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Neuronal activity-driven 3D chromatin dynamics in cortical pyramidal neurons depend on SATB2.

Code ↔ Paper

8 matches between paragraphs of the paper and lines of its authors' code, computed by the harvester (lexical-v1). Click a colored paragraph or line to see its counterpart.

The 8 matches · 5 of them tie a paragraph to a whole file, not to given lines: weak matches, whose lines are not tinted
  1. [1] § Materials and methods › RNA-seq › RNA-seq analysis ↔ RNAseq/S01_MappingAnalysis.sh, the whole file · a weak match · score 0.77 · featureCOUNTS, STAR, flagstated, subreads, trimmomatic, jar
  2. [2] § Materials and methods › Hi-C data analysis › Topologically associating domains and TAD cliques ↔ SpectralTAD/runSpectralTAD.R, the whole file · a weak match · score 0.75 · HiCcompare, SpectralTAD, hicpro2bedpe, TADs, chromosome, matrices
  3. [3] § Materials and methods › Hi-C data analysis › Topologically associating domains and TAD cliques ↔ GENOVA/TAD_N_Analysis.R, the whole file · a weak match · score 0.69 · intra_inter_TAD, interaction density, GENOVA, neighbours, HiC, resolution
  4. [4] § Materials and methods › ATAC-seq › ATAC-seq analysis ↔ RNAseq/S01_MappingAnalysis.sh, the whole file · a weak match · score 0.68 · DeepTools, R2, SAMtools, dup, R1, BAM
  5. [5] § Materials and methods › Hi-C data analysis › Mapping, filtering, normalization, and quality control ↔ HiCReproducibility/RunHiCReproducibility.R, lines 30–63 · score 0.59 · HiCRep, reproducibility, lbr, ubr, SCC, resolution
  6. [6] § Materials and methods › RNA-seq › RNA-seq analysis ↔ RNAseq/S02_Differential_analysis.R, lines 1–44 · score 0.57 · DESeq2, RUVseq, Raw, matrices, genes
  7. [7] § Materials and methods › Hi-C data analysis › Mapping, filtering, normalization, and quality control ↔ HiCReproducibility/HiCreproducibility.R, lines 11–53 · score 0.55 · get.scc, reproducibility, lbr, ubr, Hi, matrices
  8. [8] § Results › SATB2 is required for neuronal activity-triggered chromatin compaction ↔ GENOVA/TAD_N_Analysis.R, the whole file · a weak match · score 0.50 · neighbouring TADs, inter TAD, cKO, Bic, interactions

Paper

Loaded from Europe PMC by your browser, not stored by OSCR: doi.org · Europe PMC

The paper is loaded when this pane is shown.

The authors' code

Shell · 42 lines · 1.8 KB · no license · 2 matches

  1. #!/bin/bash
  2. ##
  3. #SBATCH -N 1
  4. #SBATCH --partition=skylake_0384
  5. #SBATCH --qos=skylake_0384
  6. #SBATCH --ntasks-per-node=48
  7. #SBATCH -J RNAseq
  9. source activate /SergioEG/tools/DeepTools
  11. STAR=/tools/STAR-2.7.6a/bin/Linux_x86_64/STAR
  12. bamCoverage=/tools/deepTools/bin/bamCoverage
  13. featureCOUNTS=/tools/subread-2.0.1-source/bin/featureCounts
  14. samtools=/tools/samtools-1.11/samtools
  15. trimmonatic=/tools/trimmomatic/classes/trimmomatic.jar
  17. in=/gpfs/data/fs71524/SergioEG/fastq_repository/RNAseq.rescue
  18. in2=/gpfs/data/fs71524/SergioEG/fastq_repository
  19. out=/gpfs/data/fs71524/SergioEG/analysis/RNA-seq.Rescue/mouse.rescue
  21. genomeDir=/resources/genomes/mouse/GRCm38.p6.vM25/STAR
  23. REF=/resources/genomes/mouse/GRCm38.p6.vM25/GRCm38.p6.genome.fa
  24. GTF=resources/genomes/mouse/GRCm38.p6.vM25/gencode.vM25.annotation.gtf
  27. find $in -name \*.fq.gz -printf '%f\n' | awk -F '_E' '{print $1}' | sort | uniq > $in2/filenames.txt
  30. cd $out/flx_1
  32. $STAR --runThreadN 48 --genomeDir $genomeDir --sjdbGTFfile $GTF --sjdbOverhang 100 --readFilesIn /fastq_repository/flx_1/flx_1.R1.fastq /fastq_repository/RNAseq.rescue/flx_1.R2.fastq --twopassMode Basic --outSAMtype BAM SortedByCoordinate Unsorted --quantMode TranscriptomeSAM GeneCounts
  33. $samtools index $out/flx_1/Aligned.sortedByCoord.out.bam
  34. $samtools flagstat $out/flx_1/Aligned.sortedByCoord.out.bam > $out/flx_1/flx_1.report.txt
  35. $samtools index $out/flx_1/Aligned.sortedByCoord.bam
  36. bamCoverage -b $out/flx_1/Aligned.sortedByCoord.bam -o $out/flx_1/flx_1.bw -p max
  37. mv $out/flx_1/Aligned.sortedByCoord.out.bam $out/flx_1/Aligned.sortedByCoord.bam
  40. $featureCOUNTS -T 40 --ignoreDup -a $GTF -g gene_name -O -o $out/flx_1/flx_1.exon.gene_name.txt $out/flx_1/Aligned.sortedByCoord.bam
  41. awk -F"\t" '{print $7}' $out/flx_1/flx_1.exon.gene_name.txt > $out/flx_1/flx_1.exon.gene_name.counts.txt
  42. awk -F"\t" '{print $1}' $out/flx_1/flx_1.exon.gene_name.txt > $out/features.txt

