Molecular Biology

Molecular biology is not only a fascinating subject in its own right, but it also provides other biological disciplines (cell biology, genetics, physiology, etc.) with fantastic tools for modifying and quantifying genes and their products.

The EU is deepening its understanding of the mechanisms involved in the organization, maintenance, replication, and expression (transcription, post-transcriptional modifications, translation) of eukaryotic genomes.

In particular, we will explore the properties of information-carrying macromolecules (DNA, RNA, proteins) and how interactions between them explain the functioning of eukaryotic cells and their adaptation to the environment and the development of organisms.

At the same time, the main techniques used to monitor or modify gene expression, or to study the mechanisms of this expression, will be presented in lectures and explored in greater depth in tutorials through the analysis of results.

Thus, the tutorials address these topics in the form of (1) exercises that allow students to test their understanding of the knowledge described above, and (2) experiments taken from scientific articles for analysis. In this way, the fundamentals of scientific reasoning and critical analysis of results will be acquired and/or further developed.

Knowledge:

- Understanding the exceptions and subtleties of genetic information flow, the central "dogma" in eukaryotes

- Understand the structure of eukaryotic genomes, their coding and non-coding components, and how their sequence provides fossil evidence of past molecular events (viral insertions, duplications, gene families, etc.).

- Understand the basic principles of isolation techniques (cloning vs. polony) and DNA sequencing (Sanger, pyrophosphate, nanopore).

- Understand the different levels of eukaryotic chromatin compaction and their impact on gene expression.

- Understand the mechanisms and minimal machinery involved in eukaryotic genome replication.

- Understanding the challenges of accurately replicating, at each S phase, an extensive, fragmented, linear genome, and what happens when these regulations fail.

- Know the main pathways of eukaryotic DNA repair, what damage they repair, what the cost is (fidelity, etc.), and what happens when they fail.

- Understand the mechanisms and actors involved in transcription (initiation, elongation, termination) in eukaryotes.

- Understand the steps and actors involved in the activation of a class I, II, or III eukaryotic promoter.

- Know the families of general and specific eukaryotic transcription factors and their modes of action, as well as the concepts of coactivators/corepressors and their impact on chromatin remodeling.

- Understand the mechanisms and actors involved in post-transcriptional modifications in eukaryotes, as well as regulatory RNAs.

- Understanding the mechanisms and actors involved in translation in eukaryotes

- Understand and explain how all stages of eukaryotic gene expression enable precise quantitative and qualitative measurement of the response to a stimulus.

Expertise:

- Understand immunoprecipitation-based techniques, how they account for protein/protein and protein/nucleic acid interactions, and know how to analyze the results.

- Know how to recognize and read sequencing results (Sanger, pyrophosphate, nanopore).

- Calculate the length of a nucleic acid molecule of n nucleotides; use it to calculate DNA compaction rates, replication speeds, etc.

- Know how to interpret techniques for studying replication dynamics on individual DNA strands or cell populations.

- Know how to interpret simple experiments involving chromatin digestion by nucleases and understand how this allows the state of chromatin and the activation status of genes to be determined.

- Know how to interpret techniques for studying transcription regulation (promoter mutagenesis, reporter genes, G-less cassette, etc.)

- Know how to choose the electrophoresis technique to use for each type of macromolecule and analyze complex results.

- Know how to interpret in vitro splicing experiments and other experiments monitoring post-transcriptional modifications and their regulation.

- Know how to interpret experiments aimed at monitoring translation and its regulations.

- Know how to describe and interpret a figure: understand the purpose of the experiment and the technique used, identify the variables, understand the purpose of a positive control and a negative control, follow the scientific logic (description of the results followed by their interpretation).

Basic knowledge of nucleic acid and protein biochemistry, molecular biology, and genetics.