title: Regulatory RNA at the root of animals: dynamic expression of developmental lincRNAs in the calcisponge Sycon ciliatum.
abstract: Long non-coding RNAs (lncRNAs) play important regulatory roles during animal development, and it has been hypothesized that an RNA-based gene regulation was important for the evolution of developmental complexity in animals. However, most studies of lncRNA gene regulation have been performed using model animal species, and very little is known about this type of gene regulation in non-bilaterians. We have therefore analysed RNA-Seq data derived from a comprehensive set of embryogenesis stages in the calcareous sponge Sycon ciliatum and identified hundreds of developmentally expressed intergenic lncRNAs (lincRNAs) in this species. In situ hybridization of selected lincRNAs revealed dynamic spatial and temporal expression during embryonic development. More than 600 lincRNAs constitute integral parts of differentially expressed gene modules, which also contain known developmental regulatory genes, e.g. transcription factors and signalling molecules. This study provides insights into the non-coding gene repertoire of one of the earliest evolved animal lineages, and suggests that RNA-based gene regulation was probably present in the last common ancestor of animals.
authors.affiliation: Centre for Epigenetics, Development and Evolution (CEDE), Department of Biosciences, University of Oslo, Oslo, Norway jon.brate@ibv.uio.no.
authors.forename: Jon
authors.identifier: 0000-0003-0490-1175
authors.initials: J
authors.lastname: Bråte
authors.affiliation: Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia.
authors.forename: Marcin
authors.initials: M
authors.lastname: Adamski
authors.affiliation: Centre for Epigenetics, Development and Evolution (CEDE), Department of Biosciences, University of Oslo, Oslo, Norway.
authors.forename: Ralf S
authors.initials: RS
authors.lastname: Neumann
authors.affiliation: Centre for Epigenetics, Development and Evolution (CEDE), Department of Biosciences, University of Oslo, Oslo, Norway.
authors.forename: Kamran
authors.initials: K
authors.lastname: Shalchian-Tabrizi
authors.affiliation: Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia maja.adamska@anu.edu.au.
authors.forename: Maja
authors.initials: M
authors.lastname: Adamska
mesh_terms: D000818:Animals; D018507:Gene Expression Regulation, Developmental; D011161:Porifera / Q000196:embryology / Q000235:genetics*; D025341:Principal Component Analysis; D062085:RNA, Long Noncoding / Q000235:genetics*; D059467:Transcriptome
chemical_list: D062085:RNA, Long Noncoding
keywords: development; evolution; lincRNA; lncRNA; regulatory RNA; sponges