Functional genomics of morphogenesis in filamentous ascomycetes

本项目旨在研究丝状子囊菌子实体发育的分子调控机制。在项目的第一阶段，我们对三种子囊菌进行了比较转录组学分析，以确定基因表达的进化保守模式。结果表明，子实体中的基因表达模式与营养菌丝体中的基因表达模式有一定的保守性。在这三种植物子实体发育过程中上调的83个基因中，编码在囊泡运输、膜系统或跨膜运输中具有预测作用的蛋白质的基因，以及编码在染色质组织或基因表达调控中具有预测作用的蛋白质的基因被强烈表达。在大孢子葡萄子实体发育过程中保守表达的4个基因在功能上被表征为缺失突变体。因此，鉴定出三个新的发育基因。在项目的第二阶段，我们将重点研究编码染色质修饰因子和转录因子的基因，以及它们在染色质结构、组蛋白修饰和基因表达的发育调控中的作用。初步数据表明，大孢子葡萄球菌组蛋白伴侣突变体asf1的组蛋白修饰可能与野生型不同，该突变体在早期子实体发育过程中存在阻滞。我们将在全基因组水平上使用ChIP-seq分析大孢子孢子菌野生型和发育突变体的组蛋白修饰。在发育过程中发生变化的修饰也将在不同的发育阶段对黑曲霉和黑曲霉进行分析。此外，我们将利用Hi-C分析不同发育阶段的染色质结构，并将分析结果与转录组数据和组蛋白修饰结果结合起来，建立真菌发育过程中染色质和基因表达变化的综合图谱。此外，我们将分析染色质修饰蛋白之间的蛋白质-蛋白质相互作用，确定这些相互作用所需的蛋白质结构域和蛋白质的发育功能，并根据现有的和新的基因表达数据的结果表征其他假定的发育基因。

This project aims at identifying molecular mechanisms that regulate fruiting body development in filamentous ascomycetes. During the first phase of the project, we performed comparative transcriptomics analyses of the three ascomycetes Ascodesmis nigricans, Pyronema confluens, and Sordaria macrospora to identify evolutionary conserved patterns of gene expression. The results indicate that gene expression patterns in fruiting bodies are to some degree conserved and are quite distinct from gene expression patterns in vegetative mycelium. Among 83 genes that are upregulated in developing fruiting bodies of all three species, genes encoding proteins with predicted roles in vesicle transport, the endomembrane system, or transport across membranes, and genes encoding proteins with predicted roles in chromatin organization or the regulation of gene expression are strongly represented. Four genes with conserved expression during fruiting body development were functionally characterized by generating deletion mutants in S. macrospora. Thereby, three novel developmental genes were identified. In the proposed second phase of the project, we will focus on genes encoding chromatin modifiers and transcription factors, and their role in developmental regulation of chromatin structure, histone modifications and gene expression. Preliminary data indicate that histone modifications might be different from the wild type in the S. macrospora histone chaperone mutant asf1, which has a block during early fruiting body development. We will analyze histone modifications in the S. macrospora wild type and developmental mutants at a genome-wide level using ChIP-seq. Modifications that change during development will also be analyzed in different developmental stages in A. nigricans and P. confluens. Furthermore, we will analyze the chromatin structure at different developmental stages using Hi-C, and analyze the results together with transcriptome data and results on histone modifications to establish an integrated picture of chromatin and gene expression changes during fungal development. In addition, we will analyze protein-protein interactions between chromatin modifier proteins, identify protein domains required for these interactions and for the developmental functions of the proteins, and characterize additional putative developmental genes based on the results of available and novel gene expression data.