Genomics

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Functional genomic and transcriptomic analysis of amphioxus and the origin of vertebrate genomic traits [CAGE]


ABSTRACT: What genomic changes led to the origin of vertebrates remains a mystery. On the one hand, animal evolution is thought to be driven mostly by changes in the cis-regulatory regions of a shared conserved and toolkit of developmental genes. On the other hand, vertebrates experienced two rounds of whole genome duplication (WGD) that increased their gene repertoire, particularly of regulatory genes controlling embryo development. To shed light into the origin and evolution of the vertebrate regulatory genome, we have generated an unprecedented transcriptomic and epigenomic resource for the non-duplicated genome of the European amphioxus, a closely related invertebrate chordate. These data include RNA-seq for more than 35 developmental stages and adult tissues, CAGE-seq, ChIP-seq, bisulphite-seq and ATAC-seq for several developmental stages and adult tissues. By comparing these data sets with equivalent novel and previously available data for various vertebrate species, especially zebrafish, we uncovered multiple conserved and vertebrate-specific regulatory landmarks. We first identify a conserved chordate phylotypic stage, a developmental period in which different chordate species show the highest gene expression similarity. We also shed light on the origin of enhancer demethylation in vertebrates, by identifying, for the first time in an invertebrate species, differentially methylated enhancers. Furthermore, we show that conserved clusters of co-expressed and tissue-specific genes display similar enrichments for cis-regulatory motifs between amphioxus and vertebrates. Finally, we study the impact of vertebrate WGDs on the evolution of gene regulation, providing the first genome-wide quantitative assessment of sub-functionalization and neo-functionalization processes after the vertebrate WGDs; changing the way in which these evolutionary mechanisms have been traditionally understood. Overall design: CAGE assays in different developmental stages of european amphioxus

INSTRUMENT(S): Illumina HiSeq 2500 (Branchiostoma lanceolatum)

SUBMITTER: Juan J. Tena  

PROVIDER: GSE106429 | GEO | 2018-08-15

REPOSITORIES: GEO

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Publications

Amphioxus functional genomics and the origins of vertebrate gene regulation.

Marlétaz Ferdinand F   Firbas Panos N PN   Maeso Ignacio I   Tena Juan J JJ   Bogdanovic Ozren O   Perry Malcolm M   Wyatt Christopher D R CDR   de la Calle-Mustienes Elisa E   Bertrand Stephanie S   Burguera Demian D   Acemel Rafael D RD   van Heeringen Simon J SJ   Naranjo Silvia S   Herrera-Ubeda Carlos C   Skvortsova Ksenia K   Jimenez-Gancedo Sandra S   Aldea Daniel D   Marquez Yamile Y   Buono Lorena L   Kozmikova Iryna I   Permanyer Jon J   Louis Alexandra A   Albuixech-Crespo Beatriz B   Le Petillon Yann Y   Leon Anthony A   Subirana Lucie L   Balwierz Piotr J PJ   Duckett Paul Edward PE   Farahani Ensieh E   Aury Jean-Marc JM   Mangenot Sophie S   Wincker Patrick P   Albalat Ricard R   Benito-Gutiérrez Èlia È   Cañestro Cristian C   Castro Filipe F   D'Aniello Salvatore S   Ferrier David E K DEK   Huang Shengfeng S   Laudet Vincent V   Marais Gabriel A B GAB   Pontarotti Pierre P   Schubert Michael M   Seitz Hervé H   Somorjai Ildiko I   Takahashi Tokiharu T   Mirabeau Olivier O   Xu Anlong A   Yu Jr-Kai JK   Carninci Piero P   Martinez-Morales Juan Ramon JR   Crollius Hugues Roest HR   Kozmik Zbynek Z   Weirauch Matthew T MT   Garcia-Fernàndez Jordi J   Lister Ryan R   Lenhard Boris B   Holland Peter W H PWH   Escriva Hector H   Gómez-Skarmeta Jose Luis JL   Irimia Manuel M  

Nature 20181121 7734


Vertebrates have greatly elaborated the basic chordate body plan and evolved highly distinctive genomes that have been sculpted by two whole-genome duplications. Here we sequence the genome of the Mediterranean amphioxus (Branchiostoma lanceolatum) and characterize DNA methylation, chromatin accessibility, histone modifications and transcriptomes across multiple developmental stages and adult tissues to investigate the evolution of the regulation of the chordate genome. Comparisons with vertebra  ...[more]

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