Targeting transcriptional regulators to regenerate midbrain dopaminergic axons in Parkinson's disease

Introduction： Parkinson＇s disease （PD） is a chronic, age-re- lated neurodegenerative disorder that affects 1-2% of the population over the age of 65. PD is characterised by the progressive degeneration of nigrostriatal dopaminergic （DA） neurons. This leads to disabling motor symptoms, due to the striatal DA denervation. Despite decades of research, there is still no therapy that can slow, stop or regenerate the dying midbrain DA neurons in PD.

A novel SATB1 binding site in the BCL2 promoter region possesses transcriptional regulatory function

BCL2 is a key regulator of apoptosis.Our previous work has demonstrated that special AT-rich sequence-binding protein 1 （SATB1） is positively correlated with BCL2 expression.In the present study,we report a new SATB1 binding site located between P1 and P2 promoters of the BCL2 gene.The candidate SATB1 binding sequence predicted by bioinformatic analysis was investigated in vitro and in vivo by electrophoretic gel mobility shift assays （EMSA） and chromatin immunoprecipitation （ChIP）.One 25-bp sequence,named SB1,was confirmed to be SATB1 binding site.The regulatory function of SB1 and its relevance to SATB1 were further examed with dual-luciferase reporter assay system in Jurkat cells.We found that SB1 could negatively regulate reporter gene activity.Mutation of SATB1 binding site further repressed the activity.Knockdown of SATB1 also enhanced this negative effect of SB1.Our data indicate that the SB1 sequence possesses negative transcriptional regulatory function and this function can be antagonized by SATB1.

Antagonistic MADS-box transcription factors SEEDSTICK and SEPALLATA3 form a transcriptional regulatory network that regulates seed oil accumulation

Transcriptional regulation is essential for balancing multiple metabolic pathways that influence oil accumulation in seeds.Thus far,the transcriptional regulatory mechanisms that govern seed oil accumulation remain largely unknown.Here,we identified the transcriptional regulatory network composed of MADS-box transcription factors SEEDSTICK(STK)and SEPALLATA3(SEP3),which bridges several key genes to regulate oil accumulation in seeds.We found that STK,highly expressed in the developing embryo,positively regulates seed oil accumulation in Arabidopsis(Arabidopsis thaliana).Furthermore,we discovered that SEP3 physically interacts with STK in vivo and in vitro.Seed oil content is increased by the SEP3 mutation,while it is decreased by SEP3 overexpression.The chromatin immunoprecipitation,electrophoretic mobility shift assay,and transient dual-luciferase reporter assays showed that STK positively regulates seed oil accumulation by directly repressing the expression of MYB5,SEP3,and SEED FATTY ACID REDUCER 4(SFAR4).Moreover,genetic and molecular analyses demonstrated that STK and SEP3 antagonistically regulate seed oil production and that SEP3 weakens the binding ability of STK to MYB5,SEP3,and SFAR4.Additionally,we demonstrated that TRANSPARENT TESTA 8(TT8)and ACYL-ACYL CARRIER PROTEIN DESATURASE 3(AAD3)are direct targets of MYB5 during seed oil accumulation in Arabidopsis.Together,our findings provide the transcriptional regulatory network antagonistically orchestrated by STK and SEP3,which fine tunes oil accumulation in seeds.

The transcriptional regulators of virulence for Pseudomonas aeruginosa:Therapeutic opportunity and preventive potential of its clinical infections

In Pseudomonas aeruginosa(P.aeruginosa),transcription factors(TFs)are important mediators in the genetic regulation of adaptability and pathogenicity to respond to multiple environmental stresses and host defences.The P.aeruginosa genome harbours 371 putative TFs;of these,about 70 have been shown to regulate virulence-associated phenotypes by binding to the promoters of their target genes.Over the past three decades,several techniques have been applied to identify TF binding sites on the P.aeruginosa genome,and an atlas of TF binding patterns has been mapped.The virulence-associated regulons of TFs show complex crosstalk in P.aeruginosa's regulatory network.In this review,we summarise the recent literature on TF regulatory networks involved in the quorum-sensing system,biofilm formation,pyocyanin synthesis,motility,the type III secretion system,the type VI secretion system,and oxidative stress responses.We discuss future perspectives that could provide insights and targets for preventing clinical infections caused by P.aeruginosa based on the global regulatory network of transcriptional regulators.

