Epigenetic changes in the regulation of carotenoid metabolism during honeysuckle flower development

Flower development is one of the most vital pathways in plant development, during which the epigenetic regulation of gene expression is essential. DNA methylation, the most conserved epigenetic modification, participates in gene expression regulation and transposable element silencing. Honeysuckle(Lonicera japonica) is an important medicinal plant renowned for its colorful and fragrant flowers. Honeysuckle flowers change color from white to gold as a result of carotenoid accumulation during development. However, the role of DNA methylation in flower color changes is not well understood in L. japonica. Here, we performed whole-genome bisulfite sequencing and transcriptome sequencing during flowering development in honeysuckle. The results showed that a decrease in the levels of genome-wide average DNA methylation during flower development and changes in DNA methylation were associated with the expression of demethylase genes. Moreover, many genes involved in carotenoid biosynthesis and degradation, such as Lj PSY1, LjPDS1, LjLCYE, and LjCCD4, have altered expression levels because of hypomethylation, indicating that DNA methylation plays an important role in flower color changes in honeysuckle. Taken together, our data provide epigenetic insights into flower development and color change in honeysuckles.

Plant Anthocyanin Synthesis and Gene Regulation

This paper aims to explain the biochemistry of anthocyanin synthesis based on an overview of plant anthocyanin synthesis genes and environmental factors in the regulation of anthocyanin metabolism. The results show that： ① The metabolism of anthocyanins in plants is affected by the temperature, light, ultraviolet, fertilization status, hormone levels and other factors, which affect the military anthocyanin biosynthetic genes, and then induce or inhibit the synthesis of anthocyanins. ② In the regulation of genes, some of the structural genes of anthocyanin synthesis showed promoting effect, while others showed inhibitory effect. At different environ- mental conditions, the regulation of gene activation and inhibition of the amount of different regulatory genes that anthocyanin accumulation is different, and cause different colors of plant-organs production. ③ In different environmental factors or hor-mones induced to produce the same or different regulation of gene expression changes in regulatory genes, resulting in several different anthocyanins or anthocyanin ratio changes, so that the color of plant organs in different colors.

Transcriptional Regulation of 10 Mitochondrial Genes in Different Tissues of NCa CMS System in Brassica napus L. and Their Relationship with Sterility

Northern blot analysis was conducted with mitochondrial RNA from seedling leaves, floral buds, and developing seeds of NCa CMS, maintainer line and fertile F1 using ten mitochondrial genes as probes. The results revealed that 9 out of the 10 mitochondrial genes, except for atp6, showed no difference in different tissues of the corresponding materials of NCα CMS system and that they might be constitutively expressed genes. Eight genes, such as orf139, orf222, atpl, cox1, cox2, cob, rm5S, and rm26S, showed no difference among the three tissues of all the materials detected. So the expression of these eight genes was not regulated by nuclear genes and was not tissue-specific. The transcripts of atp9 were identical among different tissues, but diverse among different materials, indicating that transcription of atp9 was neither controlled by nuclear gene nor tissue-specific. Gene atp6 displayed similar transcripts with the same size among different tissues of all the materials but differed in abundance among tissues of corresponding materials and its expression might be tissue-specific under regulation of nuclear gene. Moreover, three transcripts of orf222 were detected in the floral buds of NCa cms and fertile F1, but no transcript was detected in floral buds of the maintainer line.The transcription of orf139 was similar to that of orf222 but only two transcripts of 0.8 kb and 0.6 kb were produced. The atp9 probe detected a single transcript of 0.6 kb in NCa cms and in maintainer line and an additional transcript of 1.2 kb in fertile F1. The relationship of expression of orf222, orf139, and atp9 with NCa sterility was discussed.

Gene Expression and Regulation of Blastocyst Formation

Blastocyst formation is a crucial stage of early embryo development.Cell junction proteins and cell adhesion associated proteins are involved in the establishment of cell junction,and subsequently induce cell compaction,blastocyst formation,differentiation of trophectoderm and maintenance of blastocyst expansion.Genes regulating development and differentiation participate in embryo development and differentiation of inner cell mass and trophectoderm,which controls the transition from the undifferentiation to differentiation state.Furthermore,cytokine and growth factor have influence on the proliferation of cells of inner cell mass.In a word,many proteins and factors are involved in the gene expression and regulation of blastocyst formation.

