When the +1 nucleosome gets in the way, TFIIH fails but does not fall.

In this issue of Molecular Cell, Abril-Garrido et al.1 used cryo-EM to uncover that the +1 nucleosome inhibits transcription by interfering with the function of the TFIIH translocase via mechanisms that depend on its position relative to the transcription start site.

FACT is recruited to the +1 nucleosome of transcribed genes and spreads in a Chd1-dependent manner.

The histone chaperone FACT occupies transcribed regions where it plays prominent roles in maintaining chromatin integrity and preserving epigenetic information. How it is targeted to transcribed regions, however, remains unclear. Proposed models include docking on the RNA polymerase II (RNAPII) C-terminal domain (CTD), recruitment by elongation factors, recognition of modified histone tails, and binding partially disassembled nucleosomes. Here, we systematically test these and other scenarios in Saccharomyces cerevisiae and find that FACT binds transcribed chromatin, not RNAPII. Through a combination of high-resolution genome-wide mapping, single-molecule tracking, and mathematical modeling, we propose that FACT recognizes the +1 nucleosome, as it is partially unwrapped by the engaging RNAPII, and spreads to downstream nucleosomes aided by the chromatin remodeler Chd1. Our work clarifies how FACT interacts with genes, suggests a processive mechanism for FACT function, and provides a framework to further dissect the molecular mechanisms of transcription-coupled histone chaperoning.

Transcription-coupled nucleosome assembly.

Eukaryotic transcription occurs on chromatin, where RNA polymerase II encounters nucleosomes during elongation. These nucleosomes must unravel for the DNA to enter the active site. However, in most transcribed genes, nucleosomes remain intact due to transcription-coupled chromatin assembly mechanisms. These mechanisms primarily involve the local reassembly of displaced nucleosomes to prevent (epi)genomic instability and the emergence of cryptic transcription. As a fail-safe mechanism, cells can assemble nucleosomes de novo, particularly in highly transcribed genes, but this may result in the loss of epigenetic information. This review examines transcription-coupled chromatin assembly, with an emphasis on studies in yeast and recent structural studies. These studies shed light on how elongation factors and histone chaperones coordinate to enable nucleosome recycling during transcription.

RNA Polymerase II CTD Tyrosine 1 Is Required for Efficient Termination by the Nrd1-Nab3-Sen1 Pathway.

In Saccharomyces cerevisiae, transcription termination at protein-coding genes is coupled to the cleavage of the nascent transcript, whereas most non-coding RNA transcription relies on a cleavage-independent termination pathway involving Nrd1, Nab3, and Sen1 (NNS). Termination involves RNA polymerase II CTD phosphorylation, but a systematic analysis of the contribution of individual residues would improve our understanding of the role of the CTD in this process. Here we investigated the effect of mutating phosphorylation sites in the CTD on termination. We observed widespread termination defects at protein-coding genes in mutants for Ser2 or Thr4 but rare defects in Tyr1 mutants for this genes class. Instead, mutating Tyr1 led to widespread termination defects at non-coding genes terminating via NNS. Finally, we showed that Tyr1 is important for pausing in the 5' end of genes and that slowing down transcription suppresses termination defects. Our work highlights the importance of Tyr1-mediated pausing in NNS-dependent termination.

Yeast zinc cluster transcription factors involved in the switch from fermentation to respiration show interdependency for DNA binding revealing a novel type of DNA recognition.