Transcriptional regulation in the development and dysfunction of neocortical projection neurons

Glutamatergic projection neurons generate sophisticated excitatory circuits to integrate and transmit information among different cortical areas,and between the neocortex and other regions of the brain and spinal cord.Appropriate development of cortical projection neurons is regulated by certain essential events such as neural fate determination,proliferation,specification,differentiation,migration,survival,axonogenesis,and synaptogenesis.These processes are precisely regulated in a tempo-spatial manner by intrinsic factors,extrinsic signals,and neural activities.The generation of correct subtypes and precise connections of projection neurons is imperative not only to support the basic cortical functions(such as sensory information integration,motor coordination,and cognition)but also to prevent the onset and progression of neurodevelopmental disorders(such as intellectual disability,autism spectrum disorders,anxiety,and depression).This review mainly focuses on the recent progress of transcriptional regulations on the development and diversity of neocortical projection neurons and the clinical relevance of the failure of transcriptional modulations.

An overview of pigment gland morphogenesis and its regulatory mechanism

Cotton has enormous economic potential,providing high-quality protein,oil,and fibre.But the comprehensive utilization of cottonseed is limited by the presence of pigment gland and its inclusion.Pigment gland is a common characteristic of Gossypium genus and its relatives,appearing as visible dark opaque dots in most tissues and organs of cotton plants.Secondary metabolites,such as gossypol,synthesized and stored in the cavities of pigment glands act as natural phytoalexins,but are toxic to humans and other monogastric animals.However,only a few cotton genes have been identified as being associated with pigment gland morphogenesis to date,and the developmental processes and regulatory mechanism involved in pigment gland formation remain largely unclear.Here,the research progress on the process of pigment gland morphogenesis and the genetic basis of cotton pigment glands is reviewed,for providing a theoretical basis for cultivating cotton with the ideal pigment gland trait.

RePhine: An Integrative Method for Identification of Drug Response-related Transcriptional Regulators

Transcriptional regulators(TRs)participate in essential processes in cancer pathogenesis and are critical therapeutic targets.Identification of drug response-related TRs from cell line-based compound screening data is often challenging due to low m RNA abundance of TRs,protein modifications,and other confounders(CFs).In this study,we developed a regression-based pharmacogenomic and Ch IP-seq data integration method(Re Phine)to infer the impact of TRs on drug response through integrative analyses of pharmacogenomic and Ch IP-seq data.Re Phine was evaluated in simulation and pharmacogenomic data and was applied to pan-cancer datasets with the goal of biological discovery.In simulation data with added noises or CFs and in pharmacogenomic data,Re Phine demonstrated an improved performance in comparison with three commonly used methods(including Pearson correlation analysis,logistic regression model,and gene set enrichment analysis).Utilizing Re Phine and Cancer Cell Line Encyclopedia data,we observed that Re Phinederived TR signatures could effectively cluster drugs with different mechanisms of action.Re Phine predicted that loss-offunction of EZH2/PRC2 reduces cancer cell sensitivity toward the BRAF inhibitor PLX4720.Experimental validation confirmed that pharmacological EZH2 inhibition increases the resistance of cancer cells to PLX4720 treatment.Our results support that Re Phine is a useful tool for inferring drug response-related TRs and for potential therapeutic applications.The source code for Re Phine is freely available at https://github.com/coexps/Re Phine.

Isolation and functional analysis of SrMYB1,a direct transcriptional repressor of SrUGT76G1 in Stevia rebaudiana

SrUGT76G1,the most well-studied diterpene glycosyltransferase in Stevia rebaudiana,is key to the biosynthesis of economically important steviol glycosides(SGs).However,the molecular regulatory mechanism of SrUGT76G1 has rarely been explored.In this study,we identified a MYB transcription factor,SrMYB1,using a yeast one-hybrid screening assay.SrMYB1 belongs to the typical R2R3-type MYB protein and is specifically localized in the nucleus with strong transactivation activity.The transcript of SrMYB1 is predominantly accumulated in flowers,but is also present at a lower level in leaves.Yeast one-hybrid and electrophoretic mobility shift assays verified that SrMYB1 binds directly to the MYB binding sites in the F4-3 fragment(+50–(–141))of the SrUGT76G1 promoter.Furthermore,we found that SrMYB1 could significantly repress the expression of SrUGT76G1 in both epidermal cells of tobacco leaves and stevia callus.Taken together,our results demonstrate that SrMYB1 is an essential upstream regulator of SrUGT76G1 and provide novel insight into the regulatory network for the SGs metabolic pathway in S.rebaudiana.

