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.

Enhanced extracellular production of alpha-lactalbumin from Bacillus subtilis through signal peptide and promoter screening

Alpha-lactalbumin(α-LA)is a major whey protein found in breast milk and plays a crucial role in the growth and development of infants.In this study,Bacillus subtilis RIK1285 harboring AprE signal peptide(SP)was selected as the original strain for the production ofα-LA.It was found thatα-LA was identified in the pellet after ultrasonic disruption and centrifugation instead of in the fermentation supernatant.The original strain most likely only producedα-LA intracellular,but not extracellular.To improve the expression and secretion ofα-LA in RIK1285,a library of 173 homologous SPs from the B.subtilis 168 genome was fused with target LALBA gene in the pBE-S vector and expressed extracellularly in RIK1285.SP YjcN was determined to be the best signal peptide.Bands in supernatant were observed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and purified by nickel column to calculate the highest yield signal peptide.In addition,different promoters(P_(aprE),P_(43),and P_(glv))were compared and applied.The results indicated that the strain RIK1285-pBE-P_(glv)-YjcN-LALBA had the highestα-LA yield,reaching 122.04μg/mL.This study demonstrates successful expression and secretion of humanα-LA in B.subtilis and establishes a foundation for simulating breast milk for infant formulas and developing bioengineered milk.

Effects of CMV Enhancer on Activity and Specificity of Bovine MyoG Gene Promoter

Connected a segment of CMV enhancer to the front of MyoG gene promoter and then constructed the corresponding dual luciferase expression vector pGL3-CMV-MyoGpro. We set four eukaryotic expression vectors including pGL3-CMV, pGL3MyoGpro, pGL3-CMV-MyoGpro, and pGL3-Basic which contained CMV promoter, MyoG promoter, CMV-MyoG synthesis promoter, and a promoterless negative control, respectively. Then the four vectors and internal control Renilla luciferase report gene vector phRL-TK were transfected into bovine skeletal muscle satellite cells, mouse C2C12 cells and bovine fetal fibroblast cells to detect the promoter activity with dual luciferase report system. The results showed that CMV enhancer could significantly improve the transcription activity of bovine MyoG gene promoter in muscle satellite cells and mouse C2C12 cells, and it had certain specificity. This study provided experimental materials for increasing the high expression of exogenous gene in bovine muscle cells, and also laid the molecular theoretical basis for obtaining the high specific promoter of bovine muscle and the transgenic beef cattle.

Interaction between the Wilms tumour factor-1 element in the promoter of Amh and a downstream enhancer is required for a strong expression of the gene in pre-pubertal sertoli cells

Amh (anti-Müllerian hormone) is a single copy gene which is expressed strongly in Sertoli cells in the foetal testis and participates in the onset of sexual differentiation. Its promoter driving the expression of a reporter gene (d2EGFP) has been used to analyse the role of certain defined putative elements and a downstream enhancer element in gene expression. These experiments were carried out in vitro using a line of pre-pubertal mouse Sertoli cells, transienly transfected with circular DNA constructs with variously mutated promoter elements. A downstream enhancer element, situated immediately 3’ of the polyadenylation (PA) signal for Amh, has been inserted in an equivalent position in the d2EGFP construct. When the Amh promoter is unmodified, the downstream enhancer (DE) is positively associated with a large increase in EGFP expression. This is at least partly the consequence of an increased rate of expression by individual cells. Experiments using variously truncated Amh promoters indicate that an upstream region (-214 to -336) may play a minor role in facilitating enhancement. However mutation of the Wilms tumour factor-1 element, situated between the tata box and the start of translation, results in an almost complete suppression of enhancement.

The Cytomegalovirus Enhancer Induces an Immediate Response to the Myosin Light Chain 2v Promoter during P19CL6 Cell Differentiation

The P19CL6 mouse embryonic carcinoma cells efficiently differentiate into cardiac muscle cells in the presence of DMSO. A reporter plasmid for cardiac muscle differentiation was constructed by connecting the CMV enhancer and a 250 bp MLC-2v promoter in front of the GFP gene to further evaluate the role of the CMV enhancer. This plasmid (pCBVenh/MLC-2vpro/EGFP) was stably introduced into P19CL6 cells, and the transfectant differentiated into cardiomyocytes with DMSO. Upon DMSO addition, GFP was immediately transcribed (within 2 days) and the amount of the transcript increased with cultivation. Concomitantly, GFP fluorescence was detected in the cells under a microscope. However, native MLC-2v was transcribed later on day 4. This expression time course is different from that of GFP. Clearly the CMV enhancer responded immediately to DMSO. Since GATA DNA-binding proteins play crucial roles in the initiation of cardiomyocyte differentiation, such a response could be ascribed to the presence of multiple GATA motifs in the enhancer sequence but not in the native MLC-2v promoter. Thus the CMV enhancer may be not only useful for gene therapy and monitoring cell differentiation but also the study of the role of GATA transcription factors expressed in P19CL6 cells.

