Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters

Long-range interactions between regulatory elements and gene promoters play key roles in transcriptional regulation.The vast majority of interactions are uncharted,constituting a major missing link in understanding genome control.Here,we use promoter capture Hi-C to identify interacting regions of 31,253 promoters in 17 human primary hematopoietic cell types.We show that promoter interactions are highly cell type specific and enriched for links between active promoters and epigenetically marked enhancers.Promoter interactomes reflect lineage relationships of the hematopoietic tree,consistent with dynamic remodeling of nuclear architecture during differentiation.Interacting regions are enriched in genetic variants linked with altered expression of genes they contact,highlighting their functional role.We exploit this rich resource to connect non-coding disease variants to putative target promoters,prioritizing thousands of disease-candidate genes and implicating disease pathways.Our results demonstrate the power of primary cell promoter interactomes to reveal insights into genomic regulatory mechanisms underlying common diseases.

Theoretical study on the morphology of cobalt nanoparticles modulated by alkali metal promoters

Cobalt nanoparticles(NPs)catalysts are extensively used in heterogeneous catalytic reactions,and the addition of alkali metal promoters is a common method to modulate the catalytic performance because the catalyst's surface structures and morphologies are sensitive to the addition of promoters.However,the underlying modulation trend remains unclear.Herein,the adsorption of alkali metal promoters(Na and K)on the surfaces of face-centered-cubic(FCC)and hexagonal-closest packed(HCP)polymorphous cobalt was systematically investigated using density functional theory.Furthermore,the effect of alkali promoters on surface energies and nanoparticle morphologies was revealed on the basis of Wulff theory.For FCC-Co,the exposed area of the(111)facet in the nanoparticle increases with the adsorption coverage of alkali metal oxide.Meanwhile,the(311),(110),and(100)facets would disappear under the higher adsorption coverage of alkali metals.For HCPCo,the Wulff morphology is dominated by the(0001)and(1011)facets and is independent of the alkali metal adsorption coverage.This work provides insights into morphology modulation by alkali metal promoters for the rational design and synthesis of cobalt-based nanomaterials with desired facets and morphologies.

Effects of Supports and Promoters on in situ Hydrogenation of o-Cresol over Ni-based Catalysts

We investigated the effects of supports （CMK-3, SiO2ZrO2, MgO, Al2O3） and promoters （Cu, Ce, Fe） on textual properties of Ni based catalysts. o-Cresol was used as a probe to test the activity of these catalysts under the condition of 230 ℃ and nitrogen pres-sure of 0.1 MPa. The catalysts were characterized by X-ray diffraction, H2 temperature programmed reduction ammonium programmed desorption, and N2 adsorption-desorption isotherms. The results showed that the catalytic performance of Ni/CMK-3 （the conversion of o-cresol reached 45.4%） was significantly better than the other three kinds of supports. The modification of Ni/CMK-3 was also investigated and over 60% conversion of o-cresol was obtained after the addition of Ce （64.6%）and Cu （66.8%） in Ni/CMK-3, whereas the addition of Fe led to a decrease of conversion. In the meantime, Cu changed the products dis-tribution. The appearance of toluene indicated that another pathway existed in the reaction.Accompanied by the ascension of conversion in both sides, side effects also occurred and got more serious. The apparent order of activity for all the tested catalysts was NiCe/CMK-3〉NiCu/CMK-3〉Ni/CMK-3〉NiFe/CMK-3〉Ni/Al2O3Ni/SiO2ZrO2〉Ni/MgO. The reac-tion pathway, involving three routes, was also mentioned in this study.

Systematic identification of endogenous RNA polymeraseⅢpromoters for efficient RNA guidebased genome editing technologies in maize

Single-guide RNA(sg RNA) is one of the two core components of the CRISPR(clustered regularly interspaced short palindromic repeat)/Cas(CRISPR-associated) genome-editing technology. We established an in vitro Traffic Light Reporter(TLR) system, which is designated as the same colors as traffic lights such as green, red and yellow were produced in cells. The TLR can be readily used in maize mesophyll protoplast for a quick test of promoter activity. The TLR assay indicates the variation in transcription activities of the seven Pol III promoters, from 3.4%(U6-1) to over 21.0%(U6-6). The U6-2 promoter, which was constructed to drive sg RNA expression targeting the Zm Wx1 gene, yielded mutation efficiencies ranging from 48.5% to 97.1%. Based on the reported and unpublished data, the in vitro TLR assay results were confirmed to be a readily system and may be extended to other plant species amenable to efficient genome editing via CRISPR/Cas. Our efforts provide an efficient method of identifying native Pol III-recognized promoters for RNA guide-based genome-editing systems in maize.