The BEL1-like transcription factor GhBLH5-A05 participates in cotton response to drought stress

Drought stress impairs crop growth and development.BEL1-like family transcription factors may be involved in plant response to drought stress,but little is known of the molecular mechanism by which these proteins regulate plant response and defense to drought stress.Here we show that the BEL1-like transcription factor GhBLH5-A05 functions in cotton(Gossypium hirsutum)response and defense to drought stress.Expression of GhBLH5-A05 in cotton was induced by drought stress.Overexpression of GhBLH5-A05 in both Arabidopsis and cotton increased drought tolerance,whereas silencing GhBLH5-A05 in cotton resulted in elevated sensitivity to drought stress.GhBLH5-A05 binds to cis elements in the promoters of GhRD20-A09 and GhDREB2C-D05 to activate the expression of these genes.GhBLH5-A05 interacted with the KNOX transcription factor GhKNAT6-A03.Co-expression of GhBLH5-A05 and GhKNAT6-A03 increased the transcription of GhRD20-A09 and GhDREB2C-D05.We conclude that GhBLH5-A05 acts as a regulatory factor with GhKNAT6-A03 functioning in cotton response to drought stress by activating the expression of the drought-responsive genes GhRD20-A09 and GhDREB2C-D05.

GATA binding protein 2 mediated ankyrin repeat domain containing 26 high expression in myeloid-derived cell lines

BACKGROUND Thrombocytopenia 2,an autosomal dominant inherited disease characterized by moderate thrombocytopenia,predisposition to myeloid malignancies and normal platelet size and function,can be caused by 5’-untranslated region(UTR)point mutations in ankyrin repeat domain containing 26(ANKRD26).Runt related transcription factor 1(RUNX1)and friend leukemia integration 1(FLI1)have been identified as negative regulators of ANKRD26.However,the positive regulators of ANKRD26 are still unknown.AIM To prove the positive regulatory effect of GATA binding protein 2(GATA2)on ANKRD26 transcription.METHODS Human induced pluripotent stem cells derived from bone marrow(hiPSC-BM)INTRODUCTION Ankyrin repeat domain containing protein 26(ANKRD26)acts as a regulator of adipogenesis and is involved in the regulation of feeding behavior[1-3].The ANKRD26 gene is located on chromosome 10 and shares regions of homology with the primate-specific gene family POTE.According to the Human Protein Atlas database,the ANKRD26 protein is localized to the Golgi apparatus and vesicles,and its expression can be detected in nearly all human tissues[4].Moreover,UniProt annotation revealed that ANKRD26 is localized in the centrosome and contains coiled-coil domains formed by spectrin helices and ankyrin repeats[5,6].The most common disease related to ANKRD26 is thrombocytopenia 2(THC2),which is a rare autosomal dominant inherited disease characterized by lifelong mild-to-moderate thrombocytopenia and mild bleeding[7-9].Caused by the variants in the 5’-untranslated region(UTR)of ANKRD26,THC2 is defined by a decrease in the number of platelets in circulating blood and results in increased bleeding and decreased clotting ability[8,10].Due to the point mutations that occur in the 5’-UTR of ANKRD26,its negative transcription factors(TFs),Runt related transcription factor 1(RUNX1)and friend leukemia integration 1(FLI1),lose their repression effect[11].The persistent expression of ANKRD26 increases the activity of the mitogen activated protein kinase and extracellular signal regulated kinase 1/2 signaling pathways,which are potentially involved in the regulation of thrombopoietin-dependent signaling and further impair proplatelet formation by megakaryocytes(MKs)[11].However,the positive regulators of ANKRD26,which might be associated with THC2 pathology,are still unknown.