Increased Activity of the Human Telomerase Catalytic Subunit Promoter by the VEGF Enhancer in Human Cancer Cells

We attempted to improve the activity of hTERT promoter by fusing the vascular endothelial growth factor （VEGF） enhancer. To determine the potential as cancer specific promoters, we measured the reporter gene transfection assay driven by the hTERT promoter and the VEGF enhancer in human cancer cells. We found that the hTERT promoter containing VEGF enhancer conferred strong expression of the reporter gene only in different cancer cell lines but not in normal human cells. Retrovirus vector expressing HSV-TK controlled by the hTERT promoter and the VEGF enhancer was constructed. A549 cells infected with LN-enh-hT-TK was significantly suppressed and induced to apoptosis more than those infected with LN-hT-TK. The apoptosis ratio ofA549 cell infected with two kinds of retrovirus cell with GCV in lower concentration is 20.94% and 50.7%. It suggested that there is significant differentiation between the assay groups. Our results demonstrated the possible application of hTERT promoter and the VEGF enhancer in targeted cancer gene therapy.

Construction of retroviral vector carrying HSV tk gene under control of human AFP enhancer core sequence and human pgk promotor *

AIM Tenstruct retroviral vector bringing HSV tk gene under control by human AFP enhancer core sequence and human pgk promotor.

Flux enhancement during ultrafiltration of produced water using turbulence promoter

Concentration polarization and membrane fouling remain one of the major hurdles for the implementation of ultrafiltration of produced water. Although many applications for ultrafiltration were already suggested, only few were implemented on an industrial scale. Among those techniques, turbulence promoter can be more simple and effective in overcoming membrane fouling and enhancing membrane flux. As for the result that turbulence promoter increase fluid velocity, wall shear rates and produce secondary flows or instabilities, the influence of turbulence promoter was investigated on permeate flux during produced water ultrafiltration and the potential application of this arrangement for an industrial development. Experimental investigations were performed on 100 KDa molecular weight cut-off PVDF single-channel tubular membrane module using four kinds of turbulence promoters. It is observed that the significant flux enhancement in the range of 83%--164% was achieved while the hydraulic dissipated power per unit volume of permeate decreased from 31%--42%, which indicated that the using of turbulence promoter is more efficient than operation without the turbulence promoter. The effects of transmembrane pressure and cross-flow velocity with and without turbulence promoter were studied as well. Among the four kinds of turbulence promoters, winding inserts with 20.0 mm pitch and 1.0 mm wire diameter showed better performances than the others did.

p53 exerts anticancer effects by regulating enhancer formation and activity

The abnormality of the p53 tumor suppressor is crucial in lung cancer development,because p53 regulates target gene promoters to combat cancer.Recent studies have shown extensive p53 binding to enhancer elements.However,whether p53 exerts a tumor suppressor role by shaping the enhancer landscape remains poorly understood.In the current study,we employed several functional genomics approaches to assess the enhancer activity at p53 binding sites throughout the genome based on our established TP53 knockout(KO)human bronchial epithelial cells(BEAS-2B).A total of 943 active regular enhancers and 370 super-enhancers(SEs)disappeared upon the deletion of p53,indicating that p53 modulates the activity of hundreds of enhancer elements.We found that one p53-dependent SE,located on chromosome 9 and designated as KLF4-SE,regulated the expression of the Krüppel-like factor 4(KLF4)gene.Furthermore,the deletion of p53 significantly decreased the KLF4-SE enhancer activity and the KLF4 expression,but increased colony formation ability in the nitrosamines 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone-induced cell transformation model.Subsequently,in TP53 KO cells,the overexpression of KLF4 partially reversed the increased clonogenic capacity caused by p53 deficiency.Consistently,KLF4 expression also decreased in lung cancer tissues and cell lines.It appeared that overexpression of KLF4 significantly suppressed the proliferation and migration of lung cancer cells.Collectively,our results suggest that the regulation of enhancer formation and activity by p53 is an integral component of the p53 tumor suppressor function.Therefore,our findings offer some novel insights into the regulation mechanism of p53 in lung oncogenesis and introduce a new strategy for screening therapeutic targets.

