Cis-regulation and chromosomal rearrangement of the fgf8 locus after the teleost/tetrapod split

Abstract

The complex expression pattern of fibroblast growth factor 8 (Fgf8) and the cellular responses dependent on concentration of its mRNA in vertebrates suggest that Fgf8 should be tightly controlled at the transcriptional level. We found zebrafish conserved noncoding elements (CNEs) with pan-vertebrate as well as fish-specific orthologous sequences from across 200 kb of the zebrafish fgf8a genomic regulatory block to direct reporter expression in patterns consistent with the expression pattern of fgf8a. These included elements from inside the introns of the skin-specific slc2a15a and the ubiquitously expressed fbxw4 bystander genes. The fgf8a/fbxw4 gene pair, which has remained joined throughout three whole genome duplications in chordate evolution, is inverted in teleost genomes, but CNEs across both evolutionary breakpoints showed specific activity. While some CNEs directed highly reproducible expression patterns, others were subject to variation but showed, in a subset of transgenes, expression in the apical ectodermal ridge, the anterior boundaries of somites and the midbrain-hindbrain boundary, specific Fgf8 signaling domains, suggesting that their activity may be context specific. A human element with tetrapod-specific orthologous sequences directed reporter expression to the vasculature, possibly corresponding to a tetrapod innovation. We conclude that fgf8a transcriptional regulation employs pan-vertebrate and teleost-specific enhancers dispersed over three genes in the zebrafish genome.

A Hypomorphic Allele in the <i>FGF8 </i>Gene Contributes to Holoprosencephaly and Is Allelic to Gonadotropin-Releasing Hormone Deficiency in Humans

“…The low incidence of mutations of the FGF8 -coding region argues against mutations in this gene as a common genetic factor to explain the occurrence of midline forebrain anomalies. However, we cannot exclude the possibility that unscreened genetic elements could play a role in human disease, for example, those that control the levels or tissue distribution of FGF8 transcripts [Komisarczuk et al, 2009], or its various isoforms, which were not the focus of this study. Nor can we exclude the ability of other FGFs to compensate for any putative diminished FGF8 function.…”

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

“…Three other elements (6a, 6c, and 9d) drove GFP expression in a ubiquitous or variable way, suggesting that they may be less-specific enhancers (Supplemental Fig. S6; data not shown; Komisarczuk et al 2009). No GFP expression could be detected for the other 11 tested elements, for which cardiac and muscle expression of the control RFP was detected in several founders studied for each element (data not shown).…”

Regulatory evolution of Tbx5 and the origin of paired appendages

“…S4 D-I). Enhancers can change their position in the genome (32,33), and if zebrafish retains a Tbx5 intron2-like enhancer somewhere else in the genome along with the similar trans environment to mouse, transgenic zebrafish carrying mouse Tbx5 intron2 could express GFP in the pectoral fin. To test this possibility, we assayed mouse Tbx5 intron2 activity in transgenic zebrafish.…”