Blog post #2 Let’s meet Philippe Collas and 3D genome architecture in lineage differentiation. (Clémence Labarre)
Let’s meet Philippe Collas and 3D genome architecture in lineage differentiation.
Spatial organization of chromatin and its compaction level influence gene expression and cell fate. We learn during our studies that DNA is mainly packed via histones to form DNA-protein complex called chromatin. Moreover, histone can be enzymatically modified by the addition of acetyl, methyl or phosphate groups modifying gene accessibility. But what’s about interactions between chromatin regions and nuclear lamina?
Last week, we had the chance to meet Philippe Collas, Head of Department of the Institute of Basic Medical Sciences, University of Oslo. His laboratory investigates “principles of 3D genome architecture which pattern lineage-specific stem cell differentiation in health and disease.” In fact chromatin worth the interest of scientists as its conformations vary between cells most probably due to gene expression patterns, epigenetic pressure and stochastic interactions and movements.
Researchers have defined three types of interactions in chromatin :
Chromatin-chromatin interactions refers to topologically associated domains (TADs). When chromatin links to the nucleolus it creates nucleolus associated domains (NADs). Finally, chromatin could interact with dense fibrillar mesh lining the nuclear envelope called lamina, through lamina associated domains (LADs). The most condensed compartment (compartment B) of the chromatin interacts with LADs rather than small regions of active chromatin belonging to the compartment A bind a lot to the TADs.
How could we measure these cross-linking dynamically?
By combining cell biological, biochemical, genomics and computational modeling approaches scientists are able to explore chromosome conformation through time. Researchers study 3D chromosome-conformation through the analysis of millions of cells (Lieberman-Aiden et al. 2009).
Mostly, they resort to Hi-C Chromosome conformation capture coupled with high throughput sequencing to highlight chromosomal interactions on the entire genome.
Close chromatin regions in a cell are crosslinked with formaldehyde and then cut with restriction enzyme. Each end of a fragment is filled to stick to the other fragment and marked with biotin. The following step consists in shearing the DNA and pulling down biotin with streptavidin beads to sequence ligation products. Powerful computational approaches allows us to compare DNA sequencing, produce a catalog of interaction for each cell and determine subpopulations of 3D structures. Consensus method averages all different structures in an unique one studying the distance between chromatin regions. This method exploit the triangle inequality which assesses that the distance between any two points must be smaller than or equal to the sum of distances of these two points to a third point. On the other hand, the deconvolution method decomposes chromatin interaction patterns into subpopulations.
Other emerging single-cell, high-throughput, sequencing-based technologies could be used such as RNA sequencing for transcriptomic purposes, ChIP sequencing for protein association with the genome, DamID and Lamina associated domains (Oldenburg et al., 2016), Bisulfite to sequence DNA methylation … (Sekelja, Monika et al., 2016).
Spatial organization and cell differentiation: Why it is so important?
CollasLab has developed Chrom3D, an open program which integrates Hi-C and LADs datasets to visualize folding of the genome in single cells. This programs highlights dynamical interactions between TADs during cell differentiation within both compartments A and B. Compartments are lineage specific rather than TADs which are more conserved. However, chromosome topology within TADs can vary over time modifying the epigenetic landscape of the cell.
Adipocytes are adipose tissue cells specialized in storing energy through lipids. Their precursors adipose-derived stromal/stem cells are actually studied for their regenerative potential. During adipogenic in vitro differentiation the chromatin change of state and genes detach from the lamina : 1500 TADS are assembled, 900 are de-assembled, 500 are maintained. Carrying on exchanges between the The Institute of Basic Medical Science and Stromalab would greatly enhance our comprehension on regenerative properties to promote systems biology. Thus, we take advantage of powerful tools to visualize chromatin over time, analyze the effect of gene KO and compare observations at transcriptomic, epigenetic, genetic and histologic scale.
CollasLab : collaslab.org
Lieberman-Aiden, Erez, et al. “Comprehensive mapping of long-range interactions reveals folding principles of the human genome.” science 326.5950 (2009): 289-293.
Oldenburg, A. R., & Collas, P. (2016). Mapping Nuclear Lamin-Genome Interactions by Chromatin Immunoprecipitation of Nuclear Lamins. The Nuclear Envelope: Methods and Protocols, 315-324.
Sekelja, Monika, Jonas Paulsen, and Philippe Collas. “4D nucleomes in single cells: what can computational modeling reveal about spatial chromatin conformation?.” Genome biology 17.1 (2016): 54.
Because Science is also a game here is a video you might like :