Chromatin composition
Abstract
Wider research context: Our group is interested in understanding how fungal transcription factors function in the context of chromatin. This structure is particularly relevant for synchronized expression of physically linked gene clusters. We have studied the Aspergillus nitrate cluster (primary metabolism, PM) and also work on chromatin-level regulation of fungal secondary metabolite gene clusters (SMGCs). It is now well established in many fungi that SMGCs are silenced by heterochromatin formation and activated by wide-domain and pathway-specific regulators. The interplay between those processes is largely unknown. Hypotheses, research questions and objectives: The activation process must counteract heterochromatic silencing and we know that this requires factors such as Velvet/LaeA or histone demethylases (KdmB) but how the process works mechanistically, is poorly understood. We would like to add mechanistic information on the silencing and activation process of SMGCs and want to understand how co-regulation of these “toxin-islands” is insulated from surrounding genomic regions. Experimental approaches and methods: we will use Aspergillus nidulans as model and first plan to map the positions of the main silencing regulator HepA and the activators LaeA and KdmB by ChIP-seq. We then will apply Cas-ID, a locus-specific chromatin pull-down technique based on sgRNA-guided enzymatically disabled dCas9 fused to a biotinylating domain, to study the local proteome composition at the regulator target sites in silent and active SMGCs. We will compare these proteomes to genomic regions immediately outside with the aim to identify and then characterize factors that are specific for the chromatin of co-regulated SMGCs. Originality and innovation: Cas-ID has not yet been applied in fungi and we expect that this new technique will provide completely novel insights on chromatin composition, associated factors and their post-translational modifications (PTMs) in and around SMGCs. We expect to identify new chromatin-related SMGC regulators for repression and activation and get some novel information how they functionally or physically interact. All this together will provide a more detailed mechanistic view on chromatin-level regulation of SMGCs and their insulation from the surrounding genomic regions and will also provide possibilities for epigenetic engineering to activate orphan SMGCs and find novel metabolites. Involved scientists: Joseph Strauss´ lab has pioneered studies in chromatin-level regulation of fungal gene clusters in primary and secondary metabolism. They are publishing regularly on this topic since many years as leading lab or in collaboration with other groups in high-ranking journals. There is a long-standing and successful cooperation with the proteomics group of Friedrich Altmann who will be involved mainly in the Cas-ID part of the project and characterization of protein PTMs.
chromatin fungi bioactive metabolites
Publikationen
Project staff
Joseph Strauss
Univ.Prof. Mag.rer.nat. Dr.rer.nat. Joseph Strauss
joseph.strauss@boku.ac.at
Tel: +43 1 47654-94420
Project Leader
01.11.2019 - 10.04.2024
Paulina Arellano Perdomo
Paulina Arellano Perdomo B.Sc.
paulina.arellano-perdomo@boku.ac.at
Project Staff
01.10.2023 - 31.03.2024
Simone Bachleitner
Dipl.-Ing. Dr. Simone Bachleitner B.Sc.
simone.bachleitner@boku.ac.at
Tel: +43 1 47654-79038, 79045
Project Staff
01.11.2019 - 30.06.2021
Harald Berger
Dipl.-Ing. Dr. Harald Berger
harald.berger@boku.ac.at
Tel: +43 1 47654-94492, 94493
Project Staff
01.01.2021 - 01.01.2024
Dominik Dietrich
Dominik Dietrich
dominik.dietrich@students.boku.ac.at
Project Staff
18.09.2023 - 10.04.2024
Dominik Niederdöckl-Loibl
Dominik Niederdöckl-Loibl B.Sc.
dominik.loibl@boku.ac.at
Project Staff
01.02.2023 - 10.04.2024
Laura Scherzer
Laura Scherzer
laura.scherzer@students.boku.ac.at
Project Staff
01.10.2023 - 31.12.2023
Ayse Gizem Serin
Ayse Gizem Serin B.Sc.
ase.serin@students.boku.ac.at
Project Staff
01.11.2022 - 30.06.2023
Thomas Svoboda
DDipl.Ing. Dr.nat.techn. Thomas Svoboda MSc.
thomas.svoboda@boku.ac.at
Tel: +43 1 47654-94495
Project Staff
01.01.2022 - 17.10.2023