Learning outcomes

To be able to discuss scientific outcomes in the fields of environmental and evolutionary proteomics and epigenetics. To be able to criticize a scientific article in this field and to setup an experimental plan. To learn the main techniques to study a proteome and a methylome. To be able to analyze data from a bisulfite sequencing experiment.

Goals

Proteomics and epigenetics are currently commonly used in the field of ecology and evolution. It requires specific knowledge about the scientific questions and the techniques. The main goal is to discuss with students the scientific questions that can be tackled with proteomic and epigenetic tools. One of the main question is the role of epigenetic in adaptation and evolution of organisms and it splace in the evolutionary theories.  

Content

- Proteomics: questions and techniques

- Epigenetics: questions and techniques (DNA methylation)

- Practical: DNA methylation study using bisulfite sequencing

- Data analysis: workshop of bioinformatics to analyse data from a bisulfite sequencing experiment

Table of contents

Partim Proteomics: 12h

Definitions and history (1h)
2D SDS-PAGE (3h)
Principles of mass spectrometry : MS and MS/MS (2h)
Gel-free quantitative proteomics (2h)
Visit of the mass spectrometry platform at UNamur (2h)
Exercise : analysis of a dataset from quantitative proteomics (using Scaffold, PEAKS, Qseq, Skyline,...) (3h)
Analysis of 2 articles in environmental proteomics (1 2D gels ; 1 gel-free) (2h)

Partim Epigenetics: 18h + 18h

Prerequisites (Q/A ; main epigenetic mechanisms) : 1h

book: Introducing Epigenetics: A Graphic Guide (Ennis and Pugh 2016) : https://www.amazon.fr/Introducing-Epigenetics-Graphic-Cath- Ennis/dp/1848318626/ref=sr_1_1?ie=UTF8&qid=1542012634&sr=8- 1&keywords=introducing+epigenetics

Environmental epigenetics : 7h

The unified theory of evolution (+ discussion)
History of epidemiological studies in human populations Process of adaptation/evolution and its limitations:

link environment/epigenome
link epigenome/phenotype
link phenotype/fitness
transgenerational epigenetic inheritance
persistence of epigenetic marks
Population epigenetics and natural epigenetic variability (including clonal species)

The Weissman barrier

The DNA methylation reprogramming and the concept of critical windows How epigenetics can create phenotypic variability ?

Facilitated mutations/cryptic genetic variation
Epimutations and stochasticity > bet-hedging and epigenetics Epigenetic buffering

Epigenetics and diseases : an environmental origin of diseases : 4h (with Aniruddha Chatterjee)

The concept of maladaptive epimutations/epigenetic trap Developmental origin of Health and Diseases (DOHaD) Epigenetic and cancer
Epigenetic and ageing

Epigenetic and neurodegenerative diseases

Epigenetic approaches : 6h (with Aniruddha Chatterjee)

Histones
ncRNA
DNA methylation:

Introduction to DNA methylation techniques and biological perspectives (Genome-wide to target genes)
Pyrosequencing - two applications : LUMA and gene-specific DNAme (FS) Library preparation for RRBS, contrast with WGBS, CpG and non-

CpG, Looking at bisulfite library signatures from FastQC examples
New Trends in methylation: Single cell biology. Integration of methylation with

other omics.

Practical part : (15h)

TP pyrosequencing (6h)
Bioinformatic workshop : analysis of a RRBS dataset (12h).

 

 

Assessment method

The evaluation is split in two parts: the proteomic part concists in a critical review of a scientific article ; the epigenetic part concists in a written exam with open questions, as well as a short report on the bioinformatic workshop.

Language of instruction

Anglais