In budding yeast, fermentation is the most important pathway for energy production. Under low-glucose conditions, ethanol is used for synthesis of this sugar requiring a shift to respiration. This process is controlled by the transcriptional regulators Cat8, Sip4, Rds2 and Ert1. We characterized Gsm1 (glucose starvation modulator 1), a paralog of Rds2 and Ert1. Genome-wide analysis showed that Gsm1 has a DNA binding profile highly similar to Rds2. Binding of Gsm1 and Rds2 is interdependent at the gluconeogenic gene FBP1. However, Rds2 is required for Gsm1 to bind at other promoters but not the reverse. Gsm1 and Rds2 also bind to DNA independently of each other. Western blot analysis revealed that Rds2 controls expression of Gsm1. In addition, we showed that the DNA binding domains of Gsm1 and Rds2 bind cooperatively in vitro to the FBP1 promoter. In contrast, at the HAP4 gene, Ert1 cooperates with Rds2 for DNA binding. Mutational analysis suggests that Gsm1/Rds2 and Ert1/Rds2 bind to short common DNA stretches, revealing a novel mode of binding for this class of factors. Two-point mutations in a HAP4 site convert it to a Gsm1 binding site. Thus, Rds2 controls binding of Gsm1 at many promoters by two different mechanisms: regulation of Gsm1 levels and increased DNA binding by formation of heterodimers.

Spt6 Gets in the Way of Polycomb to Promote ESC Pluripotency.

Despite expressing high levels of Polycomb group proteins, embryonic stem cells (ESCs) are refractory to H3K27 trimethylation, notably at super-enhancers regulating key pluripotency genes. In this issue of Molecular Cell, Wang et al. (2017) report that the histone chaperone Spt6 prevents H3K27 trimethylation of key ESC super-enhancers.

Tail and Kinase Modules Differently Regulate Core Mediator Recruitment and Function In Vivo.

Mediator is a highly conserved transcriptional coactivator organized into four modules, namely Tail, Middle, Head, and Kinase (CKM). Previous work suggests regulatory roles for Tail and CKM, but an integrated model for these activities is lacking. Here, we analyzed the genome-wide distribution of Mediator subunits in wild-type and mutant yeast cells in which RNA polymerase II promoter escape is blocked, allowing detection of transient Mediator forms. We found that although all modules are recruited to upstream activated regions (UAS), assembly of Mediator within the pre-initiation complex is accompanied by the release of CKM. Interestingly, our data show that CKM regulates Mediator-UAS interaction rather than Mediator-promoter association. In addition, although Tail is required for Mediator recruitment to UAS, Tailless Mediator nevertheless interacts with core promoters. Collectively, our data suggest that the essential function of Mediator is mediated by Head and Middle at core promoters, while Tail and CKM play regulatory roles.

Oxygen and magnesium mass-independent isotopic fractionation induced by chemical reactions in plasma.

Enrichment or depletion ranging from -40 to +100% in the major isotopes 16O and 24Mg were observed experimentally in solids condensed from carbonaceous plasma composed of CO2/MgCl2/Pentanol or N2O/Pentanol for O and MgCl2/Pentanol for Mg. In NanoSims imaging, isotope effects appear as micrometer-size hotspots embedded in a carbonaceous matrix showing no isotope fractionation. For Mg, these hotspots are localized in carbonaceous grains, which show positive and negative isotopic effects so that the whole grain has a standard isotope composition. For O, no specific structure was observed at hotspot locations. These results suggest that MIF (mass-independent fractionation) effects can be induced by chemical reactions taking place in plasma. The close agreement between the slopes of the linear correlations observed between δ25Mg versus δ26Mg and between δ17O versus δ18O and the slopes calculated using the empirical MIF factor η discovered in ozone [M. H. Thiemens, J. E. Heidenreich, III. Science 219, 1073-1075; C. Janssen, J. Guenther, K. Mauersberger, D. Krankowsky. Phys. Chem. Chem. Phys 3, 4718-4721] attests to the ubiquity of this process. Although the chemical reactants used in the present experiments cannot be directly transposed to the protosolar nebula, a similar MIF mechanism is proposed for oxygen isotopes: at high temperature, at the surface of grains, a mass-independent isotope exchange could have taken place between condensing oxides and oxygen atoms originated form the dissociation of CO or H2O gas.

Connection of core and tail Mediator modules restrains transcription from TFIID-dependent promoters.

