|
| Status |
Public on Sep 24, 2020 |
| Title |
Comparative functional genome annotation of livestock species identifies core amniote regulatory features and avian enhancer versatility (DNase-Hypersensitivity) |
| Organism |
Gallus gallus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
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.
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| |
|
| Overall design |
DNase-seq in 8 tissues from chickens (2 adult male replicates per species)
|
| |
|
| Contributor(s) |
Kern C, Zhou H, Ross P |
| Citation(s) |
33758196, 34615879 |
| |
| Submission date |
Sep 23, 2020 |
| Last update date |
Oct 14, 2021 |
| Contact name |
Colin Kern |
| Organization name |
UC San Diego
|
| Street address |
9500 Gilman Dr
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL19005 |
Illumina HiSeq 2500 (Gallus gallus) |
|
| Samples (15)
|
| GSM4799703 |
DNase-seq from UC Davis FAANG chicken adipose rep A |
| GSM4799704 |
DNase-seq from UC Davis FAANG chicken adipose rep B |
| GSM4799705 |
DNase-seq from UC Davis FAANG chicken cerebellum rep A |
| GSM4799706 |
DNase-seq from UC Davis FAANG chicken cerebellum rep B |
| GSM4799707 |
DNase-seq from UC Davis FAANG chicken cerebral cortex rep A |
| GSM4799708 |
DNase-seq from UC Davis FAANG chicken cerebral cortex rep B |
| GSM4799709 |
DNase-seq from UC Davis FAANG chicken hypothalamus rep B |
| GSM4799710 |
DNase-seq from UC Davis FAANG chicken liver rep A |
| GSM4799711 |
DNase-seq from UC Davis FAANG chicken liver rep B |
| GSM4799712 |
DNase-seq from UC Davis FAANG chicken lung rep A |
| GSM4799713 |
DNase-seq from UC Davis FAANG chicken lung rep B |
| GSM4799714 |
DNase-seq from UC Davis FAANG chicken skeletal muscle rep A |
| GSM4799715 |
DNase-seq from UC Davis FAANG chicken skeletal muscle rep B |
| GSM4799716 |
DNase-seq from UC Davis FAANG chicken spleen rep A |
| GSM4799717 |
DNase-seq from UC Davis FAANG chicken spleen rep B |
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| This SubSeries is part of SuperSeries: |
| GSE158430 |
Comparative functional genome annotation of livestock species identifies core amniote regulatory features and avian enhancer versatility |
|
| Relations |
| BioProject |
PRJNA665196 |
| SRA |
SRP285096 |
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