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| Status |
Public on Apr 20, 2024 |
| Title |
Epigenetic evolution of the Ly49 gene family [NanoPore] |
| Organism |
Mus musculus |
| Experiment type |
Other
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| Summary |
Comparative genomics has revealed the rapid lineage-specific expansion of multiple gene families involved in immunity, presumably due to the complexity of ensuring pathogen defense while maintaining self-tolerance. Paralogs within these gene families often evolved distinct roles in immunity. However, less is known about how the epigenome and cis-regulation of these gene families evolved. Here we focus on the epigenetic evolution of the rapidly evolving murine Ly49 gene family. Ly49 genes mainly encode either inhibitory or activating surface receptors in natural killer (NK) cells. Together, they fine-tune NK cell activation. We systemically mapped Ly49 transcription initiation, chromatin accessibility, DNA methylation and 3D chromatin interactions. Our data revealed that each Ly49 gene forms a cis-regulatory unit consisted of one or more lowly accessible promoters and a proximal enhancer. Importantly, parallel to the functional divergence of the encoded proteins, inhibitory and activating Ly49 genes have evolved two separate sets of proximal enhancers, likely as a result of lineage-specific losses of enhancer activity. Finally, we show that some Ly49 genes can be cross-regulated by the enhancers of other Ly49 genes, suggesting that the Ly49 family have evolved a concerted regulatory mechanism. Collectively, we demonstrate the different modes of epigenetic evolution for a rapidly expanding gene family essential for host immunity, and provide a rich epigenetic dataset for NK cell research.
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| Overall design |
Assembling the Ly49 loci of the MAP8.B6.Ly49h or the MAP8.B6.Ly49m KO mice using targeted nanopore sequencing
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| Contributor(s) |
Fan C, Piersma SJ, Xing X, Yokoyama WM, Wang T |
| Citation(s) |
38844462 |
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| Submission date |
Jun 02, 2023 |
| Last update date |
Jun 26, 2024 |
| Contact name |
Changxu Fan |
| E-mail(s) |
fanc@wustl.edu
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| Organization name |
Washington University in St. Louis
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| Department |
Genetics
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| Lab |
Ting Wang Lab
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| Street address |
4515 McKinley Avenue, Room 5213
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| City |
Saint Louis |
| State/province |
Missouri |
| ZIP/Postal code |
63110 |
| Country |
USA |
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| Platforms (1) |
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| Samples (2) |
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| This SubSeries is part of SuperSeries: |
| GSE226502 |
Epigenetic evolution of the Ly49 gene family |
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| Relations |
| BioProject |
PRJNA979148 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE233982_RAW.tar |
470.0 Kb |
(http)(custom) |
TAR (of FA) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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