A comprehensive review of the effect of different kinetic promoters on methane hydrate formation

Gas hydrates have recently emerged as a better alternative for the production,storage,and transportation of natural gases.However,factors like slow formation rate and limited storage capacity obstruct the possible industrial application of this technique.Different types of promoters and synergists have been developed that can improve the kinetics and storage capacity of gas hydrates.This review focuses on different kinetic promoters and synergists that can be utilized to enhance the storage capacity of hydrates.The main characteristics,structure and the possible limitations of the use of these promoters are likewise portrayed in detail.The relationship between structure and storage capacity of hydrates have also been discussed in the review.Current status of production of gas from hydrates,their restrictions,and future difficulties have additionally been addressed in the ensuing areas of the review.

Effect of CO Combustion Promoters on Combustion Air Partition in FCC under Nearly Complete Combustion

With CO combustion promoters, the role of combustion air flow rate for concerns of economics and control is important. The combustion air is conceptually divided to three parts: the air consumed by coke burning,the air consumed by CO combustion and the air unreacted. A mathematical model of a fluid catalytic cracking(FCC)unit, which includes a quantitative correlation of CO heterogeneous combustion and the amount of CO combustion promoters, is introduced to investigate the effects of promoters on the three parts of combustion air. The results show that the air consumed by coke burning is almost linear to combustion air flow rate, while the air consumed by CO combustion promoters tends to saturate as combustion air flow rate increases, indicating that higher air flow rate can only be used as a manipulated variable to control the oxygen content for an economic concern.

Fischer–Tropsch synthesis over iron catalysts with corncob-derived promoters

A sustainable strategy for Fischer–Tropsch iron catalysts is successfully achieved by embedding of synergistic promoters from a renewable resource, corncob. The iron-based catalysts, named as 'corncob-driven'catalysts, are composed of iron species supported on carbon as primary active components and various minerals(K, Mg, Ca, and Si, etc.) as promoters. The corncob-driven catalysts are facilely synthesized by a one-pot hydrothermal treatment under mild conditions. The characterization results indicate that the formation of iron carbides from humboldtine is clearly enhanced and the morphology of catalyst particles tends to be more regular microspheres after adding corncob. It is observed that the optimized corncob-driven catalyst exhibits a higher conversion than without promoters' catalyst in Fischer–Tropsch synthesis(ca. 73% vs. ca. 49%). More importantly, a synergistic effect exists in multiple promoters from corncob that can enhance heavy hydrocarbons selectivity and lower CO_2 selectivity, obviously different from the catalyst with promoters from chemicals. The proposed synthesis route of corncob-driven catalysts provides new strategies for the utilization of renewable resources and elimination of environmental pollutants from chemical promoters.

Identification and validation of root-specific promoters in rice

Novel promoters that confer root-specific expression would be useful for engineering resistance against problems of nutrient and water absorption by roots. In this study, the reverse transcriptase polymerase chain reaction was used to identify seven genes with root-specific expression in rice. The isolation and characterization of upstream promoter regions of five selected genes rice root-specific promoter （rRSP） 1 to 5 （rRSP1-rRSP5） and A2P （the promoter of OsAct2） revealed that rRSP1, rRSP3, and rRSP5 are particularly important with respect to root-specific activities. Furthermore, rRSP1, rRSP3, and rRSP5 were observed to make different contributions to root activities in various species. These three promoters could be used for root-specific enhancement of target gene（s）.

Effects of Several Transmucosal Absorption Promoters on Buccally Administered Insulin in Rats

目的：研究吸收促进剂对大鼠胰岛素溶液（insulin solution,INS-SOL)口腔给药的吸收促进作用。方法：以血糖水平为指标，考察在各种吸收促进剂的影响下INS－SOL经正常大鼠口腔给药后的降血糖作用，以皮下注射为对照，计算不同条件下INS－SOL的药理生物利用度（pharmacological bioavailability,PA)。结果：不加吸收促进剂的条件下，10U·kg^-1的INS－SOL经口腔给药后的生物利用较低（PA＝6．9％）。十二烷基硫酸钠（5％，PA＝14．5％），苄泽78（5％，PA＝20．6％），脱氧胆酸钠（5％，PA＝6．5％）和卵磷酯（10％，PA＝13．8％）均显著地增加INS－SOL的降血糖作用。苄泽78（5％）可使INS－SOL（5U·kg^-1)的PA最高达到33％。结论：在适当的吸收促进剂的作用下INS－SOL经口腔给药后具有显著的降血糖效果。

