Among the signals that control the epigenetic landscape, non-coding (nc)RNAs have been identified to play a major role but the generalization and the mechanisms of their activity are still poorly apprehended. Recent data using high-throughput technologies have profoundly changed our view on how the genomes are organized. Indeed transcriptome analyses have shown that large genomic regions are pervasively transcribed producing a broad variety of lncRNA which functions on the epigenome remain to be deciphered. Recent works showed that S. cerevisiae’s genome also supports production of non-coding protein large transcripts, which are strongly controlled by RNA decay pathways. Of specific interest are the lncRNA XUT that we described recently, mostly antisense to class II genes and associated with a consistent regulatory potential through epigenetic modifications. Here, I will present data providing insights on their regulatory activity which is conserved also in S. pombe containing RNAi pathway. The transcription and post-transcription-mediated regulatory activities of antisense…

Mutations have been investigated for more than a century but never witnessed in action in single cells, thus preventing direct characterization of their dynamics and reliable estimation of the distribution of their fitness effects. Such estimates have wide application and are critical for most evolutionary models/studies. We accomplished this in Escherichia coli by employing microfluidics, time-lapse imaging, and by visualizing mutations in single cells by using a fluorescent tag of the Mismatch Repair System. I will present our results obtained for strains having a wide range of mutation rates and growing under controlled condition in the absence of exogenous stress.

The emerging field of compartmentalized in vitro evolution, where selection is carried out by differential reproduction in each compartment, is a promising new approach to protein engineering. From practical point of view, it is important to know the effect of the increase in the average number of genotype bearing agents per compartment. This effect is also interesting on its own in the context of primordial evolution in the hypothetical RNA world. The question is important as genotypes with different phenotypes in the same compartment share their fitness (the number of produced copies) rendering the selection frequency-dependent. I will show the results of a theoretical investigation of this problem in the context of selection dynamics for a simple model with an infinite population that is periodically redistributed among infinite number of identical compartments, inside which all molecules are copied without distinction with the success rate as a function of the total genomic composition…

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In this talk I will present some of the current knowledge regarding the cnidarian endogenous biological clock.  During the last few years our team has examined the evidence from behavioral, physiological, molecular, and evolutionary perspectives regarding the role of the clock machinery in some key cnidarians such as symbiotic corals, Aiptasia and Nematosella vectensis, an emerging model organism.  Our research is mainly focused on symbiotic corals. They are an interesting model to study the complexities and evolution of the metazoan biological clock.   A deeper understanding of this complex issue can help explain coral mass spawning, and how symbiotic organisms measure time and synchronize themselves to their environmental conditions.  Our main goal is understanding how two pacemakers, the host and the symbiont, function together in one organism and what is the cross-talk in this holobiont system. 

According to the endosymbiont theory of organelle evolution, a β cyanobacterium that was engulfed by a unicellular protist (primary endosymbiosis) evolved into the chloroplasts that are currently present in algae and plants. This successful evolutionary event was thought to have occurred once (monophyletic), about a billion years ago. The long time span separating the initial acquisition of the endosymbiont by its host and its current state as a photosynthetic organelle makes it difficult to reconstruct the evolutionary history of primary plastids. However, recently it was shown that the thecate protist Paulinella chromatophora has a photosynthetic organelle called a chromatophore that was acquired approximately 100 million years ago. Analyses of this organelle are providing us with the opportunity to deduce events that occur during early stages in organellogenesis. Overall, our studies have demonstrated that the chromatophore is a bona fide photosynthetic organelle with a reduced genome size relative to the initial endosymbiont, and it contains numerous proteins…

The spatial organization of chromosomes in eukaryotic cell nuclei has important implications for gene expression and genome stability, but has not been charted in detail and its underlying principles remain poorly known. Our lab develops imaging methods and computational models to better understand how chromatin fibers are organized and move in 3D. In this talk, I will review the methods that we developed over the years to map chromosome architecture in yeast and understand its mechanistic basis. In particular, I will show how a simple polymer model can recapitulate a host of experimental observations, and how this model can be used to infer key properties of the chromatin fiber. I will also present collaborative work addressing how chromosome architecture constrains DNA repair by homologous recombination, and how DNA damage increases chromatin mobility. Finally, I will briefly discuss an ongoing project on high-resolution imaging and modeling of human chromosomes.