PXD034464-1

PXD034464 is an original dataset announced via ProteomeXchange.

Title	Novel splicing and open reading frames revealed by long-read direct RNA sequencing of adenovirus transcripts
Description	Adenovirus is a common human pathogen that relies on host cell processes for transcription and processing of viral RNA and protein production. Although adenoviral promoters, splice junctions, and cleavage and polyadenylation sites have been characterized using low-throughput biochemical techniques or short read cDNA-based sequencing, these technologies do not fully capture the complexity of the adenoviral transcriptome. By combining Illumina short-read and nanopore long-read direct RNA sequencing approaches, we mapped transcription start sites and cleavage and polyadenylation sites across the adenovirus genome. In addition to confirming the known canonical viral early and late RNA cassettes, our analysis of splice junctions within long RNA reads revealed an additional 35 novel viral transcripts. These RNAs include fourteen new splice junctions which lead to expression of canonical open reading frames (ORF), six novel ORF-containing transcripts, and fifteen transcripts encoding for messages that potentially alter protein functions through truncations or fusion of canonical ORFs. In addition, we also detect RNAs that bypass canonical cleavage sites and generate potential chimeric proteins by linking separate gene transcription units. Of these, an evolutionary conserved protein was detected containing the N-terminus of E4orf6 fused to the downstream DBP/E2A ORF. Loss of this novel protein, E4orf6/DBP, was associated with aberrant viral replication center morphology and poor viral spread. Our work highlights how long-read sequencing technologies can reveal further complexity within viral transcriptomes.
HostingRepository	PRIDE
AnnounceDate	2022-08-30
AnnouncementXML	Submission_2022-08-30_06:28:44.753.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Richard Lauman
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2022-06-10 03:21:04	ID requested
⏵ 1	2022-08-30 06:28:45	announced
2	2024-10-22 05:39:29	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: Targeted MS, Splicing, Adenovirus

Matthew Weitzman
contact affiliation	Childrens Hospital of Pennsylvania
contact email	rlauman@mail.med.upenn.edu
lab head
Richard Lauman
contact affiliation	University of Pennsylvania
contact email	rlauman@mail.med.upenn.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/PXD034464

PRIDE project URI

• PRIDE
  1. PXD034464
     1. Label: PRIDE project
     2. Name: Novel splicing and open reading frames revealed by long-read direct RNA sequencing of adenovirus transcripts