A Polyvinyl Alcohol/Acrylamide Hydrogel with Enhanced Mechanical Properties Promotes Full-Thickness Skin Defect Healing by Regulating Immunomodulation and Angiogenesis Through Paracrine Secretion

Hydrogel-based tissue-engineered skin has attracted increased attention due to its potential to restore the structural integrity and functionality of skin.However,the mechanical properties of hydrogel scaffolds and natural skin are substantially different.Here,we developed a polyvinyl alcohol(PVA)/acrylamide based interpenetrating network(IPN)hydrogel that was surface modified with polydopamine(PDA)and termed Dopa-gel.The Dopa-gel exhibited mechanical properties similar to native skin tissue and a superior ability to modulate paracrine functions.Furthermore,a tough scaffold with tensile resistance was fabricated using this hydrogel by three-dimensional printing.The results showed that the interpenetration of PVA,alginate,and polyacrylamide networks notably enhanced the mechanical properties of the hydrogel.Surface modification with PDA endowed the hydrogels with increased secretion of immunomodulatory and proangiogenic factors.In an in vivo model,Dopa-gel treatment accelerated wound closure,increased vascularization,and promoted a shift in macrophages from a proinflammatory M1 phenotype to a prohealing and anti-inflammatory M2 phenotype within the wound area.Mechanistically,the focal adhesion kinase(FAK)/extracellular signal-related kinase(ERK)signaling pathway may mediate the promotion of skin defect healing by increasing paracrine secretion via the Dopa-gel.Additionally,proangiogenic factors can be induced through Rho-associated kinase-2(ROCK-2)/vascular endothelial growth factor(VEGF)-mediated paracrine secretion under tensile stress conditions.Taken together,these findings suggest that the multifunctional Dopa-gel,which has good mechanical properties similar to those of native skin tissue and enhanced immunomodulatory and angiogenic properties,is a promising scaffold for skin tissue regeneration.

Experimental and CFD Studies on the Performance of Microfiltration Enhanced by a Turbulence Promoter

This paper reports experimental and computational fluid dynamics(CFD) studies on the performance of microfiltration enhanced by a helical screw insert.The experimental results show that the use of turbulence pro-moter can improve the permeate flux of membrane in the crossflow microfiltration of calcium carbonate suspension,and flux improvement efficiency is strongly influenced by operation conditions.The energy consumption analysis indicates that the enhanced membrane system is more energy saving at higher feed concentrations.To explore the intrinsic mechanism of flux enhancement by a helical screw insert,three-dimensional CFD simulation of fluid flow was implemented.It reveals that hydrodynamic characteristics of fluid flow inside the channel are entirely changed by the turbulence promoter.The rotational flow pattern increases the scouring effect on the tube wall,reducing the particle deposition on the membrane surface.The absence of stagnant regions and high wall shear stress are respon-sible for the enhanced filtration performance.No secondary flow is generated in the channel,owing to the streamline shape of helical screw insert,so that the enhanced performance is achieved at relatively low energy consumption.

Understanding the catalytic performance and deactivation behaviour of second-promoter doped Pt/WO_(χ)/γ-Al_(2)O_(3) catalysts in the glycerol hydrogenolysis for selective and cleaner production of 1,3-propanediol

The selective aqueous-phase glycerol hydrogenolysis is a promising reaction to produce commercially useful 1,3-propanediol(1,3-PDO).The Pt-WOx bifunctional catalyst can catalyse the glycerol hydrogenol-ysis but the catalyst deactivation via sintering,metal leaching,and coking can predominantly occur in the aqueous phase reaction.In this work,the effect of reaction temperature,pressure and second promoter(Cu,Fe,Rh,Mn,Re,Ru,Ir,Sn,B,and P)on catalytic performance and deactivation behaviour of Pt/WOx/-Al2O3 was investigated.When doped with Rh,Mn,Re,Ru,Ir,B,and P,the second promoter boosts catalytic activity by promoting great dispersion of Pt on support and increasing Pt surface area.The increased Bronsted acid sites lead to selective synthesis of 1,3-PDO than 1,2-propanediol(1,2-PDO).The characterization studies of fresh and spent catalysts reveal that the main cause of catalyst deactivation is the Pt sintering,as interpreted based on XRD,CO chemisorption,and TEM analyses.The Pt sintering is affected depending on the second promoter that can either or reduce the interaction between Pt,WO_(χ)/γ and Al_(2)O_(3).As an electron acceptor of Pt in Pt/WO_(χ)/γ-Al_(2)O_(3),Re and Mn as second promoters resulted in increased Pt^(2+) on the catalytic surface,which strengthens the contact between Pt andγ-Al_(2)O_(3) and WO_(χ),resulting in a decrease in Pt sintering.The metal leaching and coking are not affected by the presence of second promoter.The catalyst modified with a second promoter possesses improved catalytic activity and 1,3-PDO production,however the stability continues to remain a challenge.The present work unrav-elled the determining parameters of catalytic activity and deactivation,thus providing a promising pro-tocol toward effective catalysts for glycerol hydrogenolysis.

