Identification and analysis of differentially expressed genes involved in dark-induced photoperiod response and senescence of soybean leaves by suppression subtractive hybridization

A cDNA subtractive library enriched for dark-induced up-regulated ESTs was constructed by suppression subtractive hybridization(SSH) from leaf tissues of soybean cultivar DongNong L13 treated with short-day(8-h light/16-h dark) and long-day(16-h light/8-h dark) conditions.A total of 148 clones were sequenced,representing 76 unique ESTs which corresponded to about 20% of 738 clones from the cDNA library and showed a significant up-regulation of at least three fold verified by dot blot hybridization.The putative functions of ESTs were predicted by Blastn and Blastx.The 43 differentially expressed genes identified by subtractions were classified according to their putative functions generated by Blast analysis.Genetic functional analysis indicated that putative proteins encoded by these genes were related to diverse functions during organism development,which include biological regulation pathways such as transcription,signal transduction and programmed cell death,protein,nucleic acid and carbohydrate macromolecule degradation,the cell wall modification,primary and secondary metabolism and stress response.Two soybean transcription factors enhanced in SD conditions,GAMYB-binding protein and DNA binding protein RAV cDNAs that may be involved in SD soybean photoperiod response,had been isolated using 5'-and 3'-rapid amplification of cDNA ends(RACE)(Genbank Accession numbers DQ112540 and DQ147914).

Identification of Phosphorus Starvation Inducible Genes in Rice by Suppression Subtractive Hybridization

Phosphorus is one of the three essential macroelements for plant growth. Plants respond to phosphorus starvation through adaptive mechanisms involved in morphological, biochemical and molecular changes. To investigate the molecular background of the adaptive mechanisms, the suppression subtractive hybridization (SSH) method was used to construct a rice phosphorus-starvation ( Pi-starvation) induced cDNA library. Through screening of the cDNA library and sequencing of the enriched cDNAs, 18 known genes and 47 novel genes were identified. The known genes are involved in different metabolic processes, including phosphate uptake and transport, signal transduction, protein synthesis and degradation, carbon metabolism and stress response. Northern analysis was performed to detect the expression patterns of some known genes and novel genes under different phosphorus levels. Different expression patterns of the selected genes were identified, which suggests that genes involved in different pathways may have different responses to Pi-starvation.

Identification of Differentially Expressed Genes in Sweetpotato Storage Roots Between Kokei No.14 and Its Mutant Nongdafu 14 Using PCR-Based cDNA Subtraction

The contents of earotenoids in the storage root of sweetpotato, Ipomoea batatas （L.） Lam. vary dramatically among different cultivars. However, so far little is known about the regulation of carotenoids synthesis in sweetpotato. In our laboratory, we identified a novel sweetpotato mutant, Nongdafu 14, which is a homogenous mutant derived from the wild type Kokei No. 14. The contents of carotenoids in the storage root of Nongdafu 14 were analyzed using high performance liquid chromatography （HPLC）, and it was found that the amount of carotenoids, [3-carotene, lutein and zeaxantion, three major types of earotenoids in sweetpotato storage roots, increased 2-26 folds in Nongdafu 14 compared to Kokei No. 14. Suppression subtractive hybridization （SSH） was used to identify genes that were differentially expressed in Nongdafu 14, and a differentially expressed eDNA library was constructed using the eDNA of Nongdafu 14 storage roots as tester and that of Kokei No. 14 storage roots as driver. Out of the 1 530 clones sequenced, we identified 292 nonredundant ESTs. GO and KEGG analyses of these differentially expressed ESTs indicated that diverse metabolism pathways were affected and candidate genes involved in regulation of carotenoids synthesis are suggested.

Construction of a hepatic stellate cells subtracted cDNA library of differentially expressed genes in normal mice and mice with Schistosomiasis japonica

To construct a hepatic stellate cells (HSCs) subtracted cDNA library to find differentially expressed genes in normal mice and mice infected with Schistosoma japonicum (S. japonicum). Suppression subtractive hybridization (SSH) was used. The cDNA fragments of normal mouse were compared to those of schistosoma-infected mice to find differentially expressed genes. Then differentially expressed cDNA fragments were directly inserted into T/A cloning vector to set up the subtractive library. Amplification of the library was carried out with transformation of DH5α. The amplified library contained more than 400 positive bacterial clones, which were then hybridized with forward and backward subtracted probes for differential screening. One hundred positive bacterial clones were randomly selected for sequencing and BLAST analysis. Finally, virtual Northern Blot confirmed such differential expression. The subtracted cDNA library of differentially expressed genes of HSCs was constructed successfully, the library is efficient and lays foundation for screening and cloning new and specific genes of schistosomiasis.

