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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
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
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
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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