An ancient genomic regulatory block conserved across bilaterians and its dismantling in tetrapods by retrogene replacement

Abstract

Developmental genes are regulated by complex, distantly located cis-regulatory modules (CRMs), often forming genomic regulatory blocks (GRBs) that are conserved among vertebrates and among insects. We have investigated GRBs associated with Iroquois homeobox genes in 39 metazoans. Despite 600 million years of independent evolution, Iroquois genes are linked to ankyrin-repeat-containing Sowah genes in nearly all studied bilaterians. We show that Iroquois-specific CRMs populate the Sowah locus, suggesting that regulatory constraints underlie the maintenance of the Iroquois-Sowah syntenic block. Surprisingly, tetrapod Sowah orthologs are intronless and not associated with Iroquois; however, teleost and elephant shark data demonstrate that this is a derived feature, and that many Iroquois-CRMs were ancestrally located within Sowah introns. Retroposition, gene, and genome duplication have allowed selective elimination of Sowah exons from the Iroquois regulatory landscape while keeping associated CRMs, resulting in large associated gene deserts. These results highlight the importance of CRMs in imposing constraints to genome architecture, even across large phylogenetic distances, and of gene duplication-mediated genetic redundancy to disentangle these constraints, increasing genomic plasticity.

Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints

“…First, many CAMPs show high coexpression levels in humans and/or flies, suggesting that they may share cisregulatory inputs resulting in coordinated transcription. Second, we found more than 100 putative ancient GRBs, often involving important developmental regulators, substantially adding to the Cold Spring Harbor Laboratory Press on March 31, 2019 -Published by genome.cshlp.org Downloaded from three previously known trans-phyletic GRB Irimia et al 2012;Maeso et al 2012a). The deep conservation of GRBs suggests that they may underlie the remarkable conservation of some developmental genetic programs, such as the A-P patterning of the bilaterian central nervous system (in the case of OtxEhbp1) or neuronal ontogeny (Isl-Scaper).…”

“…( McEwen et al 2006;Kikuta et al 2007;Navratilova et al 2010;Goode et al 2011;Maeso et al 2012a). Complex genes are often regulated by a redundant set of cis-regulatory elements, which increase robustness, and are continuously evolving ( Jeong et al 2006;Hong et al 2008;Frankel et al 2010;Perry et al 2010;Schmidt et al 2010).…”

“…In coregulated gene pairs, each gene of the pair could be reciprocally lost from one of the duplicated regions while keeping the common cis-regulatory elements in both, therefore becoming two nonassociated genes with fully functional regulatory landscapes. In the case of GRBs, the coding sequences of extra bystander gene copies may be erased, while the trans-dev-associated regulatory elements are conserved (McEwen et al 2006;Kikuta et al 2007;Maeso et al 2012a).…”

“…First, known GRBs are generally restricted to vertebrates (Kikuta et al 2007) or insects , with only three transphyletic GRBs described to date Irimia et al 2012;Maeso et al 2012a). Second, while tandemly duplicated Drosophila genes tend to remain linked (Quijano et al 2008), such duplicates usually reflect recent duplications (Thomas 2007;Baldwin et al 2009).…”

cis-Regulatory Complexity within a Large Non-Coding Region in the Drosophila Genome

“…For example, a 645 kb region that separates the vertebrate Iroquois genes Irx3 and Irx5 contains multiple Iroquois-specific enhancers [22]. Likewise, in Drosophila a distal non-coding region adjacent to the Drosophila iroquois gene complex contains multiple enhancers required for wild-type irx gene expression [23]. In addition, analysis of cut gene regulation has identified one of its wing margin enhancers 80 kb away from its proximal promoter region [24].…”