GEO series

SIRT6-dependent functional switch via K494 modifications of RE-1 Silencing Transcription factor [REST_experiment_1]

GSE261902 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 24 samples Submitted 2025/03/19 Platform GPL9052

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 24 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: Homo sapiens (human)
Samples: 24 samples: 8 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: SIRT6-dependent functional switch via K494 modifications of RE-1 silencing transcription factorCell death & disease · 2024

Summary (written by the submitters)

RE-1 Silencing Transcription factor (REST) is a key repressor of neural genesREST functions as a key factor for cell differentiation, repressing neural genes in non-neural somatic tissues. REST is upregulated under stress signals, aging, and neurodegenerative diseases, but loses its function in Alzheimer's Disease. However, why it becomes inactive remains unclear.

Read the full summary ↓

Here we show that the NAD-dependent deacetylase SIRT6 regulates REST expression, location, and activity. In SIRT6 absence, REST is overexpressed, but mis localized and inactive. SIRT6 deficiency abrogates REST and EZH2 interaction, perturbs its location to heterochromatin Lamin B ring, and leads to REST target gene overexpression. SIRT6 reintroduction or REST methyl-mimic K494M expression rescues this phenotype, while an acetyl-mimic mutant loses its function even in WT cells. Our studies define a novel regulatory switch, where the function of a critical repressor is regulated by post-translational modifications on K494 depending on SIRT6 existence, in turn modulating neuronal gene expression.

Published in

SIRT6-dependent functional switch via K494 modifications of RE-1 silencing transcription factor

Zaretsky A, Venzor AG, Eremenko E et al. · Cell death & disease 2024 · PMID 39511137 · doi:10.1038/s41419-024-07160-0

This dataset

Open GSE261902 in finder → Find more human ChIP / ATAC / CUT&Tag 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 GSE261902_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 PRJNA1089557 and SRA study SRP496406. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39511137) ↗

Study design

8 conditions, mostly in triplicate

C3,ChIP,IgG, ×3 C3,ChIP,REST, ×3 CC,ChIP,IgG, ×3 CC,ChIP,REST, ×3 C3,Input,IgG, ×3 C3,Input,REST, ×3 CC,Input,IgG, ×3 CC,Input,REST, ×3

Supports a between-group comparison across 24 samples.

How we read this: 8 replicated groups read from 24 sample titles; they account for 24 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

GSM8153844 C3,ChIP,IgG,rep1 C3,ChIP,IgG,
GSM8153845 C3,ChIP,IgG,rep2 C3,ChIP,IgG,
GSM8153846 C3,ChIP,IgG,rep3 C3,ChIP,IgG,
GSM8153847 C3,ChIP,REST,rep1 C3,ChIP,REST,
GSM8153848 C3,ChIP,REST,rep2 C3,ChIP,REST,
GSM8153849 C3,ChIP,REST,rep3 C3,ChIP,REST,
GSM8153850 CC,ChIP,IgG,rep1 CC,ChIP,IgG,
GSM8153851 CC,ChIP,IgG,rep2 CC,ChIP,IgG,
GSM8153852 CC,ChIP,IgG,rep3 CC,ChIP,IgG,
GSM8153853 CC,ChIP,REST,rep1 CC,ChIP,REST,
GSM8153854 CC,ChIP,REST,rep2 CC,ChIP,REST,
GSM8153855 CC,ChIP,REST,rep3 CC,ChIP,REST,
GSM8153856 C3,Input,IgG,rep1 C3,Input,IgG,
GSM8153857 C3,Input,IgG,rep2 C3,Input,IgG,
GSM8153858 C3,Input,IgG,rep3 C3,Input,IgG,
GSM8153859 C3,Input,REST,rep1 C3,Input,REST,
GSM8153860 C3,Input,REST,rep2 C3,Input,REST,
GSM8153861 C3,Input,REST,rep3 C3,Input,REST,
GSM8153862 CC,Input,IgG,rep1 CC,Input,IgG,
GSM8153863 CC,Input,IgG,rep2 CC,Input,IgG,
GSM8153864 CC,Input,IgG,rep3 CC,Input,IgG,
GSM8153865 CC,Input,REST,rep1 CC,Input,REST,
GSM8153866 CC,Input,REST,rep2 CC,Input,REST,
GSM8153867 CC,Input,REST,rep3 CC,Input,REST,

Datasets on a similar topic

GSE261903 SIRT6-dependent functional switch via K494 modifications of RE-1 Silencing Transcription factor [REST_experiment_2] 30 samples shares k494, re-1, rest, sirt6-dependent, modifications, transcription, experiment, silencing
GSE260852 Cohesin acts as a transcriptional gatekeeper by restraining pause–release to promote processive elongation [ChIP-seq] 68 samples shares rest, transcription
GSE300575 Cohesin acts as a transcriptional gatekeeper by restraining pause–release to promote processive elongation [ChIP-seq] 22 samples shares rest, transcription
GSE256345 SMARCA4 controls state plasticity in small cell lung cancer through regulation of neuroendocrine transcription factors and REST splicing [ATAC-seq] 13 samples shares rest, transcription
GSE273827 Restoration of endogenous transcription factor activity by nuclease-deficient Cas9VPR prevents cardiac failure upon stress II 13 samples shares rest, transcription
GSE296585 RESTORATION OF NOX4 SIGNALLING REVERSES ENDOTHELIAL COLONY-FORMING CELL ANGIOGENIC DYSFUNCTION ASSOCIATED WITH EXPERIMENTAL AND CLINICAL DIABETES 11 samples shares rest, experiment
GSE263716 Epigenetic Analysis of SLE Disease Activity in Resting Naive (rN) and Transitional (T1T2) B cells 62 samples shares rest
GSE240384 DNA methylation status determines the sensitivity of repeats to restriction by the HUSH-MORC2 complex [CUT&RUN] 42 samples shares rest

Search all human ChIP / ATAC / CUT&Tag datasets in GEO →

Share this dataset

Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.