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Functional redundancy between UTY and UTX in regulating the localization of transcription factors involved in pluripotency [RNA-seq]

GSE301297 Homo sapiens (human) RNA-seq (gene expression) 40 samples Submitted 2026/04/09 Platform GPL15520Platform GPL16791
At a glance

RNA-seq (gene expression) · human · 40 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
40 samples: 20 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
Functional redundancy between UTY and UTX in regulating the localization of transcription factors involved in pluripotencyDevelopment (Cambridge, England) · 2026
Summary (written by the submitters)
The Y chromosome retains a limited number of protein-coding genes, yet their biological significance remains poorly understood. Here, we find UTY, a Y-linked homolog of the histone demethylase UTX, plays an essential regulator of pluripotency in human embryonic stem cells. Despite its low expression and weak enzymatic activity, UTY co-localizes with UTX at active cis-regulatory elements and contributes to the regulation of core pluripotency genes such as NODAL and LEFTY.
Read the full summary ↓
Through genome-wide occupancy and transcriptome analyses of knockout cell lines, we show that UTY and UTX function redundantly to maintain proper localization of key transcription factors including OCT4 and SOX2. Dual loss of UTY and UTX leads to their mislocalization, widespread transcriptional dysregulation, and loss of pluripotency, without changes in H3K27 methylation. Instead, these effects are associated with changes in histone acetylation and altered chromatin accessibility, likely driven by recruitment of ATP-dependent chromatin remodelers, pointing to a non-enzymatic mechanism. Our findings uncover a novel role for UTY in stabilizing transcription factor binding and maintaining cell identity, demonstrating that even the evolutionarily compact Y chromosome retains critical regulatory functions in early human development.
Published in
Functional redundancy between UTY and UTX in regulating the localization of transcription factors involved in pluripotency
Akiyama T, Nakahara T, Sato S et al. · Development (Cambridge, England) 2026 · PMID 41906541 · doi:10.1242/dev.205328
This dataset
Open GSE301297 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 GSE301297_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 PRJNA1284767 and SRA study SRP596366. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41906541) ↗
Study design
20 conditions, mostly in duplicate
RNAseq_WT ×2 RNAseq_UTXKO ×2 RNAseq_DKO ×2 RNAseq_UTYKO_ctrl ×2 RNAseq_UTYKO ×2 RNAseq_H9-WT ×2 RNAseq_H9-UTXKO-3 ×2 RNAseq_H9-UTXKO-4 ×2 +12 more

Supports a between-group comparison across 40 samples.

How we read this: 20 replicated groups read from 40 sample titles; they account for 40 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
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