A gene regulatory network subcircuit drives a dynamic pattern of gene expression

Early specification of endomesodermal territories in the sea urchin embryo depends on a moving torus of regulatory gene expression. We show how this dynamic patterning function is encoded in a gene regulatory network (GRN) subcircuit that includes the otx, wnt8, and blimp1 genes, the cis-regulatory control systems of which have all been experimentally defined. A cis-regulatory reconstruction experiment revealed that blimp1 autorepression accounts for progressive extinction of expression in the center of the torus, whereas its outward expansion follows reception of the Wnt8 ligand by adjacent cells. GRN circuitry thus controls not only static spatial assignment in development but also dynamic regulatory patterning.     

A regulatory SNP causes a human genetic disease by creating a new transcriptional promoter

We describe a pathogenetic mechanism underlying a variant form of the inherited blood disorder alpha thalassemia. Association studies of affected individuals from Melanesia localized the disease trait to the telomeric region of human chromosome 16, which includes the alpha-globin gene cluster, but no molecular defects were detected by conventional approaches. After resequencing and using a combination of chromatin immunoprecipitation and expression analysis on a tiled oligonucleotide array, we identified a gain-of-function regulatory single-nucleotide polymorphism (rSNP) in a nongenic region between the alpha-globin genes and their upstream regulatory elements. The rSNP creates a new promoterlike element that interferes with normal activation of all downstream alpha-like globin genes. Thus, our work illustrates a strategy for distinguishing between neutral and functionally important rSNPs, and it also identifies a pathogenetic mechanism that could potentially underlie other genetic diseases.     

Evolution of shape by multiple regulatory changes to a growth gene

The genetic changes responsible for morphological differences between species are largely unidentified. Such changes can involve modifications of growth that are relevant to understanding evolution, development, and disease. We identified a gene that induces male-specific wing size and shape differences between Nasonia wasp species. Fine-scale mapping and in situ hybridization reveal that changes in at least three regions (two strictly in noncoding sequence) around the gene unpaired-like (upd-like) cause changes in spatial and temporal expression of upd-like in the developing wing and corresponding changes in wing width. Upd-like shows homology to the Drosophila unpaired gene, a well-studied signaling protein that regulates cell proliferation and differentiation. Our results indicate how multiple changes in the regulation of upd-like are involved in microevolution of morphological and sex-specific differences between species.     

农杆菌介导系统获得性抗性调节基因(NPR1)转化罗汉果的研究

以罗汉果子叶为受体,通过农杆菌介导法,将从拟南芥中克隆到的NPR1基因导入罗汉果.经抗生素筛选、PCR检测和Southern杂交分析,结果表明:NPR1基因已经整合到罗汉果基因组.通过外植体不同分化阶段的抗性筛选,获得转基因植株.在烟草花叶病毒接种6周后,转基因植株的发病程度明显低于非转基因植株.     

A genomic regulatory network for development

Development of the body plan is controlled by large networks of regulatory genes. A gene regulatory network that controls the specification of endoderm and mesoderm in the sea urchin embryo is summarized here. The network was derived from large-scale perturbation analyses, in combination with computational methodologies, genomic data, cis-regulatory analysis, and molecular embryology. The network contains over 40 genes at present, and each node can be directly verified at the DNA sequence level by cis-regulatory analysis. Its architecture reveals specific and general aspects of development, such as how given cells generate their ordained fates in the embryo and why the process moves inexorably forward in developmental time.     

Formation of regulatory patterns during signal propagation in a Mammalian cellular network

We developed a model of 545 components (nodes) and 1259 interactions representing signaling pathways and cellular machines in the hippocampal CA1 neuron. Using graph theory methods, we analyzed ligand-induced signal flow through the system. Specification of input and output nodes allowed us to identify functional modules. Networking resulted in the emergence of regulatory motifs, such as positive and negative feedback and feedforward loops, that process information. Key regulators of plasticity were highly connected nodes required for the formation of regulatory motifs, indicating the potential importance of such motifs in determining cellular choices between homeostasis and plasticity.     

