Identification of highly specific localized sequence motifs in human ribosomal protein gene promoters

Gene

Volumn 365, Issue 1-2 SPEC. ISS., 2006, Pages 48-56

  Roepcke, Stefan ^a   Zhi, Degui ^b   Vingron, Martin ^a   Arndt, Peter F ^a  

^a MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Motif search; Transcription factor binding sites; Transcription initiation; Transcription start site

Indexed keywords

MESSENGER RNA; PALINDROMIC DNA; RIBOSOME PROTEIN; TRANSCRIPTION FACTOR;

CONFERENCE PAPER; CONSENSUS SEQUENCE; CPG ISLAND; GC RICH SEQUENCE; GENE IDENTIFICATION; GENE INTERACTION; GENETIC TRANSCRIPTION; MOLECULAR EVOLUTION; ORTHOLOGY; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN BINDING; SEQUENCE ALIGNMENT; SPECIES COMPARISON; TRANSCRIPTION INITIATION SITE;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; BINDING SITES; CONSENSUS SEQUENCE; CONSERVED SEQUENCE; CPG ISLANDS; CYTOSOL; DATABASES, PROTEIN; EVOLUTION, MOLECULAR; EXONS; HUMANS; MICE; MOLECULAR SEQUENCE DATA; PROMOTER REGIONS (GENETICS); RIBOSOMAL PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID; TATA BOX; TRANSCRIPTION FACTORS; TRANSCRIPTION INITIATION SITE; TRANSCRIPTION, GENETIC;

EID: 31844446551     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2005.09.033     Document Type: Conference Paper

References (31)

1. S. Aerts, G. Thijs, M. Dabrowski, Y. Moreau, and B. De Moor Comprehensive analysis of the base composition around the transcription start site in Metazoa BMC Genomics 5 2004 34
2. M. Antoine, and P. Kiefer Functional characterization of transcriptional regulatory elements in the upstream region and intron 1 of the human S6 ribosomal protein gene Biochem. J. 336 Pt 2 1998 327 335
3. J.N. Athanikar, R.M. Badge, and J.V. Moran A YY1-binding site is required for accurate human LINE-1 transcription initiation Nucleic Acids Res. 32 2004 3846 3855
4. T.L. Bailey, and C. Elkan Fitting a mixture model by expectation maximization to discover motifs in biopolymers Proc. Int. Conf. Intell. Syst. Mol. Biol. 2 1994 28 36
5. T.L. Bailey, M.E. Baker, and C.P. Elkan An artificial intelligence approach to motif discovery in protein sequences: application to steroid dehydrogenases J. Steroid Biochem. Mol. Biol. 62 1997 29 44
6. M. Blanchette Aligning multiple genomic sequences with the threaded blockset aligner Genome Res. 14 2004 708 715
7. P. Bucher Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences J. Mol. Biol. 212 1990 563 578
8. S. Chung, and R.P. Perry The importance of downstream delta-factor binding elements for the activity of the rpL32 promoter Nucleic Acids Res. 21 1993 3301 3308
9. G.E. Crooks, G. Hon, J.M. Chandonia, and S.E. Brenner WebLogo: a sequence logo generator Genome Res. 14 2004 1188 1190
10. M. Gardiner-Garden, and M. Frommer CpG islands in vertebrate genomes J. Mol. Biol. 196 1987 261 282
11. R.R. Genuario, and R.P. Perry The GA-binding protein can serve as both an activator and repressor of ribosomal protein gene transcription J. Biol. Chem. 271 1996 4388 4395
12. J.T. Kadonaga Regulation of RNA polymerase II transcription by sequence-specific DNA binding factors Cell 116 2004 247 257
13. D. Karolchik The UCSC Genome Browser Database Nucleic Acids Res. 31 2003 51 54
14. W.J. Kent BLAT-the BLAST-like alignment tool Genome Res. 12 2002 656 664
15. S. Levy, D. Avni, N. Hariharan, R.P. Perry, and O. Meyuhas Oligopyrimidine tract at the 5′ end of mammalian ribosomal protein mRNAs is required for their translational control Proc. Natl. Acad. Sci. U. S. A. 88 1991 3319 3323
16. V. Matys TRANSFAC: transcriptional regulation, from patterns to profiles Nucleic Acids Res. 31 2003 374 378
17. O. Meyuhas Synthesis of the translational apparatus is regulated at the translational level Eur. J. Biochem. 267 2000 6321 6330
18. A. Nakao, M. Yoshihama, and N. Kenmochi RPG: the Ribosomal Protein Gene database Nucleic Acids Res. 32 Database issue 2004 D168 D170
19. R.P. Perry Architecture of Mammalian Ribosomal Protein Promoters 2003 Fox Chase Cancer Centre
20. R.P. Perry The architecture of mammalian ribosomal protein promoters BMC Evol. Biol. 5 2005 15
21. K.D. Pruitt, and D.R. Maglott RefSeq and LocusLink: NCBI gene-centered resources Nucleic Acids Res. 29 2001 137 140
22. S. Rahmann, T. Müller, and M. Vingron On the power of profiles for transcription factor binding site detection Stat. Appl. Genet. Mol. Biol. 2 2003
23. J.C. Reese Basal transcription factors Curr. Opin. Genet. Dev. 13 2003 114 118
24. G. Safrany, and R.P. Perry The relative contributions of various transcription factors to the overall promoter strength of the mouse ribosomal protein L30 gene Eur. J. Biochem. 230 1995 1066 1072
25. A. Sandelin, W. Alkema, P. Engstrom, W.W. Wasserman, and B. Lenhard JASPAR: an open-access database for eukaryotic transcription factor binding profiles Nucleic Acids Res. 32 Database issue 2004 D91 D94
26. C.D. Schmid, V. Praz, M. Delorenzi, R. Perier, and P. Bucher The Eukaryotic Promoter Database EPD: the impact of in silico primer extension Nucleic Acids Res. 32 Database issue 2004 D82 D85
27. A. Shrivastava, and K. Calame An analysis of genes regulated by the multi-functional transcriptional regulator Yin Yang-1 Nucleic Acids Res. 22 1994 5151 5155
28. S.T. Smale, and J.T. Kadonaga The RNA polymerase II core promoter Annu. Rev. Biochem. 72 2003 449 479
29. Y. Suzuki, and S. Sugano Construction of a full-length enriched and a 5′-end enriched cDNA library using the oligo-capping method Methods Mol. Biol. 221 2003 73 91
30. Y. Suzuki, R. Yamashita, S. Sugano, and K. Nakai DBTSS, DataBase of Transcriptional Start Sites: progress report 2004 Nucleic Acids Res. 32 Database issue 2004 D78 D81
31. M. Yoshihama The human ribosomal protein genes: sequencing and comparative analysis of 73 genes Genome Res. 12 2002 379 390