PXD077902

PXD077902 is an original dataset announced via ProteomeXchange.

Title	Allele-resolved monosome and polysome sequencing identifies functional cis-acting variants affecting mRNA translation efficiency
Description	To prioritize germline genetic variants affecting mRNA fate at the post-transcriptional and translational levels, we leveraged sucrose-gradient-based isolation of 80S monosomes and polysomes, followed by mRNA retrieval and paired-end sequencing. Total cytoplasmic RNA was also sequenced for comparison. Experiments were performed in the non-transformed cell line RPE-1, cultured under basal conditions or upon p53 activation by Nutlin. Differential gene expression analysis confirmed a canonical p53 response. Heterozygous SNPs and SNVs were identified from the RNA-seq data, and allelic fractions (AF) were calculated for total, monosomal, and polysomal mRNAs. Variants showing reproducible AF differences across fractions beyond experimental variability were defined as tranSNPs. Among nearly 7000 heterozygous variants analyzable in polysomal or total RNA and over 5000 in monosomal mRNA, 1155 displayed significant imbalance. Reporter assays, performed in both RPE-1 and HCT116 cells, validated allelic or haplotype effects for 17 selected variants in UTRs and coding regions, confirming differences in 15 cases, with evidence of cell line-specific responses. Proteomic analysis further supported allelic imbalance for selected missense variants. Overall, tranSNPs were identified in a non-transformed cell line at frequencies comparable to cancer cells, extending their implications in human physiology. Further, monosome profiling enabled improved detection sensitivity of tranSNPs without positional bias, suggesting that 80S profiling improves detection of allele-specific translational regulation in RPE-1 cells.
HostingRepository	PanoramaPublic
AnnounceDate	2026-09-16
AnnouncementXML	Submission_2026-09-16_09:41:29.403.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Romina Belli
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationList	Carbamidomethyl
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2026-04-30 19:46:33	ID requested
⏵ 1	2026-09-16 09:41:29	announced

no publication

submitter keyword: 80S monosome, polysome-profiling, translation efficiency, RNA-sequencing, allele-specific mRNA regulation

Romina Belli
contact affiliation	Inga Lab: Laboratory of Transcriptional Networks, DeCIBIO, University of Trento-IT
contact email	romina.belli@unitn.it
lab head
Romina Belli
contact affiliation	MS & Proteomics Core Facility, DeCIBIO, University of Trento, Trento, IT
contact email	romina.belli@unitn.it
dataset submitter

Panorama Public dataset URI