水稻响应盐胁迫关键转录因子的鉴定

盐胁迫是影响水稻生产的重要非生物胁迫之一.本研究以盐胁迫条件下的水稻转录组数据为材料,通过HTSeq和DESeq软件分析转录因子在转录组水平上的表达变化.主要结果如下:水稻在盐胁迫1、3和6h三个时间点共有26个相同的差异表达转录因子,通过蛋白互作筛选出14个基因组成的重要模块;重要模块基因GO分析主要富集在ATP结合...     

植物三螺旋Trihelix转录因子家族与环境相互作用的研究进展

植物中Trihelix转录因子的共同特征是DNA结合域含有3个连续的α-螺旋。该家族最早被发现能与光应答元件GT元件特异性结合,所以该家族也被称为GT因子家族。最新研究表明Trihelix转录因子家族不仅参与光反应应答,还广泛地参与植物对生物和非生物胁迫的应答。本研究主要介绍了植物Trihelix转录因子结构特征、家族分类,以特殊耐盐种质资源甜菜M14品系中Trihelix转录因子GT-1亚家族响应盐胁迫基因表达模式的分析为例,结合最新的研究进展,重点阐述了Trihelix转录因子与环境相互作用的功能。为今后深入探索Trihelix转录因子参与植物光响应、生物及非生物胁迫等方面的分子机理奠定良好的基础。     

水稻(Oryza satica L.)干旱胁迫响应转录因子研究进展

干旱胁迫是水稻生长发育和产量的重要限制因子。转录因子在水稻对干旱胁迫响应中起关键调控作用。水稻中参与干旱胁迫的转录因主要有DREB转录因子、NAC转录因子、b ZIP转录因子、锌指蛋白转录因子、MYB转录因子、WRKY转录因子和TIFY转录因子等。这些转录因子与特异的靶基因的顺式作用元件结合调控水稻抗旱相关基因的表达,增强水稻对干旱胁迫的适应能力,本综述对这些转录因子在干旱胁迫中的表达调控和功能进行简要概述。     

观赏植物NAC转录因子的研究进展

NAC转录因子家族在调节植物的生长发育中发挥着重要的作用,在模式植物、作物中已进行了大量研究,但是在观赏植物中的研究还缺乏系统性的梳理和探讨。本综述介绍了NAC转录因子的结构和分类,并梳理了2004-2023年NAC转录因子在观赏植物器官生长发育和胁迫响应上的生物学功能研究,其中观赏植物器官生长发育主要集中在叶缘形态建成、花器官发育、叶片衰老、花瓣衰老、种球休眠5个方面,胁迫响应则集中在干旱、盐、碱、冷、热等非生物胁迫,在生物胁迫中报道较少。最后,鉴于观赏植物NAC转录因子大部分都还停留在生物信息学分析以及表达模式分析等功能初探阶段,本文在结合观赏植物全基因组测序继续开展NAC转录因子鉴定研究、挖掘观赏植物中与模式植物存在不同作用机制的NAC转录因子、解析观赏植物NAC转录因子与其他转录因子间的调控网络、加快利用推进基因工程或编辑技术开展观赏植物的分子育种工作等4个方面,对未来NAC转录因子在观赏植物中的研究提出了展望。     

WRKY转录因子参与植物抗盐性调控的研究进展

盐胁迫是影响植物生长发育重要的环境因子之一,为了适应及抵御盐胁迫危害的逆境,作物自身会通过一系列变化来适应环境而作出相关性应激性改变,如宏观形态学、生理学改变、微观分子生物学变化等。转录调控是细胞内部调控网络中最重要的一个环节,WRKY转录因子响应并参与多种植物的生物和非生物胁迫。本综述从盐胁迫下作物形态结构的变化、盐胁迫对作物生理代谢的影响以及WRKY转录因子参与作物抗盐调控网络等方面文献,来汇总分析近年来拟南芥、水稻及其他种类植物应对胁迫的响应机制以及WRKY转录因子的功能,为提高园艺作物抗盐性生理作用及分子机制提供帮助,同时为作物抗盐栽培提供新思路。     

生长素与植物逆境胁迫关系的研究进展

生长素(IAA)是一种重要的植物激素,与植物的逆境胁迫反应关系密切。综述近年来国内外对生长素与植物逆境胁迫关系研究的一些最新进展,重点分析生长素和生长素响应基因及其相关转录因子在植物响应盐害、干旱、低温等胁迫中的反应。     

