GEO series

Evf2 enhancer lncRNA-enhancer gene guidance through direct RNA binding and RNP recruitment domains

GSE261585 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 22 samples Submitted 2025/06/19 Platform GPL24247

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 22 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: Mus musculus (mouse)
Samples: 22 samples: 22 samples, each with a distinct title — no replicated groupsGroups 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: Single-cell transcriptomics of ventral forebrain progenitors identifies Evf2 enhancer lncRNA-enhancer gene guidance through direct RNA binding and RNP recruitment domainsNature communications · 2025

Summary (written by the submitters)

During mouse embryonic brain development, the Evf2 ultraconserved enhancer lncRNA (e-lncRNA) guides the Dlx5/6UCE enhancer to ~129 sites across chr6. However, previous work identified only 4 transcriptionally regulated targets associated with Evf2 enhancer-gene guided sites (EGGs), raising questions about the significance of the majority of Evf2-EGGs.

Read the full summary ↓

Here, single cell transcriptomics shows that Evf2-regulated EGGs on chr6 coincide with subpopulation-specific Evf2 transcriptional targets, revealing far greater alignment between EGGs and transcriptional effects than previously reported. Evf2 regulation of EGGs to gene bodies (GB ±5kb) divides chr6 into short-range (<10Mb), highly activated and long/super long-range (10-129Mb), moderately repressed genes. However, chr6 clustering of Evf2 transcriptionally regulated targets in populations where Evf2 is first activated, supports that transcriptional outcomes of Evf2-EGGs are not limited to gene body guidance, but may result from EGGs as far as 3Mb, uncoupling shift distance from transcriptional effects. Analysis of directly bound Evf2 RNA binding sites on chr6 (6 RBSs), divides chr6 into 4 regions, consistent with a role for RBS spacing in Evf2-EGG mediated, chromosome-spanning transcriptional regulation. In addition to chr6 Evf2 RBSs, 141 genome-wide RBSs are identified, 69 exactly aligning (>25bp) with at least one RBS, In addition to chr6 Evf2 RBSs, 141 genome-wide RBSs are identified, 69 exactly aligning (>25bp) with at least one RBS. RBS DNA identities are associated with transcription factor enrichment rather than DNA looping, as shown by HiCseq (chromosome capture of dual crosslinked) of E13.5GEs. While 80/147 RBSs are involved in inter-or intra-chr interactions, RBS chromosomal domains are differentially enriched for intra- and inter-chromosomal interactions, and domain specific Evf2-regulated RNP binding. Together with heterogeneous Evf2 regulation of protein pool/condensates (PPCs) of diverse Evf2 ribonucleoproteins (RNPs) (Smarcc2, an RNA binding chromatin remodeler, and Nono, an RNA paraspeckle organizer, Sox2 (a homeodomain transcription factor), RNP recruitment at RBSs and transcriptional targets, we propose a model whereby direct e-lncRNA binding, combinatorial Evf2-RNP recruitment, and homeodomain transcription factor DNA motif recognition/binding/activity, enables multi-modal EGG selectivity and transcriptional outcomes.

Published in

Single-cell transcriptomics of ventral forebrain progenitors identifies Evf2 enhancer lncRNA-enhancer gene guidance through direct RNA binding and RNP recruitment domains

Li E, Chakraborty A, Kohtz SJ et al. · Nature communications 2025 · PMID 40715144 · doi:10.1038/s41467-025-62205-y

This dataset

Open GSE261585 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 GSE261585_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 PRJNA1087747 and SRA study SRP495241. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40715144) ↗

Study design

22 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 22 sample titles: 22 distinct titles with little repetition. 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

GSM8147003 Evf2++ rep1 scRNA-seq
GSM8147004 Evf2++ rep2 scRNA-seq
GSM8147005 Evf2TSTS scRNA-seq
GSM8147006 Evf2++ Nono rep1 CutandRun
GSM8147007 Evf2++ Nono rep2 CutandRun
GSM8147008 Evf2TSTS Nono rep1 CutandRun
GSM8147009 Evf2TSTS Nono rep2 CutandRun
GSM8147010 Evf2++ Smarcc2 rep1 CutandRun
GSM8147011 Evf2++ Smarcc2 rep2 CutandRun
GSM8147012 Evf2TSTS Smarcc2 rep1 CutandRun
GSM8147013 Evf2TSTS Smarcc2 rep2 CutandRun
GSM8147014 Evf12 GAPDH TSTS CHIRPseq
GSM8147015 Evf12 even TSTS CHIRPseq
GSM8147016 Evf12 even ++ rep1 CHIRPseq
GSM8147017 Evf12 even ++ rep2 CHIRPseq
GSM8147018 Evf12 odd TSTS CHIRPseq
GSM8147019 Evf12 odd ++ rep1 CHIRPseq
GSM8147020 Evf12 odd ++ rep2 CHIRPseq
GSM8147021 Evf1 GAPDH TSTS CHIRPseq
GSM8147022 Evf1 GAPDH ++ CHIRPseq
GSM8487841 Evf1_2 WT rep1 HiC
GSM8487842 Evf1_2 WT rep2 HiC

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