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.

Efficient biomass pretreatment using ionic liquids derived from lignin and hemicellulose.

Ionic liquids (ILs), solvents composed entirely of paired ions, have been used in a variety of process chemistry and renewable energy applications. Imidazolium-based ILs effectively dissolve biomass and represent a remarkable platform for biomass pretreatment. Although efficient, imidazolium cations are expensive and thus limited in their large-scale industrial deployment. To replace imidazolium-based ILs with those derived from renewable sources, we synthesized a series of tertiary amine-based ILs from aromatic aldehydes derived from lignin and hemicellulose, the major by-products of lignocellulosic biofuel production. Compositional analysis of switchgrass pretreated with ILs derived from vanillin, p-anisaldehyde, and furfural confirmed their efficacy. Enzymatic hydrolysis of pretreated switchgrass allowed for direct comparison of sugar yields and lignin removal between biomass-derived ILs and 1-ethyl-3-methylimidazolium acetate. Although the rate of cellulose hydrolysis for switchgrass pretreated with biomass-derived ILs was slightly slower than that of 1-ethyl-3-methylimidazolium acetate, 90-95% glucose and 70-75% xylose yields were obtained for these samples after 72-h incubation. Molecular modeling was used to compare IL solvent parameters with experimentally obtained compositional analysis data. Effective pretreatment of lignocellulose was further investigated by powder X-ray diffraction and glycome profiling of switchgrass cell walls. These studies showed different cellulose structural changes and differences in hemicellulose epitopes between switchgrass pretreatments with the aforementioned ILs. Our concept of deriving ILs from lignocellulosic biomass shows significant potential for the realization of a "closed-loop" process for future lignocellulosic biorefineries and has far-reaching economic impacts for other IL-based process technology currently using ILs synthesized from petroleum sources.

DSIF and RNA polymerase II CTD phosphorylation coordinate the recruitment of Rpd3S to actively transcribed genes.

Histone deacetylase Rpd3 is part of two distinct complexes: the large (Rpd3L) and small (Rpd3S) complexes. While Rpd3L targets specific promoters for gene repression, Rpd3S is recruited to ORFs to deacetylate histones in the wake of RNA polymerase II, to prevent cryptic initiation within genes. Methylation of histone H3 at lysine 36 by the Set2 methyltransferase is thought to mediate the recruitment of Rpd3S. Here, we confirm by ChIP-Chip that Rpd3S binds active ORFs. Surprisingly, however, Rpd3S is not recruited to all active genes, and its recruitment is Set2-independent. However, Rpd3S complexes recruited in the absence of H3K36 methylation appear to be inactive. Finally, we present evidence implicating the yeast DSIF complex (Spt4/5) and RNA polymerase II phosphorylation by Kin28 and Ctk1 in the recruitment of Rpd3S to active genes. Taken together, our data support a model where Set2-dependent histone H3 methylation is required for the activation of Rpd3S following its recruitment to the RNA polymerase II C-terminal domain.

Synthetic approaches to monofluoroalkenes.

Monofluoroalkenes are an important fluorinated class of compounds with applications in medicinal chemistry, material sciences and organic chemistry. An overview of methods allowing synthetic access to these fluorinated building blocks is provided. In particular, this critical review, which covers publications up to October 2010, will be divided according to the substitution pattern of the monofluoroalkenes, i.e. di-, tri- or tetra-substituted. Within each group, the various synthetic approaches will be divided according to the reaction type (282 references).

Effect of Early Supraglottic Airway Device Insertion on Chest Compression Fraction during Simulated Out-of-Hospital Cardiac Arrest: Randomised Controlled Trial.

Early insertion of a supraglottic airway (SGA) device could improve chest compression fraction by allowing providers to perform continuous chest compressions or by shortening the interruptions needed to deliver ventilations. SGA devices do not require the same expertise as endotracheal intubation. This study aimed to determine whether the immediate insertion of an i-gel® while providing continuous chest compressions with asynchronous ventilations could generate higher CCFs than the standard 30:2 approach using a face-mask in a simulation of out-of-hospital cardiac arrest. A multicentre, parallel, randomised, superiority, simulation study was carried out. The primary outcome was the difference in CCF during the first two minutes of resuscitation. Overall and per-cycle CCF quality of compressions and ventilations parameters were also compared. Among thirteen teams of two participants, the early insertion of an i-gel® resulted in higher CCFs during the first two minutes (89.0% vs. 83.6%, p = 0.001). Overall and per-cycle CCF were consistently higher in the i-gel® group, even after the 30:2 alternation had been resumed. In the i-gel® group, ventilation parameters were enhanced, but compressions were significantly shallower (4.6 cm vs. 5.2 cm, p = 0.007). This latter issue must be addressed before clinical trials can be considered.

Strain-dependent recovery of spontaneous hindlimb movement in spinal cord transected mice (CD1, C57BL/6, BALB/c).

Reorganization and plasticity after spinal cord injury have been recently shown to take place in sublesional neuronal networks, but the possibility of strain-dependent changes at that level has never been explored. The authors studied the spontaneous return of hindlimb movement in low-thoracic spinal cord transected (Tx) mice from 3 commonly used strains. Without intervention, most CD1, C57BL/6, and BALB/c mice displayed some hindlimb movement recovery after Tx. Although all assessment methods unanimously reported that CD1 displayed higher recovery levels than did the C57BL/6 and BALB/c, higher scores were generally found with the Antri-Orsal-Barthe (M. Antri, D. Orsal, & J. Y. Barthe, 2002) and the Average Combined Score (P. A. Guertin, 2005a) methods. Such spontaneous recovery in low-thoracic Tx mice is likely the result of neuronal plasticity at the lumbosacral spinal cord level, suggesting that these sublesional changes are strain dependent.

S(N)2' reaction of allylic difluorides with lithium amides and thiolates.

The synthesis of monofluoroalkenes using an S(N)2' reaction of lithium amides derived from aromatic amines or lithium thiolates with 3,3-difluoropropenes is reported. This transformation features the use of fluoride as a leaving group.

Systematic identification of fragile sites via genome-wide location analysis of gamma-H2AX.

Phosphorylation of histone H2AX is an early response to DNA damage in eukaryotes. In Saccharomyces cerevisiae, DNA damage or replication-fork stalling results in phosphorylation of histone H2A yielding gamma-H2A (yeast gamma-H2AX) in a Mec1 (ATR)- and Tel1 (ATM)-dependent manner. Here, we describe the genome-wide location analysis of gamma-H2A as a strategy to identify loci prone to engaging the Mec1 and Tel1 pathways. Notably, gamma-H2A enrichment overlaps with loci prone to replication-fork stalling and is caused by the action of Mec1 and Tel1, indicating that these loci are prone to breakage. Moreover, about half the sites enriched for gamma-H2A map to repressed protein-coding genes, and histone deacetylases are necessary for formation of gamma-H2A at these loci. Finally, our work indicates that high-resolution mapping of gamma-H2AX is a fruitful route to map fragile sites in eukaryotic genomes.