The Mediator coactivator complex is divided into four modules: head, middle, tail, and kinase. Deletion of the architectural subunit Med16 separates core Mediator (cMed), comprising the head, middle, and scaffold (Med14), from the tail. However, the direct global effects of tail/cMed disconnection are unclear. We find that rapid depletion of Med16 downregulates genes that require the SAGA complex for full expression, consistent with their reported tail dependence, but also moderately overactivates TFIID-dependent genes in a manner partly dependent on the separated tail, which remains associated with upstream activating sequences. Suppression of TBP dynamics via removal of the Mot1 ATPase partially restores normal transcriptional activity to Med16-depleted cells, suggesting that cMed/tail separation results in an imbalance in the levels of PIC formation at SAGA-requiring and TFIID-dependent genes. We propose that the preferential regulation of SAGA-requiring genes by tailed Mediator helps maintain a proper balance of transcription between these genes and those more dependent on TFIID.

In situ study of the evolution of NiFe nanocatalysts in reductive and oxidative environments upon thermal treatments.

The conversion of biomass as a sustainable path to access valuable chemicals and fuels is very attractive for the chemical industry, but catalytic conversions still often rely on the use of noble metals. Sustainability constraints require developing alternative catalysts from abundant and low-cost metals. In this context, NiFe nanoparticles are interesting candidates. In their reduced and supported form, they have been reported to be more active and selective than monometallic Ni in the hydrogenation of the polar functions of organic molecules, and the two metals are very abundant. However, unlike noble metals, Ni and Fe are easily oxidized in ambient conditions, and understanding their transformation in both oxidative and reductive atmospheres is an important though seldom investigated issue to be addressed before their application in catalysis. Three types of NiFe nanoparticles were prepared by an organometallic approach to ensure the formation of ultrasmall nanoparticles (<3.5 nm) with a narrow size distribution, controlled composition and chemical order, while working in mild conditions: Ni2Fe1 and Ni1Fe1, both with a Ni rich core and Fe rich surface, and an alloy with a Ni1Fe9 composition. Supported systems were obtained by the impregnation of silica with a colloidal solution of the preformed nanoparticles. Using advanced characterization techniques, such as wide-angle X-ray scattering (WAXS) and X-ray absorption spectroscopy (XAS) in in situ conditions, this study reports on the evolution of the chemical order and of the oxidation state of the metals upon exposure to air, hydrogen, and/or increasing temperature, all factors that may affect their degree of reduction and subsequent performance in catalysis. We show that if oxidation readily occurs upon exposure to air, the metals can revert to their initial state upon heating in the presence of H2 but with a change in structure and chemical ordering.

The Histone Chaperones FACT and Spt6 Restrict H2A.Z from Intragenic Locations.

H2A.Z is a highly conserved histone variant involved in several key nuclear processes. It is incorporated into promoters by SWR-C-related chromatin remodeling complexes, but whether it is also actively excluded from non-promoter regions is not clear. Here we provide genomic and biochemical evidence that the RNA polymerase II (RNA Pol II) elongation-associated histone chaperones FACT and Spt6 both contribute to restricting H2A.Z from intragenic regions. In the absence of FACT or Spt6, the lack of efficient nucleosome reassembly coupled to pervasive incorporation of H2A.Z by mislocalized SWR-C alters chromatin composition and contributes to cryptic initiation. Therefore, chaperone-mediated H2A.Z confinement is crucial for restricting the chromatin signature of gene promoters that otherwise may license or promote cryptic transcription.

Titanium isotopes as a tracer for the plume or island arc affinity of felsic rocks.

Indirect evidence for the presence of a felsic continental crust, such as the elevated 49Ti/47Ti ratios in Archean shales, has been used to argue for ongoing subduction at that time and therefore plate tectonics. However, rocks of intermediate to felsic compositions can be produced in both plume and island arc settings. The fact that Ti behaves differently during magma differentiation in these two geological settings might result in contrasting isotopic signatures. Here, we demonstrate that, at a given SiO2 content, evolved plume rocks (tholeiitic) are more isotopically fractionated in Ti than differentiated island arc rocks (mainly calc-alkaline). We also show that the erosion of crustal rocks from whether plumes (mafic in average) or island arcs (intermediate in average) can all produce sediments having quite constant 49Ti/47Ti ratios being 0.1-0.3 per mille heavier than that of the mantle. This suggests that Ti isotopes are not a direct tracer for the SiO2 contents of crustal rocks. Ti isotopes in crustal sediments are still a potential proxy to identify the geodynamical settings for the formation of the crust but only if combined with additional SiO2 information.

