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Series GSE35050 Query DataSets for GSE35050
Status Public on Jun 21, 2012
Title Extensive conservation of ancient microsynteny across metazoans
Organism Danio rerio
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Gene order, or microsynteny, is generally thought not to be conserved across metazoan phyla. Only a handful of exceptions, typically of tandemly duplicated genes such as Hox genes, have been discovered. Here, we performed a systematic survey for microsynteny conservation in 17 genomes and identified nearly 600 pairs of unrelated genes that have remained together across over 600 million years of evolution. Using multiple genome-wide resources, including several genomic features, epigenetic marks, sequence conservation and microarray expression data, we provide extensive evidence that many of these ancient microsyntenic arrangements have been conserved in order to preserve either (i) the coordinated transcription of neighboring genes, or (ii) Genomic Regulatory Blocks (GRBs), in which transcriptional enhancers controlling key developmental genes are contained within nearby “bystander” genes. In addition, we generated ChIP-seq data for key histone modifications in zebrafish embryos to further investigate putative GRBs in embryonic development. Finally, using chromosome conformation capture (3C) assays and stable transgenic experiments, we demonstrate that enhancers within bystander genes drive the expression of genes such as Otx and Islet, critical regulators of central nervous system development across bilaterians. These results show that ancient genomic associations are far more common in modern metazoans than previously thought – likely involving over 12% of the ancestral bilaterian genome – and that cis-regulatory constraints have played a major role in conserving the architecture of metazoan genomes.
Overall design ChIP-seq H3K27me3 of 24hpf zebrafish embryos
Contributor(s) Irimia M, Alexis MS, Fernandez-Miñan A, Maeso I, Bogdanović O, de la Calle-Mustienes E, Roy SW, Gómez-Skarmeta JL, Fraser HB
Citation(s) 22722344, 26697317
Submission date Jan 12, 2012
Last update date May 15, 2019
Contact name Ozren Bogdanovic
Organization name Garvan Institute of Medical Research
Department Genomics and Epigenetics
Street address 384 Victoria Street
City Darlinghurst
State/province NSW
ZIP/Postal code 2010
Country Australia
Platforms (1)
GPL10164 Illumina Genome Analyzer (Danio rerio)
Samples (1)
GSM861348 H3K27me3 24hpf
SRA SRP010278
BioProject PRJNA150849

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Supplementary file Size Download File type/resource
GSE35050_RAW.tar 36.6 Mb (http)(custom) TAR (of BED)
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Raw data are available in SRA
Processed data included within Sample table

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