Ontology highlight
ABSTRACT:
PROVIDER: PRJEB37735 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Gene regulatory elements are central drivers of phenotypic variation and thus of critical importance towards understanding the genetics of complex traits. Here we present a genome-wide annotation of regulatory elements in a non-mammalian vertebrate, chicken (Gallus gallus), as well as two important agricultural mammalian species: pig (Sus scrofa) and cattle (Bos taurus), with chicken and pig in particular being important to human biology and medicine. This report is the first to employ all core assays as defined by the Functional Annotation of Animal Genomes (FAANG) consortium, including information from a wide range of epigenomic assays for the same eight diverse tissues of three livestock species. Comparative analysis of these datasets and those from the human and mouse ENCODE projects revealed that although less than half of enhancers are positionally conserved between species, a core set of regulatory elements are functionally conserved independent of evolutionary distance. Further analysis suggested that tissue-specific transcription factor occupancy at regulatory elements and their predicted target genes were also conserved. Interestingly, the smaller chicken genome – relative to mammals – contains a reduced number of enhancers; however, each chicken enhancer targets more genes, on average, compared to their mammalian counterparts suggesting higher versatility. These datasets and corresponding analysis represent a unique opportunity for the emerging field of comparative epigenomics, as well as animal and human biology and medical research involving species that are globally important food resources.
2020-09-24 | GSE158418 | GEO
Project description:Gene regulatory elements are central drivers of phenotypic variation and thus of critical importance towards understanding the genetics of complex traits. Here we present a genome-wide annotation of regulatory elements in a non-mammalian vertebrate, chicken (Gallus gallus), as well as two important agricultural mammalian species: pig (Sus scrofa) and cattle (Bos taurus), with chicken and pig in particular being important to human biology and medicine. This report is the first to employ all core assays as defined by the Functional Annotation of Animal Genomes (FAANG) consortium, including information from a wide range of epigenomic assays for the same eight diverse tissues of three livestock species. Comparative analysis of these datasets and those from the human and mouse ENCODE projects revealed that although less than half of enhancers are positionally conserved between species, a core set of regulatory elements are functionally conserved independent of evolutionary distance. Further analysis suggested that tissue-specific transcription factor occupancy at regulatory elements and their predicted target genes were also conserved. Interestingly, the smaller chicken genome – relative to mammals – contains a reduced number of enhancers; however, each chicken enhancer targets more genes, on average, compared to their mammalian counterparts suggesting higher versatility. These datasets and corresponding analysis represent a unique opportunity for the emerging field of comparative epigenomics, as well as animal and human biology and medical research involving species that are globally important food resources.
2020-09-24 | GSE158417 | GEO
Project description:Gene regulatory elements are central drivers of phenotypic variation and thus of critical importance towards understanding the genetics of complex traits. Here we present a genome-wide annotation of regulatory elements in a non-mammalian vertebrate, chicken (Gallus gallus), as well as two important agricultural mammalian species: pig (Sus scrofa) and cattle (Bos taurus), with chicken and pig in particular being important to human biology and medicine. This report is the first to employ all core assays as defined by the Functional Annotation of Animal Genomes (FAANG) consortium, including information from a wide range of epigenomic assays for the same eight diverse tissues of three livestock species. Comparative analysis of these datasets and those from the human and mouse ENCODE projects revealed that although less than half of enhancers are positionally conserved between species, a core set of regulatory elements are functionally conserved independent of evolutionary distance. Further analysis suggested that tissue-specific transcription factor occupancy at regulatory elements and their predicted target genes were also conserved. Interestingly, the smaller chicken genome – relative to mammals – contains a reduced number of enhancers; however, each chicken enhancer targets more genes, on average, compared to their mammalian counterparts suggesting higher versatility. These datasets and corresponding analysis represent a unique opportunity for the emerging field of comparative epigenomics, as well as animal and human biology and medical research involving species that are globally important food resources.
2020-09-24 | GSE158416 | GEO
Project description:Gene regulatory elements are central drivers of phenotypic variation and thus of critical importance towards understanding the genetics of complex traits. Here we present a genome-wide annotation of regulatory elements in a non-mammalian vertebrate, chicken (Gallus gallus), as well as two important agricultural mammalian species: pig (Sus scrofa) and cattle (Bos taurus), with chicken and pig in particular being important to human biology and medicine. This report is the first to employ all core assays as defined by the Functional Annotation of Animal Genomes (FAANG) consortium, including information from a wide range of epigenomic assays for the same eight diverse tissues of three livestock species. Comparative analysis of these datasets and those from the human and mouse ENCODE projects revealed that although less than half of enhancers are positionally conserved between species, a core set of regulatory elements are functionally conserved independent of evolutionary distance. Further analysis suggested that tissue-specific transcription factor occupancy at regulatory elements and their predicted target genes were also conserved. Interestingly, the smaller chicken genome – relative to mammals – contains a reduced number of enhancers; however, each chicken enhancer targets more genes, on average, compared to their mammalian counterparts suggesting higher versatility. These datasets and corresponding analysis represent a unique opportunity for the emerging field of comparative epigenomics, as well as animal and human biology and medical research involving species that are globally important food resources.
