Lineage-specific expansion of DNA-binding transcription factor families

Trends in Genetics

Volumn 26, Issue 9, 2010, Pages 388-393

  Charoensawan, Varodom ^a   Wilson, Derek ^a   Teichmann, Sarah A ^a  

^a MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA BINDING PROTEIN; TRANSCRIPTION FACTOR;

ARCHAEBACTERIUM; BACTERIUM; DNA BINDING; DNA TRANSCRIPTION; EUKARYOTE; GENE SEQUENCE; GENETIC VARIABILITY; GENOME; NONHUMAN; PHYLOGENETIC TREE; PRIORITY JOURNAL; PROTEIN FAMILY; SHORT SURVEY; TAXONOMY;

EUKARYOTA;

EID: 77955846206     PISSN: 01689525     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tig.2010.06.004     Document Type: Short Survey

References (33)

1. Aravind L., Koonin E.V. DNA-binding proteins and evolution of transcription regulation in the archaea. Nucleic Acids Res. 1999, 27:4658-4670.
2. Riechmann J.L., et al. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science 2000, 290:2105-2110.
3. Coulson R.M., Ouzounis C.A. The phylogenetic diversity of eukaryotic transcription. Nucleic Acids Res. 2003, 31:653-660.
4. Perez-Rueda E., et al. Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea. Comput. Biol. Chem. 2004, 28:341-350.
5. Wilson D., et al. DBD-taxonomically broad transcription factor predictions: new content and functionality. Nucleic Acids Res. 2008, 36:D88-D92.
6. Finn R.D., et al. The Pfam protein families database. Nucleic Acids Res. 2010, 38:D211-D222.
7. Wilson D., et al. SUPERFAMILY-sophisticated comparative genomics, data mining, visualization and phylogeny. Nucleic Acids Res. 2009, 37:D380-D386.
8. Benson D.A., et al. GenBank. Nucleic. Acids Res. 2009, 37:D26-D31.
9. Wunderlich Z., Mirny L.A. Different gene regulation strategies revealed by analysis of binding motifs. Trends Genet. 2009, 25:434-440.
10. Kunin V., et al. The net of life: reconstructing the microbial phylogenetic network. Genome Res. 2005, 15:954-959.
11. Pruss B.M., et al. FlhD/FlhC-regulated promoters analyzed by gene array and lacZ gene fusions. FEMS Microbiol. Lett. 2001, 197:91-97.
12. Pavlopoulos A., Akam M. Hox go omics: insights from Drosophila into Hox gene targets. Genome Biol. 2007, 8:208.
13. Shelest E. Transcription factors in fungi. FEMS Microbiol. Lett. 2008, 286:145-151.
14. Saviola B., et al. Arm-domain interactions in AraC. J. Mol. Biol. 1998, 278:539-548.
15. Honjo M., et al. A novel Bacillus subtilis gene involved in negative control of sporulation and degradative-enzyme production. J. Bacteriol. 1990, 172:1783-1790.
16. King N., et al. The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans. Nature 2008, 451:783-788.
17. Pincus D., et al. Evolution of the phospho-tyrosine signaling machinery in premetazoan lineages. Proc. Natl. Acad. Sci. U. S. A. 2008, 105:9680-9684.
18. Rokas A. The molecular origins of multicellular transitions. Curr. Opin. Genet. Dev. 2008, 18:472-478.
19. Brown J.M., Firtel R.A. Regulation of cell-fate determination in Dictyostelium. Dev. Biol. 1999, 216:426-441.
20. Babu M.M., et al. The natural history of the WRKY-GCM1 zinc fingers and the relationship between transcription factors and transposons. Nucleic Acids Res. 2006, 34:6505-6520.
21. Balaji S., et al. Discovery of the principal specific transcription factors of Apicomplexa and their implication for the evolution of the AP2-integrase DNA binding domains. Nucleic Acids Res. 2005, 33:3994-4006.
22. Martinez-Antonio A., et al. Internal-sensing machinery directs the activity of the regulatory network in Escherichia coli. Trends Microbiol. 2006, 14:22-27.
23. Itzkovitz S., et al. Coding limits on the number of transcription factors. BMC Genomics 2006, 7:239.
24. Mukherjee S., et al. Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays. Nat. Genet. 2004, 36:1331-1339.
25. Hallikas O., Taipale J. High-throughput assay for determining specificity and affinity of protein-DNA binding interactions. Nat. Protoc. 2006, 1:215-222.
26. Gilad Y., et al. Expression profiling in primates reveals a rapid evolution of human transcription factors. Nature 2006, 440:242-245.
27. Meng X., Wolfe S.A. Identifying DNA sequences recognized by a transcription factor using a bacterial one-hybrid system. Nat. Protoc. 2006, 1:30-45.
28. Deplancke B., et al. A gateway-compatible yeast one-hybrid system. Genome Res. 2004, 14:2093-2101.
29. Coin L., et al. Enhanced protein domain discovery by using language modeling techniques from speech recognition. Proc. Natl. Acad. Sci. U. S. A. 2003, 100:4516-4520.
30. Coin L., et al. Enhanced protein domain discovery using taxonomy. BMC Bioinformatics 2004, 5:56.
31. Snel B., et al. Genomes in flux: the evolution of archaeal and proteobacterial gene content. Genome Res. 2002, 12:17-25.
32. Kunin V., Ouzounis C.A. GeneTRACE-reconstruction of gene content of ancestral species. Bioinformatics 2003, 19:1412-1416.
33. Mirkin B.G., et al. Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes. BMC Evol. Biol. 2003, 3:2.