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Series GSE216694 Query DataSets for GSE216694
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
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.
 
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.
 
Contributor(s) Kim J
Citation(s) 39165843
Submission date Oct 27, 2022
Last update date Sep 27, 2024
Contact name Jung-Woong Kim
E-mail(s) jungkim@cau.ac.kr
Organization name Chung-Ang University
Department Life Science
Lab Genome Dynamics Lab
Street address 84 Heuksuk-ro Dongjak-ku
City Seoul
ZIP/Postal code 06974
Country South Korea
 
Platforms (4)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL21273 HiSeq X Ten (Mus musculus)
Samples (38)
GSM6687444 Wild type 01M scRNA
GSM6687445 Wild type 12M scRNA
GSM6687446 Wild type 18M scRNA
Relations
BioProject PRJNA894996

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE216694_Het_12M_Cluster_Info_Top500.xlsx 225.5 Kb (ftp)(http) XLSX
GSE216694_RAW.tar 819.1 Mb (http)(custom) TAR (of BW)
GSE216694_RNA_FPKM_DESeq2.xlsx 19.1 Mb (ftp)(http) XLSX
GSE216694_WT_01M_Cluster_Info_Top500.xlsx 225.5 Kb (ftp)(http) XLSX
GSE216694_WT_12M_Cluster_Info_Top500.xlsx 152.8 Kb (ftp)(http) XLSX
GSE216694_WT_18M_Cluster_Info_Top500.xlsx 187.0 Kb (ftp)(http) XLSX
GSE216694_raw_counts_transIds.txt.gz 3.0 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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