Preparation of Nanoporous Carbonaceous Promoters for Enhanced CO2 Absorption in Tertiary Amines

Aqueous solutions of tertiary amines are promising absorbents for CO2 capture,as they are typically characterized by a high absorption capacity,low heat of reaction,and low corrosivity.However,tertiary amines also exhibit very low kinetics of CO2 absorption,which has made them unattractive options for large-scale utilization.Here,a series of novel nanoporous carbonaceous promoters(NCPs)with different properties were synthesized,characterized,and used as rate promoters for CO2 absorption in aqueous N,N-diethylethanolamine(DEEA)solutions.To prepare a DEEA–NCP nanofluid,NCPs were dispersed into aqueous 3 mol∙L1 DEEA solution using ultrasonication.The results revealed that among microporous(GC)and mesoporous(GS)carbonaceous structures functionalized with ethylenediamine(EDA)and polyethyleneimine(PEI)molecules,the GC–EDA promoter exhibited the best performance.A comparison between DEEA–GC–EDA nanofluid and typical aqueous DEEA solutions highlighted that the GC-EDA promoter enhances the rate of CO2 absorption at 40C by 38.6%(36.8–50.7 kPamin1)and improves the equilibrium CO2 absorption capacity(15 kPa;40C)by 13.2%(0.69–0.78 mol of CO2 per mole of DEEA).Moreover,the recyclability of DEEA–GC–EDA nanofluid was determined and a promotion mechanism is suggested.The outcomes demonstrate that NCP–GC–EDA in tertiary amines is a promising strategy to enhance the rate of CO2 absorption and facilitate their large-scale deployment.

Elucidating the effect of barium halide promoters on La_(2)O_(3)/CaO catalyst for oxidative coupling of methane

The industrialization of oxidative coupling of methane(OCM)is restricted by the low once through yield of C_(2)hydrocarbons.Recently,the halogen-assisted OCM process has been attempted to overcome this issue,but the reaction stability was poor due to the rapid loss of gas-phase halides or molten alkali halides.In this work,the barium salts,particularly barium halides(BaCl_(2)and BaF_(2)),were demonstrated to be efficient promoters to improve the OCM reactivity of La_(2)O_(3)/CaO catalyst by increasing both C_(2)selectivity and C_(2)H_(4)/C_(2)H_(6)ratio,and simultaneously achieving outstanding reaction stability.The promoting mechanism can be understood in two aspects.On the one hand,the introduction of barium salts increased the amount of surface electrophilic oxygen species,serving as the alkaline active sites for selective methane activation.On the other hand,the barium halide additives induced the in-situ formation of methyl halide intermediates facilitating C_(2)H_(6)dehydrogenation,and their intimate contact with catalyst substrate restricted the rapid halogen loss and thereby improved the catalytic stability.This work not only provides a class of efficient OCM catalyst,but also offers a highly stable halogen-assisted reaction strategy.

Histone methylation in Huntington's disease:are bivalent promoters the critical targets?

Huntington’s disease（HD）is a currently incurable,late onset,progressive,ultimately fatal neurological disorder（Bates et al.,2015）.We have recently published the results of comprehensive genetic interaction tests aimed at identification of histone methyltransferases and demethylases involved in HD pathogenesis in a Drosophila model of the disease（Song et al.,2018）.

Genome-wide Characterization of cis-acting Elements in the Promoters of Key Carotenoid Pathway Genes from the Main Species of Genus Citrus