2020-09-24 | GSE158414 | GEO
Project description:Gene regulatory elements are central drivers of phenotypic variation and thus of critical importance towards understanding the genetics of complex traits. Here we present a genome-wide annotation of regulatory elements in a non-mammalian vertebrate, chicken (Gallus gallus), as well as two important agricultural mammalian species: pig (Sus scrofa) and cattle (Bos taurus), with chicken and pig in particular being important to human biology and medicine. This report is the first to employ all core assays as defined by the Functional Annotation of Animal Genomes (FAANG) consortium, including information from a wide range of epigenomic assays for the same eight diverse tissues of three livestock species. Comparative analysis of these datasets and those from the human and mouse ENCODE projects revealed that although less than half of enhancers are positionally conserved between species, a core set of regulatory elements are functionally conserved independent of evolutionary distance. Further analysis suggested that tissue-specific transcription factor occupancy at regulatory elements and their predicted target genes were also conserved. Interestingly, the smaller chicken genome – relative to mammals – contains a reduced number of enhancers; however, each chicken enhancer targets more genes, on average, compared to their mammalian counterparts suggesting higher versatility. These datasets and corresponding analysis represent a unique opportunity for the emerging field of comparative epigenomics, as well as animal and human biology and medical research involving species that are globally important food resources.
2020-09-24 | GSE158429 | GEO
Project description:Gene regulatory elements are central drivers of phenotypic variation and thus of critical importance towards understanding the genetics of complex traits. Here we present a genome-wide annotation of regulatory elements in a non-mammalian vertebrate, chicken (Gallus gallus), as well as two important agricultural mammalian species: pig (Sus scrofa) and cattle (Bos taurus), with chicken and pig in particular being important to human biology and medicine. This report is the first to employ all core assays as defined by the Functional Annotation of Animal Genomes (FAANG) consortium, including information from a wide range of epigenomic assays for the same eight diverse tissues of three livestock species. Comparative analysis of these datasets and those from the human and mouse ENCODE projects revealed that although less than half of enhancers are positionally conserved between species, a core set of regulatory elements are functionally conserved independent of evolutionary distance. Further analysis suggested that tissue-specific transcription factor occupancy at regulatory elements and their predicted target genes were also conserved. Interestingly, the smaller chicken genome – relative to mammals – contains a reduced number of enhancers; however, each chicken enhancer targets more genes, on average, compared to their mammalian counterparts suggesting higher versatility. These datasets and corresponding analysis represent a unique opportunity for the emerging field of comparative epigenomics, as well as animal and human biology and medical research involving species that are globally important food resources.
2020-09-24 | GSE158427 | GEO
Project description:Gene regulatory elements are central drivers of phenotypic variation and thus of critical importance towards understanding the genetics of complex traits. Here we present a genome-wide annotation of regulatory elements in a non-mammalian vertebrate, chicken (Gallus gallus), as well as two important agricultural mammalian species: pig (Sus scrofa) and cattle (Bos taurus), with chicken and pig in particular being important to human biology and medicine. This report is the first to employ all core assays as defined by the Functional Annotation of Animal Genomes (FAANG) consortium, including information from a wide range of epigenomic assays for the same eight diverse tissues of three livestock species. Comparative analysis of these datasets and those from the human and mouse ENCODE projects revealed that although less than half of enhancers are positionally conserved between species, a core set of regulatory elements are functionally conserved independent of evolutionary distance. Further analysis suggested that tissue-specific transcription factor occupancy at regulatory elements and their predicted target genes were also conserved. Interestingly, the smaller chicken genome – relative to mammals – contains a reduced number of enhancers; however, each chicken enhancer targets more genes, on average, compared to their mammalian counterparts suggesting higher versatility. These datasets and corresponding analysis represent a unique opportunity for the emerging field of comparative epigenomics, as well as animal and human biology and medical research involving species that are globally important food resources.
2020-09-24 | GSE158419 | GEO
Project description:Gene regulatory elements are central drivers of phenotypic variation and thus of critical importance towards understanding the genetics of complex traits. Here we present a genome-wide annotation of regulatory elements in a non-mammalian vertebrate, chicken (Gallus gallus), as well as two important agricultural mammalian species: pig (Sus scrofa) and cattle (Bos taurus), with chicken and pig in particular being important to human biology and medicine. This report is the first to employ all core assays as defined by the Functional Annotation of Animal Genomes (FAANG) consortium, including information from a wide range of epigenomic assays for the same eight diverse tissues of three livestock species. Comparative analysis of these datasets and those from the human and mouse ENCODE projects revealed that although less than half of enhancers are positionally conserved between species, a core set of regulatory elements are functionally conserved independent of evolutionary distance. Further analysis suggested that tissue-specific transcription factor occupancy at regulatory elements and their predicted target genes were also conserved. Interestingly, the smaller chicken genome – relative to mammals – contains a reduced number of enhancers; however, each chicken enhancer targets more genes, on average, compared to their mammalian counterparts suggesting higher versatility. These datasets and corresponding analysis represent a unique opportunity for the emerging field of comparative epigenomics, as well as animal and human biology and medical research involving species that are globally important food resources.
2020-09-24 | GSE158412 | GEO
Project description:The human genome shares a remarkable amount of genomic sequence with our closest living primate relatives. Researchers have long sought to understand what regions of the genome are responsible for unique species-specific traits. Previous studies have shown that many genes are differentially expressed between species, but the regulatory elements contributing to these differences are largely unknown. Here we report a genome-wide comparison of active gene regulatory elements in human, chimpanzee, and macaque, and we identify hundreds of regulatory elements that have been gained or lost in the human or chimpanzee genomes since their evolutionary divergence. These elements contain evidence of natural selection and correlate with species-specific changes in gene expression. Polymorphic DNA bases in transcription factor motifs that we found in these regulatory elements may be responsible for the varied biological functions across species. This study directly links phenotypic and transcriptional differences between species with changes in chromatin structure. One biological replicate was analyzed for each of the 15 primate samples using DNase-seq.
2014-02-13 | E-GEOD-54907 | biostudies-arrayexpress