Bat Accelerated Regions Identify a Bat Forelimb Specific Enhancer in the HoxD Locus

Abstract

The molecular events leading to the development of the bat wing remain largely unknown, and are thought to be caused, in part, by changes in gene expression during limb development. These expression changes could be instigated by variations in gene regulatory enhancers. Here, we used a comparative genomics approach to identify regions that evolved rapidly in the bat ancestor, but are highly conserved in other vertebrates. We discovered 166 bat accelerated regions (BARs) that overlap H3K27ac and p300 ChIP-seq peaks in developing mouse limbs. Using a mouse enhancer assay, we show that five Myotis lucifugus BARs drive gene expression in the developing mouse limb, with the majority showing differential enhancer activity compared to the mouse orthologous BAR sequences. These include BAR116, which is located telomeric to the HoxD cluster and had robust forelimb expression for the M. lucifugus sequence and no activity for the mouse sequence at embryonic day 12.5. Developing limb expression analysis of Hoxd10-Hoxd13 in Miniopterus natalensis bats showed a high-forelimb weak-hindlimb expression for Hoxd10-Hoxd11, similar to the expression trend observed for M. lucifugus BAR116 in mice, suggesting that it could be involved in the regulation of the bat HoxD complex. Combined, our results highlight novel regulatory regions that could be instrumental for the morphological differences leading to the development of the bat wing.

Developmental loci harbor clusters of accelerated regions that evolved independently in ape lineages

“…This approach was applied genome-wide to identify Human Accelerated Regions (HARs) that experienced significantly more substitutions than expected in the human lineage since divergence from the common ancestor with chimpanzees , Prabhakar, Noonan et al 2006, Bird, Stranger et al 2007, Bush and Lahn 2008. It has also been applied to other lineages, including fruit flies (Holloway, Begun et al 2008), the common ancestor of therian mammals (Holloway, Bruneau et al 2016) and the common ancestor of bats (Booker, Friedrich et al 2016). The ~2,700 HARs identified to date are mostly non-coding, and many have epigenomic signatures suggestive of enhancer function in human cells.…”

Evaluating the Probability of CRISPR-based Gene Drive Contaminating Another Species

“…Human enhancers generally drive similar expression in mice [88 My divergence -all divergence times are from TimeTree (Kumar et al 2017) ] (Cheng et al 2014) . Enhancers have also been observed to drive expression in corresponding homologous organs in more distantly related species such as mice and bats [94 My divergence (Cretekos et al 2008;Booker et al 2016) ] or even fish species and humans [465 My divergence (Yuan et al 2018) ]. A particular enhancer was shown to drive comparable expression across 9 species of vertebrates including fishes, lizards, snakes and mice (Kvon et al 2016) .…”

Bayesian detection of convergent rate changes of conserved noncoding elements on phylogenetic trees

“…One of the major revelations of comparative genomics has been the discovery of regions of the genome falling well outside protein-coding genes that nonetheless exhibit considerable levels of conservation across evolutionary time (Bejerano et al 2004;Siepel et al 2005;Woolfe et al 2005;Venkatesh et al 2006;Lindblad-Toh et al 2011). Changes in conservation of elements, such as conserved non-coding or non-exonic elements, in a subset of lineages is often associated with altered regulatory activity and ultimately phenotypic divergence (Mclean et al 2011;Booker et al 2016). Numerous studies have used changes in sequence conservation of conserved elements as means to identify regulatory regions which may be of particular importance for lineage-specific phenotypes.…”

“…Holloway et al (2016) identified 4,797 regions accelerated at the base of therian mammals, many of which are noncoding and located close to developmental transcription factors. Booker et al (2016) discovered 166 bat-accelerated regions overlapping with enhancers in developing mouse limbs, including one that likely regulated expression of the HoxD cluster important for forelimb development. Such studies demonstrate that noncoding elements play a crucial role in molding morphological diversity across diverse clades.…”

“…These methods allow users to both estimate a phylogeny and divergence times while allowing for rate variation among lineages, but are less powerful at detecting evolutionary shifts in rate that are correlated with a specific phenotype change as they do not explicitly incorporate such correlations in the model. Moreover, although highly accurate and useful for validating various clock models, these methods are not easily scalable to genome-wide data such as is typically encountered when testing for rate changes in conserved elements across a clade for which whole-genomes have been sequenced (McLean et al 2011;Booker et al 2016;Holloway et al 2016).…”