Ancient selection for derived alleles at a GDF5 enhancer influencing human growth and osteoarthritis risk

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Abstract

Variants in GDF5 are associated with human arthritis and decreased height, but the causal mutations are still unknown. We surveyed the Gdf5 locus for regulatory regions in transgenic mice and fine-mapped separate enhancers controlling expression in joints versus growing ends of long bones. A large downstream regulatory region contains a novel growth enhancer (GROW1), which is required for normal Gdf5 expression at ends of developing bones and for normal bone lengths in vivo. Human GROW1 contains a common base-pair change that decreases enhancer activity and colocalizes with peaks of positive selection in humans. The derived allele is rare in Africa but common in Eurasia and is found in Neandertals and Denisovans. Our results suggest that an ancient regulatory variant in GROW1 has been repeatedly selected in northern environments and that past selection on growth phenotypes explains the high frequency of a GDF5 haplotype that also increases arthritis susceptibility in many human populations.

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Figure 1: A regulatory scan of the Gdf5 region.
Figure 2: Downstream BAC rescues long-bone and digit growth.
Figure 3: Fine-mapping of a human GDF5 growth-collar enhancer.
Figure 4: A functional variant in the human GDF5 growth-plate enhancer.
Figure 5: rs4911178 global allele frequencies and signatures of selection in the GROW1B region.
Figure 6: Evolutionary history of the GDF5 locus in humans.
Figure 7: GROW1 regulates long-bone length in vivo.

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Acknowledgements

The authors thank M. Hiller and G. Renaud for assistance with Neandertal and Denisovan sequence data; E. Eichler and M. Malig (University of Washington) for human fosmids; C. Lowe and F. Jones for assistance with 1000 Genomes data analysis; P. Arlotta, H.H. Chen, L. Wu, E. Brown, and M. Guo for assistance with CRISPR–Cas9 gene targeting; M. Bouxsein, D. Brooks, and M. Armanini (MGH Center for Skeletal Research Imaging and Biomechanical Testing Core (NIH P30 AR066261)) for assistance with μCT experiments; and G. Bejerano, K. Guenther, D. Mortlock, A. Pollen, and members of the laboratories of D.M.K. and T.D.C. for useful scientific discussions. This work was funded in part by grants from NSERC (RGPIN-435973-2013, A.C.D.), the Arthritis Foundation (H.C. and M.S.), the NIH (AR42236, D.M.K.), the Milton Fund of Harvard (T.D.C.), the China Scholarship Council (J.C.), and the Jason S. Bailey Fund of Harvard (J.C.). D.M.K. is supported an investigator of the Howard Hughes Medical Institute.

Author information

T.D.C. and D.M.K. conceived and oversaw the project. H.C. and M.S. designed BAC transgenic mice. M.S., H.C., and T.D.C. performed mouse rescue experiments and phenotyping. J.C. and T.D.C. performed GROW1 CRISPR–Cas9 gene editing, mouse breeding, genotyping, and phenotyping. A.M.K. and T.D.C. performed morphometric analyses on GROW1 μCT specimens. T.D.C. performed in situ hybridization expression experiments, identified and fine-mapped the growth-enhancer region, conducted coding SNP analyses, UniPROBE analyses, and HaploRegV.4.1 analyses, and performed all in vitro and in vivo tests of the effects of the rs4911178 polymorphism. T.D.C. and A.C.D. performed allele frequency, initial haplotype detection, and CMS analyses. A.C.D. processed 1000 Genomes and archaic hominin data sets; performed haplotype and visual genotype analyses, and tree-building experiments; and provided input into all computational assays. T.D.C. and D.M.K. wrote the manuscript with input from all authors.

Correspondence to Terence D Capellini or David M Kingsley.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–10, 14 and 15, and Supplementary Note. (PDF 13966 kb)

Supplementary Table 1

Allele frequencies for 1000 Genomes SNPs across 400-kb interval centered on the GDF5 locus. (XLSX 436 kb)

Supplementary Table 2

r2 linkage calculations between rs4911178 and other SNPs within 400-kb interval for all populations and continents. (XLSX 177 kb)

Supplementary Table 3

Phased 1000 Genomes haplotypes for individuals used in this study including haplotypes for archaic hominins, chimpanzee reference (panTro3) and human reference (hg19). (XLSX 7353 kb)

Supplementary Table 4

Total counts of the different 1000 Genomes population haplotypes within clades identified through phylogenetic analyses based on reduced tree used in Figure 6. (XLSX 39 kb)

Supplementary Table 5

1000 Genomes SNP frequencies in different clades for the major height and osteoarthritis GWAS variants addressed in this study based on reduced tree used in Figure 6. (XLSX 46 kb)

Supplementary Table 6

Divergence calculations for Neandertal versus all haplotypes within A, B, and B* identified in this study. (XLSX 165 kb)

Supplementary Table 7

Transcription factor binding site analysis of rs4911178. (XLSX 126 kb)

Supplementary Table 8

Primer locations, sequences, and source DNA used for constructs and genotyping in this study. (XLSX 41 kb)

Supplementary Figure 11

Maximum-likelihood analysis of 1000 Genomes, Neandertal, Denisovan, and chimpanzee haplotypes using phased variants. (PDF 3086 kb)

Supplementary Figure 12

Maximum-likelihood analysis and visual genotyping of human 1000 Genomes, Neandertal, Denisovan, and chimpanzee haplotypes using all 1,489 phased variants at MAF ≥0.05. (PDF 871 kb)

Supplementary Figure 13

Maximum-likelihood analysis and visual genotyping of human 1000 Genomes, Neandertal, Denisovan, and chimpanzee haplotypes using all 1,489 phased variants at MAF ≥0.01. (PDF 1851 kb)

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Capellini, T., Chen, H., Cao, J. et al. Ancient selection for derived alleles at a GDF5 enhancer influencing human growth and osteoarthritis risk. Nat Genet 49, 1202–1210 (2017) doi:10.1038/ng.3911

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