GEO series

SETD6 Mediates Selective Interaction and Genomic Occupancy of BRD4 and MITF in Melanoma [CUT&Run]

GSE298161 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 15 samples Submitted 2025/08/20 Platform GPL34281

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 15 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)
Topic: MelanomaThis series is part of our curated briefing on it.
Samples: 15 samples: 15 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: SETD6 mediates selective interaction and genomic occupancy of BRD4 and MITF in melanoma cellsNAR cancer · 2025

Summary (written by the submitters)

Aberrant transcriptional programs mediate malignant transformation of melanoma, the most aggressive form of skin cancer. The lysine methyltransferase SETD6 has been implicated in regulating transcription, cell adhesion, migration, and other processes in various cancers, however its role in melanoma remains unexplored. We recently reported that SETD6 mono-methylates the BRD4 at K99 to selectively regulate transcription of genes involved in mRNA translation.

Read the full summary ↓

Here, we observed that BRD4 methylation at K99 by SETD6 occurs in melanoma cells. Knockout of SETD6 or a point mutation at BRD4-K99 disrupts BRD4 genomic occupancy. In addition, we show that SETD6 interacts with MITF, a master transcription factor in melanocytes and melanoma, and influences the genomic distribution of MITF. Mechanistically, we uncover a novel chromatin- localized interaction between BRD4 and MITF in melanoma. Our data suggest that BRD4 binds MITF in melanoma cells and that this interaction is dependent on both SETD6-mediated methylation of BRD4 and MITF acetylation. This chromatin complex plays a pivotal role in selective recruitment of BRD4 and MITF to different genomic loci in melanoma cells.

Published in

SETD6 mediates selective interaction and genomic occupancy of BRD4 and MITF in melanoma cells

Biton TE, Feldman M, Davidy T et al. · NAR cancer 2025 · PMID 40809945 · doi:10.1093/narcan/zcaf023

This dataset

Open GSE298161 in finder → Find more human ChIP / ATAC / CUT&Tag datasets → Melanoma landscape →

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 GSE298161_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 PRJNA1268448 and SRA study SRP588082. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40809945) ↗

Study design

15 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 15 sample titles: 15 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

GSM9009290 Flag_Empty cells
GSM9009291 Flag_BRD4_WT1 cells
GSM9009292 Flag_BRD4_WT2 cells
GSM9009293 Flag_BRD4_K99R1 cells
GSM9009294 Flag_BRD4_K99R2 cells
GSM9009295 IgG_SETD6_Control1A cells
GSM9009296 IgG_SETD6_Control1B cells
GSM9009297 BRD4_SETD6_Control1 cells
GSM9009298 BRD4_SETD6_Control2 cells
GSM9009299 BRD4_SETD6_KO1 cells
GSM9009300 BRD4_SETD6_KO3 cells
GSM9009301 MITF_SETD6_Control1 cells
GSM9009302 MITF_SETD6_Control2 cells
GSM9009303 MITF_SETD6_KO1 cells
GSM9009304 MITF_SETD6_KO3 cells

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