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J. Dev. Biol. 2016, 4(2), 15; doi:10.3390/jdb4020015

Functional and Comparative Genomics of Hoxa2 Gene cis-Regulatory Elements: Evidence for Evolutionary Modification of Ancestral Core Element Activity

1
Department of Biology and Physical Sciences, Gordon State College, Barnesville, GA 30204, USA
2
The Scripps Research Institute, 10550 N, Torrey Pines Road, MB3, La Jolla, CA 92037, USA
3
Department of Biology, Howell Science Complex, East Carolina University, Greenville, NC 27858, USA
*
Author to whom correspondence should be addressed.
Academic Editor: Vincenzo Zappavigna
Received: 16 February 2016 / Revised: 15 March 2016 / Accepted: 17 March 2016 / Published: 26 March 2016
(This article belongs to the Special Issue Hox Genes and Development)
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Abstract

Hoxa2 is an evolutionarily conserved developmental regulatory gene that functions to specify rhombomere (r) and pharyngeal arch (PA) identities throughout the Osteichthyes. Japanese medaka (Oryzias latipes) hoxa2a, like orthologous Hoxa2 genes from other osteichthyans, is expressed during embryogenesis in r2–7 and PA2-7, whereas the paralogous medaka pseudogene, ψhoxa2b, is expressed in noncanonical Hoxa2 domains, including the pectoral fin buds. To understand the evolution of cis-regulatory element (CRE) control of gene expression, we conducted eGFP reporter gene expression studies with extensive functional mapping of several conserved CREs upstream of medaka hoxa2a and ψhoxa2b in transient and stable-line transgenic medaka embryos. The CREs tested were previously shown to contribute to directing mouse Hoxa2 gene expression in r3, r5, and PA2-4. Our results reveal the presence of sequence elements embedded in the medaka hoxa2a and ψhoxa2b upstream enhancer regions (UERs) that mediate expression in r4 and the PAs (hoxa2a r4/CNCC element) or in r3–7 and the PAs ψhoxa2b r3–7/CNCC element), respectively. Further, these elements were shown to be highly conserved among osteichthyans, which suggests that the r4 specifying element embedded in the UER of Hoxa2 is a deeply rooted rhombomere specifying element and the activity of this element has been modified by the evolution of flanking sequences that redirect its activity to alternative developmental compartments. View Full-Text
Keywords: Japanese medaka; Hox PG2 gene expression; hoxa2a; ψhoxa2b; embryonic development; cis-regulatory elements; vertebrate evolution; gene regulation Japanese medaka; Hox PG2 gene expression; hoxa2a; ψhoxa2b; embryonic development; cis-regulatory elements; vertebrate evolution; gene regulation
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Davis, A.; Reubens, M.C.; Stellwag, E.J. Functional and Comparative Genomics of Hoxa2 Gene cis-Regulatory Elements: Evidence for Evolutionary Modification of Ancestral Core Element Activity. J. Dev. Biol. 2016, 4, 15.

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