GEO series

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

GSE290680 Mus musculus (mouse) RNA-seq (gene expression) 36 samples Submitted 2026/06/02 Platform GPL28457

At a glance

RNA-seq (gene expression) · mouse · 36 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: 36 samples: 12 conditions, mostly in triplicateGroups 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 is essential for stress adaptation such as in fasting. While the core transcriptional machinery and its regulators are known, how information regarding energy availability is relayed to transcriptional complexes remains unclear. Surprisingly, we find that class 3 Phosphatidyl inositol-3 kinase (PI3K-3) lipid kinase, a master regulator of cytosolic autophagy, co-activates epigenetic writers for fasting-induced transcription.

Read the full summary ↓

To this end, chromatin distribution of PI3K-3 significantly overlapped with transcriptionally engaged RNA Pol II phosphorylated on Ser5 (RNAPII-S5p) and transcriptionally permissive H3K4me3. Mechanistically, nuclear PI3K-3 interacted with both RNAPII and the Set1a/COMPASS methyltransferase of H4K4me3. Moreover, decreased binding between RNAPII and Set1a/COMPASS was found in PI3K-3 depleted cells. Accordingly, PI3K-3 deletion led to lower H3K4me3 and RNAPII-S5p enrichment at selective loci. Conversely, PI3K-3 overexpression co-activated acetyltransferase p300/CBP in luciferase assays while its chromatin targeting promoted H3K4me3 deposition. In starved cells, PI3K-3 induced transcription of autophagy-related genes, and in fasted liver, it was critical for transcriptional remodeling of metabolism, such as activation of lipid degradation. Thus, PI3K-3 couples nutrient availability to chromatin remodeling for transcriptional activation, enabling metabolic adaptation in fasting.

This dataset

Open GSE290680 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 GSE290680_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 PRJNA1229531 and SRA study SRP566814. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

12 conditions, mostly in triplicate

RNA, Liver, Fed wt, ×3 RNA, Liver, Fast wt, ×3 RNA, Liver, Fed Vps15LKO, ×3 RNA, Liver, Fast Vps15LKO, ×3 RNA, MEF WT, basal, ×3 RNA, MEF Vps15KO, basal, ×3 RNA, MEF WT, -4h_Methionine, ×3 RNA, MEF Vps15KO, -4h_Methionine, ×3 +4 more

Supports a between-group comparison across 36 samples.

How we read this: 12 replicated groups read from 36 sample titles; they account for 36 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

GSM8819432 RNA, Liver, Fed wt, rep1 RNA, Liver, Fed wt,
GSM8819433 RNA, Liver, Fed wt, rep2 RNA, Liver, Fed wt,
GSM8819434 RNA, Liver, Fed wt, rep3 RNA, Liver, Fed wt,
GSM8819435 RNA, Liver, Fast wt, rep1 RNA, Liver, Fast wt,
GSM8819436 RNA, Liver, Fast wt, rep2 RNA, Liver, Fast wt,
GSM8819437 RNA, Liver, Fast wt, rep3 RNA, Liver, Fast wt,
GSM8819438 RNA, Liver, Fed Vps15LKO, rep1 RNA, Liver, Fed Vps15LK…
GSM8819439 RNA, Liver, Fed Vps15LKO, rep2 RNA, Liver, Fed Vps15LK…
GSM8819440 RNA, Liver, Fed Vps15LKO, rep3 RNA, Liver, Fed Vps15LK…
GSM8819441 RNA, Liver, Fast Vps15LKO, rep1 RNA, Liver, Fast Vps15L…
GSM8819442 RNA, Liver, Fast Vps15LKO, rep2 RNA, Liver, Fast Vps15L…
GSM8819443 RNA, Liver, Fast Vps15LKO, rep3 RNA, Liver, Fast Vps15L…
GSM9065503 RNA, MEF WT, basal, rep1 RNA, MEF WT, basal,
GSM9065504 RNA, MEF WT, basal, rep2 RNA, MEF WT, basal,
GSM9065505 RNA, MEF WT, basal, rep3 RNA, MEF WT, basal,
GSM9065506 RNA, MEF Vps15KO, basal, rep1 RNA, MEF Vps15KO, basal,
GSM9065507 RNA, MEF Vps15KO, basal, rep2 RNA, MEF Vps15KO, basal,
GSM9065508 RNA, MEF Vps15KO, basal, rep3 RNA, MEF Vps15KO, basal,
GSM9065509 RNA, MEF WT, -4h_Methionine, rep1 RNA, MEF WT, -4h_Methio…
GSM9065510 RNA, MEF WT, -4h_Methionine, rep2 RNA, MEF WT, -4h_Methio…
GSM9065511 RNA, MEF WT, -4h_Methionine, rep3 RNA, MEF WT, -4h_Methio…
GSM9065512 RNA, MEF Vps15KO, -4h_Methionine, rep1 RNA, MEF Vps15KO, -4h_M…
GSM9065513 RNA, MEF Vps15KO, -4h_Methionine, rep2 RNA, MEF Vps15KO, -4h_M…
GSM9065514 RNA, MEF Vps15KO, -4h_Methionine, rep3 RNA, MEF Vps15KO, -4h_M…
GSM9065515 RNA, MEF WT, -4h+1h_Methionine, rep1 RNA, MEF WT, -4h+1h_Met…
GSM9065516 RNA, MEF WT, -4h+1h_Methionine, rep2 RNA, MEF WT, -4h+1h_Met…
GSM9065517 RNA, MEF WT, -4h+1h_Methionine, rep3 RNA, MEF WT, -4h+1h_Met…
GSM9065518 RNA, MEF Vps15KO, -4h+1h_Methionine, rep1 RNA, MEF Vps15KO, -4h+1…
GSM9065519 RNA, MEF Vps15KO, -4h+1h_Methionine, rep2 RNA, MEF Vps15KO, -4h+1…
GSM9065520 RNA, MEF Vps15KO, -4h+1h_Methionine, rep3 RNA, MEF Vps15KO, -4h+1…
GSM9065521 RNA, MEF WT, -4h+4h_Methionine, rep1 RNA, MEF WT, -4h+4h_Met…
GSM9065522 RNA, MEF WT, -4h+4h_Methionine, rep2 RNA, MEF WT, -4h+4h_Met…
GSM9065523 RNA, MEF WT, -4h+4h_Methionine, rep3 RNA, MEF WT, -4h+4h_Met…
GSM9065524 RNA, MEF Vps15KO, -4h+4h_Methionine, rep1 RNA, MEF Vps15KO, -4h+4…
GSM9065525 RNA, MEF Vps15KO, -4h+4h_Methionine, rep2 RNA, MEF Vps15KO, -4h+4…
GSM9065526 RNA, MEF Vps15KO, -4h+4h_Methionine, rep3 RNA, MEF Vps15KO, -4h+4…

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