Regulatory divergence of the duplicated chromosomal loci sox11a/b by subpartitioning and sequence evolution of enhancers in zebrafish |
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Authors: | Pavla Navratilova David Fredman Boris Lenhard Thomas S Becker |
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Institution: | (1) Sars Centre for Marine Molecular Biology, University of Bergen, 5008 Bergen, Norway;(2) Computational Biology Unit, University of Bergen, 5008 Bergen, Norway;(3) Present address: Developmental Neurobiology and Genomics Laboratory, Brain and Mind Research Institute, Sydney Medical School, University of Sydney, Camperdown, NSW, 2050, Australia;(4) Present address: Department for Molecular Evolution and Development, University of Vienna, 1090 Vienna, Austria; |
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Abstract: | We used the classic example of the duplicated zebrafish sox11a and -b loci to test the duplication, degeneration, complementation (DDC) model of genome evolution through whole genome duplication.
While recent reports have demonstrated sub-partitioning of regulatory sequences in duplicated regions, a comparison of the
regulatory capabilities of extant regulatory sequences derived from ancient ancestral elements has been scarce. Consistent
with the DDC model, we find that ancestral regulatory elements distributed over several hundred kb were lost in either one
or the other zebrafish duplicate, leading to subpartitioning. However, regulatory sequences kept as duplicates near both sox11 co-orthologs diverged in sequence from each other and from human elements and in the regulatory patterns they drive in transgenic
zebrafish. Evolutionary analysis of the loci suggested that both zebrafish protein coding sox11 orthologs have been maintained by purifying selection, and have evolved at comparable rates, indicative of non-diverged protein
functions. The duplicated regulatory elements, conversely, evolved with different divergence rates and degrees of subfunctionalization.
These data show that regulatory evolution of gene expression patterns occurred both through differential loss as well as through
regulatory sequence evolution in zebrafish versus human genomes. |
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