Plant Epigenetics - MB120P172

• Anglický název: Plant Epigenetics
• Český název: Epigenetika rostlin
• Zajišťuje: Katedra botaniky (31-120)
• Fakulta: Přírodovědecká fakulta
• Platnost: od 2022
• Semestr: zimní
• E-Kredity: 4
• Způsob provedení zkoušky: zimní s.:
• Rozsah, examinace: zimní s.:2/4, Z+Zk [HT]
• Počet míst: 20
• Minimální obsazenost: 5
• 4EU+: ne
• Virtuální mobilita / počet míst pro virtuální mobilitu: ne
• Stav předmětu: vyučován
• Jazyk výuky: angličtina
• Další informace: https://lab-allience.natur.cuni.cz/plantreproevo/teaching/epigenetics
• Poznámka: povolen pro zápis po webu
• Garant: doc. Clément Lafon Placette, Dr.
• Vyučující: Mgr. Vojtěch Čermák, Ph.D.; RNDr. Lukáš Fischer, Ph.D.; doc. Clément Lafon Placette, Dr.; Iris Sammarco, Ph.D.

Anotace

čeština

Tento kurz se bude konat v angličtině. Po hlavních vědeckých pokrokech v epigenetice během posledního desetiletí je nyní jasné, že epigenetika
mechanismy hrají důležitou roli v regulaci genů, integritě genomu, fenotypové plasticitě, reprodukci a
rovnoměrný vývoj se stabilním přenosem určitých epigenetických značek po generace. Tato role se zdá být sudá
zhoršuje se v rostlinách, přisedlých organismech, které nemohou uniknout změnám prostředí a stresům, a proto
vyvinuly molekulární mechanismy, aby se s těmito omezeními vyrovnaly. Cílem tohoto kurzu je poskytnout aktuální
- znalost epigenetiky rostlin, její role v regulaci genů, umlčení transponovatelných prvků, stresová reakce a
jeho stabilní přenos mitózou a dokonce meiozou. Bude zahrnovat teoretické přednášky interní a externí
Odborníci. Praktické kurzy budou založeny na výzkumných případech a budou zahrnovat biochemii, molekulární biologii
a bioinformatika.

Poslední úprava: Lafon Placette Clément, doc., Dr. (29.10.2019)

angličtina

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.

Poslední úprava: Štefánek Michal, Mgr. (22.05.2019)

Literatura

čeština

Lämke, J., and Bäurle, I. (2017). Epigenetic and chromatin-based mechanisms in environmental stress adaptation and stress memory in plants. Genome Biol 18:124. doi 10.1186/s13059-017-1263-6.

Matzke MA, Kanno T, Matzke AJM. (2015). RNA-Directed DNA Methylation: The Evolution of a Complex Epigenetic Pathway in Flowering Plants. Annual Review of Plant Biology 66: 243–267.

Ojolo, S.P., Cao, S., Priyadarshani, S.V.G.N., Li, W., Yan, M., Aslam, M., Zhao, H., and Qin, Y. (2018). Regulation of Plant Growth and Development: A Review From a Chromatin Remodeling Perspective. Frontiers in Plant Science 9:1232. doi: 10.3389/fpls.2018.01232.

Wong, M.M., Chong, G.L., and Verslues, P.E. (2017). Epigenetics and RNA Processing: Connections to Drought, Salt, and ABA? In Plant Stress Tolerance: Methods and Protocols, R. Sunkar, ed. (New York, NY: Springer New York), pp. 3–21.

Poslední úprava: Lafon Placette Clément, doc., Dr. (29.10.2019)

Požadavky ke zkoušce

čeština

· For the theoretical part, the written exam will consist of: 1/ Knowledge test at half semester (at the end of block 1), 2/ Writing a peer-evaluated essay at the end of the semester

· V praktické části si studenti procvičí psaní článku s přípravou laboratorní zprávy.

Poslední úprava: Lafon Placette Clément, doc., Dr. (04.10.2022)

angličtina

·         For the theoretical part, the written exam will consist of: 1/ Knowledge test at half semester (at the end of block 1), 2/ Writing a peer-evaluated essay at the end of the semester

                    

·         For the practical part, students will practice the writing of article with the preparation of a lab report.

Poslední úprava: Lafon Placette Clément, doc., Dr. (04.10.2022)

Sylabus

čeština

Předběžný harmonogram:

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].

 

12^th 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 (16^th-20^th 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.

 

Poslední úprava: Lafon Placette Clément, doc., Dr. (04.10.2022)

angličtina

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].

 

12^th 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 (16^th-20^th 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.

Poslední úprava: Lafon Placette Clément, doc., Dr. (04.10.2022)