PXD057383-1

PXD057383 is an original dataset announced via ProteomeXchange.

Title	Gene expression dynamics before and after zygotic gene activation in Drosophila early embryogenesis
Description	Post-transcriptional gene regulatory mechanisms are fundamental to the determination of gene expression dynamics and especially crucial for the earliest stages of animal development in which transcription is nearly silent. Here we performed high-resolution total RNA-sequencing and quantitative mass spectrometry analysis simultaneously on Drosophila maternal-to-zygotic transition (MZT) to reveal the dynamic interchange between transcript and protein expression level at the earliest stage of animal development. Intriguingly, we found that both stable transcript expression and an increase in translation efficiency can be crucial for protein upregulation prior to zygotic gene activation (ZGA), whereas such features diminished following ZGA. Further, this study is the first to report the proteome-wide quantitative changes in protein ubiquitination in Drosophila MZT. Our results indicate that timely ubiquitination of the distinct target proteins during MZT are essential for the downregulation of protein expression levels. Profiling of the RNA-associated proteome changes in Drosophila MZT suggested that RNA-binding activities can be regulated without the respective change in net protein expression levels for over 200 proteins, including Pcid2, Sym, and Cpsf73. Taken together, we find that stable expression of transcript can be crucial for the protein expression level upregulation during the earliest stage of MZT, and also report that proteome wide and quantitative remodeling of the distinct post translational regulatory mechanisms can be crucial for the gene expression level changes and progression of the earliest stages of animal development.
HostingRepository	PRIDE
AnnounceDate	2025-09-08
AnnouncementXML	Submission_2025-09-07_16:13:44.481.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yongwoo Na
SpeciesList	scientific name: Drosophila melanogaster (Fruit fly); NCBI TaxID: 7227;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2024-10-30 23:57:59	ID requested
⏵ 1	2025-09-07 16:13:45	announced

10.1016/j.isci.2025.113272;

Na Y, Choi Y, Nguyen TTM, Pham-Bui HA, Kim J, Kim VN, Lee M, Kim JS, early embryogenesis. iScience, 28(9):113272(2025) [pubmed]

submitter keyword: Drosophila MZT development

Jongeo Kim
contact affiliation	Seoul National University
contact email	jongseokim@snu.ac.kr
lab head
Yongwoo Na
contact affiliation	Seoul National University
contact email	nyw1412@snu.ac.kr
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/2025/09/PXD057383

PRIDE project URI

• PRIDE
  1. PXD057383
     1. Label: PRIDE project
     2. Name: Gene expression dynamics before and after zygotic gene activation in Drosophila early embryogenesis