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。     

Combination of PCR subtraction and cDNA microarray for differential gene expression profiling.

PCR subtraction hybridization has been used effectively to enrich and single out differentially expressed genes. However identification of these genes by means of cloning and sequencing individual cDNAs is a tedious and lengthy process. In this report, an attempt has been made to combine the use of PCR select cDNA subtraction hybridization and cDNA microarrays to identify differentially expressed genes using a nonradioactive chemiluminescent detection method. mRNA from human prolactin (hPRL) or human prolactin antagonist (hPRL-G129R) treated and non-treated breast cancer cells was isolated, and cDNAs were synthesized and used for the PCR subtraction to enrich the differentially expressed genes in the treated cells. The PCR-amplified and subtracted cDNA pools were purified and labeled using the digoxigenin method. Labeled cDNAs were hybridized to a human apoptosis cDNA microarray membrane and identified by chemiluminescence. The results suggest that the strategy of combining all three methods will allow for a more efficient, nonradioactive way of identifying differentially expressed genes in target cells.     

Possible biomarkers for ionizing radiation exposure in human peripheral blood lymphocytes

Biomarkers to indicate past exposure to radiation have not been entirely satisfactory. Using cDNA microarray hybridization to find new potential biomarkers, we identified highly expressed genes in human peripheral blood lymphocytes (PBLs) after irradiation 1 Gy ex vivo. The present set of radiation markers in PBLs was identified 12 h after radiation. A total of 44 genes were identified. However, when RT-PCR was performed with mRNA from the PBLs of five individuals, only four genes, including TRAIL receptor 2, DRAL (now known as FHL2), cyclin G, and cyclin protein gene, showed greater than 50% agreement between gene induction as detected by microarray analysis and by RT-PCR. When more than 32 donors were tested for the above four genes, greater than 85% agreement was obtained between gene induction measured by microarray analysis and by RT-PCR. There was a linear dose-response relationship between 0.5 and 4 Gy 12 h after irradiation; however, there was less linearity at later times. These results suggested that the relative expression levels of genes such as TRAIL receptor 2, FHL2, cyclin G, and cyclin protein gene in PBLs may provide estimates of radiation exposures.     

Assignment of 118 novel cDNAs of cynomolgus monkey brain to human chromosomes

In order to isolate genes that may not be represented in current human brain cDNA libraries, we have sequenced about 20,000 sequence tags of cDNA clones derived from cerebellum and parietal lobe of cynomolgus monkeys (Macaca fascicularis). We determined the entire cDNA sequence of approximately 700 clones whose 5'-terminal sequences showed no homology to annotated putative genes or expressed sequence tags in current databases of genetic information. From this, 118 clones with sequences encoding novel open reading frames of more than 100 amino acid residues were selected for further analysis. To localize the genes corresponding to these 118 newly identified cDNA clones on human chromosomes, we performed a homology search using the human genome sequence and fluorescent in situ hybridization. In total, 108 of 118 clones were successfully assigned to specific regions of human chromosomes. This result demonstrates that genes expressed in cynomolgus monkey are highly conserved throughout primate evolution, and that virtually all had human homologs. Furthermore, we will be able to discover novel human genes in the human genome using monkey homologs as probes.     

乙肝相关性肝癌差异表达基因的获得及FOLR1分析

运用基因芯片技术获取以稳定转染HBx基因的肝癌细胞HepG2(HepG2-X)及非转染的肝癌细胞HepG2中差异表达的基因,并对其中一条基因进行的生物信息学分析。采用人肝癌G2细胞(HepG2)细胞系为对照组,以稳定转染HBx的HepG2细胞为实验组,抽取总RNA,经过反转录cDNA,对照组用Cy3实验组用Cy5荧光标记,获得cDNA探针;经杂交、洗涤后,通过ImaGene3.0软件进行分析统计。通过基因芯片筛选,获得643条与乙肝相关性肝细胞性癌相关的基因,其中FOLR1基因差异性表达最显著,HBx显著下调其表达,同源性比较分析结果表明,其碱基序列与已经报道的其他12种哺乳动物的相似率为67%-99%,且符合种属之间的进化关系。基因芯片筛选HBx诱导的HepG2差异表达基因具有样品用量少,高质量,高速度,高敏感等特性。FOLR1可能为HBV相关肝癌的发生、转移的诊断、靶基因治疗和预后评估提供一定的依据。     

The advantages of cDNA microarray as an effective tool for identification of reproductive organ-specific genes in a model legume, Lotus japonicus

To understand the molecular mechanisms intrinsic to reproductive organ development a cDNA microarray, fabricated from flower bud cDNA clones, was used to isolate genes, which are specifically expressed during the development of the anther and pistil in Lotus japonicus. Cluster analysis of the microarray data revealed 21 and 111 independent cDNA groups, which were specifically expressed in immature and mature anthers, respectively. RT-PCR was performed to provide a direct assessment of the accuracy and reproducibility of our approach. Confirmation of our results suggests that cDNA microarray technology is an effective tool for identification of novel reproductive organ-specific genes.     

