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Mechanisms governing interaction of the chromosomal protein SMCHD1 with chromatin determined by live-cell and single molecule imaging

GSE295772 Mus musculus (mouse) RNA-seq (gene expression) 36 samples Submitted 2026/04/30 Platform GPL34290Platform GPL19057
At a glance

RNA-seq (gene expression) · mouse · 36 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Mus musculus (mouse)
Samples
36 samples: 11 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
Selective interaction of SMCHD1 with chromatin is governed by LRIF1 and SMCHD1 ATPase activityNature communications · 2026
Summary (written by the submitters)
The chromosomal protein SMCHD1 is a GHKL-ATPase that plays important roles in epigenetic silencing, including on the inactive X chromosome (Xi) and at the D4Z4 macrosatellite linked to regulation of DUX4 expression in the disorders FSHD2 and BAMS. In this study we use live-cell and single-molecule imaging approaches to investigate SMCHD1 interactions with chromatin and its function in epigenetic silencing.
Read the full summary ↓
We show that chromatin binding of SMCHD1 genome wide, including on Xi, is critically dependent on the protein LRIF1 that mediates interaction with H3K9me2/3 modified nucleosomes. Using engineered mutations in the GHKL ATPase domain we show that ATP hydrolysis is required for SMCHD1 function on chromatin and gene silencing, but is dispensable for chromatin binding. A gain of function mutation, G137E, that occurs in BAMS patients, results in accelerated Xi recruitment and greater Xi chromosome compaction. Together, our findings advance mechanistic understanding of SMCHD1 function on Xi and at other target sites in the genome.
Published in
Selective interaction of SMCHD1 with chromatin is governed by LRIF1 and SMCHD1 ATPase activity
Constantinescu F, Szczurek AT, Nesterova TB et al. · Nature communications 2026 · PMID 42303997 · doi:10.1038/s41467-026-74427-9
This dataset
Open GSE295772 in finder → Find more mouse RNA-seq 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 GSE295772_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1256342 and SRA study SRP581768. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42303997) ↗
Study design
11 conditions, mostly in duplicate
SMCHD1Halo, clone G2, ML day 7 ×3 SMCHD1_G137E, clone H4, ML day 7 ×3 iXist-ChrX, ML day7 ×2 SMCHD1Halo, clone G2, ML day 5 ×2 LRIF1 KO, clone E8, ML day 7 ×2 SMCHD1 KO, clone SmA3, ML day 7 ×2 SMCHD1_E147A, clone A7, ML day 7 ×2 SMCHD1_Y353C, clone D4, ML day 7 ×2 +15 more

Supports a between-group comparison across 24 samples.

How we read this: 11 replicated groups read from 36 sample titles; they account for 24 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
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