Big Genomes Facilitate the Comparative Identification of Regulatory Elements

Abstract

The identification of regulatory sequences in animal genomes remains a significant challenge. Comparative genomic methods that use patterns of evolutionary conservation to identify non-coding sequences with regulatory function have yielded many new vertebrate enhancers. However, these methods have not contributed significantly to the identification of regulatory sequences in sequenced invertebrate taxa. We demonstrate here that this differential success, which is often attributed to fundamental differences in the nature of vertebrate and invertebrate regulatory sequences, is instead primarily a product of the relatively small size of sequenced invertebrate genomes. We sequenced and compared loci involved in early embryonic patterning from four species of true fruit flies (family Tephritidae) that have genomes four to six times larger than those of Drosophila melanogaster. Unlike in Drosophila, where virtually all non-coding DNA is highly conserved, blocks of conserved non-coding sequence in tephritids are flanked by large stretches of poorly conserved sequence, similar to what is observed in vertebrate genomes. We tested the activities of nine conserved non-coding sequences flanking the even-skipped gene of the teprhitid Ceratis capitata in transgenic D. melanogaster embryos, six of which drove patterns that recapitulate those of known D. melanogaster enhancers. In contrast, none of the three non-conserved tephritid non-coding sequences that we tested drove expression in D. melanogaster embryos. Based on the landscape of non-coding conservation in tephritids, and our initial success in using conservation in tephritids to identify D. melanogaster regulatory sequences, we suggest that comparison of tephritid genomes may provide a systematic means to annotate the non-coding portion of the D. melanogaster genome. We also propose that large genomes be given more consideration in the selection of species for comparative genomics projects, to provide increased power to detect functional non-coding DNAs and to provide a less biased view of the evolution and function of animal genomes.

Conserved noncoding elements and the evolution of animal body plans

“…In addition, sequencing the region surrounding the developmental regulatory gene even-skipped from four true fruit fly genomes (family Tephritidae) also revealed clear islands of conservation containing transcriptional enhancers. (43) This evidence is consistent with the prediction that invertebrate CNEs are transcriptional enhancers for regulatory genes, as already shown for vertebrate CNEs.…”

The First Cytogenetic Map of the Tuatara, <i>Sphenodon punctatus</i>

“…Such a map is also essential should a tuatara genome project be undertaken [Lewin et al, 2009]. Even low coverage sequencing can be of great utility [Green, 2007] and the tuatara's large genome may harbor countless novel genes and regulatory elements [Peterson et al, 2009].…”

Hox gene Ultrabithorax regulates distinct sets of target genes at successive stages of Drosophila haltere morphogenesis

“…Finally, ongoing comparative genomics with distantly related flies with larger genomes have the potential to systematically map enhancers in both Drosophila and these other species (34). Given that Hox-controlled gene circuits represent a favorable level for natural selection to drive the morphological and functional diversification of serial homologs, this cross-species comparison of the architecture of Ubx-regulated haltere networks will also help resolve how entire batteries of genes came under homeotic control to transform hind wings into halteres.…”