Roles and regulation of bone morphogenetic protein-7 in kidney development and diseases

The gene encoding bone morphogenetic protein-7(BMP7) is expressed in the developing kidney in embryos and also in the mature organ in adults. During kidney development, expression of BMP7 is essential to determine the final number of nephrons in and proper size of the organ. The secreted BMP7 acts on the nephron progenitor cells to exert its dual functions: To maintain and expand the progenitor population and to provide them with competence to respond to differentiation cues, each relying on distinct signaling pathways. Intriguingly, in the adult organ, BMP7 has been implicated in protection against and regeneration from injury. Exogenous administration of recombinant BMP7 to animal models of kidney diseases has shown promising effects in counteracting inflammation, apoptosis and fibrosis evoked upon injury. Although the expression pattern of BMP7 has been well described, the mechanisms by which it is regulated have remained elusive and the processes by which the secretion sites of BMP7 impinge upon its functions in kidney development and diseases have not yet been assessed. Understanding the regulatory mechanisms will pave the way towards gaining better insight into the roles of BMP7, and to achieving desired control of the gene expression as a therapeutic strategy for kidney diseases.

Circular RNAs: New Players in Gene Regulation

The existence of circular RNAs (circRNAs) was demonstrated over 30 years ago. They did not gain much interest at the time because they appeared to be relatively rare when compared to the abundance of the canonical linear RNAs. However, more recent evidence suggests that circRNAs are abundant in cells and tissues and possess intriguing biological properties. These recent developments have renewed our interest in this novel class of molecules. This report will provide an overview of circRNAs, discuss how they may modify our understanding of gene regulation and indicate their most likely relevance to health. The circRNAs from viruses, bacteria and archaea are not in the scope of this report, and we focused this review on circRNAs in eukaryotes.

Polyploid Gene Expression and Regulation in Polysomic Polyploids

Polyploidization is one of the most crucial pathways in introducing speciation and broadening biodiversity, especially in the Plant Kingdom. Although the majority of studies have focused only on allopolyploid or disomic polyploids, polysomic polyploid species have occurred frequently in higher plants. Due to the occurrence of the capabilities of more copies of alleles in a locus which can have additive dosage effects and/or allelic interactions, polysomic polyploids can lead to unique gene regulations to silence or adjust the expression level to create variations in organ size, metabolic products, and abiotic stress tolerance and biotic stress resistance, etc. This review aims to comprehensively summarize the contemporary understanding and findings concerning the molecular mechanisms of gene expression as well as gene regulation in natural typed and resynthesized polysomic polyploid plants. The review investigates the molecular level of phenomena in polysomic polyploid plants such as 1) typically enlarging organ size and stabilizing meiosis, 2) increasing phytochemical content and metabolic products, 3) enhancing the ability to adapt with biotic and abiotic stress, and 4) changing in gene regulation to silence or adjust the expression levels involve in sequence elimination, methylation, gene suppression, subfunctionalization, neo-functionalization, and transposon activation.

Molecular regulation mechanism of oocyte maturation in beef cattle

Bovine oocytes are one of the indispensable cells in cattle reproduction and have become a research hot spot in cattle reproduction in recent years.The maturation process of oocytes is mainly regulated by enzymes,hormones,cytokines,and other molecules.The factors affecting cattle oocyte maturation have been previously studied to clarify the molecular mechanisms of cattle oocyte maturation.In this review article,phospholipid protein-3-kinase/protein kinase B,mitogen-activated protein kinase/extracellular signal-regulated kinase,Janus kinase/signal transducer and activator of transcription,epidermal growth factor receptor/extracellular signal-regulated kinase,and other signaling pathways related to oocyte maturation are discussed.In addition,the molecular mechanisms of some coding genes(JY-1,FGF-10,CDC20,etc.)and non-coding genes(miRNA,lncRNA,and circRNA)regulating oocyte maturation have been reviewed to provide new ideas for high reproductive performance molecular breeding of high-quality cattle.

