Wintersemester 2014-2015

Principles of Epigenetics and Epigenomics

Examen: Tuesday 17.02.2015, 2:30pm, Room 0.33, Building A2.4
Re-Exam: Tuesday, 21.04.2015 6:00-7:30pm, Room 0.33, Building A2.4

The lectures provide an overview of epigenetic concepts and their relevance for human biology. Following an introduction into basic mechanisms and enzymologies of epigenetic control we will discus the developmental aspects of epigenetic modifications, particularly their importance for cell fate maintenance and cell function. Following a summary of disease related aspects we will briefly discus modern epigenomic mapping technologies and basic principles of data retrieval and interpretation.

Audience: Master Students (e.g. bioinformatics, biotechnology, biophysics and pharmacy) with basic knowledge in molecular genetics

Lecturers:
Jörn Walter, Pavlo Lutsik, Karl Nordström, Martin Simon

Venue: Seminar Room 0.33, Building A2.4 (Genetics)
Time: Tuesday 2:30 pm

Results Exam

Topics:

L1: Jörn Walter 28.10.2014
Introduction and overview
Definition and scope of epigenetics in developmental biology, genetics and molecular cell biology. Summary and short introduction into basic epigenetic concepts and mechanisms of inheritance.

pdf Lecture 1

L2: Jörn Walter 04.11.2014
Chromatin mechanisms
Bascis of chromatin: Dynamic structures in the nucleus, Discrimination of Hetero- and Euchromatin, Composition and function and dynamics of the nucleosome. Molecular control of chromatin-modifications
Description of histone modifying and demodifying enzymes (Histone methyltransferases HMTs, Histone demethylases, Histone Acetytransferases and Deacetylases).


pdf Lecture 2

L3: Jörn Walter 11.11.2014
Introduction into histone variants and histone modification types. Introduction into basic reaction mechanisms: readers, writers and erasers of histone modifications. Models of epigenetic inheritance of histone modifications.Methods to study chromatin conformations.
Methods to identify and locate chromatin modifications (ChIP, IF, MassSpec)
Distribution and local control by chromatin modifications: Transcription, Replication, Repair and Recombination.

pdf Lecture 3

L4: Jörn Walter 25.11.2014
Molecular control of DNA-methylation
Description of various types of DNA-modifications in bacteria, plants, animals and the human. Control of DNA-methylation by DNA-methyltransferases: Mechanisms of estabilishment, maintenance and (passive and active) erasure.
Distribution and role of Tet oxigenases for DNA-methylation function and stability.
Distribution of DNA-methylation in the human genome. The role of DNA-methylation in epigenetic control of transcription – interplay with chromatin modifcations. Methods to identify and locate DNA-methylation. Dynamics of DNA-methylation in development and disease.

pdf Lecture 4

L5: Martin Simon 09.12.2014
RNAi interference and RNA-induced epigenetic modifications
Basic mechanisms: enzymes and reactions; definition of small RNA classes,
link to epigenetic control (Transcriptional and posttranscriptional control); the role of small RNAs in Paramecium as a model system.

pdf Lecture 5

L6: Jörn Walter 16.12.2015
Mechanisms of epigenetic inheritance
Epigenetic control of dosage compensation: X-chromosome inactivation and genomic imprinting as classical examples. Epigenetic changes and human imprinting syndromes. Inheritance of epigenetic states across generations.

pdf Lecture 6

L7: Konstantin Lepikhov. 13.01.2015
Epigenetic reprogramming in development and in cultivated stem cells
Mechanisms of reprogramming in the zygote and germ cells, Epigenetic inheritance; Epigenetics of iPS and cloning

pdf Lecture 7

L8: Jörn Walter 20.01.2015
Epigenome Technologies
Priniciples and experimental methods for genome wide methylation analysis (WGBS, RRBS, Tab-Seq, Cap-Seq), Chromatin modification analysis (ChIP-Seq) and analysis of open chromatin, ATAC, DNAseI, NOMe-Seq. Introduction into chromatin segmentation and ENCODE classifications. Future perspectives of chromatin 3D analysis (3C, 4C and Hi-C). Epigenomics data and functional genome interpretation. Description of the goals of the international human epigenome consortium IHEC.

pdf Lecture 8

L 9: Karl Nordström/Pavlo Lutsik/Abdulrahman Sahlab 27.01.2015
Interpretation of epigenome data:
Description of primary and secondary data analysis to map and annotate epigenetic modification and to locate their association with regulatory/functional elements. Formats and QC for data deposition. Description of major data recources (Repositories and databases). Explanaition of a few basic interpretation tools such as RnBeads (DNA-Methylation data) & MACS2 (ChIP data).

pdf Lecture 9

L10: Jörn Walter 03.02.2015
Epigenetics of cancer: diagnostics and therapies
Contribution of genetic and epigenetic alterations to cellular dysfunction in cancer, basic concepts, examples of deregulation through changes in DNA-methylation
What defines a good molecular marker? From marker development to application; Epigenetic drugs and therapies.

pdf Lecture 10
Test/Examen: Tuesday 17.02.2015, 2:30pm, Room 0.33, Building A2.4
Re-Exam: Tuesday, 21.04.2015 6:00-7:30pm, Room 0.33, Building A2.4