Transcriptional mechanisms regulating gene expression and determining cell fates in plant development

Transcriptional regulatory mechanisms that control transcriptional regulators, target genes, and their interactions provide new insights into general development processes throughout the life cycle of the plant. Although different molecular mechanisms that regulate plant growth and development have been identified, detailed transcriptional mechanisms that control gene expression, modulate developmental programmes, and determine cell fates in plant development are not fully understood. To increase our understanding on transcriptional mechanisms regulating diverse processes in plant development, we have reviewed the regulation of transcription during the process of development including transcriptional mechanisms regulating root, stem, leaf, flower, seed, embryo, endosperm, ovule, fruit, and chloroplast development. We have summarized the interaction, expression, transport, signaling events of transcriptional regulators and their targets in a number of model plants and highlighted the involvement of hormones and microRNAs in plant development. Understanding the precise transcriptional mechanisms regulating gene expression in plant development will be valuable for plant molecular breeding.

Transcriptional regulation of endothelial dysfunction in atherosclerosis:an epigenetic perspective

Atherosclerosis is a progressive human pathology that encompasses several stages of development. Endothelial dysfunction represents an early sign of lesion within the vasculature. A number of risk factors for atherosclero- sis, including hyperlipidemia, diabetes, and hypertension, target the vascular endothelium by re-programming its transcriptome. These profound alterations taking place on the chromatin rely on the interplay between sequence specific transcription factors and the epigenetic machinery. The epigenetic machinery, in turn, tailor individual transcription events key to atherogenesis to intrinsic and extrinsic insults dictating the development of atheroscle- rotic lesions. This review summarizes our current understanding of the involvement of the epigenetic machinery in endothelial injury during atherogenesis.

Transcription factor ZmNAC126 plays an important role in transcriptional regulation of maize starch synthesis-related genes

Maize(Zea mays L.)is one of the most important food crops in the world,and starch is the main component of its endosperm.Transcriptional regulation plays a vital role in starch biosynthesis.However,it is not well understood in maize.We report the identification of the transcription factor ZmNAC126 and its role in regulation of starch synthesis in maize.Transcriptional expression of ZmNAC126 was higher in maize endosperm and kernels than in roots or stems.ZmNAC126 shared a similar expression pattern with starch synthesis genes during seed development,and its expression pattern was also consistent with the accumulation of starch.ZmNAC126 is a typical transcription factor with a transactivation domain between positions 201 and 227 of the amino acid sequence,is located in the nucleus,and binds to CACG repeats in vitro.Yeast one-hybrid assay revealed that ZmNAC126 bound the promoters of ZmGBSSI,ZmSSIIa,ZmSSIV,ZmISA1,and ZmISA2.Transient overexpression of ZmNAC126 in maize endosperm increased the activities of promoters pZmSh2,pZmBt2,pZmGBSSI,pZmSSIIIa,and pZmBT1 but inhibited the activities of pZmISA1 and pZmISA2.ZmNAC126 thus acts in starch synthesis by transcriptionally regulating targeted starch synthesis-related genes in maize kernels.

SIMYB1 and SIMYB2, two new MYB genes from tomato, transcriptionally regulate cellulose biosynthesis in tobacco

Cellulose, a major constituent of plant biomass, is synthesized by a cellulose synthase complex. It has been demonstrated that MYB genes transcriptionally regulate cellulose synthase in Arabidopsis. However, little is known about this process in tomato. Here, two MYB （SIMYB1/2） and three cellulose synthase （CESA） （SICESA41516） genes were isolated. SIMYB1/2 and SICESA4/5/6 accumulation was found to correspond to cellulose accumulation in different tissues of tomato. Dual luciferase assays indicated that these two MYBs were transcriptional activators that interact with promoters of SICESA4/5/6. Moreover, SIMYB2 could also activate promoters of SIMYB1/2, suggesting the possible underlying auto-activation mech- anisms for MYB transcription factors. Transient over-expression of SlMYB1/2 in Nicotiana tabacum up-regulated tobacco endogenous NtCESA genes and increased cellulose accumulation. The function of SIMYB112 was further investigated using stable transformation and the results indicated that N. tabacum lines heterologous expressing SIMYB1/2 displayed a pleiotropic phenotype, long and narrow leaves, with NtCESA induced and significant increase of cellulose. In conclusion, our data suggest that tomato SIMYB1/2 have transcriptional regulatory roles in cellulose biosynthesis and SIMYB2 was more effective than SIMYB1, which may due to the transcriptional activation by SIMYB2 on SIMYB1 and itself.

