Combinatorial Gene Regulatory Functions Underlie Ultraconserved Elements in Drosophila

Abstract

Ultraconserved elements (UCEs) are discrete genomic elements conserved across large evolutionary distances. Although UCEs have been linked to multiple facets of mammalian gene regulation their extreme evolutionary conservation remains largely unexplained. Here, we apply a computational approach to investigate this question in Drosophila, exploring the molecular functions of more than 1,500 UCEs shared across the genomes of 12 Drosophila species. Our data indicate that Drosophila UCEs are hubs for gene regulatory functions and suggest that UCE sequence invariance originates from their combinatorial roles in gene control. We also note that the gene regulatory roles of intronic and intergenic UCEs (iUCEs) are distinct from those found in exonic UCEs (eUCEs). In iUCEs, transcription factor (TF) and epigenetic factor binding data strongly support iUCE roles in transcriptional and epigenetic regulation. In contrast, analyses of eUCEs indicate that they are two orders of magnitude more likely than the expected to simultaneously include protein-coding sequence, TF-binding sites, splice sites, and RNA editing sites but have reduced roles in transcriptional or epigenetic regulation. Furthermore, we use a Drosophila cell culture system and transgenic Drosophila embryos to validate the notion of UCE combinatorial regulatory roles using an eUCE within the Hox gene Ultrabithorax and show that its protein-coding region also contains alternative splicing regulatory information. Taken together our experiments indicate that UCEs emerge as a result of combinatorial gene regulatory roles and highlight common features in mammalian and insect UCEs implying that similar processes might underlie ultraconservation in diverse animal taxa.

Ultraconserved Elements Occupy Specific Arenas of Three-Dimensional Mammalian Genome Organization

“…Consistent with this, Harmston et al (2017) recently reported that clusters of CNEs predict the span of domains, suggesting that CNEs might be involved in chromatin folding. For example, since some UCEs embody enhancer activity (Bejerano et al, 2004; Bhatia et al, 2013; Lampe et al, 2008; McBride et al, 2011; Pauls et al, 2012; Pennacchio et al, 2006; Poitras et al, 2010; Poulin et al, 2005; Sandelin et al, 2004; Vavouri et al, 2007; Visel et al, 2008; War-nefors et al, 2016; Woolfe et al, 2005) and, thus, are likely to participate in enhancer-promoter interactions, might that activity help define chromosomal contacts? Separately, but not exclusively, might selection against changes that disrupt chromosomal domains promote sequence invariance and, thus, ultraconservation?…”

“…UCEs show staggering levels of interspecies sequence conservation, demonstrating perfect sequence identity extending ≥200 bp between species that diverged 90–300 million years ago and comprising one of the most puzzling findings in comparative genomics (Harmston et al, 2013; Polychronopoulos et al, 2017). While UCEs have been found to encompass a variety of functions, including enhancer, promoter, splicing, and repressive activities (Bejerano et al, 2004; Dickel et al, 2018; Kushawah and Mishra, 2017;Pennacchio et al, 2006; Poitras et al, 2010; Sandelin et al, 2004; Warnefors et al, 2016), these functions arguably fall short of explaining ultraconservation, per se. We have suggested that UCEs may maintain their sequence conservation through a mechanism involving the pairing and comparison of allelic UCEs, followed by loss of fitness should mutations or rearrangements that disrupt UCE pairing be detected (Chiang et al, 2008; Derti et al, 2006; McCole et al, 2014) (see also Elgar and Vavouri, 2008; Kritsas et al, 2012).…”

Evolution of the complement system: from defense of the single cell to guardian of the intravascular space

“…This concept that C3 plays several somewhat distinct roles aligns with precepts of evolutionary biology purporting that nature conserves its most vital proteins by multi-tasking. 48,49 In addition to modulating the immune response, 12,14,42 intracellular C3 supports cell survival and metabolism.…”

Optimizing Phylogenomics with Rapidly Evolving Long Exons: Comparison with Anchored Hybrid Enrichment and Ultraconserved Elements

“…UCEs are often in non-coding genomic regions, though some UCEs correspond to exons (Bejerano et al 2004). A unifying functional role of UCEs is not fully understood (Harmston et al 2013), though they have been shown to often play a role in gene regulation (Lenhard et al 2003;Woolfe et al 2005;Ni et al 2007;Warnefors et al 2016) and development (Dickel et al 2018) and are undergoing purifying selection about three times higher than coding regions (Katzman et al 2007). The UCE tetrapod probeset includes approximately 5000 loci, captured using 120 bp probes .…”