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| Status |
Public on Dec 08, 2022 |
| Title |
Principles of 3D chromosome folding and evolutionary genome reshuffling in mammals |
| Organisms |
Sarcophilus harrisii; Notamacropus eugenii; Loxodonta africana; Orycteropus afer |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
|
| Summary |
Here we describe the principles of 3D genome folding dynamics in vertebrates and show how lineage-specific patterns of genome reshuffling can result in different chromatin configurations. We (i) identified different patterns of chromosome folding across vertebrate species, (ii) reconstructed ancestral marsupial and afrotherian genomes analyzing whole-genome sequences of 10 species representative of the major therian phylogroups, (iii) detected lineage-specific chromosome rearrangements and (iv) identified the dynamics of the structural properties of genome reshuffling through therian evolution.
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| Overall design |
HiC of African elephant, aardvark, Tasmanian devil and tammar wallaby fibroblasts. H3K4me3 ChIP-seq of African elephant, aardvark, Tasmanian devil and tammar wallaby fibroblasts. CTCF ChIP-seq of African elephant, aardvark fibroblasts. RNA-seq of Tasmanian devil fibroblasts
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| Web link |
https://doi.org/10.1016/j.celrep.2022.111839
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| |
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| Contributor(s) |
Álvarez-González L, Marín-Gual L, Waters P, Ruiz-Herrera A |
| Citation(s) |
36543130 |
| |
| Submission date |
Jun 14, 2022 |
| Last update date |
Mar 09, 2023 |
| Contact name |
Lucía Alvarez-Gonzalez |
| Organization name |
Universitat Autonoma de Barcelona
|
| Department |
Dept. Biologia Cel.lular, Fisiologia i Immunologia
|
| Street address |
Campus de la UAB, Bellaterra
|
| City |
Cerdanyola del Valles |
| State/province |
Barcelona |
| ZIP/Postal code |
08193 |
| Country |
Spain |
| |
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| Platforms (7)
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| GPL32347 |
Illumina HiSeq 4000 (Loxodonta africana) |
| GPL32348 |
Illumina HiSeq 4000 (Orycteropus afer) |
| GPL32349 |
Illumina HiSeq 4000 (Sarcophilus harrisii) |
| GPL32350 |
Illumina HiSeq 4000 (Notamacropus eugenii) |
| GPL32351 |
Illumina NovaSeq 6000 (Loxodonta africana) |
| GPL32352 |
Illumina NovaSeq 6000 (Orycteropus afer) |
| GPL32353 |
Illumina NovaSeq 6000 (Sarcophilus harrisii) |
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| Samples (15)
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| Relations |
| BioProject |
PRJNA849168 |
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