Distinctive regulatory architectures of germline-active and somatic genes in C. elegans.

RNA profiling has provided increasingly detailed knowledge of gene expression patterns, yet the different regulatory architectures that drive them are not well understood. To address this, we profiled and compared transcriptional and regulatory element activities across five tissues of Caenorhabditis elegans, covering ∼90% of cells. We find that the majority of promoters and enhancers have tissue-specific accessibility, and we discover regulatory grammars associated with ubiquitous, germline, and somatic tissue-specific gene expression patterns. In addition, we find that germline-active and soma-specific promoters have distinct features. Germline-active promoters have well-positioned +1 and -1 nucleosomes associated with a periodic 10-bp WW signal (W = A/T). Somatic tissue-specific promoters lack positioned nucleosomes and this signal, have wide nucleosome-depleted regions, and are more enriched for core promoter elements, which largely differ between tissues. We observe the 10-bp periodic WW signal at ubiquitous promoters in other animals, suggesting it is an ancient conserved signal. Our results show fundamental differences in regulatory architectures of germline and somatic tissue-specific genes, uncover regulatory rules for generating diverse gene expression patterns, and provide a tissue-specific resource for future studies.

Stable Caenorhabditis elegans chromatin domains separate broadly expressed and developmentally regulated genes.

Eukaryotic genomes are organized into domains of differing structure and activity. There is evidence that the domain organization of the genome regulates its activity, yet our understanding of domain properties and the factors that influence their formation is poor. Here, we use chromatin state analyses in early embryos and third-larval stage (L3) animals to investigate genome domain organization and its regulation in Caenorhabditis elegans At both stages we find that the genome is organized into extended chromatin domains of high or low gene activity defined by different subsets of states, and enriched for H3K36me3 or H3K27me3, respectively. The border regions between domains contain large intergenic regions and a high density of transcription factor binding, suggesting a role for transcription regulation in separating chromatin domains. Despite the differences in cell types, overall domain organization is remarkably similar in early embryos and L3 larvae, with conservation of 85% of domain border positions. Most genes in high-activity domains are expressed in the germ line and broadly across cell types, whereas low-activity domains are enriched for genes that are developmentally regulated. We find that domains are regulated by the germ-line H3K36 methyltransferase MES-4 and that border regions show striking remodeling of H3K27me1, supporting roles for H3K36 and H3K27 methylation in regulating domain structure. Our analyses of C. elegans chromatin domain structure show that genes are organized by type into domains that have differing modes of regulation.

The DREAM complex promotes gene body H2A.Z for target repression.

The DREAM (DP, Retinoblastoma [Rb]-like, E2F, and MuvB) complex controls cellular quiescence by repressing cell cycle genes, but its mechanism of action is poorly understood. Here we show that Caenorhabditis elegans DREAM targets have an unusual pattern of high gene body HTZ-1/H2A.Z. In mutants of lin-35, the sole p130/Rb-like gene in C. elegans, DREAM targets have reduced gene body HTZ-1/H2A.Z and increased expression. Consistent with a repressive role for gene body H2A.Z, many DREAM targets are up-regulated in htz-1/H2A.Z mutants. Our results indicate that the DREAM complex facilitates high gene body HTZ-1/H2A.Z, which plays a role in target gene repression.

Airway management success and hypoxemia rates in air and ground critical care transport: a prospective multicenter study.

