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TBP bookmarks and preserves neural stem cell fate memory by orchestrating local chromatin architecture (CUT&Tag)

GSE267892 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 32 samples Submitted 2024/12/10 Platform GPL24676Platform GPL25244
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 32 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
32 samples: 9 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
TBP bookmarks and preserves neural stem cell fate memory by orchestrating local chromatin architectureMolecular cell · 2025
Summary (written by the submitters)
Mitotic bookmarking has been posited as an important strategy for cells to faithfully propagate their fate memory though cell generations. However, the physiological significance and regulatory mechanisms of mitotic bookmarking in neural development remain unexplored. Here, we identified TBP (TATA binding protein) as a crucial mitotic bookmarker for preserving fate memory of Drosophila neural stem cells (NSCs).
Read the full summary ↓
Phosphorylation by the super elongation complex (SEC) is important for TBP to retain as discrete foci at mitotic chromosomes of NSCs to effectively transmit their fate memory. TBP depletion leads to drastic NSC loss, whereas TBP overexpression enhances the ability of SEC to induce neural progenitor dedifferentiation and tumorigenesis. Importantly, TBP achieves its mitotic retention through recruiting the chromatin remodeler EP400, which in turn increases local chromatin accessibility via depositing H2A.Z. Thus, local chromatin remodeling ensures mitotic bookmarking, which may represent a general principle underlying the preservation of cell fate memory.
Published in
TBP bookmarks and preserves neural stem cell fate memory by orchestrating local chromatin architecture
Shen Y, Liu K, Liu J et al. · Molecular cell 2025 · PMID 39662469 · doi:10.1016/j.molcel.2024.11.019
This dataset
Open GSE267892 in finder → Find more ChIP / ATAC / CUT&Tag 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 GSE267892_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 PRJNA1113604 and SRA study SRP508735. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39662469) ↗
Study design
9 conditions, mostly in duplicate
H2A.Z_NSC_CUTandTag ×3 TBP_interphase_NSC_CUTandTag ×3 TBP_mitosis_NSC_CUTandTag ×3 ELL-Myc_NSC_CUTandTag ×2 Myc_control_NSC_CUTandTag ×2 MycdEP400_TBPIR control_NSC_CUTandTag ×2 MycdEP400_TBPIR_NSC_CUTandTag ×2 hH2A.Z_HEK_CUTandTag ×2 +12 more

Supports a between-group comparison across 21 samples.

How we read this: 9 replicated groups read from 32 sample titles; they account for 21 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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