Class Ⅱ transactivator(CIITA)mediates transcriptional repression of pdk4 gene by interacting with hypermethylated in cancer 1(HIC1)

Increased accumulation and/or impaired utilization of fatty acid in extra-adipose tissues are implicated in the pathogenesis of insulin resistance and type 2 diabetes. Pyruvate dehydrogenase kinase 4 （Pdk4） is a key enzyme involved in fatty oxidation and energy expenditure, and its expression can be repressed by pro-inflammatory stimuli. Previously, we have shown that class II transactivator （CIITA） mediates the adverse effect of interferon gamma （IFN-7） in skeletal muscle cells by cooperating with hypermethylated in cancer 1 （HIC1） to repress silent informa- tion regulator 1 （SIRT1） transcription. Building upon this finding, we report here that CIITA interacted with HIC1 via the GTP-binding domain （GBD） while HIC1 interacted with CIITA via the BTB/POZ domain. The GBD domain was required for CIITA to repress SIRT1 transcription probably acting as a bridge for CIITA to bind to HIC1 and consequently to bind to the SIRT1 promoter. IFN-7 stimulation, CIITA over-expression, or HIC1 over- expression repressed Pdk4 promoter activity while silencing either CIITA or HIC1 normalized Pdk4 expression in the presence of IFN-7. An increase in SIRT1 expression or activity partially rescued Pdk4 expression in the pre- sence of CIITA, but SIRT1 inhibition abrogated Pdk4 normalization even in the absence of CIITA. Taken together, our data have identified a HIC1-CIITA-SIRT1 axis that regulates Pdk4 transcription in response to IFN-7 stimula- tion.

Molecular Characterization, Expression Pattern and Transcriptional Regulation of Figla During Gonad Development in Japanese Founder (Paralichthys olivaceus)

The factor in the germline alpha(figla), as a member of the basic helix-loop-helix family, has been reported to be involved in ovary development in mammals and teleosts. However, the regulatory mechanisms of figla in teleosts remain unclear. Here,figla in P. olivaceus(Pofigla) was characterized with encoding a 202 amino acid protein that contains a conserved basic region and helix-loop-helix(HLH) domain. Amino acids alignment and synteny analysis revealed that Pofigla was conserved with the orthologous gene sequences in other vertebrates. The results of qRT-PCR showed Pofigla was maternally inherited during embryonic development. For tissue distribution, Pofigla showed a sexually dimorphic gene expression in the gonad of different genders, with a higher expression in ovary than in testis. In situ hybridization(ISH) results demonstrated Pofigla was specifically expressed in germ cells including oocytes, spermatogonia and spermatocytes. By screening and analyzing two proximal regions(-2966/-2126 and-772/-444) with high promoter activity, we found SOX5, LEF1, FOXP1 and GATA1 may play important roles in the transcriptional regulation of Pofigla. Furthermore, we observed the co-localization between Figla and LEF1 in HEK 293T cells. And the significant up-regulation effect of the canonical Wnt signaling pathway on the expression of Pofigla was found in cultured ovarian cells. This study provided the first evidence that figla not only has an important function in ovary development, but also plays some potential roles in testis development and/or male germ cell differentiation during early testis development in P. olivaceus. The results provide valuable reference in exploring the regulatory network of figla in teleost.

Comparative genomic analyses reveal cis-regulatory divergence after polyploidization in cotton

Polyploidization has long been recognized as a driver for the evolutionary formation of superior plant traits coupled with gene expression novelty.However,knowledge of the effect of regulatory variation on expression changes following polyploidization remains limited.In this study,we characterized transcriptional regulatory divergence by comparing tetraploid cotton with its putative diploid ancestors.We identified 144,827,99,609,and 219,379 Tn5 transposase-hypersensitive sites(THSs)in Gossypium arboreum,G.raimondii,and G.hirsutum,respectively,and found that the conservation of promoter THSs was associated with coordination of orthologous genes expression.This observation was consistent with analysis of transcription-factor binding sites(TFBS)for 262 known motifs:genes with higher TFBS conservation scores(CS)showed less change than those genes with lower TFBS CS in expression levels.TFBS influenced by genomic variation were involved in the novel regulation networks between transcriptional factors and target genes in tetraploid cotton.We describe an example showing that the turnover of TFBS was linked to expression pattern divergence of genes involved in fiber development(fiber-related genes).Our findings reveal the regulatory divergence of the transcriptional network in cotton after polyploidization and characterizes the regulatory relationships of genes contributing to desirable traits.

