Glycosphingolipid metabolism in cell fate specification

Glycosphingolipids (GSLs) are ubiquitous components of eukaryotic plasma membranes that consist of a ceramide backbone linked to a glycan moiety. Both the ceramide and the glycan parts of GSLs display structural variations that result in a remarkable repertoire of diverse compounds. This diversity of GSLs is exploited during embryogenesis, when different GSLs are produced at specific developmental stages and along several differentiation trajectories. Importantly, plasma membrane receptors interact with GSLs to modify their activities. Consequently, two otherwise identical cells can respond differently to the same stimulus owing to their different GSL composition. The metabolic reprograming of GSLs is in fact a necessary part of developmental programs, as its impairment results in developmental failure or tissue-specific defects. Moreover, single-cell variability is emerging as a fundamental player in development: GSL composition displays cell-to-cell variability in syngeneic cell populations owing to the regulatory gene expression circuits involved in microenvironment adaptation and in differentiation. Here, we discuss how GSLs are synthesized and classified and review the role of GSLs in the establishment and maintenance of cell identity. We further highlight the existence of the regulatory circuits that modify GSL pathways and speculate how GSL heterogeneity might contribute to developmental patterning.

The role of MYC in bone and in the hematopoietic stem cell niche

Maike Jaworski

The nuclear protein c-Myc is one of the most potent proto-oncogenes described. Its expression is found to be deregulated in more than 50 percent of human cancers, where it has been shown to control a number of biological processes including driving proliferation, cell growth and angiogenesis while inhibiting differentiation. The effects of c-Myc are highly cell type specific and include cell autonomous and non-cell autonomous processes. In order to examine the effect of excess amounts of c-Myc in bone, we have generated a mouse line expressing the tTA transactivator under the control of the mouse 2.3 kb col1a1 promoter (named Col1a1::tTA), which directs transgene expression to mature osteoblasts. By combining this transgene with the Tet-O-Myc allele, we generated a Col1a1::tTA; Tet-O-Myc double transgenic mouse model in which it is possible to inducibly express human c-MYC in osteoblasts during development and in the adult. We document that the used 'tet-off' system directs transgene expression to bones and that c-MYC can be completely repressed by treatment with doxycycline. Using this mouse model, we demonstrate that overexpression of c-MYC leads to remarkable changes in mutant bones, which depend greatly in their severity on the developmental time point of c-MYC induction. Unrestricted c-MYC expression, starting with the first emergence of mature osteoblasts in the fetal skeleton (∼E14.0), leads to lethality of the mutants at birth; their bones are shortened and thicker than in controls. Later induction of c-MYC allows survival, but leads to significant changes in bone morphology. Mutant bones develop a very irregular bone structure with signs of excessive bone formation. Surprisingly, this also correlates with definite signs of excessive osteoclast activity, which explains the formation of cavities seen in the bone matrix. Osteoblasts not only produce bone matrix, they are also very important niche cells for hematopoietic cells, especially for hematopoietic stem cells and B cells. We find that c-MYC overexpression severely impairs B lymphopoiesis and also observe signs of extramedullary hematopoiesis in the spleen, which is indicative of a compromised HSC environment in the bone marrow. Most strikingly, these animals develop frank osteosarcomas leading to a much reduced life span. Tumors arise in various bones, with the ribs and hips being the most prominent sites. These c-MYC driven tumors are very aggressive as is evident by their capacity to spontaneously metastasize to lung and liver, a rather rare phenomenon in mouse models, indicating that these tumors share important aspects of human osteosarcomas. Molecular analysis of c-MYC overexpressing osteoblasts has revealed a defect in their terminal differentiation program, rendering them incapable to progress from a relatively immature proliferative to a quiescent, calcified matrix producing state. To our knowledge this is the first report of experimental osteosarcoma formation, originating from a mature and lineage committed osteoblast population indicating that c-MYC may be able to de-differentiate more mature cells. In summary, our novel conditional mouse model showed that c-MYC expression in mature osteoblasts can lead to the formation of highly aggressive and metastatic osteosarcomas, a lethal disease in humans. This model will be the basis for further studies elucidating the molecular effects of c-MYC on de-differentiation and metastasis formation, processes, which remain poorly understood but are critical events in highly malignant cancers.