Localization of the genes for histatins to human chromosome 4q13 and tissue distribution of the mRNAs.

A cDNA coding for histatin 1 was isolated from a human submandibular-gland library and sequenced. This cDNA was used to probe RNAs isolated from a variety of tissues to investigate tissue-specific regulation and to determine whether histatins might play a role other than in the oral cavity. The same probe was also used for Southern blot analysis of human genomic DNA restricted with various enzymes, and it showed that the genes coding for histatins are on the same chromosome. In situ hybridization of the cDNA probe to metaphase chromosome spreads was performed to determine chromosomal location of the genes for histatins. A genomic fragment isolated using the cDNA probe was also hybridized to chromosome spreads, and the same chromosome was identified. The genes for histatins are located on chromosome 4, band q13. We have shown that three histatin mRNAs are expressed in human parotid and submandibular glands but in none of the other tissues studied. These results suggest that histatins are specific to salivary secretions.     

快速老化小鼠海马差异表达cDNA芯片的制作

老年性痴呆(Alzheimer’s disease,AD)是老年人群中最普遍的痴呆类型,是一种神经退行性紊乱疾病,目前临床上还没有有效的治疗方法。快速老化小鼠亚系P8(senescence-accelerated mouse prone8,SAMP8)是研究增龄相关性认知缺陷机制以及研究脑老化机制的良好动物,同时也是研究AD较为理想的实验动物模型之一。cDNA芯片技术可以同时规模研究成千上万个基因的表达,尤其适于AD这种多机制、多靶标、多途径的复杂疾病的研究,为了揭示AD的发病机制,发现用于治疗AD的药物靶标,以SAMP8和SAMR1海马抑制消减cDNA文库中的cDNA片段为材料,以β-actin和G3PDH为内参,设计了16×(1×14)点阵方案,并点制了含有3136个点的SAM海马差异表达cDNA芯片。芯片背景均匀一致,点的大小均一,排列规则整齐。在靶分子与探针杂交过程中,进行了杂交条件和洗涤芯片的优化。将杂交结果进行统计分析,选择差异表达的cDNA进行测序并进行生物信息学分析,用实时定量RT-PCR对部分基因的表达进行了验证,检测了芯片筛选结果的可靠性。该芯片的成功制备为进一步进行差异表达基因的筛选和研究提供了良好的手段,并将成为揭示SAMP8脑老化和AD发病机制的有力手段。     

应用cDNA芯片分析79个新基因的人胚组织表达谱

大规模cDNA测序和生物信息学技术相结合,得到来自于商品化的人胚肾cDNA文库79个代表新基因的表达序列标签(EST).随后,采用高速度机械手制备这些cDNA的基因芯片,用于鉴定79个新基因的ESTs在20周、26周两个胚胎时期6种组织中的基因表达状况,以研究这些EST片段代表的新基因功能提供线索.通过芯片杂交及结果分析,得到同一个组织两个不同时相8个差异表达的基因,随后的RNA印迹分析的结果与芯片杂交的结果相一致.     

Cloning and characterization of a novel Krüppel-like zinc finger gene, ZNF268, expressed in early human embryo

With the aim of identifying genes involved in early human embryonic development, we have isolated a cDNA clone representing a novel human zinc finger gene ZNF268 from 3 week old human embryo cDNA library using a differential hybridization strategy. The complete cDNA sequence of ZNF268 contained an open reading frame of 2841 nucleotides that encodes a 947 amino acid protein with an N-terminal Krüppel-associated box (KRAB) domain and 24 C-terminal zinc fingers. Northern blot analysis showed that ZNF268 mRNA is mainly expressed in 3-5 week old human embryos suggesting it could play certain roles in the embryogenesis. The gene consists of six exons spanning about 22 kb of genomic DNA. According to the genomic sequence from the HTGS database, the ZNF268 gene is assigned to human chromosome 5.