Microsyntenic Clusters Reveal Conservation of lncRNAs in Chordates Despite Absence of Sequence Conservation

Homologous long non-coding RNAs (lncRNAs) are elusive to identify by sequence similarity due to their fast-evolutionary rate. Here we develop LincOFinder, a pipeline that finds conserved intergenic lncRNAs (lincRNAs) between distant related species by means of microsynteny analyses. Using this tool,...

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Bibliographic Details
Published in:Biology (Basel, Switzerland) Switzerland), 2019-08, Vol.8 (3), p.61
Main Authors: Herrera-Úbeda, Carlos, Marín-Barba, Marta, Navas-Pérez, Enrique, Gravemeyer, Jan, Albuixech-Crespo, Beatriz, Wheeler, Grant N, Garcia-Fernàndez, Jordi
Format: Article
Language:English
Subjects:
amphioxus
Cephalochordata
Chromosomes
Conserved sequence
Embryos
Evolution
Evolutionary genetics
Gene expression
genome_evolution
Genomes
Hybridization
lncRNAs
Non-coding RNA
Phenotypes
Synteny
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Summary:Homologous long non-coding RNAs (lncRNAs) are elusive to identify by sequence similarity due to their fast-evolutionary rate. Here we develop LincOFinder, a pipeline that finds conserved intergenic lncRNAs (lincRNAs) between distant related species by means of microsynteny analyses. Using this tool, we have identified 16 bona fide homologous lincRNAs between the amphioxus and human genomes. We characterized and compared in amphioxus and the expression domain of one of them, , located in the anterior part of the Hox cluster. In addition, we analyzed the function of this lincRNA in , showing that its disruption produces a severe headless phenotype, most probably by interfering with the regulation of the Hox cluster. Our results strongly suggest that this lincRNA has probably been regulating the Hox cluster since the early origin of chordates. Our work pioneers the use of syntenic searches to identify non-coding genes over long evolutionary distances and helps to further understand lncRNA evolution.
ISSN:2079-7737
2079-7737
DOI:10.3390/biology8030061