Revisiting the mitigation of coke formation:Synergism between support&promoters'role toward robust yield in the CO_(2)reformation of methane

CO_(2)reformation of methane(CRM)and CO_(2)methanation are two interconnected processes with significant implications for greenhouse gas reduction and sustainable energy production for industrial purposes.While Nibased catalysis suffers from poor stability due to coke formation or sintering,we report a super stable remedy.The active sites of mesoporous MgO were loaded using wet impregnation.The incorporation of Ni and promoters altered the physical features of the catalysts.Sm–Ni/MgO showed the smallest crystallite size,specific surface area,and pore volume.The Sm–Ni/MgO catalyst was selected as the most suitable candidate for CRM,with 82%CH4 and H2/CO ratio of approximately 100%and also for CO_(2)methanation with the conversion of carbon dioxide(82%)and the selectivity toward methane reaches 100%at temperatures above 300ᵒC.Furthermore,the Sm–Ni/MgO catalyst was stable for 900 min of continuous reaction,without significant carbon deposition.This stability was largely due to the high oxygen mobility on the catalyst surface in the presence of Sm.Overall,we demonstrated the efficacy of using promoted Ni catalysts supported by mesoporous magnesia for the improved reformation of greenhouse gases.

Molecular cloning,characterization and promoter analysis of LbgCWIN1 and its expression profiles in response to exogenous sucrose during in vitro bulblet initiation in lily

Lily(Lilium spp.) is an important ornamental flower, which is mainly propagated by bulbs. Cell wall invertases(CWINs), which catalyze the irreversibly conversion of sucrose into glucose and fructose in the extracellular space, are key enzymes participating in sucrose allocation in higher plants. Previous studies have shown that CWINs play an essential role in bulblet initiation process in bulbous crops, but the underlying molecular mechanism remains unclear. Here, a CWIN gene of Lilium brownii var. giganteum(Lbg) was identified and amplified from genomic DNA. Quantitative RT-PCR assays revealed that the expression level of LbgCWIN1 was highly upregulated exactly when the endogenous starch degraded in non-sucrose medium during in vitro bulblet initiation in Lbg. Phylogenetic relationship, motif, and domain analysis of LbgCWIN1 protein and CWINs in other plant species showed that all sequences of these CWIN proteins were highly conserved. The promoter sequence of LbgCWIN1 possessed a number of alpha-amylase-, phytohormone-, light-and stress-responsive cis-elements. Meanwhile, β-glucuronidase(GUS) assay showed that the 459 bp upstream fragment from the translational start site displayed maximal promoter activity. These results revealed that LbgCWIN1 might function in the process of in vitro bulblet initiation and be in the response to degradation of endogenous starch.

Utilizing the γ-Irradiated Sodium Alginate as a Plant Growth Promoter for Enhancing the Growth,Physiological Activities,and Alkaloids Production in Catharanthus roseus L.

Sodium alginate is a polysaccharide that is largely obtained from the brown algae （Sargassum sp.）.It has been used as a wonderful growth promoting substance in its depolymerized form for various plants.The aim of this study was to find out the effects of various concentrations of γ-irradiated sodium alginate （ISA）,viz.,deionized water （control,T0）,20 （T1）,40 （T2）,60 （T3）,80 （T4）,and 100 ppm （T5） on the agricultural performance of Catharanthus roseus L.（Rosea） in terms of growth attributes,photosynthesis,physiological activities,and alkaloid production.The present work revealed that ISA applied as leaf-sprays at concentrations from 20 to 100 ppm might improve growth,photosynthesis,physiological activities,and alkaloid production in C.roseus L.significantly.Of the various ISA concentrations,80 ppm proved to be the best one compared to other concentrations applied.

