Similar Datasets
Project description: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. ChIP-seq H3K27me3 of 24hpf zebrafish embryos
2012-06-21 | E-GEOD-35050 | biostudies-arrayexpress
Project description: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.
2012-06-21 | GSE35050 | GEO
Project description:DE microRNAs between normal bone and ancient osteosarcoma
2019-06-21 | GSE118540 | GEO
Project description:Centromeres ensure accurate chromosome segregation, yet their DNA evolves rapidly across eukaryotes, leaving the origin of new centromere architectures unresolved. In the brewer’s yeast Saccharomyces cerevisiae (order Saccharomycetales), compact, genetically defined “point” centromeres replaced large, repeat-rich, epigenetically specified centromeres, but how this transition occurred has been unclear. Competing models have proposed either descent with modification from ancestral epigenetic centromeres or acquisition from selfish plasmid DNA. Here we map and characterize centromeres in the sister order Saccharomycodales and identify evolutionarily related “proto-point” centromeres that bridge repeat-rich and point centromeres. Proto-point centromeres contain a single centromeric nucleosome positioned over an AT-rich core, but retain relaxed organization and sequence variability in flanking cis-elements. In two species, including Saccharomycodes ludwigii, proto-point centromeres are embedded within clusters of Ty5 long terminal repeat (LTR) retrotransposons, and their core CDEII and flanking motifs share sequence similarity to Ty5 LTR sequence. Comparative genomics, synteny, and phylogenetic analyses across multiple yeast orders show that Ty5-cluster centromeres are ancient genomic features and support a model in which proto-point and point centromeres evolved by co-option of Ty5 LTR sequences in an ancestor with retrotransposon-rich centromeres, rather than by horizontal transfer from the 2-µm plasmid. These results indicate that yeast point centromeres are direct descendants of retrotransposons and illustrate how transposable elements can be repurposed to create genetically encoded centromeres.
2025-12-15 | GSE294411 | GEO
Project description:Sexual reproduction is nearly universal among multicellular animals, but sex can be determined by cues including sex chromosomes, temperature, social status, and photoperiod. DMRT transcription factors are key regulators of sex in animals that use diverse sex-determining strategies. These proteins are related to the sexual regulators Doublesex (Dsx) and Male abnormal-3 (MAB-3) of insects and nematodes, respectively. DMRT proteins share the DM DNA binding domain, comprised of a unique intertwined double zinc-binding module flanked by a C-terminal recognition helix that binds to a pseudopalindromic target DNA. Despite the central role of DMRT proteins in metazoan sexual development, how they recognize target DNA sequences is poorly understood. Here we find that DMRT proteins employ multiple DNA binding modes due to surprising versatility in how specific base contacts are made. Human DMRT1 can bind as a dimer, trimer or tetramer, in each case using paired antiparallel recognition helices that together insert into a widened DNA major groove to make base-specific contacts. Insertion of two helices in a single major groove is, to our knowledge, a DNA binding interaction unique to DMRT proteins. High resolution in vivo DNA binding analysis (ChIP-Exo) indicates that multiple DNA binding modes also are used in the mouse testis. Finally, we show that mutations affecting amino acid residues crucial for DNA recognition are associated with sex reversal in flies and also, for the first time, with male-to-female sex reversal in humans. Our results illuminate an ancient molecular interaction that underlies much of metazoan sexual development.
2015-05-18 | GSE64892 | GEO
Project description:Metagenomics analysis of ancient microbiomes
| PRJEB31971 | ENA
Project description:Ancient Rome: a genetic crossroads of Europe and the Mediterranean
| PRJEB32566 | ENA
Project description:Ancient Hepatitis B viruses from the Bronze Age to the Medieval
| PRJEB25584 | ENA
Project description:Genomic evidence of ancient migrations along South America's Atlantic coast
| PRJEB48809 | ENA
Project description:Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe
| PRJEB30282 | ENA