PXD002525

PXD002525 is an original dataset announced via ProteomeXchange.

Title	Dynamic changes of histone H3 marks during Caenorhabditis elegans lifecycle revealed by middle-down proteomics
Description	We applied a middle-down proteomics strategy for large scale protein analysis during in vivo development of Caenorhabditis elegans. We characterized post-translational modifications (PTMs) on histone H3 N-terminal tails at eight time points during the C. elegans lifecycle, including embryo, larval stages (L1 to L4), dauer and L1/L4 post dauer. Histones were analyzed by our optimized middle-down protein sequencing platform using high mass accuracy tandem mass spectrometry. This allows quantification of intact histone tails and detailed characterization of distinct histone tails carrying co-occurring PTMs. We measured temporally distinct combinatorial PTM profiles during C. elegans development. We show that the doubly modified form H3K23me3K27me3, which is rare or non-existent in mammals, is the most abundant PTM in all stages of C. elegans lifecycle. The abundance of H3K23me3 increased during development and it was mutually exclusive of the active marks H3K18ac, R26me1 and R40me1, suggesting a role for H3K23me3 in to silent chromatin. We observed distinct PTM profiles for normal L1 larvae and for L1-post dauer larvae, or L4 and L4 post-dauer, suggesting that histone PTMs mediate an epigenetic memory that is transmitted during dauer formation. Collectively, our data describe the dynamics of histone H3 combinatorial code during C. elegans lifecycle and demonstrate the feasibility of using middle-down proteomics to study in vivo development of multicellular organisms.
HostingRepository	PRIDE
AnnounceDate	2015-11-02
AnnouncementXML	Submission_2015-11-02_06:24:24.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD002525
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Simone Sidoli
SpeciesList	scientific name: Caenorhabditis elegans; NCBI TaxID: 6239;
ModificationList	N6: N6; acetylated residue; monomethylated residue; formylated residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2015-07-13 02:17:53	ID requested
⏵ 1	2015-11-02 06:24:25	announced

Sidoli S, Vandamme J, Salcini AE, Jensen ON, Dynamic changes of histone H3 marks during Caenorhabditis elegans lifecycle revealed by middle-down proteomics. Proteomics, 16(3):459-64(2016) [pubmed]

curator keyword: Biological

submitter keyword: C. elegans, histones, lifecycle, middle-down proteomics, post-translational modifications

Ole N. Jensen
contact affiliation	University of Southern Denmark, Odense, DK
contact email	jenseno@bmb.sdu.dk
lab head
Simone Sidoli
contact affiliation	University of Pennsylvania
contact email	simone.sidoli@gmail.com
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/2015/11/PXD002525

PRIDE project URI

• PRIDE
  1. PXD002525
     1. Label: PRIDE project
     2. Name: Dynamic changes of histone H3 marks during Caenorhabditis elegans lifecycle revealed by middle-down proteomics