GEO series

Transcriptional interference drives intronic polyadenylation at the endogenous H13/Mcts2 locus

GSE308559 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 14 samples Submitted 2026/06/11 Platform GPL24247

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 14 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: 14 samples: 14 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.

Summary (written by the submitters)

ABSTRACT: Over a tenth of mammalian genes are organised as nested within distinct host genes, questioning how both can be expressed when concurrent transcription can collide in the same genetic space. DNA methylation-mediated silencing of nested genes can prevent such conflict. Alternatively, transcriptional interference can occur, but this has not been mechanistically demonstrated independently of DNA methylation outside of artificial systems.

Read the full summary ↓

We demonstrate transcriptional interference at an endogenous mammalian host/nested locus, the imprinted H13/Mcts2 pair. Here, active nested gene (Mcts2) transcription promotes host gene (H13) intronic polyadenylation, while Mcts2 silencing through promoter DNA methylation, favours distal 3′UTR polyadenylation. Using dCas9:KRAB-mediated silencing we establish that this effect depends on transcription itself, independently of DNA methylation. Moreover, nested gene transcription interferes with host gene elongation even when the upstream intronic polyadenylation site is ablated. Nested gene transcriptional interference can thus stimulate intronic termination of their host gene with implications for hundreds of loci. Allelic CUT&RUN was utilised to assay H3K36me3 to track elongation and H3K4me3 to assay promoters at the H13/Mcts2 locus within this study

This dataset

Open GSE308559 in finder → Find more mouse 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 GSE308559_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 PRJNA1330887 and SRA study SRP622019. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

14 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 14 sample titles: 14 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

GSM9248007 WT_H3K4me3
GSM9248008 WT_H3K36me3
GSM9248009 dPA_CloneA3_H3K4me3
GSM9248010 dPA_CloneA3_H3K36me3
GSM9248011 dPA_CloneF6_H3K4me3
GSM9248012 dPA_CloneF6_H3K36me3
GSM9248013 dCas9KRAB_Clone1_H3K4me3
GSM9248014 dCas9KRAB_Clone1_H3K36me3
GSM9248015 dCas9KRAB_Clone2_H3K4me3
GSM9248016 dCas9KRAB_Clone2_H3K36me3
GSM9248017 dCas9KRAB_Clone3_H3K4me3
GSM9248018 dCas9KRAB_Clone3_H3K36me3
GSM9248019 dCas9KRAB_Clone4_H3K4me3
GSM9248020 dCas9KRAB_Clone4_H3K36me3

Datasets on a similar topic

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GSE212423 FUS reads histone H3K36me3 to regulate alternative polyadenylation [CUT&Tag] 38 samples shares polyadenylation
GSE286574 Intrauterine hyperglycemia impairs primordial germ cell development and fertility by sex-specific epigenetic reprogramming interference in mice offspring [ATAC-seq] 30 samples shares interference
GSE288677 Polyadenylation at RNA polymerase III loci underlies the accumulation of noncoding retrotransposons during herpesviral infection 18 samples shares polyadenylation
GSE212425 FUS reads histone H3K36me3 to regulate alternative polyadenylation 86 samples shares polyadenylation

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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.