PXD008358

PXD008358 is an original dataset announced via ProteomeXchange.

Title	Systematic quantitative analysis of H2A and H2B variants by targeted proteomics
Description	Background: Histones organize DNA into chromatin through a variety of processes. Among them, a vast diversity of histone variants can be incorporated into chromatin to finely modulate its organization and functionality. Classically, the study of histone variants has largely relied on antibody-based assays. However, antibodies have a limited efficiency to discriminate between highly similar histone variants. Results: In this study, we established a mass spectrometry-based analysis to address this challenge. We developed a targeted proteomics method, using Single Reaction Monitoring (SRM) or Parallel Reaction Monitoring (PRM), to quantify a maximum number of histone variants in a single multiplexed assay, even when histones are present in a crude extract. This strategy was developed on H2A and H2B variants, using 55 peptides corresponding to 25 different histone sequences, among which a few differ by a single amino acid. The methodology was then applied to mouse testis extracts in which almost all histone variants are expressed. It confirmed the abundance profiles of several testis-specific histones during successive stages of spermatogenesis and the existence of predicted H2A.L.1 isoforms. This methodology was also used to explore the over-expression pattern of H2A.L.1 isoforms in a mouse model of male infertility. Conclusions: Our results demonstrate that targeted proteomics is a powerful method to quantify highly similar histone variants and isoforms. The developed method can be easily transposed to the study of human histone variants, whose abundance can be deregulated in various diseases.
HostingRepository	PRIDE
AnnounceDate	2018-01-16
AnnouncementXML	Submission_2018-01-16_02:42:27.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD008358
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Sara EL KENNANI
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	monomethylated residue; phosphorylated residue; formylated residue; monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2017-12-04 03:01:01	ID requested
⏵ 1	2018-01-16 02:42:28	announced

El Kennani S, Adrait A, Permiakova O, Hesse AM, Ialy-Radio C, Ferro M, Brun V, Cocquet J, Govin J, Pflieger D, Systematic quantitative analysis of H2A and H2B variants by targeted proteomics. Epigenetics Chromatin, 11(1):2(2018) [pubmed]

curator keyword: Biological

submitter keyword: Histone variants, Chromatin, Proteomics, Targeted proteomics, SRM, PRM, Spermatogenesis

Virginie Brun
contact affiliation	Univ. Grenoble Alpes, INSERM U1038, CEA, BIG-BGE, Grenoble, France.
contact email	Virginie.brun@cea.fr
lab head
Sara EL KENNANI
contact affiliation	CEA
contact email	sara.elkennani@cea.fr
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD008358
     1. Label: PRIDE project
     2. Name: Systematic quantitative analysis of H2A and H2B variants by targeted proteomics