S01_MappingAnalysis.sh at commit 9ffea7a, no license · at the source

Overview

Authors: Nico Wahl1, Mujahid Ali1, Sergio Espeso-Gil1, Georg Dechant1, Galina Apostolova1
ORCID iDs: Nico Wahl, Mujahid Ali, Sergio Espeso-Gil, Galina Apostolova
  1. Institute for Neuroscience, Medical University of Innsbruck, Innsbruck 6020, Austria
Institutions: Innsbruck Medical University (Austria); Universität Innsbruck (Austria)
Journal: Nucleic acids research, volume 54, issue 16, article gkag788
Dates: received 25 March 2026; accepted 21 July 2026; published online 25 August 2026; in print August 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1093/nar/gkag788 · PMID 42639793 · PMCID PMC13504278 · OpenAlex W7204189736
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: mouse (organism), cellular / molecular (subfield)
Methods: Statistics, Smoothing, state filtering, decompositions, Machine learning, Preprocessing, Connectivity
MeSH: Chromatin*, Chromatin Assembly and Disassembly*, Matrix Attachment Region Binding Proteins*, Pyramidal Cells*, Transcription Factors*, Animals, Cells, Cultured, Cerebral Cortex, Mice, Mice, Knockout (* major topic)
Journal subjects: Gene regulation, Chromatin and Epigenetics
Topic: Genomics and Chromatin Dynamics (Molecular Biology, Biochemistry, Genetics and Molecular Biology), according to OpenAlex
Funding: Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung) (10.55776/W1206, 10.55776/P32850, 10.55776/P35584, 10.55776/F44, 10.55776/P33027, 10.55776/COE16); Tyrolean research fund (F.47940/6-2023)
Citations: not cited yet (Europe PMC); 74 references in the paper

Abstract

Neuronal activity induces widespread changes in chromatin organization, yet the mechanisms of activity-dependent 3D genome remodelling remain incompletely understood. Here, we identify SATB2 as a key regulator of activity-dependent 3D chromatin dynamics in cortical pyramidal neurons. Using primary cultures from floxed and Satb2 conditional knockout mice, we combined Hi-C and chromatin accessibility mapping to capture rapid 3D epigenome reorganization following neuronal stimulation. Within 1 h of activation, floxed neurons exhibited enhanced chromatin interactions, increased chromatin accessibility, and the emergence of a novel activity-dependent (AD) compartment enriched for SATB2 binding sites. The AD compartment harbours metabolic and housekeeping genes that undergo transient repression upon neuronal activation, thereby prioritizing translation of long synaptic transcripts. Loss of SATB2 disrupted these activity-induced changes, including chromatin accessibility, long-range interactions, and AD compartment formation, resulting in attenuated induction and repression of key activity-regulated genes. These findings establish SATB2 as a central organizer of activity-dependent chromatin architecture dynamics, required for coordinated activation and repression of activity-regulated genes in cortical pyramidal neurons.

Reproduced under the paper's license (CC BY), from the paper cited above.

