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Conserved noncoding sequences are selectively constrained and not mutation cold spots

Abstract

Noncoding genetic variants are likely to influence human biology and disease, but recognizing functional noncoding variants is difficult. Approximately 3% of noncoding sequence is conserved among distantly related mammals1,2,3,4, suggesting that these evolutionarily conserved noncoding regions (CNCs) are selectively constrained and contain functional variation. However, CNCs could also merely represent regions with lower local mutation rates. Here we address this issue and show that CNCs are selectively constrained in humans by analyzing HapMap genotype data. Specifically, new (derived) alleles of SNPs within CNCs are rarer than new alleles in nonconserved regions (P = 3 × 10−18), indicating that evolutionary pressure has suppressed CNC-derived allele frequencies. Intronic CNCs and CNCs near genes show greater allele frequency shifts, with magnitudes comparable to those for missense variants. Thus, conserved noncoding variants are more likely to be functional. Allele frequency distributions highlight selectively constrained genomic regions that should be intensively surveyed for functionally important variation.

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Figure 1: DAFs (derived allele frequencies) are lower for SNPs within CNCs.
Figure 2: Fraction of evenly ascertained HapMap SNPs with DAF ≤ 0.1 in the YRI HapMap samples within and outside of CNCs and for selected functional classes.

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Acknowledgements

The authors wish to thank the International HapMap investigators, T.S. Mikkelsen for assistance determining derived alleles from chimp sequence comparisons, T. Bersaglieri for assistance genotyping SNPs, G. Rockwell for assistance implementing several statistical methods and analysis algorithms, A. Langane for DNA samples and M. Gagnebin and C. Rossier for sequencing. J.N.H. is a recipient of a Burroughs Wellcome Career Award in Biomedical Sciences, which supported this work. E.T.D. is supported by the Wellcome Trust and NIH. D.J.T. was supported by grants from the National Human Genome Research Institute. S.E.A. is supported by the Swiss National Science Foundation, NIH and EU. C.N.C. is supported by the GlaxoSmithKline Competitive Grants Award Program for Young Investigators and by a National Heart, Lung, and Blood Institute Mentored Patient Oriented Research Career Development Award.

AUTHORS' CONTRIBUTIONS

J.A.D., C.B., J.N. and D.J.T. contributed equally to this manuscript, and E.T.D. and J.N.H. co-directed this project.

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Correspondence to Emmanouil T Dermitzakis or Joel N Hirschhorn.

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Supplementary information

Supplementary Table 1

Comparisons of DAF distributions, with significance levels and percentages of SNPs in DAF frequency bins. (PDF 112 kb)

Supplementary Table 2

Positions and derived allele frequencies of SNPs from dbSNP located in ultraconserved elements. (PDF 45 kb)

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Drake, J., Bird, C., Nemesh, J. et al. Conserved noncoding sequences are selectively constrained and not mutation cold spots. Nat Genet 38, 223–227 (2006). https://doi.org/10.1038/ng1710

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