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Co-deficiency of the BLM and RECQL1 Helicases Causes Synthetic Lethality, Pronounced Replication Stress, and Loss of Chromatid Cohesion

GSE284360 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2026/07/29 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 12 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
12 samples: 3 × MEF WT vs 3 × MEF Blm -/ vs 3 × MEF Recql -/ vs 3 × MEF Blm -/- Recql -/Groups 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.
Summary (written by the submitters)
The mechanistic basis for chromosomal instability characteristic of RECQ helicase genetic disorders has been elusive, given the complexity and apparent redundancy of cellular pathways important for genome homeostasis.
Read the full summary ↓
To characterize the genetic interactions of RECQL1 helicase (recently implicated in the rare hereditary disorder RECON syndrome) essential for genome integrity, we performed an acute depletion RNA interference screen and determined a synthetic lethal interaction of RECQL1 with BLM helicase (linked to the cancer-prone disease Bloom syndrome) in cells exposed to a DNA alkylating agent that induces replication stress. The profound replication stress of cells co-deficient in RECQL1 and BLM was marked by elevated DNA damage and chromosomal instability. Strikingly, RECQL1/BLM co-deficiency induced a novel phenotype of premature sister chromatid separation that could be suppressed by depletion of the cohesion unloader WAPL, suggesting that a threshold of replication stress disrupts cohesion establishment. Primary embryonic fibroblasts from transgenic Recql-/- Blm-/- mice recapitulated the replication stress phenotypes of human cells, and the small intestines of Recql-/- Blm-/- mice showed elevated DNA damage. Our findings highlight the important role of either RECQL1 or BLM when the other is deficient, as is the case for each respective hereditary disorder. Moreover, this study suggests a potentially therapeutic vulnerability of cancers harboring somatic mutations in RECQL1, BLM, or other genome caretakers that function in pathways that confer resistance to replication stress.
This dataset
Open GSE284360 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 GSE284360_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 PRJNA1198880 and SRA study SRP551729. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
3 × MEF WT vs 3 × MEF Blm -/ vs 3 × MEF Recql -/ vs 3 × MEF Blm -/- Recql -/

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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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