Insights into the origin of carbonaceous chondrite organics from their triple oxygen isotope composition.

Dust grains of organic matter were the main reservoir of C and N in the forming Solar System and are thus considered to be an essential ingredient for the emergence of life. However, the physical environment and the chemical mechanisms at the origin of these organic grains are still highly debated. In this study, we report high-precision triple oxygen isotope composition for insoluble organic matter isolated from three emblematic carbonaceous chondrites, Orgueil, Murchison, and Cold Bokkeveld. These results suggest that the O isotope composition of carbonaceous chondrite insoluble organic matter falls on a slope 1 correlation line in the triple oxygen isotope diagram. The lack of detectable mass-dependent O isotopic fractionation, indicated by the slope 1 line, suggests that the bulk of carbonaceous chondrite organics did not form on asteroidal parent bodies during low-temperature hydrothermal events. On the other hand, these O isotope data, together with the H and N isotope characteristics of insoluble organic matter, may indicate that parent bodies of different carbonaceous chondrite types largely accreted organics formed locally in the protosolar nebula, possibly by photochemical dissociation of C-rich precursors.

A universal RNA polymerase II CTD cycle is orchestrated by complex interplays between kinase, phosphatase, and isomerase enzymes along genes.

Transcription by RNA polymerase II (RNAPII) is coupled to mRNA processing and chromatin modifications via the C-terminal domain (CTD) of its largest subunit, consisting of multiple repeats of the heptapeptide YSPTSPS. Pioneering studies showed that CTD serines are differentially phosphorylated along genes in a prescribed pattern during the transcription cycle. Genome-wide analyses challenged this idea, suggesting that this cycle is not uniform among different genes. Moreover, the respective role of enzymes responsible for CTD modifications remains controversial. Here, we systematically profiled the location of the RNAPII phosphoisoforms in wild-type cells and mutants for most CTD modifying enzymes. Together with results of in vitro assays, these data reveal a complex interplay between the modifying enzymes, and provide evidence that the CTD cycle is uniform across genes. We also identify Ssu72 as the Ser7 phosphatase and show that proline isomerization is a key regulator of CTD dephosphorylation at the end of genes.

Hydrogen isotope fractionation in methane plasma.

The hydrogen isotope ratio (D/H) is commonly used to reconstruct the chemical processes at the origin of water and organic compounds in the early solar system. On the one hand, the large enrichments in deuterium of the insoluble organic matter (IOM) isolated from the carbonaceous meteorites are interpreted as a heritage of the interstellar medium or resulting from ion-molecule reactions taking place in the diffuse part of the protosolar nebula. On the other hand, the molecular structure of this IOM suggests that organic radicals have played a central role in a gas-phase organosynthesis. So as to reproduce this type of chemistry between organic radicals, experiments based on a microwave plasma of CH4 have been performed. They yielded a black organic residue in which ion microprobe analyses revealed hydrogen isotopic anomalies at a submicrometric spatial resolution. They likely reflect differences in the D/H ratios between the various CHx radicals whose polymerization is at the origin of the IOM. These isotopic heterogeneities, usually referred to as hot and cold spots, are commensurable with those observed in meteorite IOM. As a consequence, the appearance of organic radicals in the ionized regions of the disk surrounding the Sun during its formation may have triggered the formation of organic compounds.

Bidirectional terminators in Saccharomyces cerevisiae prevent cryptic transcription from invading neighboring genes.

