Investigating the evolution of repressive gene regulatory elements in mammals

• Applicant: Dr. Lucas Esteban Wange
• Subject Area: Evolutionary Cell and Developmental Biology (Zoology) ; General Genetics and Functional Genome Biology ; Evolution, Anthropology
• Term: since 2024
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 538828098

Gene regulation has been acknowledged as the main mechanisms leading to the vast diversity of tissues, cell types and developmental transitions that arise from one genome sequence. Since the sequencing of the human genome a main focus of genome biology as well as developmental biology and biomedicine has been to understand the rules of gene regulation. A first important step in this endeavor is to identify regulatory elements and associate them to the genes they regulate. While this has been done extensively for promoters, enhancers and insulators using a combination of different epigenetic marks i.e. histone modifications, DNA methylation or transcription factor binding in the case of insulators, silencers have been more difficult to identify genome wide. Recent studies have tried to overcome this limitation by combining different types of information and predicting silencers using machine learning approaches. While these studies have shown potential ways to identify silencers, an important piece of information is still lacking. Evolutionary information, particularly sequence conservation, has been used to understand gene regulation early on. However, due to their challenging identification, silencer evolution has not been looked at systematically yet. In this project I aim to identify silencers in primates and mammals to measure their evolutionary turnover and identify and functionally validate lineage specific gains or losses in vitro. In a first step I will use an already existing dataset encompassing five primate species including humans, generated by the host laboratory. Using this dataset I will employ a strategy to identify silencers across species based on two previous studies in humans. This will generate the first catalog of candidate silencer elements in non-human primates and will enable us to identify human specific regulatory elements. Secondly, I will select human-specific, great ape-specific and primate-conserved candidate silencer elements to functionally validate them in a silencer massively parallel reporter assay (MPRA). After confirming their ability to repress gene expression I will compare their activity between species. In the third aim I will generate a comprehensive regulatory profiling of 24 placental mammals using primary fibroblast cell lines to study the evolution of silencers in a broad phylogenetic sample. Using a combination of whole genome sequencing, whole genome methylation sequencing, chromatin accessibility, histone modifications and RNA sequencing data, I will identify silencers and compare their evolution to enhancers and promoters. Using this dataset I will be able to compare conservation and regulatory turnover of silencers over the course of mammalian evolution and bridge our gap in knowledge on repressive regulatory elements.

• DFG Programme: WBP Fellowship
• International Connection: Spain
• Host: Professor Dr. Tomas Marques-Bonet