Ancient duplicated conserved noncoding elements in vertebrates: A genomic and functional analysis

Abstract

Fish-mammal genomic comparisons have proved powerful in identifying conserved noncoding elements likely to be cis-regulatory in nature, and the majority of those tested in vivo have been shown to act as tissue-specific enhancers associated with genes involved in transcriptional regulation of development. Although most of these elements share little sequence identity to each other, a small number are remarkably similar and appear to be the product of duplication events. Here, we searched for duplicated conserved noncoding elements in the human genome, using comparisons with Fugu to select putative cis-regulatory sequences. We identified 124 families of duplicated elements, each containing between two and five members, that are highly conserved within and between vertebrate genomes. In 74% of cases, we were able to assign a specific set of paralogous genes with annotation relating to transcriptional regulation and/or development to each family, thus removing much of the ambiguity in identifying associated genes. We find that duplicate elements have the potential to up-regulate reporter gene expression in a tissue-specific manner and that expression domains often overlap, but are not necessarily identical, between family members. Over two thirds of the families are conserved in duplicate in fish and appear to predate the large-scale duplication events thought to have occurred at the origin of vertebrates. We propose a model whereby gene duplication and the evolution of cis-regulatory elements can be considered in the context of increased morphological diversity and the emergence of the modern vertebrate body plan.

Ultraconserved Elements: Analyses of Dosage Sensitivity, Motifs and Boundaries

“…The ultraconservation of nonexonic UCEs may therefore reflect a multiplicity of constraints, such as dual regulatory roles at the DNA and RNA levels (Feng et al 2006) or a superimposition of binding sites for multiple transcription factors [Bejerano et al 2004;Boffelli et al 2004;De La Calle-Mustienes et al 2005;Siepel et al 2005;Derti et al 2006;Pennacchio et al 2006;Vavouri et al 2007; also see related arguments for exonic UCEs (Derti et al 2006)]. The latter explanation is consistent with the putative enhancer-like activity of nonexonic UCEs as well as other highly conserved noncoding elements (CNEs) (Woolfe et al 2005;McEwen et al 2006;Pennacchio et al 2006;Ahituv et al 2007;Paparidis et al 2007;Visel et al 2008) and has also been hypothesized for invertebrate highly conserved elements (Siepel et al 2005;Vavouri et al 2007). In support of these proposals, multiple transcription factor binding sites have been observed in an intronic UCE at the GLI3 locus (Paparidis et al 2007).…”

“…Aligned with this proposal is evidence supporting the hypothesis that these UCEs and CNEs function as highly important gene regulatory elements, such as enhancers, thereby providing a reason for their perfect or remarkably high conservation. This interpretation is widely supported by the capacity of these elements to direct transcription (Woolfe et al 2005;McEwen et al 2006;Pennacchio et al 2006;Ahituv et al 2007;Paparidis et al 2007;Visel et al 2008) and is also consistent with the enrichment in nonexonic UCEs for the recognition sequence of the homeodomain protein DNA-binding module (also see Abnizova et al 2007), which is found in many transcription factors (Fraenkel et al 1998).…”

“…These and related observations demonstrating that CNEs experienced a deceleration of the molecular clock prior to the divergence of tetrapods and teleosts (McEwen et al 2006) have suggested that nonexonic UCEs and such CNEs played and continue to play key roles in vertebrate evolution and development. Aligned with this proposal is evidence supporting the hypothesis that these UCEs and CNEs function as highly important gene regulatory elements, such as enhancers, thereby providing a reason for their perfect or remarkably high conservation.…”

An evolutionarily conserved three-dimensional structure in the vertebrate Irx clusters facilitates enhancer sharing and coregulation

“…Eight of the IrxA HCNRs are partially conserved in the IrxB cluster in largely equivalent genomic locations 18 indicating an origin that predates the duplication of the clusters. Interestingly, of these eight paralogous sequences, fi ve were positive in our Xenopus transgenic assay (2,165, 2,695, 3,173, 3,240 and 3,565) and all IrxA and IrxB paralogues show similar regulatory activities, with the exception of the paralogue region of 3,240 which showed no enhancer activity ( Supplementary Fig.…”

Conserved noncoding elements and the evolution of animal body plans

“…(8,11,(14)(15)(16)(17) These highly conserved regulatory elements and the associated genes appear to be among the key components of core gene regulatory networks (GRNs) that control the development of different animal body plans.…”