Click here to close
Hello! We notice that you are using Internet Explorer, which is not supported by Xenbase and may cause the site to display incorrectly.
We suggest using a current version of Chrome,
FireFox, or Safari.
Biology (Basel)
2019 Aug 24;83:. doi: 10.3390/biology8030061.
Show Gene links
Show Anatomy links
Microsyntenic Clusters Reveal Conservation of lncRNAs in Chordates Despite Absence of Sequence Conservation.
Herrera-Úbeda C, Marín-Barba M, Navas-Pérez E, Gravemeyer J, Albuixech-Crespo B, Wheeler GN, Garcia-Fernàndez J.
???displayArticle.abstract???
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 Xenopus the expression domain of one of them, Hotairm1, located in the anterior part of the Hox cluster. In addition, we analyzed the function of this lincRNA in Xenopus, 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.
Figure 1. Diagram of LincOFinder mechanism. (A) Representation of the Ref species region where a lincRNA is present. (B) Formatted table of orthologs and virtual coordinates from the three upstream and downstream coding genes fed to the algorithm. (C) Selection of the best cluster according to the minimum distance between genes. (D) Representation of a conserved mycrosyntenic cluster in the Int species, where the presence of a lincRNA is manually confirmed (above) or discarded (below).
Figure 2. Schematic representation of the genomic locus of Hotairm1 across several chordate species. Genome or scaffold position is indicated above each HotairM1 locus.
Figure 3. In situ hybridization (ish) in B. lanceolatum and X. tropicallis. Anterior to the left, dorsal is up. (A,A’) Fluorescent HCR ish in B. lanceolatum in whole mount for (A) Hox1 and (A’) Hotairm1 in 30 hpf embryos. White arrows mark the anterior and posterior limits of the expression domain. (B,B’) Colorimetric whole mount ish in X. tropicalis tadpoles for (B) hoxa1 and (B’) hotairm1. Black arrows mark the anterior and posterior limits of the expression domain. (C,C’) Fluorescent double HCR ish in B. lanceolatum in whole mount ish of (C) Hox1 and Hotairm1 in a 36 hpf embryo and (C’) the detailed zone where Hotairm1 peaks its expression. Green arrows mark the anterior and posterior limits of Hox1 expression and red arrows mark the ones of Hotairm1.
Figure 4. Isoform switch of hotairm1 expression towards the unspliced state using a morpholino. (A) Detail of the primers (black and red arrowheads) and morpholino (purple box) used for the amplification of the spliced and unspliced isoforms of hotairm1 in X.tropicalis and for the impairment of the splicing in the MO-treated embryos. (B) Expression of hotairm1 across Xenopus developmental stages. (C) Inhibition of the spliced isoform in MO treated embryos of Xenopus at st18. (D) Assessment of the presence of the unspliced isoform of hotairm1 in MO treated embryos as well as in the control embryos at st18.
Figure 5. MO treated embryos and in situ hybridization in MO treated embryos. Anterior to the left, dorsal is up. (A) Control X. tropicalis MO treated embryos with normal development. 60ng hotairm1-MO treated embryos with a posteriorization of the anterior part of the embryo. (B) Whole mount colorimetric ish of otx2 in X. tropicalis stage 26 control embryos and MO treated embryos showing the reduced expression domain of otx2 in MO treated embryos. (C) Whole mount colorimetric ish of engrailed in X. tropicalis stage 26 control embryos and MO treated embryos showing a clear reduction in the expression in the MO treated embryos.
Figure 6. qPCRs between 60 ng MO treated embryos and control samples at stage 18. * shows statistically significance compared with control samples (Student’s t-test, * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001). Gapdh was used as a reference gene.
Albuixech-Crespo,
Molecular regionalization of the developing amphioxus neural tube challenges major partitions of the vertebrate brain.
2017, Pubmed
Albuixech-Crespo,
Molecular regionalization of the developing amphioxus neural tube challenges major partitions of the vertebrate brain.
2017,
Pubmed Albuixech-Crespo,
Origin and evolution of the chordate central nervous system: insights from amphioxus genoarchitecture.
2017,
Pubmed Bertrand,
Evolutionary crossroads in developmental biology: amphioxus.
2011,
Pubmed Bush,
Cross-species inference of long non-coding RNAs greatly expands the ruminant transcriptome.
2018,
Pubmed Choi,
Third-generation in situ hybridization chain reaction: multiplexed, quantitative, sensitive, versatile, robust.
