Transcription induces context-dependent remodeling of chromatin architecture during differentiation.

Metazoan chromosomes are organized into discrete spatial domains (TADs), believed to contribute to the regulation of transcriptional programs. Despite extensive correlation between domain organization and gene activity, a direct mechanistic link is unclear, with perturbation studies often showing little effect. To follow chromatin architecture changes during development, we used Capture Hi-C to interrogate the domains around key differentially expressed genes during mouse thymocyte maturation, uncovering specific remodeling events. Notably, one TAD boundary was broadened to accommodate RNA polymerase elongation past the border, and subdomains were formed around some activated genes without changes in CTCF binding. The ectopic induction of some genes was sufficient to recapitulate domain formation in embryonic stem cells, providing strong evidence that transcription can directly remodel chromatin structure. These results suggest that transcriptional processes drive complex chromosome folding patterns that can be important in certain genomic contexts.

Glucose depletion decreases cell viability without triggering degenerative changes in a physiological nucleus pulposus explant model.

Although the etiology of intervertebral disc degeneration is still unresolved, the nutrient paucity resulting from its avascular nature is suspected of triggering degenerative processes in its core: the nucleus pulposus (NP). While severe hypoxia has no significant effects on NP cells, the impact of glucose depletion, such as found in degenerated discs (0.2-1 mM), is still uncertain. Using a pertinent ex-vivo model representative of the unique disc microenvironment, the present study aimed, therefore, at determining the effects of "degenerated" (0.3 mM) glucose levels on bovine NP explant homeostasis. The effects of glucose depletion were evaluated on NP cell viability, apoptosis, phenotype, metabolism, senescence, extracellular matrix anabolism and catabolism, and inflammatory mediator production using fluorescent staining, RT-qPCR, (immuno)histology, ELISA, biochemical, and enzymatic assays. Compared to the "healthy" (2 mM) glucose condition, exposure to the degenerated glucose condition led to a rapid and extensive decrease in NP cell viability associated with increased apoptosis. Although the aggrecan and collagen-II gene expression was also downregulated, NP cell phenotype, and senescence, matrix catabolism, and inflammatory mediator production were not, or only slightly, affected by glucose depletion. The present study provided evidence for glucose depletion as an essential player in NP cell viability but also suggested that other microenvironment factor(s) may be involved in triggering the typical shift of NP cell phenotype observed during disc degeneration. The present study contributes new information for better understanding disc degeneration at the cellular-molecular levels and thus helps to develop relevant therapeutical strategies to counteract it.

The Lower in Vivo Osteogenicity of Adipose Tissue-Derived Stem Cells Correlates with a Higher Innate Immune Response.

Adipose tissue-derived mesenchymal stem cells (ATSCs) have been used as an alternative to bone marrow-derived mesenchymal stem cells (BMSCs) for bone tissue engineering applications. The ability of ATSCs to promote new bone formation remains lower than that of BMSCs. This study aimed to investigate the mechanisms underlying osteogenicity differences between human ATSCs and BMSCs in ceramic constructs, focusing on the effects of inflammation on this process. In contrast to ATSC-containing constructs, which did not induce bone formation in an ectopic mouse model, BMSC constructs consistently did so. Gene expression analysis revealed that human BMSCs, concomitantly with host murine progenitors, differentiated into the osteogenic lineage early post-implantation. In contrast, ATSCs differentiated later, when few implanted viable cells remained post-implantation, while the host murine cells did not differentiate. Comparison of the inflammatory profile in the cell constructs indicated concomitant upregulation of some human and murine inflammatory genes in the ATSC-constructs compared to the BMSC-constructs during the first-week post-implantation. The high level of chemokine production by the ATSCs was confirmed at the gene and protein levels before implantation. The immune cell recruitment within the constructs was then explored post-implantation. Higher numbers of TRAP-/ MRC1 (CD206) + multinucleated giant cells, NOS2 + M1, and ARG1 + M2 macrophages were present in the ATSC constructs than in the BMSC constructs. These results proved that ATSCs are a transient source of inflammatory cytokines promoting a transient immune response post-implantation; this milieu correlates with impaired osteogenic differentiation of both the implanted ATSCs and the host osteoprogenitor cells.

Precise measurements of chromatin diffusion dynamics by modeling using Gaussian processes.

The spatiotemporal organization of chromatin influences many nuclear processes: from chromosome segregation to transcriptional regulation. To get a deeper understanding of these processes, it is essential to go beyond static viewpoints of chromosome structures, to accurately characterize chromatin's diffusion properties. We present GP-FBM: a computational framework based on Gaussian processes and fractional Brownian motion to extract diffusion properties from stochastic trajectories of labeled chromatin loci. GP-FBM uses higher-order temporal correlations present in the data, therefore, outperforming existing methods. Furthermore, GP-FBM allows to interpolate incomplete trajectories and account for substrate movement when two or more particles are present. Using our method, we show that average chromatin diffusion properties are surprisingly similar in interphase and mitosis in mouse embryonic stem cells. We observe surprising heterogeneity in local chromatin dynamics, correlating with potential regulatory activity. We also present GP-Tool, a user-friendly graphical interface to facilitate usage of GP-FBM by the research community.