PXD069390-1

PXD069390 is an original dataset announced via ProteomeXchange.

Title	Integrative multi-omics analysis of growth plate regulation underlying body size in miniature pigs
Description	Body size represents a complex phenotype driven by genetic variation and epigenetic regulation, with the molecular processes underlying this trait remaining a central challenge to disentangle. To elucidate these fundamental mechanisms, we applied a multi-omics approach to investigate the regulatory architecture of growth in the growth plates of the long bones from pigs, a valuable model species for skeletal development. Taking advantage of divergent selection that separates pig breeds into miniature and larger-sized types, we targeted homozygous genomic regions under this intense selection for height, which harbor functional variants with pronounced effects. We sampled two miniature breeds, namely Aachen Minipig (AM) and Mini-LEWE (ML), as well as two larger pig breeds, Angeln Saddleback (AS) and Mangalitza (MA) and assembled an integrated multi-omics dataset comprising the results of WGS, Hi-C, ATAC-seq and RNA-seq, available at ENA Browser with accession number provided in our manuscript, and LC-MS analyses (data available with this submission). Data analyses led to the identification of 23 homozygous mutant variants in Aachen Minipigs and 13 distinct variants in Mini-LEWE predicted to affect cis-regulatory elements and potentially interact with differentially expressed genes that drive body size in breed-dependent ways. Our results pointed to HPX, an lncRNA (ENSSSCG00000048200) located near SDR16C5 and PLAG1, as well as NET-related pathways, as central players in impaired growth in the growth plates. Furthermore, protein-protein interaction networks highlighted 16 proteins that interacted significantly, of which GC vitamin D binding was identified as a regulatory element acting downstream of the key variants for body size across miniature pig breeds. In summary, our study offers a multi-layered characterization of regulatory mechanisms in the growth plates, using miniature pigs as a model to understand the genetic and epigenetic control of long-bone growth.
HostingRepository	PRIDE
AnnounceDate	2026-06-11
AnnouncementXML	Submission_2026-06-11_01:54:14.590.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Karsten Cirksena
SpeciesList	scientific name: Sus scrofa (Pig); NCBI TaxID: NEWT:9823;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2025-10-13 04:08:42	ID requested
⏵ 1	2026-06-11 01:54:15	announced

Dataset with its publication pending

submitter keyword: miniaturization, growth, miniature pigs, functional genomics,multi-omics, gene regulation, body size, growth plates

Gisa Gerold
contact affiliation	Institute of Virology Medical University of Innsbruck Schöpfstraße 41 6020 Innsbruck, Austria
contact email	gisa.gerold@i-med.ac.at
lab head
Karsten Cirksena
contact affiliation	Helmholtz Centre for Infection Research
contact email	karsten.cirksena.research@posteo.de
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/2026/06/PXD069390

PRIDE project URI

• PRIDE
  1. PXD069390
     1. Label: PRIDE project
     2. Name: Integrative multi-omics analysis of growth plate regulation underlying body size in miniature pigs