Wintersemester 2016-2017

Principles of Epigenetics and Epigenomics

Lecturers:
Jörn Walter, Abdulrahman Salhab, Karl Nordström, Martin Simon

Venue: Seminar Room 0.33, Building A2.4 (Dpt. of Epigenetics)

Time: 8:30 - 10:00

Starting date: 21st November, daily until 1st December 2016
Last lecture: 17th January, 8:30 - 10:00

Because of technical issues the Re-Examen had to be re-scheduled to May 11th, 5pm in room 0.33, building A2.4 .

Note that this PDF (new) contains the correct grades - the previous included some mistakes.
pdf Results 1. Examen new


Registration for the re-examen via the LSF/HISPOS is only necessary for those who have not been registered before.

pdf Results Re-Examen


pdf Overview


pdf introduction and links

pdf Lecture 1 - Introduction

pdf Lecture 2 - Chromatin

pdf Lecture 3 - DNA-methylation

pdf Lecture 4 - RNA

pdf Lecture 5 - Epigenetics & Cancer

pdf Lecture 6 - Pluripotency

pdf Lecture 7 - Epigenomics

pdf Lecture 8 - Summary


Suggested textbooks for Epigenetics:

"Epigenetics", by David Allis, Marie-Laure Caparros, Thomas Jenuwein, Danny Reinberg, Monika Lachlan, 2015, 984 pages, ISBN 978-1-936113-59-0

"Molekulare Genetik" (mit einem Kapitel über Epigenetik), Hrsg.: Alfred Nordheim, Rolf Knippers, 10. Auflage 2015, 568 S. , 620 Abb. , ISBN: 9783134770100 (only in german available)

Additional introductory literature for cancer epigenetics:
"Cancer Genetics and Epigenetics: Two Sides of the Same Coin?" Review by You & Jones http://dx.doi.org/10.1016/j.ccr.2012.06.008


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 finally the basic principles of epigenetic data production, data managment and data interpretation.

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

L1: Introduction and basics of chromatin modifications 21.11.2016 (Walter)
Definition of epigenetics. Introduction into basic epigenetic concepts and mechanisms of inheritance. Role in development and molecular cell biology. Principles of chromatin organisation: nucleosomes, histones, histone variants, histone modifications, higher order structure, chromatin dynamics in the nucleus, methods to study chromatin structure. Basic principles of epigenetic modifications in chromatin: Introduction into key reaction mechanisms: readers, writers and erasers. Short description of key histone modifications and their role, models for inheritance of histone modifications.

L2: Histone-modifications 22.11.2016 (Walter)
Introduction of histone „modifying“ and „demodifying“ enzymes (Histone methyltransferases, demethylases, acetytransferases and deacetylases). Methods to identify and locate histone modifications in chromatin (ChIP, IF, MassSpec). Processes controlled by chromatin modifications: Transcription, Replication, Repair and Recombination.

L3: DNA-methylation 23.11.2016 (Walter)
Short description of various types of DNA-modifications. Enzymtic control of cytosine specific DNA-methylation: Mechanisms of establishment, maintenance and (passive and active) erasure. Oxidized forms of DNA-methylation, role of Tet enzymes. Bisulfite based methods to detect DNA-methylation in the genome. Role of DNA-methylation in gene regulation and genome stability. Dynamics of DNA-methylation in development and disease.

L4: RNA-induced epigenetic effects 24.11.2016 (Simon)
Basic mechanisms of RNAi: 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. The epigenetic role of long non-coding RNAs.

L5: Epigenetics and cancer 25.11.2016 (Walter)
Contribution of genetic and epigenetic dysregulation to cellular dysfunction in cancer, basic concepts for epigenetic contributions in cancer development,
The use of epigenetic signatures for cancer diagnostic. Epigenetic mechanisms as targets for new cancer therapies.

L6: Epigenetics and development 28.11.2016 (Lepikhov)
From the zygote to adult cells. Epigenetic control of X-chromosome inactivation and genomic imprinting. Epigenetic changes and human imprinting syndromes. Inheritance of epigenetic states across generations.

L7: Epigenetics and cancer 29.11.2016 (Walter)
Contribution of genetic and epigenetic dysregulation to cellular dysfunction in cancer, basic concepts for epigenetic contributions in cancer development,
The use of epigenetic signatures for cancer diagnostic. Epigenetic mechanisms as targets for new cancer therapies.

L8: Epigenomics part I 30.11.2016 (Walter)
Definition, main questions and basic concepts of Epigenomics. Introduction in experimental methods to produce epigenomic data: ChIP-Seq, WGB-Seq,(RRB-Seq), ATAC/NOMe-Seq, Hi-C/3C, RNA-Seq.

L9: Epigenomics part II 01.12.2016 (Salhab, Nordström)
Handling of data generated in epigenomics: Procedures for raw data processing, quality control and mapping. Methods for calling and quantification of epigenetic modifications. Methods for data visualisation. Data storage and data retrival. Processes and programs used for low and high level analysis of epigenomic data.

L10: Summary and Discussion (Walter) date to be determined