GEO series

Deciphering the role of RNA in regulating CTCF’s DNA binding affinity in leukemia cells [CTCF-ChIP]

GSE281633 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 14 samples Submitted 2024/11/11 Platform GPL24676

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 14 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: 14 samples: 5 conditions, mostly in duplicateGroups 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: Deciphering the role of RNA in regulating CTCF's DNA binding affinity in leukemia cellsGenome biology · 2025

Summary (written by the submitters)

CTCF, a highly studied transcription factor, is essential for chromatin interaction maintenance. Several independent studies have reported that CTCF interacts with RNAs in vitro and in cells. Yet continuous debates about the authenticity of the RNA-binding affinity of CTCF and its biological role remain in large part due to limited research techniques available, such as CLIP-seq.

Read the full summary ↓

Here, we investigated the role RNA plays on CTCF’s transcription factor function through its chromatin occupancy. To systematically investigate whether RNAs affect CTCF’s ability to bind DNA, we perturbed CTCF-RNA interactions by three independent approaches and examined CTCF genome occupancy by ChIP-seq. Although RnaseA A and Triptolide treatment each affected a certain number of CTCF-binding peaks, few peaks overlapped between treatment groups indicating the effect of RNA in regulating CTCF’s DNA binding affinity was modest and variable between loci. In addition, limited transcriptional or chromatin accessibility changes were observed between cells expressing wild-type CTCF or CTCF lacking the RNA binding region. Our data provide a complementary approach and in silico evidence to reconsider the significance of RNA affecting CTCF’s DNA-binding affinity in a global manner.

Published in

Deciphering the role of RNA in regulating CTCF's DNA binding affinity in leukemia cells

Hyle J, Qi W, Djekidel MN et al. · Genome biology 2025 · PMID 40355969 · doi:10.1186/s13059-025-03582-x

This dataset

Open GSE281633 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 GSE281633_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 PRJNA1184930 and SRA study SRP544570. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40355969) ↗

Study design

5 conditions, mostly in duplicate

CTCF_minusRnaseA_45min ×3 CTCF_plusRnaseA_45min ×3 CTCF_WT_Endogenous ×2 CTCF_plusDMSO_8hrs ×2 CTCF_plusTRIP_8hrs ×2 CTCF_plusTRIP_8hrs_Rep3.bw ×1 CTCF_INPUT ×1

Supports a between-group comparison across 12 samples.

How we read this: 5 replicated groups read from 14 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

GSM8625131 CTCF_WT_Endogenous_Rep1 CTCF_WT_Endogenous
GSM8625132 CTCF_WT_Endogenous_Rep2 CTCF_WT_Endogenous
GSM8625133 CTCF_plusDMSO_8hrs_Rep1 CTCF_plusDMSO_8hrs
GSM8625134 CTCF_plusDMSO_8hrs_Rep2 CTCF_plusDMSO_8hrs
GSM8625135 CTCF_plusTRIP_8hrs_Rep1 CTCF_plusTRIP_8hrs
GSM8625136 CTCF_plusTRIP_8hrs_Rep2 CTCF_plusTRIP_8hrs
GSM8625137 CTCF_plusTRIP_8hrs_Rep3.bw
GSM8625138 CTCF_minusRnaseA_45min_Rep1 CTCF_minusRnaseA_45min
GSM8625139 CTCF_minusRnaseA_45min_Rep2 CTCF_minusRnaseA_45min
GSM8625140 CTCF_minusRnaseA_45min_Rep3 CTCF_minusRnaseA_45min
GSM8625141 CTCF_plusRnaseA_45min_Rep1 CTCF_plusRnaseA_45min
GSM8625142 CTCF_plusRnaseA_45min_Rep2 CTCF_plusRnaseA_45min
GSM8625143 CTCF_plusRnaseA_45min_Rep3 CTCF_plusRnaseA_45min
GSM8625144 CTCF_INPUT

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