Analysis of genome structure and cellular fates in the early mouse embryo

Línea de investigación

Functional Genomics.

Descripción

DNA is folded and packed in particular ways to dictate the accessibility of specific regions of the genome. The result is the coordination of regulatory elements and genes leading to spatial, temporal and quantitative transcriptional patterns that determine the final phenotype of the cell. This 3D structure must be reproduced when an organism is growing during embryonic development and rules genome function. Crucial for its establishment and maintenance is the presence of architectural proteins that bind to the chromatin and modulate the interactions between distal regions of the genome. Among these, CTCF and the Cohesin complex are considered key factors. Disruptions of this regulation will result in organism malfunction and disease, but at the same time, variations in its balance can be ground for evolutionary change. The first stages of mouse development as a model, starting at fertilization, offers a unique opportunity to dissect these processes as they are established starting from a totally naïve genome, while at the same time the embryo is growing and the first lineage decisions that lead to different cell types take place.

The principal aim of this proposal is to understand how the loss of CTCF at peri-implantation stages in the pluripotent epiblast of the mouse embryo affects critical developmental decisions such as germ layer specification. The phenotypic consequences of CTCF depletion will be analysed by RNA-seq and genome accessibility and structure will be studied by ATAC-seq and Hi-C on single embryos. This project will generate essential information and complementary results to previous research in the lab showing that lack of zygotic CTCF leads to lethality by late blastocyst stage.

In parallel, the student to join our group will characterize a new pharmacological model to alter chromatin structure by using the anti-cancer drug CBL0137 (curaxin), that has been shown to displace CTCF leading to structural changes of the chromatin in cell lines. We plan to use curaxin to deplete CTCF from mouse embryonic stem cells (ESCs) and mouse embryos to elucidate the effects of its loss in structure and transcription, which at the same time will influence viability and/or progression. This approach will allow us to better control the stages on which we induce the depletion and to substantially reduce the use of genetically modified mice, what we believe is in line with the future perspectives of biological sciences.

Contacto

Miguel Manzanares.

Correo electrónico: mmanzanares@cbm.csic.es.

Centro de Biología Molecular Severo Ochoa (CBM).

Número de plazas ofertadas: 1.