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LAP2alpha facilitates myogenic gene expression by preventing spreading of nucleoplasmic lamin A/C to active chromatin regions (ChIP-Seq)

GSE247771 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 42 samples Submitted 2024/08/08 Platform GPL17021Platform GPL24247
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 42 samples

What it is
ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism
Mus musculus (mouse)
Samples
42 samples: 14 conditions, mostly in duplicateGroups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper
LAP2alpha facilitates myogenic gene expression by preventing nucleoplasmic lamin A/C from spreading to active chromatin regionsNucleic acids research · 2024
Summary (written by the submitters)
A-type lamins form a filamentous meshwork beneath the nuclear membrane that anchors large heterochromatic chromatin domains at the nuclear envelope. They also exist as a more dynamic, non-filamentous pool in the nuclear interior, where they interact with gene-rich euchromatin. Lamin-associated polypeptide 2 alpha (LAP2alpha) binds to and maintains the nucleoplasmic lamin pool, but the functional significance of this interaction is poorly understood.
Read the full summary ↓
Here we investigate the genome-wide chromatin association of A-type lamins during myogenic differentiation in the presence and absence of LAP2alpha. We find that A-type lamins are significantly reorganized on chromatin upon depletion of LAP2alpha, spreading towards active chromatin and accumulating at regions of active H3K27ac and H3K4me3 histone marks close to the genes whose expression is impaired in the absence of LAP2alpha. This reorganization of A-type lamins on chromatin is accompanied by depletion of the active chromatin mark H3K27ac and a significant delay of myogenic differentiation. Thus, the interplay of lamins and LAP2alpha is crucial for proper positioning of intranuclear lamins on chromatin to allow normal myogenic differentiation. This research was funded in whole or in part by the Austrian Science Fund (FWF) to Roland Foisner: P32512-B/DOI:10.55776/P36503 https://www.doi.org/10.55776/P36503 P36503-B/DOI:10.55776/P32512 https://www.doi.org/10.55776/P32512
Published in
LAP2alpha facilitates myogenic gene expression by preventing nucleoplasmic lamin A/C from spreading to active chromatin regions
Ferraioli S, Sarigol F, Prakash C et al. · Nucleic acids research 2024 · PMID 39228367 · doi:10.1093/nar/gkae752
This dataset
Open GSE247771 in finder → Find more mouse ChIP / ATAC / CUT&Tag datasets →
Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE247771_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1040295 and SRA study SRP471889. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39228367) ↗
Study design
14 conditions, mostly in duplicate
wildtype myoblasts, proliferating, Input ×3 wildtype myoblasts, differentiating (D2), Inp… ×3 LAP2alpha knockout myoblasts, proliferating, … ×3 LAP2alpha knockout myoblasts, differentiating… ×3 wildtype myoblasts, proliferating, LAP2alpha … ×2 wildtype myoblasts, differentiating (D2), LAP… ×2 wildtype myoblasts, proliferating, lamin AC 3… ×2 wildtype myoblasts, differentiating (D2), lam… ×2 +16 more

Supports a case/control comparison: 18 samples read as cases, 24 as controls.

How we read this: 14 replicated groups read from 42 sample titles; they account for 32 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

+ 2 more — browse all 42 samples with per-sample file links →

Datasets on a similar topic

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