Carotenoids are indispensable for both human health and plant survival.Citrus,is one of the fruit crops richest in carotenoid compounds,with approximately 115 kinds of carotenoids;tremendous diversity in carotenoids composition and concentration exists among various species,showing different colors from nearly white to crimson.The carotenoid biosynthetic pathway and the key carotenogenic genes have been identified in citrus;however,the underlying regulatory mechanisms remain unclear.In this study,among the main species of genus Citrus(primitive,wild,and cultivated),we detected carotenoids in flavedo using High-Performance Liquid Chromatography,and analyzed variations in cis-acting elements in the promoters of key carotenoid pathway genes.Intriguingly,both carotenoid composition and content were generally increased during the evolution of citrus,and the corresponding variations in the promoters were identified,including the gain or loss of critical environmental stress-responsive elements and hormone-responsive elements,which are closely associated with carotenoid enhancement.In addition,pummelo has the most heat-responsive elements,but the Mangshan mandarin does not have this element in the promoters of PSY,which is highly related to their geographical origin and indicate that temperature is a critical environmental signal influencing carotenoid accumulation.Moreover,the abscisic acid-responsive motif was rich in almost all the seven species,but the ethylene-responsive motif was deficient,which demystified the unique phytohormone regulation mechanism of carotenoid accumulation in citrus.Overall,our study provides new insights into the molecular regulatory mechanism of carotenoid enhancement in the evolution of citrus,which can facilitate breeding and cultivation efforts to improve the nutritional quality and esthetic value in citrus and hopefully other fruit crops.

Analysis of the methylation pattern of six gene promoters in sperm of men with abnormal protamination

It has recently been shown that alteration of the methylation pattern of imprinted genes is associated with different types of male infertility. The objective of our study was to investigate the methylation pattern of selected gene promoters in sperm of patients with abnormal protamine replacement. The promoters of OCT4, SOX2, NANOG, HOXC11, miR-17and CREMwere analyzed using bisulfite sequencing and the percentage of DNA methylation was compared between patients with an abnormal protamine l/protamine 2 （P1/ P2） ratio and normozoospermic controls. No significant quantitative differences were found between groups of patients with either an abnormally high or low P1/P2 ratio compared to normal controls. However, two individual samples from infertile subjects （2/20, 10%） showed an altered methylation pattern for the CREMgene promoter that was not found in control samples. These two samples had a significantly higher （P〈0.05） promoter methylation （5.58 and 4.23%, respectively） compared to the control group （0.46%）. In conclusion, in our pilot study, extreme methylations defects were not seen broadly in severely infertile men. However, two patients exhibited altered methylation of the CREMgene, which may be either causative or a result of abnormal protmaine replacement.

Effect of promoters on the selective hydrogenolysis of glycerol over Pt/W-containing catalysts

Diverse promoters,including noble metals（such as Ru,Ir and Rh） and transition metal oxides（such as Re,La,Fe,Zr,Sn and Ce oxides） were introduced into Pt/WOx and Pt/WOx/Al2O3 catalysts to investigate the ability of these promoters to modify activity and selectivity during glycerol hydrogenolysis to 1,3-propanediol.Among these,La exhibited the greatest promotional effect;the introduction of 0.1% La to the Pt/WOx improved activity,selectivity and stability,although the significant increase in selectivity came at the cost of a slight activity loss in the case of the Pt/WOx/Al2O3 catalyst.Transmission electron microscopy,high angle annular dark field scanning tunneling electron microscopy and NH3-temperature programmed desorption all demonstrated that the introduction of La generates a greater quantity of acidic sites on the catalyst surface,and that the majority of the La species are associated with Pt particles.Most of the other additives resulted in only minimal improvements or even detrimental effects with regard to both activity and selectivity,although some appear to improve the stability of the catalyst.

Effects of Potassium and Manganese Promoters on Nitrogen-Doped Carbon Nanotube-Supported Iron Catalysts for CO_2 Hydrogenation

Nitrogen-doped carbon nanotubes （NCNTs） were used as a support for iron （Fe） nanoparticles applied in car- bon dioxide （CO_2） hydrogenation at 633 K and 25 bar （1 bar = 10-5 Pa）. The Fe/NCNT catalyst promoted with both potassium （K） and manganese （Mn） showed high performance in CO_2 hydrogenation, reaching 34.9% conversion with a gas hourly space velocity （GHSV） of 3.1 L-（g·h）-1. Product selectivities were high for olefin products and low for short-chain alkanes for the K-promoted catalysts. When Fe/NCNT catalyst was promot- ed with both K and Mn, the catalytic activity was stable for 60 h of reaction time. The structural effect of the Mn promoter was demonstrated by X-ray diffraction （XRD）, temperature-programmed reduction （TPR） with molecular hydrogen （H2）, and in situ X-ray absorption near-edge structure （XANES） analysis. The Mn pro- moter stabilized wtistite （FeO） as an intermediate and lowered the TPR onset temperature. Catalytic ammo- nia （NH_3） decomposition was used as an additional probe reaction for characterizing the promoter effects. The Fe/NCNT catalyst promoted with both K and Mn had the highest catalytic activity, and the Mn-promoted Fe/NCNT catalysts had the highest thermal stability under reducing conditions.

