PXD001211

PXD001211 is an original dataset announced via ProteomeXchange.

Title	Circadian clock-dependent and -independent rhythmic proteomes implement distinct diurnal functions in mouse liver.
Description	Diurnal oscillations of gene expression controlled by the circadian clock underlie rhythmic physiology across most living organisms. Although such rhythms have been extensively studied at the level of transcription and mRNA accumulation, little is known about the accumulation patterns of proteins. Here, we quantified temporal profiles in the murine hepatic proteome under physiological light–dark conditions using stable isotope labeling by amino acids quantitative MS. To measure the daily accumulation of proteins, we designed an SILAC MS experiment, in which total protein extracts were harvested from C57BL/6J mice every 3 h for 2 d (eight samples per day). Relative protein abundance in each of 16 samples was quantified against a common reference sample labeled using the SILAC method. The generated mass spectra allowed the identification of a total of 5,827 distinct proteins, of which 70% yielded relative measurements in at least 8 of 16 samples. Our analysis identified over 5,000 proteins, of which several hundred showed robust diurnal oscillations with peak phases enriched in the morning and during the night and related to core hepatic physiological functions. Combined mathematical modeling of temporal protein and mRNA profiles indicated that proteins accumulate with reduced amplitudes and significant delays, consistent with protein half-life data. Moreover, a group comprising about one-half of the rhythmic proteins showed no corresponding rhythmic mRNAs, indicating significant translational or posttranslational diurnal control. Such rhythms were highly enriched in secreted proteins accumulating tightly during the night. Also, these rhythms persisted in clock-deficient animals subjected to rhythmic feeding, suggesting that food-related entrainment signals influence rhythms in circulating plasma factors
HostingRepository	PRIDE
AnnounceDate	2014-10-23
AnnouncementXML	Submission_2014-10-23_05:00:59.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Manfredo Quadroni
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	6x(13)C labeled residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2014-08-08 02:12:22	ID requested
1	2014-08-08 07:38:10	announced
⏵ 2	2014-10-23 05:01:00	announced	Updated project metadata.

Mauvoisin D, Wang J, Jouffe C, Martin E, Atger F, Waridel P, Quadroni M, Gachon F, Naef F, Circadian clock-dependent and -independent rhythmic proteomes implement distinct diurnal functions in mouse liver. Proc Natl Acad Sci U S A, 111(1):167-72(2014) [pubmed]

curator keyword: Biological

submitter keyword: mouse, liver proteins, SILAC, quantitative proteomics, circadian rhythms, LC-MSMS

Frederic Gachon
contact affiliation	Diabetes and Circadian Rhythms Department, Nestlé Institute of Health Sciences, CH-1015 Lausanne, Switzerland
contact email	frederic.gachon@rd.nestle.com
lab head
Manfredo Quadroni
contact affiliation	University of Lausanne
contact email	manfredo.quadroni@unil.ch
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD001211
     1. Label: PRIDE project
     2. Name: Circadian clock-dependent and -independent rhythmic proteomes implement distinct diurnal functions in mouse liver.