Transcription can be quite disruptive for chromatin so cells have evolved mechanisms to preserve chromatin integrity during transcription, thereby preventing the emergence of cryptic transcripts from spurious promoter sequences. How these transcripts are regulated and processed remains poorly characterized. Notably, very little is known about the termination of cryptic transcripts. Here, we used RNA-Seq to identify and characterize cryptic transcripts in Spt6 mutant cells (spt6-1004) in Saccharomyces cerevisiae. We found polyadenylated cryptic transcripts running both sense and antisense relative to genes in this mutant. Cryptic promoters were enriched for TATA boxes, suggesting that the underlying DNA sequence defines the location of cryptic promoters. While intragenic sense cryptic transcripts terminate at the terminator of the genes that host them, we found that antisense cryptic transcripts preferentially terminate near the 3΄-end of the upstream gene. This finding led us to demonstrate that most terminators in yeast are bidirectional, leading to termination and polyadenylation of transcripts coming from both directions. We propose that S. cerevisiae has evolved this mechanism in order to prevent/attenuate spurious transcription from invading neighbouring genes, a feature that is particularly critical for organisms with small compact genomes.

Bidirectional terminators: an underestimated aspect of gene regulation.

Recent experimental and computational work revealed that transcriptional terminators in Saccharomyces cerevisiae can terminate transcription coming from both directions. This mechanism helps budding yeast cope with the pervasive nature of transcription by limiting aberrant transcription from invading neighboring genes.

Histone chaperones FACT and Spt6 prevent histone variants from turning into histone deviants.

Histone variants are specialized histones which replace their canonical counterparts in specific nucleosomes. Together with histone post-translational modifications and DNA methylation, they contribute to the epigenome. Histone variants are incorporated at specific locations by the concerted action of histone chaperones and ATP-dependent chromatin remodelers. Recent studies have shown that the histone chaperone FACT plays key roles in preventing pervasive incorporation of two histone variants: H2A.Z and CenH3/CENP-A. In addition, Spt6, another histone chaperone, was also shown to be important for appropriate H2A.Z localization. FACT and Spt6 are both associated with elongating RNA polymerase II. Based on these two examples, we propose that the establishment and maintenance of histone variant genomic distributions depend on a transcription-coupled epigenome editing (or surveillance) function of histone chaperones.

Yeast RNase III triggers polyadenylation-independent transcription termination.

Transcription termination of messenger RNA (mRNA) is normally achieved by polyadenylation followed by Rat1p-dependent 5'-3' exoribonuleolytic degradation of the downstream transcript. Here we show that the yeast ortholog of the dsRNA-specific ribonuclease III (Rnt1p) may trigger Rat1p-dependent termination of RNA transcripts that fail to terminate near polyadenylation signals. Rnt1p cleavage sites were found downstream of several genes, and the deletion of RNT1 resulted in transcription readthrough. Inactivation of Rat1p impaired Rnt1p-dependent termination and resulted in the accumulation of 3' end cleavage products. These results support a model for transcription termination in which cotranscriptional cleavage by Rnt1p provides access for exoribonucleases in the absence of polyadenylation signals.

The negligible chondritic contribution in the lunar soils water.

Recent data from Apollo samples demonstrate the presence of water in the lunar interior and at the surface, challenging previous assumption that the Moon was free of water. However, the source(s) of this water remains enigmatic. The external flux of particles and solid materials that reach the surface of the airless Moon constitute a hydrogen (H) surface reservoir that can be converted to water (or OH) during proton implantation in rocks or remobilization during magmatic events. Our original goal was thus to quantify the relative contributions to this H surface reservoir. To this end, we report NanoSIMS measurements of D/H and (7)Li/(6)Li ratios on agglutinates, volcanic glasses, and plagioclase grains from the Apollo sample collection. Clear correlations emerge between cosmogenic D and (6)Li revealing that almost all D is produced by spallation reactions both on the surface and in the interior of the grains. In grain interiors, no evidence of chondritic water has been found. This observation allows us to constrain the H isotopic ratio of hypothetical juvenile lunar water to δD ≤ -550‰. On the grain surface, the hydroxyl concentrations are significant and the D/H ratios indicate that they originate from solar wind implantation. The scattering distribution of the data around the theoretical D vs. (6)Li spallation correlation is compatible with a chondritic contribution <15%. In conclusion, (i) solar wind implantation is the major mechanism responsible for hydroxyls on the lunar surface, and (ii) the postulated chondritic lunar water is not retained in the regolith.