Periodic Reporting for period 4 - PlasmoSilencing (Exoribonuclease-mediated degradation of nascent RNA in Malaria Parasites: A Novel Mechanism in Virulence Gene Silencing)
Berichtszeitraum: 2020-05-01 bis 2020-10-31
Taken together, our work has resulted in 17 publications with support of this grant and two manuscripts are in preparation that will be published in 2021. This includes work directly linked to the main objectives of PlasmoSilencing and work aimed to develop new methods to overcome technical hurdles in chromatin analysis and genome editing of P. falciparum. Due to space limits, only some of the achievements will be mentioned here. One highlight is that the exoribonuclease-controlled ncRNA gene family (called GC-rich element) acts in trans as an enhancer-like ncRNA in monoallelic expression of virulence genes. A second discovery shows, that a second type of 3’-5’ exoribonuclease (Dis3) controls mainly antisense RNA, that is an emerging regulator of gene expression in malaria parasites. A third highlight is the identification of mRNA adenosine methylation as a regulator of mRNA stability and translation in P. falciparum. One of the objectives, the role of RNase II transcript levels in virulence gene regulation, could not be completed, due to technical problems to establish a genetic system to dose the transcript levels of a given gene in P. falciparum.
Final conclusions: The initial project outlined for PlasmoSilencing has not been always had a linear evolution due to different technical challenges. At least two of the three aims have been moved forward and resulted in fundamental new insight into the exoribonuclease regulators of RNA (ncRNA and mRNA) degradation and RNA modifications (mainly m6A) that modulate the RNA. Technical challenges were often the motivation to overcome roadblocks for this pathogen, that is far from being a model system and difficult to manipulate. We developed dCas9 genome engineering tools to isolate locus specific chromatin components and to shut down multiple promoters from a gene family. Furthermore, we adapted for the first time a method, to identify RNA-binding proteins from native RNA-protein complexes using a method called ChIRP (chromatin isolation by RNA isolation). These methods put us in a unique situation to further explore the precise molecular events that involve ncRNA activity in virulence gene expression. In conclusion, PlasmoSilencing has had a huge impact in the field of exoribonuclease/ncRNA/mRNA biology of P. falciparum. It has helped to move this field to an unprecedented level of insight.
As a result of the high scientific output, one postdoc (S. Baumgarten) has further developed one emerging aspect of PlasmoSilencing and has obtained in 2020 an ERC Starting grant to explore as group leader at the Institut Pasteur the role of RNA modifications in P. falciparum. Another postdoc who has been hired to work on PlasmoSilencing, has obtained a staff position (Charge de Recherche) at the Institut Pasteur to build a new team on plasmodial chromatin biology (J. Bryant). In addition, two students financed by this project have obtained their PhD in 2019 and continue to work in the field of molecular parasitology (A. Barcons Simmons & E. Hammam). Last but not least, new grants have been obtained in 2020 on results obtained from PlasmoSilencing.