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

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F68378050%3A_____%2F16%3A00472853" target="_blank" >RIV/68378050:_____/16:00472853 - isvavai.cz</a>

Result on the web

<a href="http://dx.doi.org/10.1093/gbe/evw158" target="_blank" >http://dx.doi.org/10.1093/gbe/evw158</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1093/gbe/evw158" target="_blank" >10.1093/gbe/evw158</a>

Result language

angličtina

Original language name

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

Original language description

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 inseveral 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.

Czech name

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Czech description

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Type

J_x - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)

CEP classification

EB - Genetics and molecular biology

OECD FORD branch

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Project

<a href="/en/project/GC15-21285J" target="_blank" >GC15-21285J: Reconstruction of an ancestral chordate organizer: the role of Wnt/beta-catenin signaling.</a><br>

Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2016

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Genome Biology and Evolution

ISSN

1759-6653

e-ISSN

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Volume of the periodical

8

Issue of the periodical within the volume

8

Country of publishing house

GB - UNITED KINGDOM

Number of pages

19

Pages from-to

2387-2405

UT code for WoS article

000382523500011

EID of the result in the Scopus database

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