2018,
Pubmed Dehal,
Two rounds of whole genome duplication in the ancestral vertebrate.
2005,
Pubmed Diederichs,
The four dimensions of noncoding RNA conservation.
2014,
Pubmed Emms,
OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy.
2015,
Pubmed Esfandi,
Expression of long non-coding RNAs (lncRNAs) has been dysregulated in non-small cell lung cancer tissues.
2019,
Pubmed Fico,
Long non-coding RNA in stem cell pluripotency and lineage commitment: functions and evolutionary conservation.
2019,
Pubmed Fuentes,
Insights into spawning behavior and development of the European amphioxus (Branchiostoma lanceolatum).
2007,
Pubmed Garcia-Fernàndez,
It's a long way from amphioxus: descendants of the earliest chordate.
2009,
Pubmed Gardner,
Conservation and losses of non-coding RNAs in avian genomes.
2015,
Pubmed Holland,
Gene duplications and the origins of vertebrate development.
1994,
Pubmed Irimia,
Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints.
2012,
Pubmed Jathar,
Technological Developments in lncRNA Biology.
2017,
Pubmed Kent,
The human genome browser at UCSC.
2002,
Pubmed Li,
Over-expressed lncRNA HOTAIRM1 promotes tumor growth and invasion through up-regulating HOXA1 and sequestering G9a/EZH2/Dnmts away from the HOXA1 gene in glioblastoma multiforme.
2018,
Pubmed Lin,
RNA-Seq of human neurons derived from iPS cells reveals candidate long non-coding RNAs involved in neurogenesis and neuropsychiatric disorders.
2011,
Pubmed Marlétaz,
Amphioxus functional genomics and the origins of vertebrate gene regulation.
2018,
Pubmed McNulty,
Knockdown of the complete Hox paralogous group 1 leads to dramatic hindbrain and neural crest defects.
2005,
Pubmed
,
Xenbase Monsoro-Burq,
A rapid protocol for whole-mount in situ hybridization on Xenopus embryos.
2007,
Pubmed
,
Xenbase Morris,
The rise of regulatory RNA.
2014,
Pubmed Neme,
Fast turnover of genome transcription across evolutionary time exposes entire non-coding DNA to de novo gene emergence.
2016,
Pubmed Paps,
A genome-wide view of transcription factor gene diversity in chordate evolution: less gene loss in amphioxus?
2012,
Pubmed Pascual-Anaya,
Hagfish and lamprey Hox genes reveal conservation of temporal colinearity in vertebrates.
2018,
Pubmed Pegueroles,
Transcriptomic analyses reveal groups of co-expressed, syntenic lncRNAs in four species of the genus Caenorhabditis.
2019,
Pubmed Ponting,
Evolution and functions of long noncoding RNAs.
2009,
Pubmed Putnam,
The amphioxus genome and the evolution of the chordate karyotype.
2008,
Pubmed Rivas,
A statistical test for conserved RNA structure shows lack of evidence for structure in lncRNAs.
2017,
Pubmed Schmitz,
Mechanisms of transcription factor evolution in Metazoa.
2016,
Pubmed Schubert,
A retinoic acid-Hox hierarchy controls both anterior/posterior patterning and neuronal specification in the developing central nervous system of the cephalochordate amphioxus.
2006,
Pubmed Sekigami,
Hox gene cluster of the ascidian, Halocynthia roretzi, reveals multiple ancient steps of cluster disintegration during ascidian evolution.
2017,
Pubmed Song,
Genome-wide identification of lncRNAs as novel prognosis biomarkers of glioma.
2019,
Pubmed Ulitsky,
Evolution to the rescue: using comparative genomics to understand long non-coding RNAs.
2016,
Pubmed Wan,
Understanding the transcriptome through RNA structure.
2011,
Pubmed Wang,
Reciprocal regulation of chromatin state and architecture by HOTAIRM1 contributes to temporal collinear HOXA gene activation.
2017,
Pubmed Yu,
Evolution of coding and non-coding genes in HOX clusters of a marsupial.
2012,
Pubmed Zampetaki,
Long Non-coding RNA Structure and Function: Is There a Link?
2018,
Pubmed Zerbino,
Ensembl 2018.
2018,
Pubmed Zhang,
A myelopoiesis-associated regulatory intergenic noncoding RNA transcript within the human HOXA cluster.
2009,
Pubmed Zieger,
Roles of Retinoic Acid Signaling in Shaping the Neuronal Architecture of the Developing Amphioxus Nervous System.
2018,
Pubmed
