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Accession: PRJNA940495 ID: 940495

Characterizing Pneumocystis carinii centromeres with ChIP-seq

See Genome Information for Pneumocystis carinii
Pneumocystis is a relevant genetic system to study centromere formation in relation with host adaptation. How centromeres are formed and maintained in strongly host adapted fungal pathogens is poorly investigated. Centromeres are genomic regions that coordinate accurate chromosomal segregation during mitosis and meiosis. Yet, despite their essential function, centromeres evolve rapidly across eukaryotes. CENP-A, a variant of histone H3 is the epigenetic marker that define centromeres in most eukaryotes. Centromeres are often the sites of chromosomal breaks which contribute to genome shuffling and promote speciation by inhibiting gene flow. Genome shuffling allows genome reconfiguration suitable for survival in new environment such as pathogen adaptation to new hosts. Here, we study the evolution of centromeres in closely related species of mammalian specific pathogens of the fungal phylum of Ascomycota. Long term culture of Pneumocystis species is currently untenable. Using heterologous complementation, we show that Pneumocystis CENP-A ortholog is functionally equivalent to fission yeast Cnp1. Using a short-term in vitro culture, infected animal models and ChIP-seq, we identified centromeres in three Pneumocystis species that diverged ~100 Mya ago. Each species has 17 unique short regional centromeres (< 10kb) in 17 monocentric chromosomes. The centromeres are flanked by heterochromatin. They span active genes, lack conserved DNA sequence motifs, and repeats.These features suggest an epigenetic specification of centromere function. Overall design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for centromeric histone CENP-A and CENP-C in Pneumocystis carinii. P. carinii organisms were collected from infected lungs of corticoids-induced immunocompromised Sprague-Dawley male rats
AccessionPRJNA940495; GEO: GSE226536
Data TypeEpigenomics
ScopeMultiisolate
OrganismPneumocystis carinii[Taxonomy ID: 4754]
Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Pneumocystomycetes; Pneumocystaceae; Pneumocystis; Pneumocystis carinii
Publications
  • Cissé OH et al., "Regional centromere configuration in the fungal pathogens of the Pneumocystis genus.", mBio, 2024 Mar 13;15(3):e0318523
  • Cissé OH et al., "The Host Adapted Fungal Pathogens of Pneumocystis Genus Utilize Genic Regional Centromeres.", bioRxiv, 2023 May 12;
SubmissionRegistration date: 2-Mar-2023
National Institutes of Health
RelevanceUnknown
Project Data:
Resource NameNumber
of Links
Sequence data
SRA Experiments4
Publications
PubMed2
PMC2
Other datasets
BioSample4
GEO DataSets1
GEO Data Details
ParameterValue
Data volume, Supplementary Mbytes57
SRA Data Details
ParameterValue
Data volume, Gbases70
Data volume, Mbytes29441

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