Séminaire de Bioinformatique et Biologie Computationnelle sur la thématique d’analyse de régulation transcriptionnelle par des méthodes statistiques. L’exposé sera suivi d’une pause café.
Laurent Bréhélin
LIRMM, Univ. Montpellier, CNRS
Probing transcriptional regulation with statistical models
Lieu : Salle de Conférences du Centre de Génomique Fonctionnelle
Abstract :
Gene expression in Eukaryotes is orchestrated by distinct regulatory mechanisms to ensure a wide variety of cell types and functions. While these regulations include actors as different as transcription factors (TFs), histone marks, or chromatin structure, the DNA sequence itself is invariably involved in the different processes. Hence, a key challenge in regulatory genomics is to decipher the links between gene regulation and DNA sequence. In this talk, I will present two attempts to this problem based on statistical machine learning and feature selection approaches.
In the first work [1], we probe sequence-level instructions for gene expression and develop a method to explain mRNA levels based solely on nucleotide features. Our method positions nucleotide composition as a critical component of gene expression. In the second one [2], we study TF combinations involved in the binding of a target TF in a particular cell type. We show that TF combinations are different between promoters and enhancers, but similar for promoters of mRNAs, lncRNAs and pri-miRNAs.
[1] https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005921
[2] https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-5408-0