Funding: MINIATURA, NCN
Project period: 2019 - 2019
Project leader: Teresa Szczepińska
Institutions:
Centre of New Technologies, University of Warsaw
Contacts of structural chromatin domains investigated by GAM method. A scientific internship at the laboratory of Professor Ana Pombo in Berlin.
Introduction: The three-dimensional structure of the genome plays a key role in controlling cell regulation. Chromosome conformation capture methods (e.g. Hi-C) have demonstrated the existence of chromatin structural domains called TADs (topologically associating domains). TAD is defined as a chromosome region that has many internal interactions, but much less interaction with neighboring and other more distant TADs (Dixon et al., 2012). The concept of ~ 1 Mbp TADs in mammals is consistent with microscopic observations. It is still not known how the active and silent TADs are placed relative to each other and to the other structures of the cell nucleus.
Placement: The Laboratory of Professor Ana Pombo at the Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molekulare Medizin, deals with the mechanisms of epigenetic regulation of gene expression and chromatin architecture. It is a molecular biology laboratory in which innovative research techniques that require new computational solutions are being developed. Professor Ana Pombo invented and introduced new techniques to study chromatin structure: cryoFISH (Fluorescence In Situ Hybridization in thin cryosections) and GAM (Genome Architecture Mapping). She uses two different approaches in her research: in situ imaging of DNA, RNA and proteins in the nucleus by means of microscopy and next-generation sequencing. She is an expert in the field of functional genomics and has extensive experience in the study of gene regulation systems in mammalian cells, including the process of cell differentiation.
The scientific goal of the project: I will develop bioinformatic methods to study contacts between chromatin structural domains. In Professor Ana Pombo’s laboratory, I will gain access to newly created data from the GAM method for embryonic human stem cells (hESC-H1 cell line). The GAM (Genome Architecture Mapping) method (Beagrie et al., 2017) is an alternative to methods using ligation to capture spatially colocalized DNA fragments (such as the Hi-C method). This method combines the cutting of frozen nuclei into ultrathin sections using a laser and DNA sequencing. Determining the presence/absence of all genomic regions in a set of individual slices collected randomly from the population of nuclei, GAM measures the parameters of chromatin spatial organization, including the frequency of chromatin contacts in the entire genome, distance to the nuclear envelope and chromatin packing. It is an extremely valuable method for discovering further neighborhood in the genome structure and not just directly contacting regions. It allows identification of more than two genome regions in close proximity. Working on bioinformatic methods of data analysis at the place of their creation will allow me to understand in greater depth the nature of data obtained from GAM experiments. Being on the spot, I will have the possibility of deep discussions, and this will help me see interesting, yet unknown properties of the chromatin structure. It will also allow me to interpret the data more critically.
Literature:
Beagrie, R. A., Scialdone, A., Schueler, M., Kraemer, D. C. A., Chotalia, M., Xie, S. Q., ... Pombo, A. (2017). Complex multi-enhancer contacts captured by genome architecture mapping. Nature, 543 (7646), 519-524.
Dixon, J. R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., ... Ren, B. (2012). Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature, 485 (7398), 376-380.