Cloning of BjNAC102 Promoter and Construction of Expression Vector in Brassica juncea

Transcription factor NAC102 plays an important role in the abiotic stress responses of plants.In this study,the promoter sequence of 3000 bp located in the upstream of the BjNAC102 gene was cloned from Brassica juncea‘Sichuan Yellow Seed’by using the homologous cloning method.The expression vector of the GUS gene driven by the BjNAC102 promoter was constructed by seamless cloning technology.The results showed that the sequence of the promoter of the BjNAC102 gene contained many cis-acting elements involved in light responsiveness,gibberellinresponsive element,and auxin-responsive element.It was speculated that BjNAC102 played an important role in the abiotic stress response in Brassica juncea.The expression vector of the promoter of the BjNAC102 gene was constructed,which layed a foundation for further studies of the expression pattern of the BjNAC102 gene in Brassica juncea.

Enhanced stability of Pt/Al_(2)O_(3) modified by Zn promoter for catalytic dehydrogenation of ethane

Catalytic ethane dehydrogenation(EDH) to ethylene over Pt-based catalysts has received increasing interests in recent years as it is a potential alternative route to conventional steam cracking. However, the catalysts used in this reaction often suffer from rapid deactivation due to serious coke deposition and metal sintering. Herein, we reported the effects of Zn modification on the stability of Pt/Al2 O3 for EDH.The Zn-modified sample(PtZn2/Al2 O3) exhibits stable ethane conversion(20%) with over 95% ethylene selectivity. More importantly, it exhibits a significantly low deactivation rate of only 0.003 h-1 at 600 °C for70 h, which surpasses most of previously reported catalysts. Detailed characterizations including in situ FT-IR, ethylene adsorption microcalorimetry, and HAADF-STEM etc. reveal that Zn modifier reduces the number of Lewis acid sites on the catalyst surface. Moreover, it could modify Pt sites and preferentially cover the step sites, which decrease surface energy and retard the sintering of Pt particle, then prohibiting the further dehydrogenation of ethylene to ethylidyne. Consequently, the good stability is realized due to anti-sintering and the decrease of coke formation on the Pt Zn2/Al2 O3 catalyst.

Procollagen C-proteinase enhancer 1 promotes physiologic retinal angiogenesis via regulating the process of collagen

AIM:To investigate the role of procollagen C-proteinase enhancer 1(PCPE1)in retinal angiogenesis and relevant mechanisms.METHODS:The Pcolce1-knockout(KO)mice were used to explore the effect of PCPE1 on retinal angiogenesis in vivo.Pcolce1 si RNA were designed,cell count kit 8(CCK8)assays and tube formation assays were performed to investigate the cell proliferation and tube formation abilities of retinal microvascular endothelial cells(h RMECs)in vitro.Mouse embryo fibroblasts(MEF)cells were isolated and cultured to analyze the effect of PCPE1 on enhancing procollagen cleavage.RESULTS:In vivo studies showed that the retinal vascular density of Pcolce1-/-mice was significantly lower than that of the control group.Furthermore,silencing of Pcolce1 inhibited cell proliferation and tube formation abilities of h RMECs in vitro.Additionally,much more procollagen was found in Pcolce1-/-MEF cells,compared to wild type MEF cells.CONCLUSION:PCPE1 may promote physiological retinal angiogenesis by regulating the processing of collagen,which may provide a potential therapeutic target of retinal vascular disease.

The enhancing effect and promoting mechanisms of the stereoisomeric monoterpene alcohol esters as enhancers for drugs with different physicochemical properties

To explore the structure-activity connections of amphiphilic permeation enhancers containing the length of the hydrophobic chains as well as the properties of the polar head,O-acylgeraniol and O-acylnerol derivatives were synthesized from geraniol/nerol(cis-isomer of geraniol) and pharmaceutical excipient acids in this research. Their promotion of the percutaneous absorption of three drugs as the model, flurbiprofen(FP), isosorbide dinitrate(ISDN) and donepezil(DNP), which were selected based on their physicochemical properties,was tested by in vitro skin penetration and in vivo. Molecular simulation, ATR-FTIR, CLSM and histological observation were implement to evaluate the mode of action of the enhancers.The results indicated that(E)-3,7-dimethyl-2,6-octadien-1-yl tetradecanoate(GER-C14, trans-)achieved the highest enhancement ability for the three drugs;additionally, the in vivo results obtained were in good correlation with the in vitro data. Molecular docking results suggested that enhancers loosen the hydrogen bonds between ceramides, and the results of molecular simulation indicated that GER-C14, NER-C14 could insert into the middle of the lipid bilayer to form an independent phase. According to ATR-FTIR and histological evaluation, the enhancers extracted lipids and influenced the protein region, thereby disturbing the skin array. In addition, CLSM described the dynamic effects of enhancers on lipids between stratum corneum(SC) cells. In conclusion, GER-C14 had a better penetration promotion effect, which broadened our understanding of stereoisomeric penetration enhancers.