GEO series

The BOD1L subunit of the SETD1A complex sustains the expression of DNA damage repair genes despite restraining H3K4 trimethylation [paired_end_RNAseq]

GSE319676 Mus musculus (mouse) DNA methylation 12 samples Submitted 2026/02/18 Platform GPL24247

At a glance

DNA methylation · mouse · 12 samples

What it is: DNA methylationChemical marks on DNA that help switch genes on or off.
Organism: Mus musculus (mouse)
Samples: 12 samples
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.

Summary (written by the submitters)

Background SETD1A is the histone 3 lysine 4 (H3K4) methyltransferase central to the mammalian version of the highly conserved eight subunit Set1 complex (Set1C) that apparently conveys H3K4 trimethylation (H3K4me3) onto all active Pol II promoters. Accordingly, the Setd1a mouse knock-out dies in early embryogenesis at the epiblast stage and mouse embryonic stem cells (ESCs) die when SETD1A is removed.

Read the full summary ↓

Results We report that ESC death is accompanied by loss of expression of DNA repair genes and accumulating DNA damage. BOD1L and BOD1 are homologs of the yeast Set1C subunit, Shg1, and subunits of the mammalian SETD1A and B complexes. We show that the Shg1 homology region binds to a highly conserved central a-helix in SETD1A and B. Like mutagenesis of Shg1 in yeast, conditional mutagenesis of Bod1l in ESCs promoted increased H3K4 di- and tri-methylation but also, like loss of SETD1A, loss of expression of DNA repair genes, increased DNA damage and cell death. Conclusions In contrast to similar losses of DNA repair gene expression, the converse changes in H3K4 methylation after loss of SETD1A or BOD1L implies that H3K4 methylation is not essential for expression of the DNA repair network genes. Because BOD1L becomes highly phosphorylated after DNA damage and acts to protect damaged replication forks, the SETD1A complex, and BOD1L in particular, are key nodes for the DNA damage repair network.

This dataset

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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 GSE319676_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 beta-value tables or raw IDAT files among the supplementary files.

Also filed as BioProject PRJNA1424947 and SRA study SRP677717. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Samples in this study

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+ 12 more — browse all 12 samples with per-sample file links →

Datasets on a similar topic

GSE319677 The BOD1L subunit of the SETD1A complex sustains the expression of DNA damage repair genes despite restraining H3K4 trimethylation [single_end_RNAseq] 36 samples shares setd1a, bod1l, h3k4, trimethylation, restraining, sustains, subunit, complex
GSE165460 Induction of senescence upon loss of the Ash2l subunit of histone H3K4 methyltransferase complexes (ChIP-Seq) 20 samples shares h3k4, subunit, complex
GSE208365 Identify H3K4Me3 occupancy on genome in Setd1a Knock out (KO) mouse undifferentiated pleomorphic sarcoma cells 10 samples shares setd1a, h3k4
GSE7815 Histone H3K4 and H3K27 trimethylation analysis in ES cells, Mefs and induced pluriptent cells. 26 samples shares h3k4, trimethylation
GSE250276 Epigenetic maintenance of neural stem cell quiescence in the adult mouse hippocampus via Setd1a [RNA-Seq] 48 samples shares setd1a
GSE229238 DNA methylation constrains nucleosome retention in sperm and H3K4 methylation deposition in early mouse embryos [RNA-seq 2] 42 samples shares h3k4
GSE335970 KMT2C catalytic activity regulates enhancer H3K4me1 and synaptic gene expression in cortical excitatory neurons [RNA-Seq] 39 samples shares h3k4
GSE309712 Broad H3K4me3 domains support oocyte genome silencing and maturation but are dispensable for repression in early embryos 35 samples shares h3k4

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