Insights into functional genomics: Exploring Phenotype Evolution in Non-Model Organisms

One key question in evolutionary biology is how new phenotypes emerge in populations. Recent studies show that regulatory mutations very often contribute to new phenotypes by modulating gene expression while carrying lower pleiotropic effects. However, the molecular and cellular mechanisms through which regulatory mutations impact phenotype evolution remain widely unknown. Advances in molecular and cellular methodologies now allow us to explore how these mutations affect phenotype evolution in non-model organisms. This course will delve into functional genomics, and how using multiple sources of data can be used to infer how such mutations lead to the emergence of new, adaptive phenotypes.

Course Introduction

An overview of phenotype evolution - Why is regulatory variation important?

Different mechanisms of regulatory evolution (e.g. cis/trans).

An introduction to functional genomics.

Exploring genome features and what they do (e.g., promoters, enhancers, UTRs).

The complex interactions that form regulatory networks.

Using chromatin accessibility to identify regulatory elements.

Histone modifications as markers for gene expression (e.g., ChIP-seq).

Impact of Nucleotide Modifications (e.g., DNA methylation, RNA acetylation) in gene expression.

Hands-on data analysis.

Leveraging 3D genomic techniques (e.g., Hi-C) to identify promoter-enhancer interactions.

One genome, multiple tissues – exploring how single-cell information can inform on tissue/cell-specific processes.

Hands-on data analysis.

Using machine learning to annotate some regulatory features.

A quick overview of other sources of information that can be used (e.g., protein-protein interactions, in-situs).

Preparing presentations for general discussion.

Presentations by the participants.

5 days - 32 hours - Schedule: 09:30 - 13:00 & 14:00 - 17:30 (Friday only in the morning)

Coordination

Paulo Pereira | BIOPOLIS-CIBIO

Miguel Carneiro | BIOPOLIS-CIBIO

Instructors

Paulo Pereira | BIOPOLIS-CIBIO

Roberto Arbore | BIOPOLIS-CIBIO

Soraia Barbosa | BIOPOLIS-CIBIO

Yohei Ogawa | National Institute of Genetics, Mishima, Japan

The topics covered in this course can be often complex and require understanding of fundamental molecular and cellular processes to fully comprehend them. Therefore, it is expected that the participants have a strong foundation in molecular and cellular biology, including topics on gene regulation, population genetics and evolutionary biology. Furthermore, due to the necessity of using both command-line based software and statistical frameworks like R, it is expected that the participants will have sufficient experience in both. For BIODIV students, it is required to have attended the "Introduction to R” and the "Linux and HPC cluster” courses. Participants will need to use their personal laptops for this course and to install specific software. The respective instructions will be sent by email one week prior to the course's start.

The course will be open to a maximum number of 20 participants.

75% of available student slots are reserved for BIODIV students.

Priority will be given to:

• 1st year and other PhD students attending the BIODIV Doctoral Program;

• PhD students attending other courses;

• Other post-graduate students and researchers.

(A minimum number of participants is required for the course to take place)

Official applications for this course will be managed directly by FCUP. Detailed information will be available soon.

If you would like to be notified as soon as registrations open, please let us know by filling out our short form: Express Your Interest Here

⚠️ Please note: This form is not an official application. It simply allows us to keep you updated and helps us gauge the level of interest for each course.

No ECTS credits are awarded for attending the course. Participants receive a certificate of attendance without quantitative evaluation.

Education & Training Unit (Post graduation office)

+351 252 660 425