Project Details
Projekt
An integrative epigenomic approach to discover small RNA mediated regulatory programs in Paramecium tetraurelia
Subject Area
General Genetics and Functional Genome Biology
Term
from 2016 to 2021
Project identifier
Deutsche Forschungsgemeinschaft (DFG) - Project number 292631656
Recent advances in RNA Biology show that small RNA molecules control phenotypic variation at the epigenetic level either by post-transcriptional or transcriptional inactivation of gene expression. However, the ongoing work mostly focuses on individual loci and individual mechanisms rather than estimating the extent to which such mechanisms contribute to transcriptome dynamics, and as a consequence, to phenotypic plasticity or phenotypic robustness. The epigenetic model organism Paramecium allows us to study genome wide RNA and chromatin dynamics to get an insight into small RNA controlled short-term regulation of gene expression and long-term manifestation of gene expression patterns by epigenetic mechanisms. Recently, we described different RNA-mediated silencing pathways acting at different levels. Now, we will analyse genome wide small RNA/chromatin associations in different metabolic states dissecting post-transcriptional and transcriptional silencing pathways. This will be achieved by an integrative approach using bioinformatics to differentiate between newly identified siRNA clusters associated or not associated with heterochromatin formation, as well as biochemical analysis of siRNAs and dissection of their genetic requirements such as RNAi components involved in post-transcriptional or transcriptional silencing. Further, a new integrative analysis approach will be used to associate short RNA abundance and chromatin modifications with gene expression. We will model trans acting siRNA networks enabling coordinated activation and silencing of gene groups, as well as identification of trans acting RNAs derived from gene duplicates. As a consequence, we will not only be able to describe the extent of epigenetic pathways controlling gene expression and adaptation of this unicellular organism during vegetative growth, we will moreover analyse which of these epigenetic characters can be passed on to sexual progeny. This will be done by crosses of genetically identical but epigenetically different individuals and subsequent analysis of F1 clones. We will thus identify genetic requirements for epigenetic inheritance, which will allow for brand new conclusions on the possibilities for inheritance of gene expression: manifestation of positively selected gene expression patterns by small RNAs, which are mobile elements between generations, will be the key to understand short-time Lamarckian adaptation in contrast to long-term Darwinian evolution.
DFG Programme
Research Grants
