GEO series

FBXO11-Mediated Proteolysis of BAHD1 Relieves PRC2-dependent Transcriptional Repression in Erythropoiesis

GSE290717 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 10 samples Submitted 2025/06/24 Platform GPL20301

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 10 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: 10 samples
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.

Summary (written by the submitters)

The histone mark H3K27me3 and its reader/writer Polycomb repressive complex 2 (PRC2) mediate widespread transcriptional repression in stem and progenitor cells. Mechanisms that regulate this activity are critical for tissue development but poorly understood. Here we show that the E3 ubiquitin ligase FBXO11 relieves PRC2-mediated repression during erythroid maturation by targeting its newly identified substrate BAHD1, an H3K27me3 reader that recruits transcriptional co-repressors.

Read the full summary ↓

Erythroblasts lacking FBXO11 are developmentally delayed, with reduced expression of maturation-associated genes, most of which harbor bivalent histone marks (activating H3K4me3 and repressive H3K27me3), bind BAHD1, and fail to recruit the erythroid transcription factor GATA1. The BAHD1 complex interacts physically with PRC2 and depletion of either component restores FBXO11-deficient erythroid gene expression. Previous studies showed that FBXO11 promotes B-cell development and inhibits lymphomagenesis by degrading the transcriptional repressor BCL6. We show that in aggressive B-cell lymphoma lines, depletion of FBXO11 causes the accumulation of both BCL6 and BAHD1, and that suppression of BAHD1 slows cell expansion. Our studies identify BAHD1 as a novel effector of PRC2-mediated repression and reveal how a single E3 ubiquitin ligase eliminates PRC2 repression at developmentally poised bivalent genes during erythropoiesis. The FBXO11-BAHD1 regulatory axis may function in other developmental pathways, including B-lymphopoiesis and lymphomagenesis.

This dataset

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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 GSE290717_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 PRJNA1229620 and SRA study SRP566864. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Samples in this study

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+ 10 more — browse all 10 samples with per-sample file links →

Datasets on a similar topic

GSE291329 Omics of FBXO11-Mediated Proteolysis of BAHD1 Relieves PRC2-dependent Transcriptional Repression in Erythropoiesis 60 samples shares bahd1, fbxo11-mediated, prc2-dependent, erythropoiesis, proteolysis, repression, relieves
GSE293474 KMT2D-Mediated H3K4methylation is Essential for GATA1 Transcriptional Activation in Erythropoiesis [ChIP-seq] 24 samples shares erythropoiesis
GSE272339 Noncoding RNA, ncRNA-a3, epigenetically regulates TAL1 transcriptional program during erythropoiesis (CUT&Run) 15 samples shares erythropoiesis
GSE272338 Noncoding RNA, ncRNA-a3, epigenetically regulates TAL1 transcriptional program during erythropoiesis (ATAC-Seq) 3 samples shares erythropoiesis
GSE283793 BCL11A is required for normal erythropoiesis [ATAC-seq] 24 samples shares erythropoiesis
GSE248804 MED16 negatively regulates erythropoiesis and myelopoiesis through modulation of chromatin accessibility [ChIP-Seq human] 12 samples shares erythropoiesis
GSE222296 Nuclear IDH1 regulates human erythropoiesis by eliciting chromatin state reprogramming 10 samples shares erythropoiesis
GSE248802 MED16 negatively regulates erythropoiesis and myelopoiesis through modulation of chromatin accessibility [ATAC-Seq human] 8 samples shares erythropoiesis

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