Control of stress-dependent cardiac growth and gene expression by a microRNA

The heart responds to diverse forms of stress by hypertrophic growth accompanied by fibrosis and eventual diminution of contractility, which results from down-regulation of alpha-myosin heavy chain (alphaMHC) and up-regulation of betaMHC, the primary contractile proteins of the heart. We found that a cardiac-specific microRNA (miR-208) encoded by an intron of the alphaMHC gene is required for cardiomyocyte hypertrophy, fibrosis, and expression of betaMHC in response to stress and hypothyroidism. Thus, the alphaMHC gene, in addition to encoding a major cardiac contractile protein, regulates cardiac growth and gene expression in response to stress and hormonal signaling through miR-208.     

基于基因调控网络对鸡胚皮肤发育的枢纽基因和关键通路分析

为挖掘脊椎动物胚胎发育过程中皮肤调控模式的改变,以鸡胚作为模型,利用来源于NCBI数据库的SRA数据子库中胚胎发育第6～21天的皮肤组织RNA-Seq数据进行聚类分析,在基因共表达网络、信号通路、蛋白互作网路3个层面基于网络拓扑属性逐步挖掘核心基因集,并分析核心基因集在不同发育阶段的互作网络变化.结果表明:1)鸡胚皮肤...     

Contingent genetic regulatory events in T lymphocyte activation

Interaction of antigen in the proper histocompatibility context with the T lymphocyte antigen receptor leads to an orderly series of events resulting in morphologic change, proliferation, and the acquisition of immunologic function. In most T lymphocytes two signals are required to initiate this process, one supplied by the antigen receptor and the other by accessory cells or agents that activate protein kinase C. Recently, DNA sequences have been identified that act as response elements for one or the other of the two signals, but do not respond to both signals. The fact that these sequences lie within the control regions of the same genes suggests that signals originating from separate cell membrane receptors are integrated at the level of the responsive gene. The view is put forth that these signals initiate a contingent series of gene activations that bring about proliferation and impart immunologic function.     

利用rbcL基因序列比对分析广西优质红锥种质资源的遗传多样性

通过PCR扩增得到10个红锥品系的rbcL基因全序列,均为1.513 kb.核苷酸序列比对结果表明,在256-1 455 bp区间10个红锥品系共有16处碱基发生变异,变异率为1%,其中在306 bp和634 bp处10个红锥品系较同属对照castanopsis lucida均发生相同的变异,可以看作属内进化信息碱基.对表达的氨基酸序列进行比对分析,发现16处碱基变异共引起8处氨基酸序列变异.     

农杆菌介导iaaM基因黄瓜遗传转化体系的建立

以已经建立的高频黄瓜再生体系为基础,从影响黄瓜转基因体系的农杆菌侵染时间,共培养时是否加入乙酰丁香酮等因素优化了黄瓜遗传转化体系;将单性结实基因iaaM以农杆菌介导法导入到东农649品种黄瓜子叶节中,经过不定芽诱导和生根等过程获得了转基因株系,通过特异性引物的PCR鉴定,40个株系扩增出iaaM目的基因片段。PCR-Southern检测为阳性。转基因阳性植株移栽到温室中,其果实经检测80%为单性结实黄瓜。     

Cloning and genetic transformation of a novel rice gene OsAPT2

A novel rice gene OsAPT2,which encodes a putative adenine phosphoribosyl transferase(APRT),was cloned.Its full-length cDNA is 1125bp,composing an ORF encoding 212 amino acid residues and a stop cordon,a 5‘ UTR of 123 bp and a 3‘ UTR of 363 bp.The sequence data have been submitted to the DDBJ/EMBL/GenBank databases(accession number:AY238894).The deduced amino acid sequence of OsAPT2 is highly homologous to those of previously reported APRTs.The genomic OsAPT2 gene contains 7 exons and 6 introns.Its total len...     

