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PXD027030-1

PXD027030 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleTime-series transcriptomics and proteomics reveal alternative modes to decode p53 oscillations
DescriptionTranscription factors (TFs) can relay signals through temporal alterations in their levels. The cell stress responsive TF p53 exhibits different dynamics depending on the type of stress, which influence the magnitude and dynamics of expression of its target genes and subsequent cellular outcomes. The mechanisms decoding p53 dynamics into levels and dynamics of RNA and protein of its targets remain unclear. We systematically quantified p53 target mRNA and protein levels over time under two p53 dynamical regimes – oscillatory and sustained – using RNA-seq and quantitative mass spectrometry. We categorized the mRNA dynamical patterns arising from oscillatory or sustained p53 expression, as well as the corresponding protein dynamics. We found that in both cases oscillatory dynamics allowed for the greatest variety of dynamical patterns of the downstream species. Target proteins from a wide range of functional categories were induced under both p53 dynamic conditions, with induction levels being overall higher under sustained dynamics. Mathematical modeling combined with analysis of empirical data revealed three mechanisms of decoding p53 dynamics: adjustment of mRNA and protein degradation rates, adjustment of activation thresholds for expression of mRNA and corresponding protein levels, and usage of coherent and incoherent feed-forward loop motifs in generating exclusive responses to p53 oscillatory or sustained dynamics, respectively. Our results highlight the diversity of mechanisms that decode complex TF dynamics into dynamical patterns of mRNA and proteins.
HostingRepositoryPRIDE
AnnounceDate2022-02-11
AnnouncementXMLSubmission_2022-02-11_04:34:05.202.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterMarian Kalocsay
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListiodoacetamide derivatized residue
InstrumentOrbitrap Fusion Lumos
Dataset History
RevisionDatetimeStatusChangeLog Entry
02021-07-01 02:35:18ID requested
12022-02-11 04:34:05announced
Publication List
Dataset with its publication pending
Keyword List
submitter keyword: P53 targets dynamic oscillatory sustained proteomics TMT multiplex mRNA RNAseq
Contact List
Galit Lahav
contact affiliationDepartment of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
contact emailgalit@hms.harvard.edu
lab head
Marian Kalocsay
contact affiliationHarvard Medical School
contact emailmarian_kalocsay@hms.harvard.edu
dataset submitter
Full Dataset Link List
Dataset FTP location
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