Regulatory role of NFAT1 signaling in articular chondrocyteactivities and osteoarthritis pathogenesis

Osteoarthritis (OA), the most common form of joint disease, is characterized clinically by joint pain, stiffness,and deformity. OA is now considered a whole joint disease;however, the breakdown of the articular cartilage remains themajor hallmark of the disease. Current treatments targeting OA symptoms have a limited impact on impeding orreversing the OA progression. Understanding the molecular and cellular mechanisms underlying OA development isa critical barrier to progress in OA therapy. Recent studies by the current authors’ group and others have revealedthat the nuclear factor of activated T cell 1 (NFAT1), a member of the NFAT family of transcription factors, regulatesthe expression of many anabolic and catabolic genes in articular chondrocytes of adult mice. Mice lacking NFAT1exhibit normal skeletal development but display OA in both appendicular and spinal facet joints as adults. Thisreview mainly focuses on the recent advances in the regulatory role of NFAT1 transcription factor in the activities ofarticular chondrocytes and its implication in the pathogenesis of OA.

Review of the genetic basis of emotion dysregulation in children and adolescents

Previous evidence suggests that emotion dysregulation may have different biological correlates between adults and children/adolescents. Although the role of genetic factors has been extensively studied in adult-onset emotion dysregulation, the genetic basis for pediatriconset emotion dysregulation remains elusive. The current review article presents a summary of previous studies that have suggested a few genetic variants associated with pediatric emotion dysregulation. Among these candidate loci, many prior studies have been focused on serotonin transporter promoter gene polymorphism 5-HTTLPR. Certain alleles of the 5-HTTLPR gene polymorphism have been found to be associated with traits associated with emotion dysregulation, such as aggression, affect reactivity, and insecure attachment. Additionally, genetic variants involving dopamine and neurophysiological biomarkers like the COMT Val158Met(rs460) and dopamine receptor D2/ ankyrin repeat and kinase domain containing one polymorphisms may play a role in emotion dysregulation. Inconsistent findings have been noted, possibly due to the heterogeneity in study designs and characteristics of different populations. Further research on the role of genetic predetermination of emotion dysregulation in children and adolescents is warranted.

Long Non-coding RNA ANRIL in Gene Regulation and Its Duality in Atherosclerosis

The antisense transcript long non-coding RNA（lnc RNA）（antisense non-coding RNA in the INK4 locus, ANRIL） is an antisense of the cyclin-dependent kinase inhibitor 2 B（CDKN2B） gene on chromosome 9 p21 that contains an overlapping 299-bp region and shares a bidirectional promoter with alternate open reading frame（ARF）. In the context of gene regulation, ANRIL is responsible for directly recruiting polycomb group（Pc G） proteins, including polycomb repressive complex-1（PRC-1） and polycomb repressive complex-2（PRC-2）, to modify the epigenetic chromatin state and subsequently inhibit gene expression in cis-regulation. On the other hand, previous reports have indicated that ANRIL is capable of binding to a specific site or sequence, including the Alu element, E2 F transcription factor 1（E2F1）, and CCCTC-binding factor（CTCF）, to achieve trans-regulation functions. In addition to its function in cell proliferation, adhesion and apoptosis, ANRIL is very closely associated with atherosclerosis-related diseases. The different transcripts and the SNPs that are related to atherosclerotic vascular diseases（ASVD-SNPs） are inextricably linked to the development and progression of atherosclerosis. Linear transcripts have been shown to be a risk factor for atherosclerosis, whereas circular transcripts are protective against atherosclerosis. Furthermore, ANRIL also acts as a component of the inflammatory pathway involved in the regulation of inflammation, which is considered to be one of the causes of atherosclerosis. Collectively, ANRIL plays an important role in the formation of atherosclerosis, and the artificial modification of ANRIL transcripts should be considered following the development of this disease.