通过整合转录组与代谢组解析不同类型椰子的脂肪酸调控网络

为了探究不同类型椰子中脂质种类和含量的差异,本研究利用非靶向代谢组学方法对海南高种和矮种椰子椰肉组织的代谢物进行了分析,共检测到12 579种代谢信号,其中鉴定了564种代谢物,包括氨基酸、脂肪酸、类黄酮等。定量分析表明高种椰子的脂质总体含量高于矮种椰子,其中绿矮椰子脂质含量最低。甘油脂、鞘脂和脂肪酰是不同类型椰子中主要的差异物质。转录组数据结果表明,不同类型椰子中的差异基因主要参与脂肪酸代谢、α-亚麻酸代谢、木质素代谢和苯丙烷代谢。基于表达模式的不同将差异基因划分为20个不同的模块,其中“Melightyellow”模块与差异积累的脂肪酸高度相关。通过分析模块中脂质途径结构基因启动子区的cis-element,发现大多数脂质途径基因的启动子区存在多个MYB家族的结合位点及大量的激素信号响应元件。结果表明,MYB家族的转录因子可能在脂质的合成调控中发挥重要作用,并且激素可能作为一种信号分子参与到脂质的合成调控中。本研究通过组合策略对不同品种椰肉组织脂质差异的分子机理进行分析,并进一步构建了转录因子-结构基因-代谢物的合成调控网络,为后续解析脂质合成调控的分子机制提供了资源,为油脂椰子品...     

Global mapping of the yeast genetic interaction network

A genetic interaction network containing approximately 1000 genes and approximately 4000 interactions was mapped by crossing mutations in 132 different query genes into a set of approximately 4700 viable gene yeast deletion mutants and scoring the double mutant progeny for fitness defects. Network connectivity was predictive of function because interactions often occurred among functionally related genes, and similar patterns of interactions tended to identify components of the same pathway. The genetic network exhibited dense local neighborhoods; therefore, the position of a gene on a partially mapped network is predictive of other genetic interactions. Because digenic interactions are common in yeast, similar networks may underlie the complex genetics associated with inherited phenotypes in other organisms.     

农杆菌介导冷调节基因（Cbcor15a）遗传转化甘蔗体系的建立

【目的】利用农杆菌介导法,将外源冷调节基因Cbcor15a导入甘蔗愈伤组织,建立快速、高效的甘蔗遗传转化体系,为培育具抗寒性甘蔗品种奠定基础。【方法】以新台糖22号（ROC22）为材料,通过对愈伤组织诱导、分化、生根等培养基进行优化,筛选出外源基因转化甘蔗的适合激素种类与用量、PPT用量、抗生素种类与用量;利用甘蔗转基因二元植物表达载体pCambia1300-Cbcor15a-bar,通过农杆菌介导法将目的基因Cbcor15a导入甘蔗愈伤组织。【结果】当农杆菌菌液OD600为0.4、侵染20 min时有利于愈伤组织分化;甘蔗愈伤组织诱导和分化培养阶段的最佳PPT为0.50mg/L。侵染后在共培养中添加500.00 mg/L抗生素Cef能有效抑制农杆菌,添加300.00 mg/L抗生素Cef能促进愈伤组织分化成苗,添加200.00 mg/L抗生素Cef能促进幼苗生根。MS培养基中添加低量NAA更有利于甘蔗愈伤组织的分化;在促进细胞分裂时KT的效果明显优于6-BA。MS培养基中添加5.00 mg/LNAA和70.00g/L蔗糖能有效促进分化苗生根。利用建立的遗传转化体系可获得286株转冷调节基因Cbcor15a的甘蔗转化植株;选取83株通过PPT抗性筛选后长势良好的转化植株进行阳性检测,其中有4株呈阳性。【结论】利用农杆菌介导的Cbcor15a基因转化甘蔗的遗传转化体系能成功将Cbcor15a基因整合到甘蔗基因组。     

Evolution of a polyphenism by genetic accommodation

Polyphenisms are adaptations in which a genome is associated with discrete alternative phenotypes in different environments. Little is known about the mechanism by which polyphenisms originate. We show that a mutation in the juvenile hormone-regulatory pathway in Manduca sexta enables heat stress to reveal a hidden reaction norm of larval coloration. Selection for increased color change in response to heat stress resulted in the evolution of a larval color polyphenism and a corresponding change in hormonal titers through genetic accommodation. Evidently, mechanisms that regulate developmental hormones can mask genetic variation and act as evolutionary capacitors, facilitating the origin of novel adaptive phenotypes.