Comparative studies on mammalian
            <i>Hoxc8</i>
            early enhancer sequence reveal a baleen whale-specific deletion of a cis-acting element

Shashikant, Cooduvalli S.; Kim, Chang B.; Borbély, Marc A.; Wang, Wayne C. H.; Ruddle, Frank H.

doi:10.1073/pnas.95.26.15446

Cited by 62 publications

(30 citation statements)

References 44 publications

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“…Finally, it should be emphasized that sequence similarity in noncoding DNA only suggests a functional role for conserved motifs. However, we and others have shown that a functional analysis is possible with a transgenic approach (37,38).…”

Section: Discussionmentioning

confidence: 99%

Hox cluster genomics in the horn shark, Heterodontus francisci

Kim

Amemiya

Bailey

et al. 2000

Proc. Natl. Acad. Sci. U.S.A.

101

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Reconstructing the evolutionary history of Hox cluster origins will lead to insights into the developmental and evolutionary significance of Hox gene clusters in vertebrate phylogeny and to their role in the origins of various vertebrate body plans. We have isolated two Hox clusters from the horn shark, Heterodontus francisci. These have been sequenced and compared with one another and with other chordate Hox clusters. The results show that one of the horn shark clusters (HoxM) is orthologous to the mammalian HoxA cluster and shows a structural similarity to the amphioxus cluster, whereas the other shark cluster (HoxN) is orthologous to the mammalian HoxD cluster based on cluster organization and a comparison with noncoding and Hox genecoding sequences. The persistence of an identifiable HoxA cluster over an 800-million-year divergence time demonstrates that the Hox gene clusters are highly integrated and structured genetic entities. The data presented herein identify many noncoding sequence motifs conserved over 800 million years that may function as genetic control motifs essential to the developmental process.T he Hox gene clusters, first described in Drosophila as the Antenapedia and Bithorax clusters, control pattern formation along the anterior-posterior axis in bilateral animals (1). There is a single Hox gene cluster in all invertebrate species reported to date (2-5). In contrast, multiple Hox clusters have been reported in all vertebrate species examined (6-9). Reconstructing the evolutionary history of vertebrate Hox cluster duplication is necessary to identify orthologous clusters in different vertebrate species, to establish phylogenetic relationships among and between clades, and to elucidate the role of Hox cluster duplication in the vertebrate radiation.We have isolated two genomic clones containing Hox clusters from the primitive horn shark, Heterodontus francisci. One (Het1) is 81.2 kilobases (kb) in length, and the other (Het2) is 98.8 kb. Both have been sequenced completely and compared inter se and with other vertebrate Hox sequences. The Heterodontus Hox cluster data reported herein provide definitive map positions for the Hox genes within the shark clusters as well as extensive sequence information in coding and noncoding domains. Materials and MethodsGenomic DNA Sequencing. Nucleotide sequences were primarily determined by using the shotgun method, and unsequenced gaps were filled by the primer walking method (10). Two distinct dye termination kits (dRhodamine terminator cycle sequencing kit and BigDye terminator cycle sequencing kit, Perkin-Elmer) were used and analyzed by a 377 PRISM DNA sequencer (Perkin-Elmer). Regions covered with only one shotgun clone were resequenced with the other dye termination kit. The entire sequencing region was ensured by covering at least one highly reliable reading (Ͻ550-nucleotides-long from a sequencing primer). For regions covered by unidirectional readings or covered by less than three readings, all the sequence trace patterns were inspected to elimina...

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Section: Discussionmentioning

confidence: 99%

Hox cluster genomics in the horn shark, Heterodontus francisci

Kim

Amemiya

Bailey

et al. 2000

Proc. Natl. Acad. Sci. U.S.A.

101

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“…Another possibility is that the loss of transcription factor binding sites in one location might be compensated by de novo evolution of binding sites in another location, as has been demonstrated for the stripe 2 enhancer of even-skipped gene in Drosophila (44). Notwithstanding these possibilities, several studies have shown that changes in cis-regulatory sequences, ranging from subtle differences to extensive restructuring, can account for the altered expression pattern of Hox genes (6,7,(45)(46)(47). For example, the duplicate fugu HoxA2a and HoxA2b genes show distinct expression patterns in the hindbrain.…”

Section: Pattern Of Cne Evolution In Hox Clusters Of Fugu Human Andmentioning

confidence: 99%

Elephant shark ( Callorhinchus milii ) provides insights into the evolution of Hox gene clusters in gnathostomes

