Characterizing Novel CypA-RNA Interactions

RNA-binding proteins are a diverse and essential class of proteins with critical roles in key processes such as gene regulation, mRNA processing, and cell metabolism1,2. While hundreds of RNA binding proteins (RBPs) have functions relating to RNA executed by well characterized RNA binding domains, a recent set of mRNA pulldown studies has uncovered a rich set of unexpected RBPs with no known binding domains and functions that do not obviously require RNA2-4.&nbsp; Among these putative RNA binders are proteins belonging to the cyclophilin family, proteins that isomerize the amino acid proline from the lower energy trans conformation to the higher energy cis conformation5. Cyclophilin A (CypA), a highly conserved cyclophilin comprising a single isomerase domain6, was among the identified novel RBPs2-4. CypA is ubiquitous in the cell, as it abundant in the nucleus and cytoplasm as well as being secreted6,7. It plays an essential role in protein folding and trafficking, cell signaling, and immune system response6,7 and has recently been shown to interact with key transcription factors to mediate their transcriptional activity8,9.&nbsp; CypA is also biomedically relevant as the target of the immunosuppressive drug Cyclosporin A and is overexpressed in various cancers7. In addition to the mRNA studies, CypA and homologues have been implicated as RNA binders in several studies10-12 though its isomerase activity does not seem to require RNA. It is thus an exciting model to study novel RNA-protein interactions. Here, I take a two-pronged approach to investigate CypA&rsquo;s RNA interactome: in vitro binding with previously implicated RNAs and in vivo RNA immunoprecipitation with subsequent bioinformatic analysis to identify relevant endogenous RNA classes that CypA may bind. The in vitro results suggest that CypA binds RNA with some specificity, as certain RNAs interacted with CypA while others did not. The in vivo results differentiate a set of statistically significant enriched genes from a set of depleted genes, suggesting that CypA interacts sets of transcribed genes in the cell whose functional groups relate to known CypA activity.</p

Characterizing Novel CypA-RNA Interactions

RNA-binding proteins are a diverse and essential class of proteins with critical roles in key processes such as gene regulation, mRNA processing, and cell metabolism1,2. While hundreds of RNA binding proteins (RBPs) have functions relating to RNA executed by well characterized RNA binding domains, a recent set of mRNA pulldown studies has uncovered a rich set of unexpected RBPs with no known binding domains and functions that do not obviously require RNA2-4.&nbsp; Among these putative RNA binders are proteins belonging to the cyclophilin family, proteins that isomerize the amino acid proline from the lower energy trans conformation to the higher energy cis conformation5. Cyclophilin A (CypA), a highly conserved cyclophilin comprising a single isomerase domain6, was among the identified novel RBPs2-4. CypA is ubiquitous in the cell, as it abundant in the nucleus and cytoplasm as well as being secreted6,7. It plays an essential role in protein folding and trafficking, cell signaling, and immune system response6,7 and has recently been shown to interact with key transcription factors to mediate their transcriptional activity8,9.&nbsp; CypA is also biomedically relevant as the target of the immunosuppressive drug Cyclosporin A and is overexpressed in various cancers7. In addition to the mRNA studies, CypA and homologues have been implicated as RNA binders in several studies10-12 though its isomerase activity does not seem to require RNA. It is thus an exciting model to study novel RNA-protein interactions. Here, I take a two-pronged approach to investigate CypA&rsquo;s RNA interactome: in vitro binding with previously implicated RNAs and in vivo RNA immunoprecipitation with subsequent bioinformatic analysis to identify relevant endogenous RNA classes that CypA may bind. The in vitro results suggest that CypA binds RNA with some specificity, as certain RNAs interacted with CypA while others did not. The in vivo results differentiate a set of statistically significant enriched genes from a set of depleted genes, suggesting that CypA interacts sets of transcribed genes in the cell whose functional groups relate to known CypA activity.</p

CST does not evict elongating telomerase but prevents initiation by ssDNA binding

The CST complex (CTC1-STN1-TEN1) has been shown to inhibit telomerase extension of the G-strand of telomeres and facilitate the switch to C-strand synthesis by DNA polymerase alpha-primase (pol α-primase). Recently the structure of human CST was solved by cryo-EM, allowing the design of mutant proteins defective in telomeric ssDNA binding and prompting the reexamination of CST inhibition of telomerase. The previous proposal that human CST inhibits telomerase by sequestration of the DNA primer was tested with a series of DNA-binding mutants of CST and modeled by a competitive binding simulation. The DNA-binding mutants had substantially reduced ability to inhibit telomerase, as predicted from their reduced affinity for telomeric DNA. These results provide strong support for the previous primer sequestration model. We then tested whether addition of CST to an ongoing processive telomerase reaction would terminate DNA extension. Pulse-chase telomerase reactions with addition of either wild-type CST or DNA-binding mutants showed that CST has no detectable ability to terminate ongoing telomerase extension in vitro. The same lack of inhibition was observed with or without pol α-primase bound to CST. These results suggest how the switch from telomerase extension to C-strand synthesis may occur

Global warming and recurrent mass bleaching of corals

During 2015–2016, record temperatures triggered a pan-tropical episode of coral bleaching, the third global-scale event since mass bleaching was first documented in the 1980s. Here we examine how and why the severity of recurrent major bleaching events has varied at multiple scales, using aerial and underwater surveys of Australian reefs combined with satellite-derived sea surface temperatures. The distinctive geographic footprints of recurrent bleaching on the Great Barrier Reef in 1998, 2002 and 2016 were determined by the spatial pattern of sea temperatures in each year. Water quality and fishing pressure had minimal effect on the unprecedented bleaching in 2016, suggesting that local protection of reefs affords little or no resistance to extreme heat. Similarly, past exposure to bleaching in 1998 and 2002 did not lessen the severity of bleaching in 2016. Consequently, immediate global action to curb future warming is essential to secure a future for coral reefs

Search for an extended VHE gamma-ray emission from Mrk 421 and Mrk 501 with the MAGIC Telescope

Context. Part of the very high energy gamma-ray radiation coming from extragalactic sources is absorbed through the pair production process on the extragalactic background light photons. Extragalactic magnetic fields alter the trajectories of these cascade pairs and, in turn, convert cosmic background photons to.-ray energies by inverse Compton scattering. These secondary photons can form an extended halo around bright VHE sources. Aims. We searched for an extended emission around the bright blazars Mrk 421 and Mrk 501 using the MAGIC telescope data. Methods. If extended emission is present, the angular distribution of reconstructed gamma-ray arrival directions around the source is broader than for a point-like source. In the analysis of a few tens of hours of observational data taken from Mrk 421 and Mrk 501 we used a newly developed method that provides better angular resolution. This method is based on the usage of multidimensional decision trees. Comparing the measured shapes of angular distributions with those expected from a point-like source one can detect or constrain possible extended emission around the source. We also studied the influence of different types of systematic errors on the shape of the distribution of reconstructed gamma-ray arrival directions for a point source. Results. We present upper limits for an extended emission calculated for both sources for various source extensions and emission profiles. We obtain upper limits on the extended emission around the Mrk 421 (Mrk 501) on the level of <5% (<4%) of the Crab Nebula flux above the energy threshold of 300 GeV. Using these results we discuss possible constraints on the extragalactic magnetic fields strength around a few times 10(-15) G