Abstract
Abstract
Vertebrate limb bones grow at different rates within and between species to achieve a striking variety of proportions and functions. However, most coding mutations that alter bone growth in mice and humans affect the entire skeleton, pointing to
cis-
regulatory modularity as the primary mechanism to diversify proportion. In a search for causative loci, we previously identified 1,755 disproportionately differentially expressed genes associated with the extreme hindlimb elongation in bipedal jerboas,
Jaculus jaculus
, compared to laboratory mice. We then took a focused approach to identify putative
cis
-regulatory elements near select candidate genes in a highly fragmented draft
Jaculus jaculus
genome assembly. We identified an ATAC-seq peak near
Shox2
that was reproducible in jerboa metatarsals and not in radius/ulna.
Shox2
gained a novel expression domain in jerboa metatarsals and is both necessary and sufficient to modulate mouse limb bone length. This 139 bp putative enhancer in the jerboa genome centers on a ∼1 kb deletion of sequence found broadly throughout placental mammals. Here, we show that replicating the deletion and replacement with the 139 bp jerboa sequence in mice causes no detected phenotype. A genome-wide analysis of our ATAC-seq data using a high-quality
Jaculus jaculus
genome assembly replicated the peak called at this location but also identified 7,445 peaks that are similarly reproducible in metatarsals and not in radius/ulna. Certainly not all of these peaks are causative, but it is likely that many small-effect mutations diversified proportion. It is therefore crucial to apply unbiased filters to genome-wide analyses and to not assume that the few historically favored genes will have the largest effect.