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Status |
Public on Jul 01, 2024 |
Title |
Identifying the binding sites for miRSome on miR-9 genomic locus with ChIP-seq |
Organism |
Mus musculus |
Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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Summary |
Recent studies have attributed multiple etiological factors for NDDs. miR-9/29a/107 is a key regulator in NDD. Therefore, understanding the upstream regulation of miR-9/29a/107 is critical for NDDs. We have used a unique multi-animal model-CC line that gives greater genetic diversity because miR upstream regulators could involve single or multiple factors. Using mirQTL mapping of CC we identified three candidates-Panx2/Polr1c/Mgea5. We showed that they modulate neuronal differentiation through miR-9. Next, we determined by ChIP that these genes are recruited to the regulatory region of the miR-9 locus. We showed that Panx2 is cleaved by RIP and translocated to the nucleus to interact with Polr1c and Mgea5. ChIP-combined-loop and 3C assays established the interaction on the miR-9 genomic locus through chromatin loops and histone modifications. We also proved that Panx2/Polr1c/Mgea5-miR-9 crosstalk to alter neuronal differentiation. Overall, we established a miRSome complex that govern transcriptional events during adult hippocampal neurogenesis.
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Overall design |
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for Panx2, Polr1c and Mgea5 in duplicates with treatment and control files
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Contributor(s) |
Kuriakose D |
Citation missing |
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Submission date |
May 10, 2022 |
Last update date |
Jul 01, 2024 |
Contact name |
Diji Kuriakose |
E-mail(s) |
diji.kuriakose@monash.edu
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Organization name |
Monash University
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Lab |
ADB
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Street address |
Wellington road
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City |
Melbourne |
State/province |
Victoria |
ZIP/Postal code |
3800 |
Country |
Australia |
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Platforms (1) |
GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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Samples (8)
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Relations |
BioProject |
PRJNA836876 |
Supplementary file |
Size |
Download |
File type/resource |
GSE202645_Control_repeat_1.bedgraph.gz |
102.1 Mb |
(ftp)(http) |
BEDGRAPH |
GSE202645_Control_repeat_2.bedgraph.gz |
100.8 Mb |
(ftp)(http) |
BEDGRAPH |
GSE202645_Mgea5peaks_peaks_repeat_1.broadPeak.gz |
9.7 Mb |
(ftp)(http) |
BROADPEAK |
GSE202645_Mgea5peaks_peaks_repeat_2.broadPeak.gz |
9.6 Mb |
(ftp)(http) |
BROADPEAK |
GSE202645_Mgea5peaks_treatment_repeat_1.bedgraph.gz |
280.2 Mb |
(ftp)(http) |
BEDGRAPH |
GSE202645_Mgea5peaks_treatment_repeat_2.bedgraph.gz |
407.6 Mb |
(ftp)(http) |
BEDGRAPH |
GSE202645_Panx2peaks_peaks_repeat_1.broadPeak.gz |
2.4 Mb |
(ftp)(http) |
BROADPEAK |
GSE202645_Panx2peaks_peaks_repeat_2.broadPeak.gz |
9.6 Mb |
(ftp)(http) |
BROADPEAK |
GSE202645_Panx2peaks_treatment_repeat_1.bedgraph.gz |
122.1 Mb |
(ftp)(http) |
BEDGRAPH |
GSE202645_Panx2peaks_treatment_repeat_2.bedgraph.gz |
156.8 Mb |
(ftp)(http) |
BEDGRAPH |
GSE202645_Polr1cpeaks_peaks_repeat_1.narrowPeak.gz |
17.3 Kb |
(ftp)(http) |
NARROWPEAK |
GSE202645_Polr1cpeaks_peaks_repeat_2.narrowPeak.gz |
652.6 Kb |
(ftp)(http) |
NARROWPEAK |
GSE202645_Polr1cpeaks_treatment_repeat_1.bedgraph.gz |
147.9 Mb |
(ftp)(http) |
BEDGRAPH |
GSE202645_Polr1cpeaks_treatment_repeat_2.bedgraph.gz |
305.7 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |