GEO series

Human CCR4-NOT is a global regulator of gene expression and is a novel silencer of retrotransposon activation [TT-seq]

GSE308749 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2026/03/12 Platform GPL30173

At a glance

RNA-seq (gene expression) · human · 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: Homo sapiens (human)
Samples: 12 samples: 12 samples, each with a distinct title — no replicated groupsGroups 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: Human CCR4-NOT suppresses pervasive transcription and retrotransposable elementsbioRxiv : the preprint server for biology · 2026

Summary (written by the submitters)

CCR4-NOT regulates multiple steps in gene regulation, including transcription, mRNA decay, protein ubiquitylation, and translation. It has been well studied in budding yeast; however, relatively less is known about its regulation and functions in mammals. To characterize the functions of the human CCR4-NOT complex, we developed a rapid auxin-induced degron system to deplete CNOT1 (the scaffold of the complex) and CNOT4 (E3 ubiquitin ligase) in cell culture.

Read the full summary ↓

To investigate the role of CCR4-NOT in transcription, we used transient transcriptome sequencing (TT-seq) to measure ongoing RNA synthesis. Depletion of either subunit resulted in increased RNA synthesis of several thousand genes. In contrast to most of the genome, a rapid reduction in the synthesis of KRAB-Zinc-Finger-proteins (KZNFs) genes, especially those clustered on chromosome 19, was observed. KZNFs are transcriptional repressors of retro-transposable elements (rTEs), and consistent with the decreased KZNFs expression, we observed a significant and rapid activation of rTEs, mainly Long interspersed Nuclear Elements (LINEs). Our data reveal that CCR4-NOT regulates gene expression and silences retrotransposons across the genome by maintaining KZNF expression. These data establish CCR4-NOT as a global regulator of gene expression, and we have identified a novel mammalian-specific function of the complex, the suppression of rTEs.

Published in

Human CCR4-NOT suppresses pervasive transcription and retrotransposable elements

Kulkarni S, Morrissey A, Sebastian A et al. · bioRxiv : the preprint server for biology 2026 · PMID 41648255 · doi:10.64898/2026.01.16.699749

This dataset

Open GSE308749 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 GSE308749_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 PRJNA1332651 and SRA study SRP624823. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41648255) ↗

Study design

12 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 12 sample titles: 12 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

GSM8516908 WT_2h_rep1_ttseq
GSM8516909 WT_2h_rep2_ttseq
GSM8516910 CNOT1_2h_rep1_ttseq
GSM8516911 CNOT1_2h_rep2_ttseq
GSM8516912 CNOT4_2h_rep1_ttseq
GSM8516913 CNOT4_2h_rep2_ttseq
GSM8516914 WT_8h_rep1_ttseq
GSM8516915 WT_8h_rep2_ttseq
GSM8516916 CNOT1_8h_rep1_ttseq
GSM8516917 CNOT1_8h_rep2_ttseq
GSM8516918 CNOT4_8h_rep1_ttseq
GSM8516919 CNOT4_8h_rep2_ttseq

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