GEO series

Nuclear class 3 PI3K co-activates fasting-specific chromatin remodeling

GSE320350 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2026/06/02 Platform GPL28457

At a glance

RNA-seq (gene expression) · mouse · 12 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: Mus musculus (mouse)
Samples: 12 samples: 3 × MEF WT, basal, vs 3 × MEF Vps15KO, basal, vs 3 × MEF WT, EBSS2h, vs 3 × MEF Vps15KO, EBSS2h,Groups 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.

Summary (written by the submitters)

Transcriptional remodeling in fasting assures metabolic adaptation that provides health benefits across species1-5. While the regulators of transcription and chromatin organization in fasting are known6-10, how lack of nutrients impacts RNA Pol II (RNAPII) and epigenetic writers remains unclear. Surprisingly, we find that class 3 Phosphatidyl inositol-3 kinase (PI3K-3) lipid kinase, a master regulator of autophagy11, is present at chromatin where it co-activates epigenetic writers for transcriptional activation.

Read the full summary ↓

To this end, the chromatin distribution of PI3K-3 largely overlapped with transcriptionally engaged RNAPII phosphorylated on Ser5 (RNAPII-S5p) and Setd1a/COMPASS, the transcription activating H3K4me3 methyltransferase complex12. Mechanistically, nuclear PI3K-3 interacted with RNAPII and the Set1a/COMPASS transcriptional complexes and facilitated their binding. Accordingly, PI3K-3 deletion resulted in lower H3K4me3 and RNAPII-S5p enrichment at selective loci. Conversely, PI3K-3 overexpression co-activated acetyltransferase p300/CBP while chromatin targeting of PI3K-3 promoted H3K4me3 deposition. In starved cells, PI3K-3 was needed for the transcriptional induction of autophagy-related genes, and in fasted liver, it was critical for metabolic shift, such as ketogenesis and lipid degradation. Thus, PI3K-3 couples nutrient availability to chromatin remodeling enabling adaptive transcriptional activation during nutrient stress.

This dataset

Open GSE320350 in finder → Find more mouse 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 GSE320350_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 PRJNA1427638 and SRA study SRP679016. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

3 × MEF WT, basal, vs 3 × MEF Vps15KO, basal, vs 3 × MEF WT, EBSS2h, vs 3 × MEF Vps15KO, EBSS2h,

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 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

GSM9541293 MEF WT, basal, rep1 MEF WT, basal,
GSM9541294 MEF WT, basal, rep2 MEF WT, basal,
GSM9541295 MEF WT, basal, rep3 MEF WT, basal,
GSM9541296 MEF Vps15KO, basal, rep1 MEF Vps15KO, basal,
GSM9541297 MEF Vps15KO, basal, rep2 MEF Vps15KO, basal,
GSM9541298 MEF Vps15KO, basal, rep3 MEF Vps15KO, basal,
GSM9541299 MEF WT, EBSS2h, rep1 MEF WT, EBSS2h,
GSM9541300 MEF WT, EBSS2h, rep2 MEF WT, EBSS2h,
GSM9541301 MEF WT, EBSS2h, rep3 MEF WT, EBSS2h,
GSM9541302 MEF Vps15KO, EBSS2h, rep1 MEF Vps15KO, EBSS2h,
GSM9541303 MEF Vps15KO, EBSS2h, rep2 MEF Vps15KO, EBSS2h,
GSM9541304 MEF Vps15KO, EBSS2h, rep3 MEF Vps15KO, EBSS2h,

Datasets on a similar topic

GSE290680 Nuclear class 3 PI3K co-activates fasting-specific chromatin remodeling 36 samples shares pi3k, fasting-specific, co-activates, remodeling, chromatin, nuclear, class
GSE228366 Chromatin remodeling in HIF-1a deficient B cell during IgA class switching [ChIP-seq] 12 samples shares remodeling, chromatin, class
GSE274492 The remodeling of bivalent chromatin is essential for mouse peri-implantation embryogenesis [Valid RNA-Seq] 200 samples shares remodeling, chromatin
GSE300757 Efferocytosis induces proangiogenic function and chromatin remodeling in tumor-associated macrophages 127 samples shares remodeling, chromatin
GSE299114 Endothelial Cells retain inflammatory memory through chromatin remodeling [RNA-Seq 2] 53 samples shares remodeling, chromatin
GSE253693 Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [mESC_d0246_DMSO_BPK25_IAA_RNA_Seq] 36 samples shares remodeling, chromatin
GSE239469 Condensate-promoting ENL mutation induces tumorigenesis via chromatin remodeling [RNA-seq] 28 samples shares remodeling, chromatin
GSE327619 Murine Endothelial Chromatin Remodeling Enzymes Modulate Plasmin Activity and Sterile Inflammation to Prevent Lethal Embryonic Liver Deterioration 24 samples shares remodeling, chromatin

Search all mouse RNA-seq 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.