Genetic engineering and lignin biosynthetic regulation in forest tree species

Genetic engineering of forest tree species is regarded as a strategy to reduce worldwide pressure on natural forests, to conserve genetic resources and ameliorate stress on global climate, and to meet growing demand for forest wood and timber products. Genetic engineering approaches toward the control or management of fungal pathogens, arthropod herbivores, bacterial and viral diseases, the use of pest resistance genes, and weed competitors are being studied. Although the production of transgenic trees is relatively recent and only a few species have been successfully genetically engineered in forest tree species, very useful and valuable information is available on the application of transgenic trees. Genes involved in important agricultural traits such as herbicide resistance, insect resistance, and wood quality have been isolated and have been used to genetically engineer trees. New technologies of plant molecular biology and genomics now make it possible high-efficient genetic improvement of forest trees. Genetic engineering promises to expand greatly the potential for genetic manipulation as new genes of commercial interest are discovered and utilized. Lignification is a process essential to the nature and evolution of vascular plants that is still poorly understood, even though it has been studied for more than a century. Recent studies on mutant and transgenic plants indicate that lignification may be far more flexible than previously realized. Rines with a mutation affecting the biosynthesis of the major lignin precursor, coniferyl alcohol, show a high level of an unusual subunit, dihydroconiferyl alcohol. It is also unusual as a plant polymer in that there are no plant enzymes for its degradation. These results have significant implications regarding the tradiational definition of lignin, and highlight the need for a better understanding of the lignin precursor biosynthetic pathway. In this review, we describe the progress made recently in genetic engineering of forest tree species.

坝上长尾鸡PPAR基因多态性及其与脂肪酸性状关联分析

为了明确坝上长尾鸡氧化物酶体增殖物激活受体(peroxisome proliferation activated receptors,PPAR)基因单核苷酸多态性(single nucleotide polymorphism,SNP)与腿肌脂肪酸性状间的关联性,试验扩增了54只坝上长尾鸡的PPAR基因并进行SNP检测,同时测定鸡只腿肌中的脂肪酸含量,并对SNP位点进行基因型和等位基因频率及遗传特性分析,以及SNP位点与腿肌脂肪酸含量的关联性分析。结果表明:坝上长尾鸡PPAR基因有3个SNP位点,分别为g.43738C>T、g.43916C>T、g.44063T>C位点;g.43738C>T位点存在CT和CC两种基因型,优势基因型为CC基因型,优势基因为C;g.43916C>T位点存在CC、CT和TT 3种基因型,优势基因型为CC基因型,优势基因为C;g.44063T>C位点存在CT和TT两种基因型,优势基因型为TT基因型,优势基因为T;3个SNP位点均处于哈代-温伯格平衡状态(P>0.05),其中g.43738C>T和g.44063T>C属于低度多态,g.43916C>T属于中度多态;g.43738C>T和g.44063T>C与腿肌脂肪酸含量相关性均不显著(P>0.05),g.43916C>T与腿肌肉豆蔻油酸含量显著相关(P<0.05),与其他脂肪酸含量相关性不显著(P>0.05)。说明PPAR基因g.43916C>T可作为坝上长尾鸡腿肌肉豆蔻油酸选育的分子标记。

Regulation of fim genes in uropathogenic Escherichia coli

Uropathogenic Escherichia coli(UPEC)is the leading cause of urinary tract infections in women,causing significant morbidity and mortality in this population.Adherence to host epithelial cells is a pivotal step in the pathogenesis of UPEC.One of the most important virulence factors involved in mediating this attachment is the type 1 pilus(type 1 fimbria)encoded by a set of fim genes arranged in an operon.The expression of type 1 pili is controlled by a phenomenon known as phase variation,which reversibly switches between the expression of type 1 pili(Phase-ON)and loss of expression(Phase-OFF).Phase-ON cells have the promoter for the fimA structural gene on an invertible DNA element called fimS,which lines up to allow transcription,whereas transcription of the structural gene is silenced in Phase-OFF cells.The orientation of the fimS invertible element is controlled by two site-specific recombinases,FimB and FimE.Environmental conditions cause transcriptional and post-transcriptional changes in UPEC cells that affect the level of regulatory proteins,which in turn play vital roles in modulating this phase switching ability.The role of fim gene regulation in UPEC pathogenesis will be discussed.

