Probing the Dynamic Organization of Transcription Compartments and Gene Loci within the Nucleus of Living Cells

AbstractThe three-dimensional organization of nuclear compartments within living cells determines genome function and yet their underlying self-organizing principles are unclear. We visualize in real-time transcriptionally active compartments (TCs) by the transient enrichment of fluorescently-labeled uridine 5′-triphosphate molecules within living cells. These TCs partially colocalize with active RNA-Pol II in the cell nucleus. Fluorescence anisotropy maps of chromatin compaction evidences a more open chromatin structure at the TCs. Using live-cell timelapse imaging, heterogeneity in the dynamic behavior of TCs has been revealed which falls into three distinct classes: subdiffusive, super-diffusive, and normal diffusive behavior. In contrast, the mobility of a candidate gene locus, either in the repressed or activated state, undergoes a differential restricted motion that is coupled to TC movement. Further TC dynamics is directly affected by small molecule chromatin structure modulators and adenosine triphosphate depletion. This heterogeneous behavior in TC dynamics within living cells could provide an interesting paradigm to explore the spatiotemporal dimension to gene transcription control

Mechanical stimulation induces formin-dependent assembly of a perinuclear actin rim

Proceedings of the National Academy of Sciences of the United States of America11220E2595-E260

Chromosome Intermingling: Mechanical Hotspots for Genome Regulation

Cells sense physical and chemical signals from their local microenvironment and transduce them to the nucleus to regulate genomic programs. In this review, we first discuss different modes of mechanotransduction to the nucleus. Then we highlight the role of the spatial organization of chromosomes for integrating these signals. In particular, we emphasize the importance of chromosome intermingling for gene regulation. We also discuss various geometric models and recent advances in microscopy and genomics that have allowed accessing these nanoscale chromosome intermingling regions. Taken together, the recent work summarized in this review culminates in the hypothesis that the chromosome intermingling regions are mechanical hotspots for genome regulation. Maintenance of such mechanical hotspots is crucial for cellular homeostasis, and alterations in them could be precursors for various cellular reprogramming events including diseases.DARPA (Contract W911NF-16-1-0551)NSF (Grant DMS-1651995)ONR (Grant N00014-17-1-2147

Analysis of transcriptional modules during human fibroblast ageing

For systematic identification of transcription signatures of human cell aging, we carried out Weighted Gene Co-expression Network Analysis (WGCNA) with the RNA-sequencing data generated with young to old human dermal fibroblasts. By relating the modules to the donor's traits, we uncovered the natural aging- and premature aging disease-associated modules. The STRING functional association networks built with the core module memberships provided a systematic overview of genome-wide transcriptional changes upon aging. We validated the selected candidates via quantitative reverse transcription PCR (RT-qPCR) assay with young and aged human fibroblasts, and uncovered several genes involved in ECM, cell, and nuclear mechanics as a potential aging biomarker. Collectively, our study not only provides a snapshot of functional changes during human fibroblast aging but also presents potential aging markers that are relevant to cell mechanics.ISSN:2045-232

Mechanogenomic coupling of lung tissue stiffness, EMT and coronavirus pathogenicity

In this Current Opinion, we highlight the importance of the material properties of tissues and how alterations therein, which influence epithelial-to-mesenchymal transitions, represent an important layer of regulation in a number of diseases and potentially also play a critical role in host-pathogen interactions. In light of the current SARS-CoV-2 pandemic, we here highlight the possible role of lung tissue stiffening with ageing and how this might facilitate increased SARS-CoV-2 replication through matrix-stiffness dependent epithelial-to-mesenchymal transitions of the lung epithelium. This emphasizes the need for integrating material properties of tissues in drug discovery programs

Nuclear Mechanopathology and Cancer Diagnosis

Abnormalities in nuclear and chromatin organization are hallmarks of many diseases including cancer. This review provides our understanding of how the cellular microenvironment regulates nuclear morphology and with it the spatial organization of chromosomes and genes, resulting in cell-type specific genomic programs. We also discuss the molecular basis for maintaining nuclear and genomic integrity and how alterations in nuclear mechanotransduction pathways result in various diseases. Finally, we highlight the importance of digital pathology based on nuclear morphometric features combined with single-cell genomics for early cancer diagnostics.NSF (Grant DMS-1651995)ONR (Grant N00014-17-1-2147