EPFL2009

Rhythmic and clock-dependent chromatin loops regulate circadian gene expression

Jérôme Mermet

In mammals the circadian clock drives daily behavioural and physiological changes that resonate with environmental cues, which can be observed, for example, in the intricate timing of rest during the night and activity during the day in humans. The circadian clock consists of a network of hierarchical clocks in which the central pacemaker is located in the suprachiasmatic nucleus, which is sensitive to external light and propagates time to the peripheral organ-based clocks. Within organs, clocks tick in each individual cell and are molecularly encoded in the genome as a network of dynamic feedback loops. By mediating the expression of the appropriate gene products at the correct moment of the day, the molecular clocks op-timize physiological functions of virtually every cell in our body, allowing us to synchronize with daily fluc-tuations in the environment. In mammalian cells the chromatin organization in the nucleus consists of a topological network, in which chromatin interactions between distal regulatory elements such as enhancers and target genes are essen-tial to regulate gene expression. Important questions remain: is the complex chromatin folding dynamic and if so on which genomic and temporal scales? In fact, dynamic rearrangements of the chromatin have been reported on multiple genomic and time scales, from the entire genome to enhancer-promoter con-tacts, across developmental transitions, cellular differentiation, and transcription cycles. With this per-spective in mind, the circadian oscillator provides a unique model to study the dynamics of genomic inter-actions in the context of fluctuating transcription. Here, we explored chromatin contacts of core-clock and clock-controlled gene promoters in the mouse. We aimed at evaluating the putative dynamics of chromatin contacts, at estimating their conservation across tissues, and at exploring the contribution of the circadian clock to this interaction network. To achieve this goal, we performed 4C-sequencing assays at two circadian time points in the liver and kidney of WT and clock-deficient animals. Overall, we observe that chromatin contacts are largely conserved across circadian time points and genetic backgrounds, and are tissue-specific. Our experiments reveal that the promoters of core-clock and clock-controlled genes contact distal genomic regions containing en-hancer chromatin signatures, suggesting a functional role of these distal sites in target gene regulation. Our data also suggest a clock-driven module of rhythmic genes that are colocalized in the nucleus. However, we also observe dynamic contacts between oscillating gene promoter and enhancer-like ge-nomic regions. In this thesis, we discuss in detail two examples of dynamic chromatin looping that are ob-served at the Cry1 and Gys2 loci. Our data reveal not only a dynamic coupling between the chromatin loop and the transcriptional state but also that the dynamic of chromatin looping depends on a functional clock. Furthermore, genome editing experiments using CRISPR-Cas9 tools reveal that the Cry1 distal site is essential for the transcriptional regulation of Cry1 and contributes to the circadian clock robustness both in-vivo and in cultured cells. These results demonstrate how local chromatin rearrangements take place in a 24-hour time-scale and set chromatin looping between gene promoters and distal regions as a new reg-ulatory layer for circadian gene expression.

EPFL2017

Comparative Transcriptomics Analyses across Species, Organs, and Developmental Stages Reveal Functionally Constrained lncRNAs

Fabrice Daniel Darbellay, Anamaria Necsulea

The functionality of long noncoding RNAs (lncRNAs) is disputed. In general, lncRNAs are under weak selective pressures, suggesting that the majority of lncRNAs may be nonfunctional. However, although some surveys showed negligible phenotypic effects upon lncRNA perturbation, key biological roles were demonstrated for individual lncRNAs. Most lncRNAs with proven functions were implicated in gene expression regulation, in pathways related to cellular pluripotency, differentiation, and organ morphogenesis, suggesting that functional lncRNAs may be more abundant in embryonic development, rather than in adult organs. To test this hypothesis, we perform a multidimensional comparative transcriptomics analysis, across five developmental time points (two embryonic stages, newborn, adult, and aged individuals), four organs (brain, kidney, liver, and testes), and three species (mouse, rat, and chicken). We find that, overwhelmingly, lncRNAs are preferentially expressed in adult and aged testes, consistent with the presence of permissive transcription during spermatogenesis. LncRNAs are often differentially expressed among developmental stages and are less abundant in embryos and newborns compared with adult individuals, in agreement with a requirement for tighter expression control and less tolerance for noisy transcription early in development. For differentially expressed lncRNAs, we find that the patterns of expression variation among developmental stages are generally conserved between mouse and rat. Moreover, lncRNAs expressed above noise levels in somatic organs and during development show higher evolutionary conservation, in particular, at their promoter regions. Thus, we show that functionally constrained lncRNA loci are enriched in developing organs, and we suggest that many of these loci may function in an RNA-independent manner.

OXFORD UNIV PRESS2020