Drosophila TET acts with PRC1 to activate gene expression independently of its catalytic activity

Enzymes of the ten-eleven translocation (TET) family play a key role in the regulation of gene expression by oxidizing 5-methylcytosine (5mC), a prominent epigenetic mark in many species. Yet, TET proteins also have less characterized noncanonical modes of action, notably in Drosophila, whose genome is devoid of 5mC. Here, we show that Drosophila TET activates the expression of genes required for larval central nervous system (CNS) development mainly in a catalytic-independent manner. Genome-wide profiling shows that TET is recruited to enhancer and promoter regions bound by Polycomb group complex (PcG) proteins. We found that TET interacts and colocalizes on chromatin preferentially with Polycomb repressor complex 1 (PRC1) rather than PRC2. Furthermore, PRC1 but not PRC2 is required for the activation of TET target genes. Last, our results suggest that TET and PRC1 binding to activated genes is interdependent. These data highlight the importance of TET noncatalytic function and the role of PRC1 for gene activation in the Drosophila larval CNS

Acquisition of isotopic composition for surface snow in East Antarctica and the links to climatic parameters

The isotopic compositions of oxygen and hydrogen in ice cores are invaluable tools for the reconstruction of past climate variations. Used alone, they give insights into the variations of the local temperature, whereas taken together they can provide information on the climatic conditions at the point of origin of the moisture. However, recent analyses of snow from shallow pits indicate that the climatic signal can become erased in very low accumulation regions, due to local processes of snow reworking. The signal-to-noise ratio decreases and the climatic signal can then only be retrieved using stacks of several snow pits. Obviously, the signal is not completely lost at this stage, otherwise it would be impossible to extract valuable climate information from ice cores as has been done, for instance, for the last glaciation. To better understand how the climatic signal is passed from the precipitation to the snow, we present here results from varied snow samples from East Antarctica. First, we look at the relationship between isotopes and temperature from a geographical point of view, using results from three traverses across Antarctica, to see how the relationship is built up through the distillation process. We also take advantage of these measures to see how second-order parameters (d-excess and O-17-excess) are related to delta O-18 and how they are controlled. d-excess increases in the interior of the continent (i.e., when delta O-18 decreases), due to the distillation process, whereas O-17-excess decreases in remote areas, due to kinetic fractionation at low temperature. In both cases, these changes are associated with the loss of original information regarding the source. Then, we look at the same relationships in precipitation samples collected over 1 year at Dome C and Vostok, as well as in surface snow at Dome C. We note that the slope of the delta O-18 vs. temperature (T) relationship decreases in these samples compared to those from the traverses, and thus caution is advocated when using spatial slopes for past climate reconstruction. The second-order parameters behave in the same way in the precipitation as in the surface snow from traverses, indicating that similar processes are active and that their interpretation in terms of source climatic parameters is strongly complicated by local temperature effects in East Antarctica. Finally we check if the same relationships between delta O-18 and second-order parameters are also found in the snow from four snow pits. While the d-excess remains opposed to delta O-18 in most snow pits, the O-17-excess is no longer positively correlated to delta O-18 and even shows anti-correlation to delta O-18 at Vostok. This may be due to a stratospheric influence at this site and/or to post-deposition processes

DNA:RNA Immunoprecipitation from S. pombe Cells for qPCR and Genome-Wide Sequencing

International audienceBy temporarily distorting the DNA double helix, the moving RNA polymerases can lead to the formation of non-B DNA structures. One of the most abundant and largest non-B DNA structures in the genome is the R-loop, a three-stranded structure forming when the nascent RNA hybridizes with its DNA template, thereby extruding the non-template DNA strand. Growing evidence suggests that at least a subset of R-loops could induce transcription stress and genome instability, although the direct, primary consequences of R-loop formation on the surrounding chromatin are still unclear.To understand the direct impact of R-loops on transcription and genome stability, accurate and quantitative mapping of R-loops is essential. R-loop mapping is commonly achieved using the antibody-based DNA:RNA Immunoprecipitation (DRIP) strategy. While it is reasonably straightforward to obtain robust DRIP enrichments from human cells, this has proved harder in yeast, where DRIP signals are often relatively weak, with a poor signal-to-noise ratio. Although it is unclear whether such weak signals stem from a technical or a biological reality, they make the accurate quantification of DRIP signals all the more important, especially when deep sequencing is used to monitor and quantify the distribution of R-loops genome-wide. Here we propose a DRIP protocol that has been optimized for the mapping and the quantification of R-loops in Schizosaccharomyces pombe but that can also be used in Saccharomyces cerevisiae. As a result, this protocol can be used to generate calibrated DRIP-seq data, where genomic DNA extracted from S. cerevisiae serves as spike-in reference

Senataxin homologue Sen1 is required for efficient termination of RNA polymerase III transcription

International audienceR‐loop disassembly by the human helicase Senataxin contributes to genome integrity and to proper transcription termination at a subset of RNA polymerase II genes. Whether Senataxin also contributes to transcription termination at other classes of genes has remained unclear. Here, we show that Sen1, one of two fission yeast homologues of Senataxin, promotes efficient termination of RNA polymerase III (RNAP3) transcription in vivo. In the absence of Sen1, RNAP3 accumulates downstream of RNAP3‐transcribed genes and produces long exosome‐sensitive 3′‐extended transcripts. Importantly, neither of these defects was affected by the removal of R‐loops. The finding that Sen1 acts as an ancillary factor for RNAP3 transcription termination in vivo challenges the pre‐existing view that RNAP3 terminates transcription autonomously. We propose that Sen1 is a cofactor for transcription termination that has been co‐opted by different RNA polymerases in the course of evolution