Plant epigenetics

Introduction

Genetic information in a multicellular organism remains generally the same throughout ontogenesis irrespective of the surrounding conditions therefore the activity of individual parts of genomes must be carefully regulated. This is extremely important for plants as they tolerate an enormous amount of transposable elements (TE) inserted in between their genes and which number can be as high as 85% of the size of their genomes. Plants are also able to effectively cope with whole-genome duplications that are the ultimate drive of plant evolution. Plants have evolved a wide range of epigenetic mechanisms to mark chromatin at both DNA and histone levels to ensure a desirable management and activity of their genomes. These mechanisms are, furthermore, tightly interconnected which makes them even more effective. Histone marks are highly complex and involve a series of posttranslational modifications of histone ends as well as different representation of histone variations in nucleosomes. Unlike histones, DNA is marked predominantly by the only mark - cytosine methylation. Chromatin marks are often temporary or easily reversible but they can sometimes be very stable and also heritable into the next generation. De novo epigenetic marks are only established under reasonable circumstances and require a high specificity. Sequence-specific silencing of chromatin activity mediated by DNA methylation is controlled through small RNAs (sRNAs) in a process known as “RNA-directed DNA methylation” (RdDM). RdDM combines chromatin modifications with RNA interference (RNAi) that regulates gene expression through sRNAs derived from dsRNA precursors. sRNAs in a complex with Argonaute (AGO) allow sequence-specific silencing of gene expression at the posttranscriptional level (PTGS) and can also cause transcriptional silencing (TGS) when inducing methylation in a promoter area.

Main research topics:

Proteins of RdDM pathway are relatively well described in the literature but initial stages of this process, transitions from active to inactive stages of chromatin and reversibility of epigenetic changes remain poorly understood. Our model system based on inducible expression of constructs that serve as a source of sRNAs in highly homogeneous tobacco cell cultures BY-2 is a unique tool to study the dynamics of these processes in detail. Our major research questions are:

• what factors affect the establishment and stability of repressive chromatin marks;
• what is the relationship between posttranscriptional and transcriptional silencing;
• what is the dynamics of these processes;
• what are the roles and interactions of putative AGO-binding transcription factor SPT6-L.

For more information contact the head of the group Lukáš Fischer or visit us in our lab Viničná 5, 2nd floor, door 210 (at the end of the corridor).