盐胁迫下两个甜瓜品种转录因子的转录组分析

利用新一代高通量测序手段——转录组测序（RNA-Seq）技术研究在300 mmol.L-1NaCl胁迫下两个甜瓜（Cucumis melo L.）品种‘玉露’和‘冰雪脆’的转录因子基因表达变化。这两个甜瓜品种在叶绿素荧光参数上的差异表明其在盐胁迫下有不同的生理反应。转录组测序结果表明,盐胁迫与对照相比,‘玉露’共有属于19个转录因子家族的56个转录因子基因表达发生变化（在转录水平,属于7个转录因子家族的22个转录因子上调表达,属于14个转录因子家族的34个转录因子下调表达）。‘冰雪脆’有属于20个转录因子家族的47个转录因子基因表达发生变化（在转录水平上,属于5个转录因子家族的17个转录因子上调表达,属于17个转录因子家族的30个转录因子下调表达）。盐胁迫下,两个甜瓜品种差异表达的转录因子既表现特异性,也存在部分重叠。‘玉露’有29个转录因子特异响应,‘冰雪脆’有20个特异响应。盐胁迫响应重叠的转录因子有27个,其中9个上调表达,18个下调表达。采用实时荧光定量PCR对几个转录因子进行了盐胁迫下的表达检测,其趋势与转录组分析结果基本一致。     

日本结缕草‘胶东青’DREB2.2基因克隆及表达模式研究

DREB(dehydration responsive element binding protein)是植物中普遍存在的一类重要转录因子,参与植物逆境响应和生长发育过程。以日本结缕草‘胶东青’为材料,克隆获得了DREB2.2基因的编码区序列,分析了该基因的生物信息学特征,通过半定量PCR技术检测其逆境表达模式。测序结果表明,‘胶东青’DREB2.2基因存在长、短两个转录本。长转录本DREB2.2-L编码区长1 067 bp,多含一个长50 bp的序列,阅读框提前终止,仅推测编码65个氨基酸。短转录本DREB2.2-S编码区长1 017 bp,推测编码338个氨基酸,蛋白质分子量37.3 KD,等电点p I为4.86,含有一个保守的AP2结构域和核定位序列,属于DREB亚家族A-2组成员。半定量PCR结果显示,DREB2.2-S和DREB2.2-L在正常生长条件下有表达,低温胁迫时表达量上调,胁迫2 h时最高,干旱胁迫2 h和24 h时轻度上调表达,高盐胁迫下表达量无显著变化。在相同条件下,DREB2.2-L的表达量均略高于DREB2.2-S。     

中国辣椒热胁迫转录因子的全基因组鉴定及热胁迫响应的初步分析

采用生物信息学方法,从中国辣椒(Capsicum chinense Jacq.)全基因组序列中鉴定得到28个热胁迫转录因子(HSF)候选基因,并对这些候选基因的染色体分布、基因结构及编码蛋白的3D结构特征进行了分析。结果显示:28个候选基因的编码蛋白长度为128~526 aa;系统发育分析结果表明,HSF可分为A、B、C 3个亚家族。进一步对热胁迫处理后的中国辣椒种质进行转录组分析,共检测到27个HSF转录本,与对照组相比,实验组中有25个基因对热胁迫有不同程度的响应。     

绿色杜氏藻转录组分析

为了深入了解绿色杜氏藻(Dunaliella viridis)基因信息及功能、耐盐相关通路(甘油脂代谢)及关键酶,本文首次通过Illumina HiSeq^TM 2000高通量测序技术对绿色杜氏藻转录组进行测序,利用Trinity软件将数据组装形成转录本,对所有转录本进行COG(Clusters of Orthologous Groups)、GO(Gene Ontology)和KEGG(Kyoto Encyclopedia of Genes and Genomes)分类和功能注释、Pathway注释以及蛋白编码区(Opening reading fragment,ORF)的预测,并对甘油脂代谢通路关键酶基因进行了分析。转录组测序共获得81 593个转录本,其中ORF共有77 117条,约占所有转录本的94.50%。COG分类结果表明,16 569条转录本被分为24个类别。GO分类结果表明,76 436条转录本被注释。在所有注释分类中,生物学过程转录本数量最多,为30 678条,占总转录本数的40.14%。KEGG分析结果表明,317个标准途径中包含26 428条转录本,含转录本最多的类别是代谢,为9949条(37.65%)。与代谢有关的途径为131条,占所有注释途径的41.32%。在甘油脂代谢通路中仅发现1条关键酶转录本(二羟丙酮激酶),该酶可能与绿色杜氏藻耐盐胁迫中甘油的合成有较大关系。本研究进一步完善了绿色杜氏藻的基因信息,为绿色杜氏藻代谢途径研究奠定了坚实的基础。     

