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Deletion of an evolutionary conserved TAD boundary leads to changes in gene expression, histology and function in mouse testis.

GSE242235 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 27 samples Submitted 2025/01/31 Platform GPL24247
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 27 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
27 samples: 9 conditions, mostly in triplicateGroups 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
Deletion of an evolutionarily conserved TAD boundary compromises spermatogenesis in micebioRxiv : the preprint server for biology · 2024
Summary (written by the submitters)
Spermatogenesis is a complex process that can be disrupted by genetic and epigenetic changes, potentially leading to male infertility. Recent research has rapidly increased the number of protein coding mutations causally linked to impaired spermatogenesis in humans and mice. However, the role of non-coding mutations remains largely unexplored.
Read the full summary ↓
As a case study to evaluate the effects of non-coding mutations on spermatogenesis, we first identified an evolutionarily conserved topologically associated domain (TAD) boundary near two genes with important roles in mammalian testis function: Dmrtb1 and Lrp8 . We then used CRISPR-Cas9 to generate a mouse line where 26kb of the boundary was removed including a strong and evolutionarily conserved CTCF binding site. ChIP-seq and Hi-C experiments confirmed the removal of the CTCF site and a resulting increase in the DNA-DNA interactions across the domain boundary. Mutant mice displayed significant changes in testis gene expression, abnormal testis histology, a 35% drop in the estimated efficiency of spermatogenesis and a 28% decrease in daily sperm production compared to littermate controls. Despite these quantitative changes in testis function, mutant mice show no significant changes in fertility. This suggests that non-coding deletions affecting testis gene regulation may have smaller effects on fertility compared to coding mutations of the same genes. Our results demonstrate that disruption of a TAD boundary can have a negative impact on sperm production and highlight the importance of considering non-coding mutations in the analysis of patients with male infertility.
Published in
Deletion of an evolutionarily conserved TAD boundary compromises spermatogenesis in mice
Lima AC, Okhovat M, Stendahl AM et al. · bioRxiv : the preprint server for biology 2024 · PMID 39026739 · doi:10.1101/2024.07.08.602428
This dataset
Open GSE242235 in finder → Find more mouse 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 GSE242235_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 PRJNA1012337 and SRA study SRP458173. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39026739) ↗
Study design
9 conditions, mostly in triplicate
KO_hom_testis_CaptureHiC ×3 WT_hom_testis_CaptureHiC ×3 KO_hom_testis_RNAseq ×3 Wild-type_testis_RNAseq ×3 KO_het_testis_RNAseq ×3 KO_hom_testis_CTCF.ChIPseq ×3 WT_hom_testis_CTCF.ChIPseq ×3 KO_hom_testis_input.ChIPseq ×3 +1 more

Supports a between-group comparison across 27 samples.

How we read this: 9 replicated groups read from 27 sample titles; they account for 27 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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