OBJECTIVE: To assess critical care transport (CCT) crews' endotracheal intubation (ETI) attempts, success rates, and peri-ETI oxygenation. METHODS: Participants were adult and pediatric patients undergoing attempted advanced airway management during the period from July 2007 to December 2008 by crews from 11 CCT programs varying in geography, crew configuration, and casemix; all crews had access to neuromuscular-blocking agents. Data collected included airway management variables defined per national consensus criteria. Descriptive analysis focused on ETI success rates (reported with exact binomial 95% confidence intervals [CIs]) and occurrence of new hypoxemia (oxygen saturation [SpO(2)] dropping below 90% during or after ETI); to assess categorical variables, Fisher's exact test, Pearson chi(2), and logistic regression were employed to explore associations between predictor variables and ETI failure or new hypoxemia. For all tests, p < 0.05 defined significance. RESULTS: There were 603 total attempts at airway management, with successful oral or nasal ETI in 582 cases, or 96.5% (95% CI 94.7-97.8%). In 182 cases (30.2%, 95% CI 26.5-34.0%), there were failed ETI attempts prior to CCT crew arrival; CCT crew ETI success on these patients (96.2%, 95% CI 92.2-98.4%) was just as high as in the patients in whom there was no pre-CCT ETI attempt (p = 0.81). New hypoxemia occurred in only six cases (1.6% of the 365 cases with ongoing SpO(2) monitoring; 95% CI 0.6-3.5%); the only predictor of new hypoxemia was pre-ETI hypotension (p < 0.001). A requirement for multiple ETI attempts by CCT crews was not associated with new hypoxemia (Fisher's exact p = 0.13). CONCLUSIONS: CCT crews' ETI success rates were very high, and even when ETI required multiple attempts, airway management was rarely associated with SpO(2) derangement. CCT crews' ETI success rates were equally high in the subset of patients in whom ground emergency medical services (EMS) ETI failed prior to arrival of transport crews.

C. elegans HLH-2/E/Daughterless controls key regulatory cells during gonadogenesis.

The Caenorhabditis elegans distal tip cell (DTC) provides a niche for germline stem cells in both hermaphrodites and males. The hermaphrodite distal tip cell (hDTC) also provides "leader" function to control gonadal elongation and shape, while in males, leader function is allocated to the linker cell (LC). Therefore, the male distal tip cell (mDTC) serves as a niche but not as a leader. The C. elegans homolog of E/Daughterless, HLH-2, was previously implicated in hDTC specification. Here we report that HLH-2 is also critical for hDTC maintenance, hDTC niche function and hDTC expression of a lag-2/DSL ligand reporter. We also find that HLH-2 functions in males to direct linker cell specification and to promote both mDTC maintenance and the mDTC niche function. We conclude that HLH-2 functions in both sexes to promote leader cell specification and DTC niche function.

Wnt signaling and CEH-22/tinman/Nkx2.5 specify a stem cell niche in C. elegans.

Wnt signaling regulates many aspects of metazoan development, including stem cells. In C. elegans, Wnt/MAPK signaling controls asymmetric divisions. A recent model proposed that the POP-1/TCF DNA binding protein works together with SYS-1/beta-catenin to activate transcription of target genes in response to Wnt/MAPK signaling. The somatic gonadal precursor (SGP) divides asymmetrically to generate distal and proximal daughters of distinct fates: only its distal daughter generates a distal tip cell (DTC), which is required for stem cell maintenance. No DTCs are produced in the absence of POP-1/TCF or SYS-1/beta-catenin, and extra DTCs are made upon overexpression of SYS-1/beta-catenin. Here we report that POP-1/TCF and SYS-1/beta-catenin directly activate transcription of ceh-22/nkx2.5 isoforms in SGP distal daughters, a finding that confirms the proposed model of Wnt/MAPK signaling. In addition, we demonstrate that the CEH-22/Nkx2.5 homeodomain transcription factor is a key regulator of DTC specification. We speculate that these conserved molecular regulators of the DTC niche in nematodes may provide insight into specification of stem cell niches more broadly.

gon-14 functions with class B and class C synthetic multivulva genes to control larval growth in Caenorhabditis elegans.

