Origin and evolution of developmental enhancers in the mammalian neocortex

Abstract

Morphological innovations such as the mammalian neocortex may involve the evolution of novel regulatory sequences. However, de novo birth of regulatory elements active during morphogenesis has not been extensively studied in mammals. Here, we use H3K27ac-defined regulatory elements active during human and mouse corticogenesis to identify enhancers that were likely active in the ancient mammalian forebrain. We infer the phylogenetic origins of these enhancers and find that ∼20% arose in the mammalian stem lineage, coincident with the emergence of the neocortex. Implementing a permutation strategy that controls for the nonrandom variation in the ages of background genomic sequences, we find that mammal-specific enhancers are overrepresented near genes involved in cell migration, cell signaling, and axon guidance. Mammal-specific enhancers are also overrepresented in modules of coexpressed genes in the cortex that are associated with these pathways, notably ephrin and semaphorin signaling. Our results also provide insight into the mechanisms of regulatory innovation in mammals. We find that most neocortical enhancers did not originate by en bloc exaptation of transposons. Young neocortical enhancers exhibit smaller H3K27ac footprints and weaker evolutionary constraint in eutherian mammals than older neocortical enhancers. Based on these observations, we present a model of the enhancer life cycle in which neocortical enhancers initially emerge from genomic background as short, weakly constrained "proto-enhancers." Many proto-enhancers are likely lost, but some may serve as nucleation points for complex enhancers to evolve.regulatory innovation | neocortical development | epigenetics | brain evolution T he evolution of animal morphology requires changes in fundamental developmental processes. Recent studies suggest that altered gene regulation during development contributes to morphological differences between species (1-4). In several cases, individual regulatory changes have been shown to have strong effects on morphology, including reduction or loss of existing anatomical units (5-7). However, the mechanisms underlying morphological innovation, which includes the emergence of entirely novel anatomical structures and radical transformations of existing structures, remain unclear (see ref. 8).One hypothesis is that morphological innovations are driven by the widespread emergence of new regulatory functions. These may arise through several potential mechanisms: modification of regulatory elements with ancestral functions, exaptation of specific classes of transposons to generate new regulatory sequences, and emergence of new regulatory elements in situ from nonfunctional, unconstrained genomic sequences. Although recent theoretical work in flies suggests that entire regulatory elements can evolve from genomic background on relatively short time scales (9), the de novo generation of regulatory elements by transposon exaptation is a particularly compelling mechanism. Many transposons include binding sites for multiple ...

Transposable elements are the primary source of novelty in primate gene regulation

“…3; Supplemental Table S2). Together, our differential histone state analysis results are broadly supported by several studies that have consistently suggested a high degree of regulatory element conservation between closely related species in metazoans (Cotney et al 2013;Boyle et al 2014;Prescott et al 2015;Emera et al 2016). We note that the estimated fraction of conserved CRE is lower (36.2%: 39.6% of promoters and 24.3% of enhancers) when analyses are not restricted to six-way orthologous regions (i.e., treating all human CREs lacking an ortholog in any of the other species as not conserved).…”

“…Similarly, the recruitment of novel regulatory networks in the uterus was likely mediated by ancient mammalian TEs (Lynch et al 2011(Lynch et al , 2015. Conversely, neocortical enhancers do not exhibit strong evidence of transposon co-option (Emera et al 2016).…”

“…The contribution of cis-regulatory elements (CREs) to phenotypic and behavioral evolution has been shown in many taxa (King and Wilson 1975;Prabhakar et al 2008;Schmidt et al 2010;Cain et al 2011;Marnetto et al 2014;Zhou et al 2014;Prescott et al 2015;Reilly et al 2015;Villar et al 2015;Emera et al 2016;Berthelot et al 2017). Although previous studies have suggested a role for transposable elements (TEs) in the evolution of gene regulation, validating the functional contribution of TEs in mammalian gene regulation remains a challenge (McClintock 1950(McClintock , 1984Britten and Davidson 1969;Davidson and Britten 1979;Jordan et al 2003;Bejerano et al 2006;Wang et al 2007;Bourque et al 2008;Sasaki et al 2008;Markljung et al 2009;Kunarso et al 2010;Lynch et al 2011Lynch et al , 2015Schmidt et al 2012;Chuong et al 2013Chuong et al , 2016Jacques et al 2013;Xie et al 2013;del Rosario et al 2014;Sundaram et al 2014;Du et al 2016;Rayan et al 2016;Ward et al 2017).…”

Regulatory activities of transposable elements: from conflicts to benefits

“…Recent work suggests that TEs can extensively remodel regulatory networks that are involved in specific processes including dosage compensation 103 , immunity 44 , and early embryonic development 24 . Other comparative studies of enhancer evolution in the liver 148 and the neocortex 149 among mammals found only a minor contribution for host co-option of TE activity. These observations raise the question of whether TE-mediated regulatory evolution may be inherently biased for certain biological processes, or if it is a more general mechanism for large-scale genetic innovation.…”

Origin and evolution of the metazoan non-coding regulatory genome: Insights from the sponge Amphimedon queenslandica

“…Distal enhancers are rapidly evolving (Villar et al, 2015). In mammals, their origin often involves exaptation of ancestral DNA (Villar et al, 2015) or de novo emergence from neutral genomic background (proto-enhancers) (Emera et al, 2016). The finding of only a couple of conserved cis-regulatory elements, located in the vicinity of SOX21 and HMX3 genes, across eumetazoans Royo et al, 2011) underscores the dynamic nature of enhancer sequence evolution.…”