Identification of Dss1 as a 12-O-tetradecanoylphorbol-13-acetate-responsive gene expressed in keratinocyte progenitor cells,with possible involvement in early skin tumorigenesis

This study identifies genes expressed early in 12-O-tetradecanoylphorbol-13-acetate (TPA)-induced skin carcinogenesis in genetically initiated Tg.AC v-Ha-ras transgenic mice. Keratinocyte progenitor cells from TPA-treated Tg.AC mice were isolated with fluorescence-activated cell sorting and expression was analyzed using cDNA microarray technology. Eleven genes were identified whose expression changed significantly in response to carcinogen treatment. Deleted in split hand/split foot 1 (Dss1) is a gene associated with a heterogeneous limb developmental disorder called split hand/split foot malformation. cDNA microarray expression analysis showed that the mouse homologue of Dss1 is induced by TPA. Dss1 overexpression was detected by Northern blot analysis in early TPA-treated hyperplastic skins and in JB6 Cl 41-5a epidermal cells. Interestingly, Dss1 expression was also shown to be elevated in skin papillomas relative to normal skins, and further increased in squamous cell malignancies. Functional studies by ectopically constitutive expression of Dss1 in JB6 Cl 41-5a preneoplastic cells strongly increased focus formation and proliferation of these cells and enhanced efficiency of neoplastic transformation of the cells in soft agar. These results strongly suggest that Dss1 is a TPA-inducible gene that may play an important role in the early stages of skin carcinogenesis.     

The influence of RNA integrity,purity and cDNA labelling on glass slide cDNA microarray image quality

The accuracy of gene expression measurements generated using cDNA microarrays is dependent on the quality of the image generated following hybridization of fluorescently labelled cDNA. It is not known how this image is influenced by sample preparation factors which such as RNA quality, cDNA synthesis and labelling efficiency. In this study we used a simple metric based on the ratio of the total feature (F) and background (B) fluorescence, which correlates with the visual assessment of 60 microarray images, to determine the influence of sample preparation on image quality. Results indicate that RNA purity (A260/A280) and integrity (18S:28S ratio) do not strongly influence microarray image quality. cDNA having an nucleotide to dye ratio greater than 100 produced poor microarray images, however, cDNA labelled more efficiently was not a guarantee of a better image. The data also indicate that the array image quality is not improved by loading more cDNA into the hybridization mixture however poor image quality did result from a disproportionate amounts of Cy5 and Cy3 labelled cDNA. This study provides insight into the source of variation in microarray image analysis introduced during sample preparation and will assist in the standardisation of cDNA glass slide microarray protocols.     

Resource and hardware options for microarray-based experimentation.

DNA microarray technology permits the study of biological systems and processes on a genome-wide scale. Arrays based on cDNA clones, oligonucleotides and genomic clones have been developed for investigations of gene expression, genetic analysis and genomic changes associated with disease. Over the past 3-4 years, microarrays have become more widely available to the research community. This has occurred through increased commercial availability of custom and generic arrays and the development of robotic equipment that has enabled array printing and analysis facilities to be established in academic research institutions. This brief review examines the public and commercial resources, the microarray fabrication and data capture and analysis equipment currently available to the user.     

Spatial and temporal analysis of the local response to wounding

Plant Molecular Biology - We studied the local response to wounding in Arabidopsis thaliana leaves using a two-step microarray analysis. A microarray containing 3500 cDNA clones was first screened...     

cDNA微阵列技术研究干旱胁迫下星星草基因的表达

运用cDNA微阵列技术研究干旱胁迫下星星草基因的表达。制备了载有660条星星草单一基因的cDNA微阵列。分别对干旱胁迫和对照星星草的mRNA进行荧光标记,并与载有星星草基因的cDNA微阵列进行杂交,通过芯片的杂交信号强度分析,共获得22个下调表达和17个上调表达的基因。BLASTX分析表明这些基因按功能可以分为脱水保护、信号转导与调控、活性氧清除、代谢、核糖体蛋白等几大类。发现了一些与干旱胁迫相关的功能未知基因和新基因。     

Evaluation of experimental designs for two-color cDNA microarrays.

