Transposable elements: from junk DNA toad to Prince Major Driver of biodiversity - MB120P186

• Title: Transposable elements: from junk DNA toad to Prince Major Driver of biodiversity
• Guaranteed by: Department of Botany (31-120)
• Faculty: Faculty of Science
• Actual: from 2023
• Semester: winter
• E-Credits: 6
• Examination process: winter s.:
• Hours per week, examination: winter s.:2/2, C+Ex [HT]
• Capacity: 20
• Min. number of students: 5
• 4EU+: no
• Virtual mobility / capacity: no
• State of the course: taught
• Language: English
• Note: enabled for web enrollment
• Guarantor: doc. Clément Lafon Placette, Dr.
• Teacher(s): doc. Clément Lafon Placette, Dr.
• Incompatibility : MB120P177

Annotation

Last update: Mgr. Michal Štefánek (24.05.2023)

This course will be held in English.
Transposable elements (TEs), since their discovery, have been considered either as useless pieces of DNA, as
selfish parasitic genes or as major elements driving biodiversity. The aim of this course is to bring a holistic
knowledge of TEs, from the molecular mechanisms underlying their function to their impact on populations and
species in eukaryotes. It will involve lectures gathering current research issues as well as practicals involving
modern tools used in current research.

Literature

Last update: doc. Clément Lafon Placette, Dr. (21.06.2023)

Bourque G, Burns KH, Gehring M, et al. Ten things you should know about transposable elements. Genome Biol. 2018;19:199.

Bousios A, Gaut BS. Mechanistic and evolutionary questions about epigenetic conflicts between transposable elements and their plant hosts. Curr Opin Plant Biol. 2016;30:123–133.

Cosby RL, Chang N-C, Feschotte C. Host–transposon interactions: conflict, cooperation, and cooption. Genes Dev. 2019;33:1098–1116.

Blumenstiel JP. Birth, school, work, death, and resurrection: the life stages and dynamics of transposable element proliferation. Genes (Basel). 2019;10:336.

Requirements to the exam

Last update: doc. Clément Lafon Placette, Dr. (21.06.2023)

The theory part will be assessed with a written essay.

The practical part exam will consist in lab reports.

Syllabus

Last update: doc. Clément Lafon Placette, Dr. (21.06.2023)

Preliminary schedule:

Block 1: molecular aspects and developmental roles of TEs

· Week 1. Lecture: Introduction [CLP].

· Week 2. Lecture: TE families, modes of actions and evolution [CLP].

· Week 3. Lecture: Epigenetic silencing of TEs by host genomes [LF].

· Week 4. Lecture: TEs and sexual reproduction [CLP].

· Week 5. Homework.

· Week 6. Knowledge consolidation. Presentations. Essay practice [CLP].


Block 2: evolutionary implications of TEs

· Week 7. Lecture: Natural selection and TEs [CLP].

· Week 8. Lecture: Stress impact on TE activity [CLP].

· Week 9. Lecture: Molecular domestication of TEs [RB].

· Week 10. Lecture: TEs and biodiversity [CLP].

· Week 11. Knowledge consolidation. Presentations. Essay practice [CLP].



Block 3: hands on TEs! (practical classes)

One week in January. Teachers: VC and CLP. Detailed program TBA.

· Day 1. Profiling the epigenetics of TEs 1.

· Day 2. Profiling the epigenetics of TEs 2.

· Day 3. Profiling the epigenetics of TEs 3.

· Day 4. Identify and annotate TEs in genomes with RepeatExplorer 1.

· Day 5. Identify and annotate TEs in genomes with RepeatExplorer 2.