Direct somatic embryogenesis and related gene expression networks in leaf explants of Hippeastrum ‘Bangkok Rose’

Hippeastrum, a highly diverse genus in the Amaryllidaceae family, is a valuable ornamental bulbous flowering plant. Somatic embryogenesis(SE) is an efficient method for mass production of Hippeastrum plantlets. Previous studies have been devoted to the in vitro propagation of Hippeastrum, but the SE and its regulatory networks are rarely reported. In this study, we established a direct SE method of Hippeastrum Bangkok Rose' using leaf bases as explants. MS supplemented with 1.00 mg·L^(-1)NAA +1.00 mg·L^(-1)KT + 0.25 mg·L^(-1)TDZ was the optimal medium for SE. Histological observations showed that the bipolar somatic embryo originated from the epidermal cell layer and underwent initiation,globular, scutellar and coleoptile stages. During SE, endogenous hormones of IAA, CTK, ABA, and SA were highly accumulated. Transcriptomic analysis revealed the genes encoding auxin biosynthesis/metabolic enzymes and efflux carriers were induced, while the auxin receptor of TIR1 and ARF transcriptional repressor of Aux/IAA were down-regulated and up-regulated, respectively, leading to suppression of auxin signaling. In contrast, cytokine signaling was promoted at the early stage of SE, as biosynthesis, transport, and signaling components were up-regulated.Various stress-related genes were up-regulated at the early or late stages of SE. Chromatin remodeling could also be dynamically regulated via distinct expression enzymes that control histone methylation and acetylation during SE. Moreover, key SE regulators, including WOXs and SERKs were highly expressed along with SE. Overall, the present study provides insights into the SE regulatory mechanisms of the Hippeastrum.

The virulence regulator AbsR in avian pathogenic Escherichia coli has pleiotropic effects on bacterial physiology

Avian pathogenic Escherichia coli(APEC)belonging to extraintestinal pathogenic E.coli(ExPEC)can cause severe infections in extraintestinal tissues in birds and humans,such as the lungs and blood.MprA(microcin production regulation,locus A,herein renamed AbsR,a blood survival regulator),a member of the MarR(multiple antibiotic resistance regulator)transcriptional regulator family,governs the expression of capsule biosynthetic genes in human ExPEC and represents a promising druggable target for antimicrobials.However,a deep understanding of the AbsR regulatory mechanism as well as its regulon is lacking.In this study,we present a systems-level analysis of the APEC AbsR regulon using ChIP-Seq(chromatin immunoprecipitation sequencing)and RNA-Seq(RNA sequencing)methods.We found that AbsR directly regulates 99 genes and indirectly regulates 667 genes.Furthermore,we showed that:1)AbsR contributes to antiphagocytotic effects by macrophages and virulence in a mouse model for systemic infection by directly activating the capsular gene cluster;2)AbsR positively impacts biofilm formation via direct regulation of the T2SS(type II secretion system)but plays a marginal role in virulence;and 3)AbsR directly upregulates the acid tolerance signaling system EvgAS to withstand acid stress but is dispensable in ExPEC virulence.Finally,our data indicate that the role of AbsR in virulence gene regulation is relatively conserved in ExPEC strains.Altogether,this study provides a comprehensive analysis of the AbsR regulon and regulatory mechanism,and our data suggest that AbsR likely influences virulence primarily through the control of capsule production.Interestingly,we found that AbsR severely represses the expression of the type I-F CRISPR(clustered regularly interspaced short palindromic repeats)-Cas(CRISPR associated)systems,which could have implications in CRISPR biology and application.