Previous work showed that C. elegans gon-14 is required for gonadogenesis. Here we report that gon-14 encodes a protein with similarity to LIN-15B, a class B synMuv protein. An extensive region of GON-14 contains blocks of sequence similarity to transposases of the hAT superfamily, but key residues are not conserved, suggesting a distant relationship. GON-14 also contains a putative THAP DNA-binding domain. A rescuing gon-14::GON-14::VENUS reporter is broadly expressed during development and localizes to the nucleus. Strong loss-of-function and predicted null gon-14 alleles have pleiotropic defects, including multivulval (Muv) defects and temperature-sensitive larval arrest. Although the gon-14 Muv defect is not enhanced by synMuv mutations, gon-14 interacts genetically with class B and class C synMuv genes, including lin-35/Rb, let-418/Mi-2beta, and trr-1/TRRAP. The gon-14; synMuv double mutants arrest as larvae when grown under conditions supporting development to adulthood for the respective single mutants. The gon-14 larval arrest is suppressed by loss of mes-2/E(Z), mes-6/ESC, or mes-4, which encodes a SET domain protein. Additionally, gon-14 affects expression of pgl-1 and lag-2, two genes regulated by the synMuv genes. We suggest that gon-14 functions with class B and class C synMuv genes to promote larval growth, in part by antagonizing MES-2,3,6/ESC-E(z) and MES-4.

The sys-1 and sys-3 genes cooperate with Wnt signaling to establish the proximal-distal axis of the Caenorhabditis elegans gonad.

To form the proximal-distal axis of the C. elegans gonad, two somatic gonadal precursor cells, Z1 and Z4, divide asymmetrically to generate one daughter with a proximal fate and one with a distal fate. Genes governing this process include the lin-17 frizzled receptor, wrm-1/beta-catenin, the pop-1/TCF transcription factor, lit-1/nemo-like kinase, and the sys-1 gene. Normally, all of these regulators promote the distal fate. Here we show that nuclear levels of a pop-1 GFP fusion protein are less abundant in the distal than in the proximal Z1/Z4 daughters. This POP-1 asymmetry is lost in mutants disrupting Wnt/MAPK regulation, but retained in sys-1 mutants. We find that sys-1 is haplo-insufficient for gonadogenesis defects and that sys-1 and pop-1 mutants display a strong genetic interaction in double heterozygotes. Therefore, sys-1 is a dose-sensitive locus and may function together with pop-1 to control Z1/Z4 asymmetry. To identify other regulatory genes in this process, we screened for mutants resembling sys-1. Four such genes were identified (gon-14, -15, -16, and sys-3) and shown to interact genetically with sys-1. However, only sys-3 promotes the distal fate at the expense of the proximal fate. We suggest that sys-3 is a new key gene in this pathway and that gon-14, gon-15, and gon-16 may cooperate with POP-1 and SYS-1 at multiple stages of gonad development.

Differential uptake of volatile agents into brain tissue in vitro. Measurement and application of a diffusion model to determine concentration profiles in brain slices.

BACKGROUND: The rate of onset of drug actions in experiments with brain slices in vitro can vary widely. One factor that influences the rate is access to tissue sites of action. To study the effects of the nonimmobilizer 1,2-dichlorohexafluorocyclobutane (F6, also termed 2N in the literature) on physiologic processes under defined tissue concentrations, the authors performed electrophysiologic measurements of the effects of F6 and halothane, measured the uptake of these agents into brain tissue, and performed computational modeling to determine concentration-depth profiles during drug application. METHODS: Hippocampal brain slices 500 microm thick were prepared from adult rats. Evoked population responses in the CA1 region were obtained using extracellular recordings and electrical stimulation of the Schaffer collateral pathway. F6 (24 microm) and halothane (270 microm) were applied via superfusion for 40 min. Uptake of drug into tissue slices was measured using gas chromatography. Computational modeling was used to obtain estimates of drug diffusion coefficients in brain tissue and to calculate tissue concentration as a function of time and depth during drug application. RESULTS: Halothane reduced the amplitude of the evoked population spike and reduced the population excitatory postsynaptic potential slope. F6 had no effect on either measure. Uptake experiments yielded a diffusion coefficient of 0.1 x 10-6 cm2/s for F6 and 0.8 x 10-6 cm2/s for halothane. After 40 min of drug application, the concentration reached at tissue depths from which physiologic signals were obtained, approximately the top 200 microm of the slice, was estimated to be 58% of the final equilibrium value for F6 and 93% for halothane. CONCLUSIONS: Diffusion into tissue is substantially slower for F6 than for halothane, and its impact is great enough that this must be considered when designing or interpreting in vitro experiments. However, impaired access does not account for the lack of effect of F6 on electrophysiologic responses in rat hippocampal slices.