Dynamical Analysis of Protein Regulatory Network in Budding Yeast Nucleus

Recent progresses in the protein regulatory network of budding yeast Saccharomyces cerevisiae have provided a global picture of its protein network for further dynamical research. We simplify and modularize the protein regulatory networks in yeast nucleus, and study the dynamical properties of the core 37-node network by a Boolean network model, especially the evolution steps and final fixed points. Our simulation results show that the number of fixed points N（k） for a given size of the attraction basin k obeys a power-law distribution N（k） χ k^-2.024. The yeast network is more similar to a scale-free network than a random network in the above dynamical properties.

Type-B response regulator OsRR22 forms a transcriptional activation complex with OsSLR1 to modulate OsHKT2;1 expression in rice

Soil salinity severely limits crop yields and quality.Plants have evolved several strategies to mitigate the adverse effects of salinity,including redistribution and compartmentalization of toxic ions using ion-specific transporters.However,the mechanisms underlying the regulation of these ion transporters have not been fully elucidated.Loss-of-function mutants of OsHKT2;1,which is involved in sodium uptake,exhibit strong salt stress-resistant phenotypes.In this study,OsHKT2;1 was identified as a transcriptional target of the type-B response regulator OsRR22.Loss-of-function osrr22 mutants showed resilience to salt stress,and OsRR22-overexpression plants were sensitive to salt stress.OsRR22 was found to activate the expression of OsHKT2;1 by directly binding to the promoter region of OsHKT2;1 via a consensus cis-element of type-B response regulators.Moreover,rice DELLA protein OsSLR1 directly interacted with OsRR22 and functioned as a transcriptional co-activator.This study has uncovered a novel transcriptional regulatory mechanism by which a type-B response regulator controls sodium transport under salinity stress.

A novel candidate gene CLN8 regulates fat deposition in avian

Background The fat deposition has a crucial role in animal meat flavor,and fat deposition-related traits are vital for breeding in the commercial duck industry.Avian fat-related traits are typical complex phenotypes,which need a large amount of data to analyze the genetic loci.Results In this study,we performed a new phenotypic analysis of fat traits and genotyped whole-genome varia-tions for 1,246 ducks,and combed with previous GWAS data to reach 1,880 ducks for following analysis.The carcass composition traits,subcutaneous fat weight(SFW),subcutaneous fat percentage(SFP),abdominal fat weight(AFW),abdominal fat percentage(AFP)and the body weight of day 42(BW42)for each duck were collected.We identified a set of new loci that affect the traits related to fat deposition in avian.Among these loci,ceroid-lipofuscinosis,neuronal 8(CLN8)is a novel candidate gene controlling fat deposition.We investigated its novel function and regulation in avian adipogenesis.Five significant SNPs(the most significant SNP,P-value=21.37E-12)and a single haplotype were detected in the upstream of CLN8 for subcutaneous fat percentage.Subsequently,luciferase assay demonstrated that 5 linked SNPs in the upstream of the CLN8 gene significantly decreased the transcriptional activity of CLN8.Further,ATAC-seq analysis showed that transcription factor binding sites were identified in a region close to the haplotype.A set of luciferase reporter gene vectors that contained different deletion fragments of the CLN8 promoter were con-structed,and the core promoter area of CLN8 was finally identified in the-1,884/-1,207 bp region of the 5′flanking sequences,which contains adipogenesis-related transcription factors binding sites.Moreover,the over-expression of CLN8 can remarkably facilitate adipocyte differentiation in ICPs.Consistent with these,the global transcriptome profiling and functional analysis of the over-expressed CLN8 in the cell line further revealed that the lipid biosynthetic process during the adipogenesis was significantly enriched.Conclusions Our results demonstrated that CLN8 is a positive regulator of avian adipocyte differentiation.These findings identify a novel function of CLN8 in adipocyte differentiation,which provides important clues for the further study of the mechanism of avian fat deposition.