Highly conserved elements discovered in vertebrates are present in non-syntenic loci of tunicates, act as enhancers and can be transcribed during development

Remo Sanges, Yavor Hadzhiev, Marion Gueroult-Bellone, Agnes Roure, Marco Ferg, Nicola Meola, Gabriele Amore, Swaraj Basu, Euan R Brown, Marco De Simone, Francesca Petrera, Danilo Licastro, Uwe Strahle, Sandro Banfi, Patrick Lemaire, Ewan Birney, Ferenc Muller, Elia Stupka

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19 Citations (Scopus)
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Abstract

Co-option of cis-regulatory modules has been suggested as a mechanism for the evolution of expression sites during development. However, the extent and mechanisms involved in mobilization of cisregulatory modules remains elusive. To trace the history of non-coding elements, which may represent candidate ancestral cis-regulatory modules affirmed during chordate evolution, we have searched for conserved elements in tunicate and vertebrate (Olfactores) genomes. We identified, for the first time, 183 non-coding sequences that are highly conserved between the two groups. Our results show that all but one element are conserved in non-syntenic regions between vertebrate and tunicate genomes, while being syntenic among vertebrates. Nevertheless, in all the groups, they are significantly associated with transcription factors showing specific functions fundamental to animal development, such as multicellular organism development and sequence-specific DNA binding. The majority of these regions map onto ultraconserved elements and we demonstrate that they can act as functional enhancers within the organism of origin, as well as in cross-transgenesis experiments, and that they are transcribed in extant species of Olfactores. We refer to the elements as ‘Olfactores conserved non-coding elements’.
Original languageEnglish
Article number1
Pages (from-to)3600-3618
Number of pages19
JournalNucleic Acids Research
Volume41
Issue number6
Early online date7 Feb 2013
DOIs
Publication statusPublished - Apr 2013

Keywords

  • Animals
  • Base Sequence
  • Conserved Sequence
  • Dogs
  • Enhancer Elements, Genetic
  • Fishes
  • Gene Expression Regulation, Developmental
  • Gene Regulatory Networks
  • Genes, Homeobox
  • Genetic Loci
  • Genome
  • Humans
  • Mammals
  • Mice
  • Synteny
  • Transcription, Genetic
  • Urochordata
  • Vertebrates

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  • Cite this

    Sanges, R., Hadzhiev, Y., Gueroult-Bellone, M., Roure, A., Ferg, M., Meola, N., Amore, G., Basu, S., Brown, E. R., De Simone, M., Petrera, F., Licastro, D., Strahle, U., Banfi, S., Lemaire, P., Birney, E., Muller, F., & Stupka, E. (2013). Highly conserved elements discovered in vertebrates are present in non-syntenic loci of tunicates, act as enhancers and can be transcribed during development. Nucleic Acids Research, 41(6), 3600-3618. [1]. https://doi.org/10.1093/nar/gkt030