Use of Rich BHI Medium Instead of Synthetic TMH Medium for Gene Regulation Study in Yersinia pestis

Objective This study is to verify the use of rich BHI medium to substitute synthetic media for gene regulation studies in Yersinia pestis. Methods The transcriptional regulation of rovA by PhoP or via temperature upshift, and that of pla by CRP were investigated when Y. pestis was cultured in BHI. After cultivation under 26 ~C, and with temperature shifting from 26 to 37 ~C, the wild-type （WT） strain or its phoP or crp null mutant （AphoP or Acrp, respectively） was subject to RNA isolation, and then the promoter activity of rovA or plo in the above strains was detected by the primer extension assay. The rovA promoter-proximal region was cloned into the pRW50 containing a promoterless lacZ gene. The recombinant LacZ reporter plasmid was transformed into WT and AphoP to measure the promoter activity of rovA in these two strains with the ^-Galactosidase enzyme assay system. Results When Y. pestis was cultured in BHI, the transcription of rovA was inhibited by PhoP and upon temperature upshift while that ofpla was stimulated by CRP. Conclusion The rich BHI medium without the need for modification to be introduced into the relevant stimulating conditions （which are essential to triggering relevant gene regulatory cascades）, can be used in lieu of synthetic TMH media to cultivate Y. pestis for gene regulation studies.

Epigenetic regulation of stemness maintenance in the neurogenic niches

In the adult mouse brain, the subventricular zone lining the lateral ventricles and the subgranular zone in the dentate gyrus of the hippocampus are two zones that contain neural stem cells(NSCs) with the capacity to give rise to neurons and glia during the entire life of the animal. Spatial and temporal regulation of gene expression in the NSCs populationis established and maintained by the coordinated interaction between transcription factors and epigenetic regulators which control stem cell fate. Epigenetic mechanisms are heritable alterations in genome function that do not involve changes in DNA sequence itself but that modulate gene expression, acting as mediators between the environment and the genome. At the molecular level, those epigenetic mechanisms comprise chemical modifications of DNA such as methylation, hydroxymethylation and histone modifications needed for the maintenance of NSC identity. Genomic imprinting is another normal epigenetic process leading to parentalspecific expression of a gene, known to be implicated in the control of gene dosage in the neurogenic niches. The generation of induced pluripotent stem cells from NSCs by expression of defined transcription factors, provide key insights into fundamental principles of stem cell biology. Epigenetic modifications can also occur during reprogramming of NSCs to pluripotency and a better understanding of this process will help to elucidate the mechanisms required for stem cell maintenance. This review takes advantage of recent studies from the epigenetic field to report knowledge regarding the mechanisms of stemness maintenance of neural stem cells in the neurogenic niches.

PPAR gamma2:The main isoform of PPARγthat positively regulates the expression of the chicken Plin1 gene

Perilipin1(PLIN1)is a major phosphorylated protein that specifically coats the surface of neutral lipid droplets(LDs)in adipocytes and plays a crucial role in regulating the accumulation and hydrolysis of triacylglycerol(TG).Mammalian studies have shown that Plin1 gene transcription is mainly regulated by peroxisome proliferator-activated receptorgamma(PPARγ),the master regulator of adipogenesis.However,the regulatory mechanism of the chicken Plin1(c Plin1)gene is poorly understood.The present study aimed to investigate whether Plin1 is regulated by PPARγin chickens and identify its exact molecular mechanism.Reporter gene and expression assays showed that PPARγ2,but not PPARγ1,activated(P<0.01)the cPlin1 gene promoter.An electrophoretic mobility shift assay and mutational analysis revealed that PPARγ2 bound to a special site in the cPlin1 gene promoter to enhance its expression.In summary,our results show that PPARγpromotes the expression of the cPlin1 gene and that PPARγ2 is the main regulatory isoform.

Expression Regulation of Starch and Storage Protein Synthesis Related Genes in Rice Grains

Starch and the storage proteins are the main nutritious substances in crop grains,and their composition and content in grains play a decisive role in the grain quality of rice and other staple food crops.This review has mainly summarized the new advances in the expression regulation of starch and storage protein synthesis related genes in rice grains.Moreover,the challenges of the starch and storage protein synthesis substances in rice genetic improvement were also discussed.This review will provide important information for genetic improvement of grain quality in rice and,potentially,other staple cereals.