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Genome Biol Evol. 2016 Aug 25;8(8):2387-405. doi: 10.1093/gbe/evw158.

Conserved Noncoding Elements in the Most Distant Genera of Cephalochordates: The Goldilocks Principle.

Author information

1
Biosciences at Rice, Rice University, Houston, Texas Present address: Institute for Research on Cancer and Aging, Nice (IRCAN), CNRS UMR 7284, INSERM U1081, Nice 06107 France.
2
Department of Transcriptional Regulation, Institute of Molecular Genetics, Prague 14220, Czech Republic.
3
Marine Biology Research Division, Scripps Institution of Oceanography, UC San Diego, La Jolla, California.
4
Biosciences at Rice, Rice University, Houston, Texas Present address: Gene by Gene Ltd., Houston, TX 77008.
5
Biosciences at Rice, Rice University, Houston, Texas Present address: Dovetail Genomics, Santa Cruz, CA 95060.
6
Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan.
7
Marine Biology Research Division, Scripps Institution of Oceanography, UC San Diego, La Jolla, California lzholland@ucsd.edu.

Abstract

Cephalochordates, the sister group of vertebrates + tunicates, are evolving particularly slowly. Therefore, genome comparisons between two congeners of Branchiostoma revealed so many conserved noncoding elements (CNEs), that it was not clear how many are functional regulatory elements. To more effectively identify CNEs with potential regulatory functions, we compared noncoding sequences of genomes of the most phylogenetically distant cephalochordate genera, Asymmetron and Branchiostoma, which diverged approximately 120-160 million years ago. We found 113,070 noncoding elements conserved between the two species, amounting to 3.3% of the genome. The genomic distribution, target gene ontology, and enriched motifs of these CNEs all suggest that many of them are probably cis-regulatory elements. More than 90% of previously verified amphioxus regulatory elements were re-captured in this study. A search of the cephalochordate CNEs around 50 developmental genes in several vertebrate genomes revealed eight CNEs conserved between cephalochordates and vertebrates, indicating sequence conservation over >500 million years of divergence. The function of five CNEs was tested in reporter assays in zebrafish, and one was also tested in amphioxus. All five CNEs proved to be tissue-specific enhancers. Taken together, these findings indicate that even though Branchiostoma and Asymmetron are distantly related, as they are evolving slowly, comparisons between them are likely optimal for identifying most of their tissue-specific cis-regulatory elements laying the foundation for functional characterizations and a better understanding of the evolution of developmental regulation in cephalochordates.

KEYWORDS:

CNE; amphioxus; asymmetron; cephalochordate; regulatory element

PMID:
27412606
PMCID:
PMC5010895
DOI:
10.1093/gbe/evw158
[Indexed for MEDLINE]
Free PMC Article

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