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Series GSE222606 Query DataSets for GSE222606
Status Public on Jan 22, 2024
Title SATB2 organizes the 3D genome architecture of cognition in cortical neurons [Hi-C]
Organism Mus musculus
Experiment type Other
Summary The DNA-binding protein SATB2 is genetically linked to human intelligence. We studied its influence on 3D epigenome by mapping chromatin interactions and accessibility in control versus SATB2-deficient cortical neurons. We find that SATB2 affects the chromatin looping between enhancers and promoters of neuronal activity-regulated genes, thus influencing their expression. It also alters A/B compartments, Topologically Associating Domains and Frequently Interacting Regions. Genes linked to SATB2-dependent 3D genome changes are implicated in highly specialized neuronal functions and contribute to cognitive ability and risk for neuropsychiatric and neurodevelopmental disorders. Non-coding DNA regions with SATB2-dependent structure are enriched for common variants associated with educational attainment, intelligence and schizophrenia. Our data establish SATB2 as a cell-type specific 3D genome modulator, which operates both independently and in cooperation with CTCF to set up the chromatin landscape of pyramidal neurons for cognitive processes.
 
Overall design To explore a role of SATB2 in shaping 3D epigenome, cultured cortical neurons derived from Satb2flx/flx::Nes-Cre (cKO) and Satb2flx/flx (floxed) mice were used. On DIV14, Satb2 cKO and floxed cultures were treated with bicuculline, a GABA-A receptor antagonist, which stabilizes/increased neuronal activity in all neurons. To identify changes in chromatin accessibility and chromatin interactions, three ATAC-seq and six Hi-C libraries were prepared per genotype, respectively. To map SATB2 binding sites genome-wide, two CUT&RUN libraries were prepared from floxed cultures.
Web link https://doi.org/10.1016/j.molcel.2023.12.024
 
Contributor(s) Wahl N, Espeso-Gil S, Dechant G, Apostolova G, Chietera P
Citation(s) 38244545
Submission date Jan 11, 2023
Last update date Jan 22, 2024
Contact name Nico Wahl
E-mail(s) nico.wahl@i-med.ac.at
Phone 0043512900371255
Organization name Medical University Innsbruck
Department Institute for Neuroscience
Street address Innrain 66
City Innsbruck
ZIP/Postal code 6020
Country Austria
 
Platforms (2)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (12)
GSM6927709 HiC_Flx1: Satb2 flx/flx DIV14 primary cortical cultures, 1h bic, rep1
GSM6927710 HiC_Flx2: Satb2 flx/flx DIV14 primary cortical cultures, 1h bic, rep2
GSM6927711 HiC_Flx3: Satb2 flx/flx DIV14 primary cortical cultures, 1h bic, rep3
This SubSeries is part of SuperSeries:
GSE222609 SATB2 organizes the 3D genome architecture of cognition in cortical neurons
Relations
BioProject PRJNA922869

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Supplementary file Size Download File type/resource
GSE222606_Compartments_Flx.bedGraph.gz 268.2 Kb (ftp)(http) BEDGRAPH
GSE222606_Compartments_cKO.bedGraph.gz 268.1 Kb (ftp)(http) BEDGRAPH
GSE222606_Differentail_Boundary_Analysis.txt.gz 214.1 Kb (ftp)(http) TXT
GSE222606_FIREs_Analysis_Flx.txt.gz 2.9 Mb (ftp)(http) TXT
GSE222606_FIREs_Analysis_cKO.txt.gz 2.9 Mb (ftp)(http) TXT
GSE222606_loops_5kb_Flx.bedpe.gz 294.2 Kb (ftp)(http) BEDPE
GSE222606_loops_5kb_cKO.bedpe.gz 265.0 Kb (ftp)(http) BEDPE
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