PXD069944-1

PXD069944 is an original dataset announced via ProteomeXchange.

Title	Diversity and evolution of chromatin regulatory states across eukaryotes
Description	Histone post-translational modifications (hPTMs) are key regulators of chromatin states, influencing gene expression, epigenetic memory, and transposable element repression across eukaryotic genomes. While many hPTMs are evolutionarily conserved, the extent to which the chromatin states they define are similarly preserved remains unclear. Here, we developed a combinatorial indexing ChIP-seq method to simultaneously profile specific hPTMs across diverse eukaryotic lineages, including amoebozoans, rhizarians, discobans, and cryptomonads. Our analyses revealed highly conserved euchromatin states at active gene promoters and gene bodies. In contrast, we observed diverse configurations of repressive heterochromatin states associated with silenced genes and transposable elements, characterized by various combinations of hPTMs such as H3K9me3, H3K27me3 and/or different H3K79 methylations. These findings suggest that while core hPTMs are ancient and broadly conserved, their functional readout has diversified throughout eukaryotic evolution, shaping lineage-specific chromatin landscapes.
HostingRepository	PRIDE
AnnounceDate	2026-04-30
AnnouncementXML	Submission_2026-04-30_04:42:06.401.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Cristina Chiva
SpeciesList	scientific name: Tetrahymena thermophila; NCBI TaxID: NEWT:5911; scientific name: Dictyostelium discoideum (Slime mold); NCBI TaxID: NEWT:44689; scientific name: Spizellomyces punctatus; NCBI TaxID: NEWT:109760; scientific name: Physcomitrella patens subsp. patens (Moss); NCBI TaxID: NEWT:3218; scientific name: Nematostella vectensis; NCBI TaxID: NEWT:45351; scientific name: Acanthamoeba castellanii; NCBI TaxID: NEWT:5755; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: NEWT:4932; scientific name: Bigelowiella natans; NCBI TaxID: NEWT:227086; scientific name: Guillardia theta; NCBI TaxID: NEWT:55529; scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: NEWT:3702; scientific name: Naegleria gruberi; NCBI TaxID: NEWT:5762; scientific name: Creolimax fragrantissima; NCBI TaxID: NEWT:470921;
ModificationList	N6-methyl-L-lysine; N6; acetylated residue; N6
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2025-10-27 08:21:49	ID requested
⏵ 1	2026-04-30 04:42:06	announced

Dataset with its publication pending

submitter keyword: histones, eukaryotes,chromatin

Arnau Sebé-Pedrós
contact affiliation	Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain.
contact email	arnau.sebe@crg.eu
lab head
Cristina Chiva
contact affiliation	University Pompeu Fabra
contact email	cristina.chiva@upf.edu
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD069944

PRIDE project URI

• PRIDE
  1. PXD069944
     1. Label: PRIDE project
     2. Name: Diversity and evolution of chromatin regulatory states across eukaryotes