PXD067760-1

PXD067760 is an original dataset announced via ProteomeXchange.

Title	CUT&Tag Overcomes Biases of ChIP and Establishes Chromatin Patterns for Repetitive Genomic Loci
Description	Determining the genomic localization of chromatin features is an essential aspect of investigating gene expression control, and ChIP-Seq has long been the gold standard technique for interrogating chromatin landscapes. Recently, the development of alternative methods, such as CUT&Tag, have provided researchers with alternative strategies that eliminate the need for chromatin purification, and allow for in situ investigation of histone modifications and chromatin bound factors. Mindful of technical differences, we set out to investigate whether distinct chromatin modifications were equally compatible with these different chromatin interrogation techniques. We found that ChIP-Seq and CUT&Tag performed similarly for modifications known to reside at gene regulatory regions, such as promoters and enhancers, but major differences were observed when we assessed enrichment over heterochromatin-associated loci. Unlike ChIP-Seq, CUT&Tag detects robust levels of H3K9me3 at a substantial number of repetitive elements, with especially high sensitivity over evolutionarily young retrotransposons. IAPEz-int elements for example, exhibited underrepresentation in mouse ChIP-Seq datasets but strong enrichment using CUT&Tag. Additionally, we identified several euchromatin-associated proteins that co-purify with repetitive loci and are similarly depleted when applying ChIP-based methods. This study reveals that our current knowledge of chromatin states across the heterochromatin portions of the mammalian genome is extensively incomplete, largely due to36 limitations of ChIP-Seq. We also demonstrate that newer in situ chromatin fragmentation-based techniques, such as CUT&Tag and CUT&RUN, are more suitable for studying chromatin modifications over repetitive elements and retrotransposons.
HostingRepository	PRIDE
AnnounceDate	2025-08-26
AnnouncementXML	Submission_2025-08-26_13:11:50.591.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Kyle Swovick
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Astral

Revision	Datetime	Status	ChangeLog Entry
0	2025-08-26 12:17:20	ID requested
⏵ 1	2025-08-26 13:11:50	announced

Dataset with its publication pending

submitter keyword: Repetitive Loci,Mouse, IP-MS, Chromatin, Retrotransposons, ChIP

Patrick Murphy
contact affiliation	Molecular Biology and Genetics, Cornell University, USA
contact email	pjm249@cornell.edu
lab head
Kyle Swovick
contact affiliation	University of Rochester Medical Center Mass Spectrometry Shared Resource Laboratory
contact email	kswovick@ur.rochester.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD067760
     1. Label: PRIDE project
     2. Name: CUT&Tag Overcomes Biases of ChIP and Establishes Chromatin Patterns for Repetitive Genomic Loci