverged U4 and U6 small nuclear RNAs required for splicing rare AT-AC introns. Science, 273, 1824-1832.
42. Peterson,R.C., Doering,J.L. and Brown,D.D. (1980) Characterization of two Xenopus somatic 5S DNAs and one minor oocyte-specific 5S DNA. Cell, 20, 131-141.
43. Bogenhagen,D.F., Wormington,W.M. and Brown,D.D. (1982) Stable transcription complexes of Xenopus 5S RNA genes: a means to maintain the differentiated state. Cell, 28, 413-421.
44. ala. Proc. Natl Acad. Sci. USA, 83, 374-378.
45. Lobo,S.M., Lister,J., Sullivan,M.L. and Hernandez,N. (1991) The cloned RNA polymerase II transcription factor IID selects RNA polymerase III to transcribe the human U6 gene in vitro. Genes Dev., 5, 1477-1489.
46. Waldschmidt,R., Wanandi,I. and Seifart,K.H. (1991) Identification of transcription factors required for the expression of mammalian U6 genes in vitro. EMBO J., 10, 2595-2603.
47. Simmen,K.A., Waldschmidt,R., Bernues,J., Parry,H.D., Seifart,K.H. and Mattaj,I.W. (1992) Proximal sequence element factor binding and species specificity in vertebrate U6 snRNA promoters. J. Mol. Biol., 223, 873-884.
48. Cabart,P. and Murphy,S. (2002) Assembly of human small nuclear RNA gene-specific transcription factor IIIB complex de novo on and off promoter. J. Biol. Chem., 277, 26831-26838.
49. Wang,Y. and Stumph,W.E. (1998) Identification and topological arrangement of Drosophila proximal sequence element (PSE)-binding protein subunits that contact the PSEs of U1 and U6 small nuclear RNA genes. Mol. Cell. Biol., 18, 1570-1579.
50. Hardin,S.B., Ortler,C.J., McNamara-Schroeder,K.J. and Stumph,W.E. (2000) Similarities and differences in the conformation of protein-DNA complexes at the U1 and U6 snRNA gene promoters. Nucleic Acids Res., 28, 2771-2778.
51. Sec promoters. J. Biol. Chem., 274, 24241-24249.
52. Dahlberg,J.E. and Lund,E. (1988) The genes and transcription of the major small nuclear RNAs. In Birnstiel,M.L. (ed.), Structure and Function of Major and Minor Small Nuclear Ribonucleoprotein Particles. Springer-Verlag, Berlin,Germany pp. 38-70.