PXD031991

PXD031991 is an original dataset announced via ProteomeXchange.

Title	A phylogenetic and proteomic reconstruction of eukaryotic chromatin evolution
Description	Histones and associated chromatin proteins have essential functions in eukaryotic genome organization and regulation. Despite this fundamental role in eukaryotic cell biology, we lack a phylogenetically-comprehensive understanding of chromatin evolution. Here, we combine comparative proteomics and genomics analysis of chromatin in eukaryotes and archaea. Proteomics uncovers the existence of histone post-translational modifications in Archaea. However, archaeal histone modifications are scarce, in contrast with the highly conserved and abundant marks we identify across eukaryotes. Phylogenetic analysis reveals that chromatin-associated catalytic functions (e.g., methyltransferases) have pre-eukaryotic origins, whereas histone mark readers and chaperones are eukaryotic innovations. We show that further chromatin evolution is characterized by expansion of readers, including capture by transposable elements and viruses. Overall, our study infers detailed evolutionary history of eukaryotic chromatin: from its archaeal roots, through the emergence of nucleosome-based regulation in the eukaryotic ancestor, to the diversification of chromatin regulators and their hijacking by genomic parasites
HostingRepository	PRIDE
AnnounceDate	2022-08-12
AnnouncementXML	Submission_2022-08-12_02:03:00.510.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Cristina Chiva
SpeciesList	scientific name: Sycon ciliatum; NCBI TaxID: 27933; scientific name: Gefionella okellyi; NCBI TaxID: 2853422; scientific name: Corallochytrium limacisporum; NCBI TaxID: 98351; scientific name: Methanobrevibacter cuticularis; NCBI TaxID: 47311; scientific name: Naegleria gruberi; NCBI TaxID: 5762; scientific name: Fabomonas tropica; NCBI TaxID: 1246791; scientific name: Guillardia theta; NCBI TaxID: 55529; scientific name: Thecamonas trahens; NCBI TaxID: 529818; scientific name: Emiliania huxleyi; NCBI TaxID: 2903; scientific name: Methanospirillum stamsii; NCBI TaxID: 1277351; scientific name: Spizellomyces punctatus; NCBI TaxID: 109760; scientific name: Thalassiosira pseudonana; NCBI TaxID: 35128; scientific name: Capsaspora owczarzaki; NCBI TaxID: 192875; scientific name: Dictyostelium discoideum (Slime mold); NCBI TaxID: 44689; scientific name: Phytophthora infestans; NCBI TaxID: 4787; scientific name: Physcomitrella; NCBI TaxID: 3217; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Chlamydomonas reinhardtii; NCBI TaxID: 3055; scientific name: Nitrososphaera viennensis; NCBI TaxID: 1034015; scientific name: Bigelowiella natans; NCBI TaxID: 227086; scientific name: Acanthamoeba castellanii; NCBI TaxID: 5755;
ModificationList	monomethylated residue; acetylated residue; dimethylated residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2022-03-02 01:13:53	ID requested
⏵ 1	2022-08-12 02:03:01	announced

Grau-Bov, é X, Navarrete C, Chiva C, Pribasnig T, Ant, ó M, Torruella G, Galindo LJ, Lang BF, Moreira D, L, ó, pez-Garcia P, Ruiz-Trillo I, Schleper C, Sabid, ó E, Seb, é, -Pedr, ó, s A, A phylogenetic and proteomic reconstruction of eukaryotic chromatin evolution. Nat Ecol Evol, 6(7):1007-1023(2022) [pubmed]

ProteomeXchange project tag: Human Proteome Project

submitter keyword: proteogenomics,histones, evolution, chromatin

Arnau Sebé-Pedrós
contact affiliation	Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Catalonia, 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/2022/08/PXD031991

PRIDE project URI

• PRIDE
  1. PXD031991
     1. Label: PRIDE project
     2. Name: A phylogenetic and proteomic reconstruction of eukaryotic chromatin evolution