Repositories

Its files are read in the Code ↔ Paper reader above, with 8 matches between paragraphs and lines of code.

sespesogil/satb2_3d_genome

License: none: the authors keep all their rights
State: the link answers, verified on 26 September 2026
Evidence: files inventoried
Commit: 9ffea7a7eec0e161bf5eb618abdf2f0950886ae5, 24 January 2024
Languages: R (10), Shell (8)
Size: 41 files, 18 scripts
Software Heritage: not archived
Found in: the text, “Mapping, filtering, normalization, and quality c”
Holds: README
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: tidyverse (3 files), data.table (1 file), deepTools (1 file), DESeq2 (1 file), edgeR (1 file), ggplot2 (1 file), limma (1 file), pheatmap (1 file)
Availability: 1 check, the latest on 26 September 2026: the link answers
  • 26 September 2026: the link answers
19 files
At the source: github.com/sespesogil/SATB2_3D_Genome/blob/main/HiCReproducibility

ay-lab/dchic

License: MIT
State: the link answers, verified on 26 September 2026
Evidence: files inventoried
Commit: 144b4dfed665a8ddbd90ab3bff778736e8fde796, 10 January 2024
Languages: R (4), Perl (2), Shell (1), Python (1)
Size: 33 files, 8 scripts
Software Heritage: not archived
Found in: the text, “A/B compartment analysis”
Holds: README, license file, documentation
Not found: CITATION.cff, environment file, tests, continuous integration
Tools: data.table (3 files), BEDTools (2 files), ggplot2 (1 file), limma (1 file), reshape2 (1 file)
Availability: 1 check, the latest on 26 September 2026: the link answers
  • 26 September 2026: the link answers
10 files
At the source: github.com/ay-lab/dcHiC/tree/master

Ali-Mujahid/Satb2-3D-Genome-organization

License: none: the authors keep all their rights
State: the link answers, verified on 26 September 2026
Evidence: files inventoried
Commit: 7a0c5d488472589da7095448d3e2ccaeff484858, 17 March 2026
Size: 30 files, 0 scripts
Software Heritage: not archived
Found in: “Data availability”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 26 September 2026: the link answers
  • 26 September 2026: the link answers
At the source: github.com/Ali-Mujahid/Satb2-3D-Genome-organization

Zenodo 21534635

License: CC-BY-4.0
State: the link answers, verified on 26 September 2026
Evidence: files inventoried
Size: 1 file
Software Heritage: not checked
Found in: “Data availability”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 26 September 2026: the link answers (HTTP 200)
  • 26 September 2026: the link answers (HTTP 200)
At the source:

The paper's code and data availability statement is in the Data section.

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

  • 4 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 26 scripts, each with its path and the digest of its content;
  • 8 matches between paragraphs of the paper and lines of the code (method lexical-v1);
  • neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

No dataset and no data link were found in the paper.

Data availability

Original data generated in this study have been deposited at GEO and are available as the following GEO records: GSE307197 (CUT&Tag), GSE307098 (RNA-seq), GSE307096 (ATAC-seq), GSE307097 (Hi-C). Published datasets used in this study are: GSE222609, GSE157375, GSE175965, GSE163113, GSM5738208, GSM5738212, GSM5738214, GSM5343756, GSM5343757. Histone modification ChIP-seq data were downloaded from ENCODE (ENCFF160SCR, ENCSR093DWU, ENCSR094TTT). Study analysis pipelines and codes are available at the following GitHub repository: https://github.com/Ali-Mujahid/Satb2-3D-Genome-organization and Zenodo at DOI: 10.5281/zenodo.21534635.

Reproduced under the paper's license (CC BY), from the paper cited above.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 5 authors, 10 MeSH terms, 2 funders, 73 references.

Cite

This paper

Wahl, N., Ali, M., Espeso-Gil, S., Dechant, G., & Apostolova, G. (2026). Neuronal activity-driven 3D chromatin dynamics in cortical pyramidal neurons depend on SATB2. Nucleic acids research, 54(16), gkag788. https://doi.org/10.1093/nar/gkag788

BibTeX

@article{wahl2026neuronal,
author = {Wahl, Nico and Ali, Mujahid and Espeso-Gil, Sergio and Dechant, Georg and Apostolova, Galina},
title = {{Neuronal activity-driven 3D chromatin dynamics in cortical pyramidal neurons depend on SATB2}},
journal = {Nucleic acids research},
year = {2026},
month = aug,
volume = {54},
number = {16},
pages = {gkag788},
publisher = {Oxford University Press},
issn = {0305-1048},
doi = {10.1093/nar/gkag788},
url = {https://doi.org/10.1093/nar/gkag788},
pmid = {42639793},
pmcid = {PMC13504278}
}

RIS

TY - JOUR
AU - Wahl, Nico
AU - Ali, Mujahid
AU - Espeso-Gil, Sergio
AU - Dechant, Georg
AU - Apostolova, Galina
TI - Neuronal activity-driven 3D chromatin dynamics in cortical pyramidal neurons depend on SATB2
T2 - Nucleic acids research
J2 - Nucleic Acids Res
PY - 2026
DA - 2026/08/01
VL - 54
IS - 16
SP - gkag788
SN - 0305-1048
PB - Oxford University Press
DO - 10.1093/nar/gkag788
UR - https://doi.org/10.1093/nar/gkag788
LA - en
ER -

CSL-JSON

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