ArticlePloS one2014
Allele frequencies of variants in ultra conserved elements identify selective pressure on transcription factor binding.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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4 citing papers in PubMed.
- Computational identification of ultra-conserved elements in the human genome: a hypothesis on homologous DNA pairing.NAR genomics and bioinformatics · 2024Article
- Genetic Variations of Ultraconserved Elements in the Human Genome.Omics : a journal of integrative biology · 2019Article
- Introduction of 'Generalized Genomic Signatures' for the quantification of neighbour preferences leads to taxonomy- and functionality-based distinction among sequences.Scientific reports · 2019Article
- Conserved non-coding elements: developmental gene regulation meets genome organization.Nucleic acids research · 2017Review
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8 authors.
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Abstract
Ultra-conserved genes or elements (UCGs/UCEs) in the human genome are extreme examples of conservation. We characterized natural variations in 2884 UCEs and UCGs in two distinct populations; Singaporean Chinese (n = 280) and Italian (n = 501) by using a pooled sample, targeted capture, sequencing approach. We identify, with high confidence, in these regions the abundance of rare SNVs (MAF<0.5%) of which 75% is not present in dbSNP137. UCEs association studies for complex human traits can use this information to model expected background variation and thus necessary power for association studies. By combining our data with 1000 Genome Project data, we show in three independent datasets that prevalent UCE variants (MAF>5%) are more often found in relatively less-conserved nucleotides within UCEs, compared to rare variants. Moreover, prevalent variants are less likely to overlap transcription factor binding site. Using SNPfold we found no significant influence of RNA secondary structure on UCE conservation. All together, these results suggest UCEs are not under selective pressure as a stretch of DNA but are under differential evolutionary pressure on the single nucleotide level.
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