Genomic Analysis of MicroRNA Promoters and Their Cis-Acting Elements in Soybean

MicroRNAs （miRNAs） are derived from distinct loci in the genome and play crucial roles in RNA-mediated gene silencing mechanisms that regulate cellular processes during development and stress responses of plants. The miRNAs are approximately 21 nucleotides long and code for the complementary strand to a larger genic mRNA. They are often found within the complementary primary transcript （pri-miRNAs）. In the past few years, a growing number of soybean miRNAs have been discovered, however, little is known about the transcriptional regulation of these miRNAs. In this study, promoters and cis-acting elements of soybean miRNAs were analyzed using the genomic data for the first time. A total of 82 miRNAs were located among 122 loci in genome, some were present as double or multiple copies. Five clusters that included ten miRNAs were found in genome, and only one cluster share the same promoter. A total of 191 promoters from 122 loci of the soybean miRNA sequences were found and further analyzed. The results indicated that the conserved soybean miRNA genes had a greater proportion of promoters than that of non-conserved ones, and the distribution of the transcript start sites （TSSs） and TATA-boxes found had different motif styles between conserved and non-conserved miRNA genes. Furthermore, the cis-acting elements 5＇ of the TSSs were analyzed to obtain potential function and spatiotemporal expression pattern of miRNAs. The data obtained here may lead to the identification of specific sequences upstream of pre-miRNAs and the functional annotation of miRNAs in soybean.

Regulated Gene Expression with Promoters Responding to Inducers

Genetically engineered transgenic animals and plants have proven to be extremely useful for analyzing biochemical and developmental processes.Promoters responding to chemical inducers will be powerful tools for basic research in molecular biology and biotechnological applications.Various chemical inducible systems based on activation and inactivation of the target gene had been described.The transfer of regulatory elements from prokaryotes,insects,and mammals has opened new avenues to construct chemically inducible promoters that differ in their ability to regulate the temporal and spatial expression patterns,and this will dramatically increase the application of transgenic technology.This review provides an overview on regulation of gene expression,promoter activating systems,promoter inactivation systems,inducible gene over expression,and inducible anti suppression.

Partial Oxidation of Methane to Syngas over Monolithic Ni/γ-Al_2O_3 Catalyst——Effects of Rare Earths and Other Basic Promoters

A series of monolithic Ni/γ-Al2O3 catalysts with and without basic promoters （Na, Sr, La, Ce） were prepared. Partial oxidation of methane （POM） to syngas was carried out in a continuous-flow, fixed-bed reactor. The influences of reaction conditions, including temperature, CH4/O2 ratio and space velocity, on the performance of the catalyst were investigated. The results show that at a high space velocity of 1 ×10^5 h^-1, optimal CH4 conversion can be obtained. Effects of promoters such as Na, Sr, Ce, La were also investigated, and the catalyst samples were characterized by means of temperature-programmed reduction and XRD techniques. XRD suggests that the addition of promoters has no influence on the crystal structure of Ni/γ-Al2O3 catalyst. The results show that the addition of a small amount of promoters improves the reducibility and activity of the catalyst. The side reaction CH4 ＋ 2O2→CO2 ＋ H2O, is fully restrained and 100% H2 selectivity is achieved when Ce and La are used as promoters, respectively.

Effect of Cr and Co Promoters Addition on Vanadium Phosphate Catalysts for Mild Oxidation of n-Butane

In this study, Cr and Co promoted, as well as unpromoted vanadium phosphate （VPO） catalysts were synthesized by the reaction of V2O5 and o-H3PO4 in organic medium followed by calcination in n-butane/air environment at 673 K. The physico-chemical properties and the catalytic behavior were affected by the addition of Cr and Co dopants. H2-TPR was used to investigate the nature of oxidants in the unpromoted and promoted catalysts. The results showed that both the Cr and Co promoters remarkably lowered the temperature of the reduction peak associated with V^5＋. The amount of oxygen species originated from the active phase, V^4＋, removed was significantly increased for Co and Cr-promoted catalysts. Both Cr and Co dopants improve strongly the n-butane conversion without sacrificing the MA selectivity. A good correlation was observed between the amount of oxygen species removed from V^4＋ phase and the activity for n-butane oxidation to maleic anhydride. This suggested that V^4＋-O was the center for the activation of n-butane.