Regulatory evolution of Tbx5 and the origin of paired appendages

Abstract

The diversification of paired appendages has been a major factor in the evolutionary radiation of vertebrates. Despite its importance, an understanding of the origin of paired appendages has remained elusive. To address this problem, we focused on T-box transcription factor 5 (Tbx5), a gene indispensable for pectoral appendage initiation and development. Comparison of gene expression in jawless and jawed vertebrates reveals that the Tbx5 expression in jawed vertebrates is derived in having an expression domain that extends caudal to the heart and gills. Chromatin profiling, phylogenetic footprinting, and functional assays enabled the identification of a Tbx5 fin enhancer associated with this apomorphic pattern of expression. Comparative functional analysis of reporter constructs reveals that this enhancer activity is evolutionarily conserved among jawed vertebrates and is able to rescue the finless phenotype of tbx5a mutant zebrafish. Taking paleontological evidence of early vertebrates into account, our results suggest that the gain of apomorphic patterns of Tbx5 expression and regulation likely contributed to the morphological transition from a finless to finned condition at the base of the vertebrate lineage.paired fins | evolution | development | Tbx5 enhancer P aired appendages are one of the fundamental novelties of vertebrates. Having emerged in Paleozoic taxa, they have been associated with major patterns of phylogenetic, ecological, and functional diversification ever since. An understanding of the origin of paired appendages is a problem that links multiple approaches-from paleontology to genomics (1-7). The main challenge to progress in the field derives from understanding the similarities and differences between taxa with and without paired fins: How did the mechanisms that pattern paired appendages arise from taxa that lack them altogether? Whereas jawed vertebrates have two sets of paired fins-pectoral and pelvic-their outgroups, jawless vertebrates, have a range of conditions. Extant jawless fish such as the lamprey and hagfish do not have any paired appendages. The fossil record, however, reveals extinct jawless fish that have pectoral appendages but lack pelvic ones (8). The phylogenetic distribution of extant and extinct species supports the notion that pectoral fins arose before the pelvics (7-12). Therefore, an understanding of pectoral fin development looms large in analyses of the origin of paired appendages.Tbx5, and its homolog in jawless fish, Tbx4/5, have emerged as attractive candidates to explore the origin of pectoral fins. Phylogenetic analysis reveals that Tbx4/5 of an ancestral jawless vertebrate split into two functional paralogs in species with paired appendages, Tbx4 and Tbx5. These paralogs are involved in the initiation of the pectoral and pelvic appendages, respectively (6, 13-17). Of particular interest is Tbx5 because of its role in pectoral fin development (16)(17)(18)(19)(20)(21)(22). The expression pattern of Tbx5 has been studied in multiple chordate species, including...

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

“…This suggests that even modest changes in gene regulation produce significant differences, and confirms that cis-regulatory evolution plays a central role in primate diversification (Davidson 2001(Davidson , 2006Wray 2007;Ho et al 2009;Tsankov et al 2010;Martin et al 2012;Coolon et al 2014;Martin and Reed 2014;Guo et al 2015;Lynch et al 2015;Villar et al 2015;Adachi et al 2016;Landeen et al 2016;Lesch et al 2016;Zhang and Reed 2016).…”

Tbx5

“…This forelimb enhancer is regulated in part through Hox4/5 genes, expressed in the region of the lateral plate mesoderm that gives rise to the forelimb, and has been proposed as the mechanism by which forelimb Tbx5 expression is positionally defined along the anterior–posterior body axis (Minguillon et al, 2012). The second forelimb enhancer identified is known as CNS12 and is located approximately 120 kbp downstream of the Tbx5 coding region (Adachi, Robinson, Goolsbee, & Shubin, 2016). The CNS12 enhancer drives expression in the lateral plate mesoderm and is sufficient to drive Tbx5 expression for forelimb formation (Adachi et al, 2016).…”

“…The second forelimb enhancer identified is known as CNS12 and is located approximately 120 kbp downstream of the Tbx5 coding region (Adachi, Robinson, Goolsbee, & Shubin, 2016). The CNS12 enhancer drives expression in the lateral plate mesoderm and is sufficient to drive Tbx5 expression for forelimb formation (Adachi et al, 2016). …”

Functional genetic analysis in a jawless vertebrate, the sea lamprey: insights into the developmental evolution of early vertebrates

“…In the past several years the field of vertebrate evo-devo has witnessed an explosion of research into so-called 'non-model' systems, including several chondrichthyans (sharks and other cartilaginous fishes), actinopterygians (ray-finned fishes) and agnathan ( jawless) fisheslampreys and hagfishes ( Fig. 1) (Adachi et al, 2016;Braasch et al, 2015;Dahn et al, 2007;Gillis and Hall, 2016;Gillis and Tidswell, 2017;Green and Bronner, 2014;McCauley et al, 2015;Modrell et al, 2017a,b;Oisi et al, 2013aOisi et al, ,b, 2007Pasquier et al, 2017;Shapiro et al, 2004;Tarazona et al, 2016). Unfortunately, these animals often lack one or more of the features (described above) that make the mainstream developmental models appealing to most embryologists.…”