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| Status |
Public on Jan 01, 2018 |
| Title |
DNA Damage Response in Elephant Cells |
| Organism |
Loxodonta africana |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The identity of most functional elements in the mammalian genome and the phenotypes they impact are unclear. Here, we perform a genome-wide comparative analysis of patterns of accelerated evolution in species with highly distinctive traits to discover candidate functional elements for clinically important phenotypes. We identify accelerated regions (ARs) in the elephant, hibernating bat, orca, dolphin, naked mole rat and thirteen-lined ground squirrel lineages in mammalian conserved regions, uncovering ~33,000 elements that bind hundreds of different regulatory proteins in humans and mice. ARs in the elephant, the largest land mammal, are uniquely enriched at elephant DNA damage response genes and changed conserved regulatory sites. The genomic hotspot for elephant ARs is the E3 ligase subunit of the Fanconi Anemia Complex, a master regulator of DNA repair. Additionally, ARs in the six species are associated with specific human clinical phenotypes that have apparent concordance with overt traits in each species.
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| Overall design |
Perfrom RNA-seq to identgy genes differentially expressed in irradiated and untreated cells
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| Contributor(s) |
Abegglen L, Schiffman J, Ferris E, Gregg C |
| Citation(s) |
29514101 |
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| Submission date |
Nov 19, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Chris Gregg |
| E-mail(s) |
chris.gregg@neuro.utah.edu
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| Organization name |
University of Utah
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| Department |
Neurobiology and Anatomy
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| Lab |
Chris Gregg Lab
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| Street address |
20 South 2030 East
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| City |
Salt Lake City |
| State/province |
UT |
| ZIP/Postal code |
84112 |
| Country |
USA |
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| Platforms (1) |
| GPL24284 |
Illumina HiSeq 2500 (Loxodonta africana) |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA419061 |
| SRA |
SRP125259 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE107117_3_NT5h_6_2Gy5h.txt.gz |
2.3 Mb |
(ftp)(http) |
TXT |
| GSE107117_4_NT24h_7_2Gy24h.txt.gz |
2.3 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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