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Proc Natl Acad Sci U S A. 2018 Apr 24;115(17):4429-4434. doi: 10.1073/pnas.1721381115. Epub 2018 Apr 11.

Nucleus-specific expression in the multinuclear mushroom-forming fungus Agaricus bisporus reveals different nuclear regulatory programs.

Author information

1
Delft Bioinformatics Lab, Delft University of Technology, 2628XE Delft, The Netherlands; t.abeel@tudelft.nl t.gehrmann@tudelft.nl.
2
Microbiology, Utrecht University, 3584CH Utrecht, The Netherlands.
3
Plant Breeding, Wageningen University and Research, 6708PB Wageningen, The Netherlands.
4
Delft Bioinformatics Lab, Delft University of Technology, 2628XE Delft, The Netherlands.
5
Broad Institute of MIT and Harvard, Cambridge, MA 02142.

Abstract

Many fungi are polykaryotic, containing multiple nuclei per cell. In the case of heterokaryons, there are different nuclear types within a single cell. It is unknown what the different nuclear types contribute in terms of mRNA expression levels in fungal heterokaryons. Each cell of the mushroom Agaricus bisporus contains two to 25 nuclei of two nuclear types originating from two parental strains. Using RNA-sequencing data, we assess the differential mRNA contribution of individual nuclear types and its functional impact. We studied differential expression between genes of the two nuclear types, P1 and P2, throughout mushroom development in various tissue types. P1 and P2 produced specific mRNA profiles that changed through mushroom development. Differential regulation occurred at the gene level, rather than at the locus, chromosomal, or nuclear level. P1 dominated mRNA production throughout development, and P2 showed more differentially up-regulated genes in important functional groups. In the vegetative mycelium, P2 up-regulated almost threefold more metabolism genes and carbohydrate active enzymes (cazymes) than P1, suggesting phenotypic differences in growth. We identified widespread transcriptomic variation between the nuclear types of A. bisporus Our method enables studying nucleus-specific expression, which likely influences the phenotype of a fungus in a polykaryotic stage. Our findings have a wider impact to better understand gene regulation in fungi in a heterokaryotic state. This work provides insight into the transcriptomic variation introduced by genomic nuclear separation.

KEYWORDS:

RNA-seq; fungi; heterokaryon; nuclear-specific expression; quantification

PMID:
29643074
PMCID:
PMC5924919
DOI:
10.1073/pnas.1721381115
[Indexed for MEDLINE]
Free PMC Article

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