The effects of selection against spurious transcription factor binding sites
- PMID: 12716998
- DOI: 10.1093/molbev/msg096
The effects of selection against spurious transcription factor binding sites
Abstract
Most genomes contain nucleotide sequences with no known function; such sequences are assumed to be free of constraints, evolving only according to the vagaries of mutation. Here we show that selection acts to remove spurious transcription factor binding site motifs throughout 52 fully sequenced genomes of Eubacteria and Archaea. Examining the sequences necessary for polymerase binding, we find that spurious binding sites are underrepresented in both coding and noncoding regions. The average proportion of spurious binding sites found relative to the expected is 80% in eubacterial genomes and 89% in archaeal genomes. We also estimate the strength of selection against spurious binding sites in the face of the constant creation of new binding sites via mutation. Under conservative assumptions, we estimate that selection is weak, with the average efficacy of selection against spurious binding sites, Nes, of -0.12 for eubacterial genomes and -0.06 for archaeal genomes, similar to that of codon bias. Our results suggest that both coding and noncoding sequences are constrained by selection to avoid specific regions of sequence space.
Similar articles
-
Selection against spurious promoter motifs correlates with translational efficiency across bacteria.PLoS One. 2007 Aug 15;2(8):e745. doi: 10.1371/journal.pone.0000745. PLoS One. 2007. PMID: 17710145 Free PMC article.
-
Relaxed selection against accidental binding of transcription factors with conserved chromatin contexts.Gene. 2010 Oct 15;466(1-2):43-8. doi: 10.1016/j.gene.2010.07.002. Epub 2010 Jul 15. Gene. 2010. PMID: 20637845
-
Expected rates and modes of evolution of enhancer sequences.Mol Biol Evol. 2004 Jun;21(6):1064-73. doi: 10.1093/molbev/msh105. Epub 2004 Mar 10. Mol Biol Evol. 2004. PMID: 15014138
-
Integrating genomic data to predict transcription factor binding.Genome Inform. 2005;16(1):83-94. Genome Inform. 2005. PMID: 16362910
-
Divergent transcriptional and translational signals in Archaea.Environ Microbiol. 2005 Jan;7(1):47-54. doi: 10.1111/j.1462-2920.2004.00674.x. Environ Microbiol. 2005. PMID: 15643935
Cited by
-
Pervasive Selection against MicroRNA Target Sites in Human Populations.Mol Biol Evol. 2020 Dec 16;37(12):3399-3408. doi: 10.1093/molbev/msaa155. Mol Biol Evol. 2020. PMID: 32585012 Free PMC article.
-
FELINES: a utility for extracting and examining EST-defined introns and exons.Nucleic Acids Res. 2003 Nov 15;31(22):e141. doi: 10.1093/nar/gng141. Nucleic Acids Res. 2003. PMID: 14602934 Free PMC article.
-
Unusual mammalian usage of TGA stop codons reveals that sequence conservation need not imply purifying selection.PLoS Biol. 2022 May 12;20(5):e3001588. doi: 10.1371/journal.pbio.3001588. eCollection 2022 May. PLoS Biol. 2022. PMID: 35550630 Free PMC article.
-
Random sequences rapidly evolve into de novo promoters.Nat Commun. 2018 Apr 18;9(1):1530. doi: 10.1038/s41467-018-04026-w. Nat Commun. 2018. PMID: 29670097 Free PMC article.
-
Pervasive transcription: detecting functional RNAs in bacteria.Transcription. 2014;5(4):e944039. doi: 10.4161/21541272.2014.944039. Epub 2014 Oct 30. Transcription. 2014. PMID: 25483405 Free PMC article.
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
