GEO series

Assessing the impact of loss of HUSH or HUSH2 subunits on the transcriptome

GSE268797 Homo sapiens (human) RNA-seq (gene expression) 14 samples Submitted 2024/07/15 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 14 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: Homo sapiens (human)
Samples: 14 samples: 11 distinct titles, 2 of them repeatedGroups 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: Competition between two HUSH complexes orchestrates the immune response to retroelement invasionMolecular cell · 2024

Summary (written by the submitters)

The HUSH complex preserves genome integrity through the epigenetic repression of invasive genetic elements. However, despite our understanding of HUSH as an obligate complex of three subunits, only loss of MPP8 or Periphilin, but not TASOR, triggers interferon signaling following derepression of endogenous retroelements. Here we resolve this paradox by characterising a second HUSH complex which shares MPP8 and Periphilin but assembles around TASOR2, an uncharacterized paralog of TASOR.

Read the full summary ↓

Whereas HUSH represses LINE-1 retroelements marked by the repressive histone modification H3K9me3, HUSH2 is recruited by the transcription factor IRF2 to repress interferon-stimulated genes. Mechanistically, HUSH-mediated retroelement silencing sequesters the limited pool of the shared subunits MPP8 and Periphilin, preventing TASOR2 from forming HUSH2 complexes and hence relieving the HUSH2-mediated repression of interferon-stimulated genes. Thus, competition between two HUSH complexes intertwines retroelement silencing with the induction of an immune response, coupling epigenetic and immune aspects of genome defense.

Published in

Competition between two HUSH complexes orchestrates the immune response to retroelement invasion

Danac JMC, Matthews RE, Gungi A et al. · Molecular cell 2024 · PMID 39013473 · doi:10.1016/j.molcel.2024.06.020

This dataset

Open GSE268797 in finder → Find more human 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 GSE268797_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 PRJNA1118768 and SRA study SRP511069. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39013473) ↗

Study design

11 distinct titles, 2 of them repeated

CRISPRi-HUSH2, sgAAVS1, ×3 CRISPRi-HUSH2, dCas9, ×2

How we read this: Read from 14 sample titles: 11 distinct titles with little repetition. 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

GSM8299608 CRISPRi-HUSH2, dCas9, rep1
GSM8299609 CRISPRi-HUSH2, dCas9, rep2
GSM8299610 CRISPRi-HUSH2, sgAAVS1, rep1
GSM8299611 CRISPRi-HUSH2, sgAAVS1, rep2
GSM8299612 CRISPRi-HUSH2, sgAAVS1, rep3
GSM8299613 CRISPRi-HUSH2, sg1-TASOR
GSM8299614 CRISPRi-HUSH2, sg2-TASOR
GSM8299615 CRISPRi-HUSH2, sg1-TASOR2
GSM8299616 CRISPRi-HUSH2, sg2-TASOR2
GSM8299617 CRISPRi-HUSH2, sg3-TASOR2
GSM8299618 CRISPRi-HUSH2, sg1-MPP8
GSM8299619 CRISPRi-HUSH2, sg2-MPP8
GSM8299620 CRISPRi-HUSH2, sg1-PPHLN1
GSM8299621 CRISPRi-HUSH2, sg2-PPHLN1

Datasets on a similar topic

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GSE268798 Assessing the impact of loss of IRF2 on the transcriptome 8 samples shares assessing, impact, loss
GSE269262 Assessing the impact of loss of IRF2 on TASOR2 localization 3 samples shares assessing, impact, loss
GSE268794 Profiling the genome-wide distribution of HUSH subunits 8 samples shares hush, subunits
GSE279633 Assessing the Impact of Cell Isolation Method on B cell Gene Expression using Next-Generation Sequencing 11 samples shares assessing, impact
GSE267825 Assessing the impact of GXYLT2 knockdown on the expression levels of genes associated with malignant characteristics, including proliferation, invasion, and stemness, in HGC-27 gastric cancer cells. 6 samples shares assessing, impact
GSE296915 Assessing the Impact of Metabolic Competence on Estrogenic Chemical Bioactivity in High-Throughput Profiling Assays 0 samples shares assessing, impact
GSE240386 DNA methylation status determines the sensitivity of repeats to restriction by the HUSH-MORC2 complex [Bulk RNA-seq] 27 samples shares hush

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