The spatial organization of the genome impinges on all genomic processes, including gene regulation, maintenance of genome stability and chromosome transmission to daughter cells. A detailed understanding of the spatial arrangement of the human genome, referred to as the 4D nucleome, and the biological and physical principles that drive chromosome folding requires combining approaches from the fields of molecular and cell biology, imaging, genetics and genomics with approaches from physics, computational biology, and computer simulation. We have assembled a highly interdisciplinary center with the goal of generating extensively validated maps of the 4D nucleome, its physical and dynamic properties and its role in regulating the activity of the genome. First, the center will further optimize and extensively validate a suite of genome-wide molecular methodologies, based on chromosome conformation capture (3C) that can probe the folding of chromosomes at the scale of single nucleosomes, chromatin fibers, chromosomes and the entire nucleus, across cell populations and in single cells. Given that chromosome and nuclear organization is tightly linked to biological state of the cell, the center will map the 4D nucleome for four key biological states representing different conformations during the cell cycle (interphase and mitosis), and during cell differentiation (pluripotent and differentiated states). We will obtain complementary data regarding the structure and dynamics of chromatin, at different length scales and in single cells using extensive high-throughput imaging, live cell imaging and super resolution microscopy. Data obtained with all approaches will be analyzed, integrated and modeled using a set of methods we will further develop to gain insights into the structure, physics and dynamics of chromosome folding over different length scales. Finally, a critical component of our proposal is the biological validation and further elaboration of the chromatin interaction maps that are generated from our conformational analyses. This validation will be achieved through site-specific editing of genomic sequence and epigenetic marks, the creation of new contact points within the genome, and the identification of factors (both protein and nucleic acid) that facilitat or restrict these interactions. Effects of such perturbations in the chromosome conformation on transcription will reveal relationships between specific chromosome structural features and gene expression.
The research proposed here will determine how the human genome is folded inside the cell nucleus. Insights into this process will lead to a deeper understanding of how cells regulate genes, transmit chromosomes to daughter cells, and maintain genome stability. All these processes are essential for normal development and homeostasis, and defects in any of these processes have been linked to human diseases such as cancer, diabetes and developmental disorders.
| Chong, Shasha; Dugast-Darzacq, Claire; Liu, Zhe et al. (2018) Imaging dynamic and selective low-complexity domain interactions that control gene transcription. Science 361: |
| Gibcus, Johan H; Samejima, Kumiko; Goloborodko, Anton et al. (2018) A pathway for mitotic chromosome formation. Science 359: |
| Andrews, J O; Conway, W; Cho, W -K et al. (2018) qSR: a quantitative super-resolution analysis tool reveals the cell-cycle dependent organization of RNA Polymerase I in live human cells. Sci Rep 8:7424 |
| Skoruppa, Enrico; Nomidis, Stefanos K; Marko, John F et al. (2018) Bend-Induced Twist Waves and the Structure of Nucleosomal DNA. Phys Rev Lett 121:088101 |
| Nuebler, Johannes; Fudenberg, Geoffrey; Imakaev, Maxim et al. (2018) Chromatin organization by an interplay of loop extrusion and compartmental segregation. Proc Natl Acad Sci U S A 115:E6697-E6706 |
| Erba?, Aykut; de la Cruz, Monica Olvera; Marko, John F (2018) Effects of electrostatic interactions on ligand dissociation kinetics. Phys Rev E 97:022405 |
| Stephens, Andrew D; Liu, Patrick Z; Banigan, Edward J et al. (2018) Chromatin histone modifications and rigidity affect nuclear morphology independent of lamins. Mol Biol Cell 29:220-233 |
| Mir, Mustafa; Stadler, Michael R; Ortiz, Stephan A et al. (2018) Dynamic multifactor hubs interact transiently with sites of active transcription in Drosophila embryos. Elife 7: |
| Adriaens, Carmen; Serebryannyy, Leonid A; Feric, Marina et al. (2018) Blank spots on the map: some current questions on nuclear organization and genome architecture. Histochem Cell Biol 150:579-592 |
| Brahmachari, Sumitabha; Dittmore, Andrew; Takagi, Yasuharu et al. (2018) Defect-facilitated buckling in supercoiled double-helix DNA. Phys Rev E 97:022416 |
Showing the most recent 10 out of 49 publications
