Syllabus
Preliminary schedule:
Block 1: Introduction to concepts and molecular mechanisms of epigenetics.
· Week 1 (6/10). General introduction to the content & learning outcomes of the course, practical information. [CLP]
· Week 2 (13/10). Lecture: Basic concept of epigenetics (genetic and epigenetic information; chromatin structure; main components of epigenetic information (introduction): histones, DNA methylation; basic principles of introducing (targeting) and erasing epigenetic information, mitotic inheritance). [LF].
· Week 3 (20/10). Lecture: Histone PT modifications (enzymes; interpretation – interactions; basic functions) [LF]
· Week 4 (27/10). Lecture: DNA methylation (enzymes - sequence contexts; RNA-directed DNA methylation; interpretation, basic functions) [LF].
· Week 4 (3/11). Recap on epigenetic mechanisms: Group work, discussion, presentations [CLP] + [IS].
· Week 5 (10/11). Lecture: Methodologies to study epigenetics/epigenomics (methylation analysis by restriction, methylation analysis by bisulfite conversion; ChIP; dCAS9-ChIP/MS) [LF].
Block 2: biological roles of epigenetic mechanisms
· Week 6 (17/11). Lecture: Epigenetics, stress response, priming [CLP].
· Week 7 (25/11). Lecture: Epigenetics and sexual reproduction [CLP].
Block 3: plant epigenetics and evolution
· Week 8 (1/12). Lecture: Evolutionary perspectives I. Epigenetics and natural variation [IS] + [CLP].
· Week 9 (8/12). Lecture: Evolutionary perspectives II. Transgenerational memory: meiotic heritability vs clonal transmission. Group work [CLP] + [IS].
· Week 10 (15/12). Lecture: Evolutionary perspectives III. Meiotic heritability: how good is the evidence. Essay feedback and presentations [CLP]. 12th of January 2023 (date to be confirmed): “Miniconference” day with 2-3 external experts: o Histone modifications: role in plant development [IM] o Epigenetics in evolution [CB] o Stress and breeding applications [SM]
Program of practical classes (16th-20th Jan; lab in Viničná 5, Prague 2) [VC] + [IS] + [CLP]:
· Searching for local histone modifications: Chromatin immunoprecipitation (ChIP), ChIP-PCR.
· Searching for DNA methylation silencing of a specific gene: Microscopy observation of reporter gene silencing, bisulfite conversion (BS) of DNA, BS-PCR, Sanger sequencing.
· Profiling epigenetic marks across the genome: Epigenomics: BS-Seq analysis, ChIP-Seq analysis.
Annotation
Content:
After the major scientific advances in epigenetics during the last decade, it is now clear that epigenetic mechanisms play an important role in gene regulation, genome integrity, phenotypic plasticity, reproduction, and even evolution with the stable transmission of certain epigenetic marks over generations. This role seems even exacerbated in plants, sessile organisms that cannot escape environmental changes and stresses, and therefore evolved molecular mechanisms to cope with such constraints. The aim of this course is to deliver the current knowledge on plant epigenetics, its role in gene regulation, transposable elements silencing, stress response and its stable transmission through mitosis and even meiosis. It will involve theoretical lectures by internal and external experts. The practical classes will be based on research cases and will include biochemistry, molecular biology and bioinformatics.