The major goal of two-color cDNA microarray experiments is to measure the relative gene expression level (i.e., relative amount of mRNA) of each gene between samples in studies of gene expression. More specifically, given an N-sample experiment, we need all N(N - 1)/2 relative expression levels of all sample pairs of each gene for identification of the differentially expressed genes and for clustering of gene expression patterns. However, the intensities observed from two-color cDNA microarray experiments do not simply represent the relative gene expression level. They are composed of signal (gene expression level), noise, and other factors. In discussions on the experimental design of two-color cDNA microarray experiments, little attention has been given to the fact that different combinations of test and control samples will produce microarray intensities data with varying intrinsic composition of factors. As a consequence, not all experimental designs for two-color cDNA microarray experiments are able to provide all possible relative gene expression levels. This phenomenon has never been addressed. To obtain all possible relative gene expression levels, a novel method for two-color cDNA microarray experimental design evaluation is necessary that will allow the making of an accurate choice. In this study, we propose a model-based approach to illustrate how the factor composition of microarray intensities changed with different experimental designs in two-color cDNA microarray experiments. By analyzing 12 experimental designs (including 5 general forms), we demonstrate that not all experimental designs are able to provide all possible relative gene expression levels due to the differences in factor composition. Our results indicate that whether an experimental design can provide all possible relative expression levels of all sample pairs for each gene should be the first criterion to be considered in an evaluation of experimental designs for two-color cDNA microarray experiments.     

Combined transcript and metabolite analysis reveals genes involved in spider mite induced volatile formation in cucumber plants

Many plants have an indirect defense against herbivores by emitting volatiles that attract carnivorous enemies of the herbivores. In cucumber (Cucumis sativus) the production of carnivore attractants can be induced by herbivory or jasmonic acid spraying. From the leaves of cucumber plants with and without spider mite infestation, two subtractive cDNA libraries were made that were enriched in cDNA fragments up- or down-regulated by spider mite infestation. A total of 713 randomly selected clones from these libraries were used to make a cDNA microarray. Subsequently, cucumber plants were sprayed with jasmonic acid, mechanically damaged, infested with spider mites, or left untreated (control). Leaf samples were taken at a range of different time points, and induced volatile compounds and mRNA (from the same leaves) were collected. cDNAs prepared from the mRNA were hybridized to the clones on the microarray. The resulting gene expression profiles were analyzed in combination with volatile production data in order to gain insight in the possible involvement of the studied genes in the synthesis of those volatiles. The clones on the microarray and the induced cucumber volatiles could be grouped into a number of clusters in which specific biosynthetic genes clustered with the product of that pathway. For example, lipoxygenase cDNA clones clustered with the volatile (Z)-3-hexenyl acetate and the volatile sesquiterpene (E,E)- alpha-farnesene clustered with an up-regulated sesquiterpene synthase fragment. This fragment was used to screen a cDNA library which resulted in the cloning of the cucumber (E,E)-alpha-farnesene and (E)-beta-caryophyllene synthases. The use of combined global gene expression analysis and metabolite analysis for the discovery of genes involved in specific biosynthetic processes is discussed.     

Differences in gene expression between B-cell chronic lymphocytic leukemia and normal B cells: a meta-analysis of three microarray studies

MOTIVATION: A major focus of current cancer research is to identify genes that can be used as markers for prognosis and diagnosis, and as targets for therapy. Microarray technology has been applied extensively for this purpose, even though it has been reported that the agreement between microarray platforms is poor. A critical question is: how can we best combine the measurements of matched genes across microarray platforms to develop diagnostic and prognostic tools related to the underlying biology? RESULTS: We introduce a statistical approach within a Bayesian framework to combine the microarray data on matched genes from three investigations of gene expression profiling of B-cell chronic lymphocytic leukemia (CLL) and normal B cells (NBC) using three different microarray platforms, oligonucleotide arrays, cDNA arrays printed on glass slides and cDNA arrays printed on nylon membranes. Using this approach, we identified a number of genes that were consistently differentially expressed between CLL and NBC samples.