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Status |
Public on Jun 18, 2024 |
Title |
Reorganization of H3K9me heterochromatin leads the neuronal impairment via the cascading destruction of KDM3B-centered epigenomic network |
Organism |
Mus musculus |
Experiment type |
Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing
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Summary |
Histone H3K9 methylated heterochromatin silences repetitive non-coding sequences and lineage-specific genes during development, but how tissue-specific genes escape from heterochromatin in differentiated cells is unclear. Here, we examine age-dependent transcriptomic profiling of terminally differentiated mouse retina to identify epigenetic regulators involved in heterochromatin reorganization. The single-cell RNA sequencing analysis reveal a gradual downregulation of Kdm3b in cone photoreceptors during aging. Disruption of Kdm3b (Kdm3b+/-) of 12-month-old mouse retina leads to the decreasing number of cones via apoptosis, and it changes the morphology of cone ribbon synapses. Integration of transcriptome with epigenomic analysis in Kdm3b+/- retinas demonstrate gains of heterochromatin feature in synapse assembly and vesicle transport genes that are downregulated via the accumulation of H3K9me1/2. Contrary, losses of heterochromatin in apoptotic genes exacerbated retinal neurodegeneration. We propose that KDM3B-centered epigenomic network is crucial for balancing of cone photoreceptor homeostasis via the modulation of gene-set specific heterochromatin features during aging.
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Overall design |
We compared gene expression profiles between mouse retina of wild type and Kdm3b heterozygous. ChIP-seq for H3K9me1, H3K9me2 and H3K9me3 were performed in mouse retina between wild type and heterozygous.
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Contributor(s) |
Kim J |
Citation(s) |
39165843 |
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Submission date |
Oct 27, 2022 |
Last update date |
Sep 27, 2024 |
Contact name |
Jung-Woong Kim |
E-mail(s) |
jungkim@cau.ac.kr
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Organization name |
Chung-Ang University
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Department |
Life Science
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Lab |
Genome Dynamics Lab
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Street address |
84 Heuksuk-ro Dongjak-ku
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City |
Seoul |
ZIP/Postal code |
06974 |
Country |
South Korea |
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Platforms (4)
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GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
GPL21273 |
HiSeq X Ten (Mus musculus) |
GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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Samples (38)
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Relations |
BioProject |
PRJNA894996 |