Ravi

Lam

Tay

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

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We have sequenced and analyzed Hox gene clusters from elephant shark, a holocephalian cartilaginous fish. Elephant shark possesses 4 Hox clusters with 45 Hox genes that include orthologs for a higher number of ancient gnathostome Hox genes than the 4 clusters in tetrapods and the supernumerary clusters in teleost fishes. Phylogenetic analysis of elephant shark Hox genes from 7 paralogous groups that contain all of the 4 members indicated an ((AB)(CD)) topology for the order of Hox cluster duplication, providing support for the 2R hypothesis (i.e., 2 rounds of wholegenome duplication during the early evolution of vertebrates). Comparisons of noncoding sequences of the elephant shark and human Hox clusters have identified a large number of conserved noncoding elements (CNEs), which represent putative cis-regulatory elements that may be involved in the regulation of Hox genes. Interestingly, in fugu more than 50% of these ancient CNEs have diverged beyond recognition in the duplicated (HoxA, HoxB, and HoxD) as well as the singleton (HoxC conserved noncoding elements ͉ gene loss ͉ genome duplication ͉ teleost fish ͉ fugu H ox genes encode homeodomain-containing transcription factors that specify the identities of body segments along the anterior-posterior axis of metazoans. Hox genes occur in clusters that were generated by a series of tandem duplications of ancestral gene(s) before the divergence of cnidarians and bilaterians (1). The Hox clusters exhibit a striking phenomenon of spatial collinearity whereby genes in the 3Ј-end of the cluster are expressed in the anterior part of the embryo, whereas those in the 5Ј-end are expressed in the posterior part. In vertebrates, Hox cluster genes also exhibit temporal collinearity; that is, genes located in the 3Ј-end of the cluster are expressed early during development, whereas genes in the 5Ј-end are expressed later (2). Recent comparative studies of Hox clusters in model genomes have shown that Hox clusters have experienced repeated molecular changes, including fragmentation, cluster duplication, gene loss, coding-sequence divergence, and cisregulatory element evolution (3-7). Because of their critical role in defining the identities of body segments, Hox genes are believed to have played a key role in driving the morphologic diversification of animals (8-10) and thus are of particular interest in understanding the genetic basis of morphologic diversity of metazoans.Among chordates, the cephalochordate amphioxus possesses a single Hox cluster (11,12). In urochordates such as Ciona and Oikopleura, the single cluster is highly fragmented and dispersed in the genome (13,14). In contrast to these invertebrate chordates, vertebrates contain multiple Hox clusters that are tightly organized. However, the number of Hox clusters and Hox genes varies among vertebrates. Mammals and other tetrapods contain 4 Hox clusters (HoxA, HoxB, HoxC, and HoxD) resulting from 2 rounds of genome duplication early during the evolution of vertebrates. Most teleost fishes contain 7 Hox clusters o...

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“…Whether separate elements of other dentally expressed genes control expression in di¡erent types of teeth remains to be demonstrated. Analyses of cis-regulatory elements from one species in a related model organism (see, for example, Shashikant et al (1998), for the evolution of the vertebral column) might reveal whether di¡erences in expression relevant to dental pattern are due to di¡erences in cis-or trans-acting factors.…”

Section: Approaches To the Further Study Of Modularity And Dissociatimentioning

confidence: 99%

The genetic basis of modularity in the development and evolution of the vertebrate dentition

Stock

2001

Phil. Trans. R. Soc. Lond. B

109

121

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The construction of organisms from units that develop under semi-autonomous genetic control (modules) has been proposed to be an important component of their ability to undergo adaptive phenotypic evolution. The organization of the vertebrate dentition as a system of repeated parts provides an opportunity to study the extent to which phenotypic modules, identi¢ed by their evolutionary independence from other such units, are related to modularity in the genetic control of development. The evolutionary history of vertebrates provides numerous examples of both correlated and independent evolution of groups of teeth. The dentition itself appears to be a module of the dermal exoskeleton, from which it has long been under independent genetic control. Region-speci¢c tooth loss has been a common trend in vertebrate evolution. Novel deployment of teeth and reacquisition of lost teeth have also occurred, although less frequently. Tooth shape di¡erences within the dentition may be discontinuous (referred to as heterodonty) or graded. The occurrence of homeotic changes in tooth shape provides evidence for the decoupling of tooth shape and location in the course of evolution. Potential mechanisms for regionspeci¢c evolutionary tooth loss are suggested by a number of mouse gene knockouts and human genetic dental anomalies, as well as a comparison between fully-developed and rudimentary teeth in the dentition of rodents. These mechanisms include loss of a tooth-type-speci¢c initiation signal, alterations of the relative strength of inductive and inhibitory signals acting at the time of tooth initiation and the overall reduction in levels of proteins required for the development of all teeth. Ectopic expression of tooth initiation signals provides a potential mechanism for the novel deployment or reacquisition of teeth; a single instance is known of a gene whose ectopic expression in transgenic mice can lead to ectopic teeth. Di¡er-ences in shape between incisor and molar teeth in the mouse have been proposed to be controlled by the region-speci¢c expression of signalling molecules in the oral epithelium. These molecules induce the expression of transcription factors in the underlying jaw mesenchyme that may act as selectors of tooth type. It is speculated that shifts in the expression domains of the epithelial signalling molecules might be responsible for homeotic changes in tooth shape. The observation that these molecules are regionally restricted in the chicken, whose ancestors were not heterodont, suggests that mammalian heterodonty may have evolved through the use of patterning mechanisms already acting on skeletal elements of the jaws. In general, genetic and morphological approaches identify similar types of modules in the dentition, but the data are not yet su¤cient to identify exact correspondences. It is speculated that modularity may be achieved by gene expression di¡erences between teeth or by di¡erences in the time of their development, causing mutations to have cumulative e¡ects on later-developing teeth. The mam...

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Comparative studies on mammalian Hoxc8 early enhancer sequence reveal a baleen whale-specific deletion of a cis-acting element

Cited by 62 publications

References 44 publications

Hox cluster genomics in the horn shark, Heterodontus francisci

Hox cluster genomics in the horn shark, Heterodontus francisci

Elephant shark ( Callorhinchus milii ) provides insights into the evolution of Hox gene clusters in gnathostomes

The genetic basis of modularity in the development and evolution of the vertebrate dentition

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