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Abstract Detail

Gene regulatory networks in fungal development and morphogenesis - towards fungal evo-devo

Ohm, Robin A. [1].

ChIP-Seq reveals the epigenetic landscape in the mushroom-forming fungus Schizophyllum commune during development and lignocellulose degradation.

Mushroom-forming fungi are a nutritious and sustainable source of food, and they play an important role in nutrient recycling in nature by degrading the complex polymers of wood. In recent years, several transcription factors have been identified that regulate the development of mushrooms. However, little is known about the epigenetic changes during mushroom formation. We have developed ChIP-Seq protocols for H3K4me2 (dimethylation of lysine 4 on histone H3) to study the epigenetic landscape during development, and we have developed transcription factor specific ChIP-Seq to map the binding sites of important transcriptional regulators.
With H3K4me2 ChIP-Seq we identified a total of 6032 and 5889 sites during monokaryotic and dikaryotic development, respectively. The sites were strongly enriched near translation initiation sites of genes. Although the overall epigenetic landscape was similar between both conditions, we identified 837 sites of differential enrichment during monokaryotic or dikaryotic development, associated with 965 genes. Six transcription factor genes were enriched in H3K4me2 during dikaryotic development, indicating that these are epigenetically regulated during development. Deletion of two of these genes (fst1 and zfc7) resulted in arrested development of fruiting bodies, resulting in immature mushrooms.
In parallel, we developed a ChIP-Seq protocol to map the binding sites of specific transcription factors. Comparative genomics and transcriptomics revealed a Zn2Cys6-type transcription factor gene (roc1) that was highly up-regulated during growth on cellulose, when compared to glucose. A roc1 knockout strain showed an inability to grow on medium with cellulose as a sole carbon source, and growth on cellobiose and xylan (other components of wood) was inhibited. We performed ChIP-Seq with Roc1, which identified 1474 binding sites of this transcription factor. Promoters of genes involved in lignocellulose degradation were strongly enriched with these binding sites, especially those of LPMO (lytic polysaccharide monooxygenase) CAZymes, indicating that Roc1 directly regulates these genes. A GC-rich motif was identified as the binding site of Roc1, which was confirmed by a functional promoter analysis.
These two ChIP-Seq analyses have allowed us to gain more insights into the epigenetic landscape and gene regulatory network during mushroom development and lignocellulose degradation.

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1 - Utrecht University, Biology, Padualaan 8, 3584 CH, Utrecht, Netherlands

transcription factor
lignocellulose degradation.

Presentation Type: Symposium Presentation
Session: SY1, Gene regulatory networks in fungal development and morphogenesis - towards fungal evo-devo
Location: /
Date: Monday, July 19th, 2021
Time: 10:45 AM(EDT)
Number: SY1003
Abstract ID:1127
Candidate for Awards:None

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