An Integrated Technique for Identification of Differential Genes Expressed in Patients with Cancer

Summary: To develop a method for identification of differential gene expression between different cell populations, several convenient techniques of molecular biology, including subtractive hybridization, suppression PCR, T/A cloning and sequencing, were used to identify genes expressed differentially in CD45+ and CD45-cells isolated from U266 cell line of multiple myeloma. Our results showed that the levels of abundant genes scale down 20 times through subtractive hybridization. Plasmid DNA from CD45+ cell clones was hybridized with forward or backward cDNA probes synthesized from CD45+ and CD45-cells, respectively. A few of differentially expressed genes reconfirmed by RT-PCR were identified from 500 expressed clones of CD45+ cells. It is concluded that a strategy for gene expression identification developed from conventional molecular biological methods can be used in different laboratories.

Identification of differently expressed genes in human colorectal adenocarcinoma

AIM： To investigate the differently expressed genes in human colorectal adenocarcinorna.METHODS： The integrated approach for gene expression profiling that couples suppression subtractive hybridization, high-throughput cDNA array, sequencing, bioinformatics analysis, and reverse transcriptase real- time quantitative polymerase chain reaction （PCR） was carried out. A set of cDNA clones including 1260 SSH inserts amplified by PCR was arrayed using robotic printing. The cDNA arrays were hybridized with florescent-labeled probes prepared from RNA of human colorectal adenocarcinoma （HCRAC） and normal colorectal tissues.RESULTS： A total of 86 genes were identified, 16 unknown genes and 70 known genes. The transcription factor Sox9 influencing cell differentiation was downregulated. At the same time, Heat shock protein 10 KDis downregulated and Calmoulin is up-regulated.CONCLUSION： Downregulation of heat shock protein 10 KD lost its inhibition of Ras, and men attenuated the Ras GTPase signaling pathway, increased cell proliferation and inhibited cell apoptosis. Down-regulated transcription factor Sox9 influences cell differentiation and cell-specific gene expression. Down-regulated Sox9 also decreases its binding to calmodulin, accumulates calmodulin as receptor-activated kinase and phosphorylase kinase due to the activation of PhK.

Identification and Expression Analysis of Salinity-induced Genes in Rangpur lime(Citrus limonia)

Among the economically important horticultural crops,citrus is one of the most vulnerable crops to soil salinity.Rangpur lime is more tolerant to high soil salinity than other commonly used citrus rootstocks.However,the molecular mechanism involved in salinity tolerance has not been explored in Rangpur lime.In this study,a cDNA library was constructed from leaves of Rangpur lime watered for 30 days with 100mmol·L^−1 NaCl in tap water or tap water using suppression subtractive hybridization(SSH).Two hundred cDNA clones randomly selected from this library were sequenced,and an average of 569 bp was obtained from the majority of clones.Fifty-six salinity-induced genes,showing 2-to 6-fold increases in their expression levels,were identified by macroarray hybridizations.Salinity-induced genes were associated with transcription(5.36%),stress response and signaling(21.43%),metabolism(16.07%),transport facilitation(10.71%),photosynthesis(10.71%),protein synthesis and fate(19.64%)and cellular biogenesis(3.57%).Stress response-and signaling-related genes constituted the largest functional group,associated with the production of compatible solutes,regulation of stomatal movement,lipid modification,oxidative stress,antioxidant defense,and stress signaling.Expression levels of 13 identified genes were induced 1.8-to 3.1-fold,which were validated in salt-treated and untreated Rangpur lime.The functions of salinity-induced,stress-related genes and their potential roles in salinity tolerance in Rangpur lime were discussed.

Identification and Expression Analysis of Regulatory Genes Induced by Near-Ultraviolet Irradiation in <i>Bipolaris oryzae</i>

Bipolaris oryzae is the causal agent of brown leaf spot disease in rice, and its asexual spore (conidium) formation is known to be induced by near-ultraviolet (NUV) irradiation. In order to reveal the photomorphogenic response and to identify new genes upregulated by NUV irradiation, suppression subtractive hybridization (SSH) was carried out in B. oryzae. To confirm the differential gene expression in NUV-irradiated mycelia, quantitative real-time PCR (qRT-PCR) analysis was performed among 301 genes arbitrarily chosen from 1170 cDNA clones. The expression of 46 genes (named NUV01 to NUV46) was found to be significantly enhanced (>4-fold) by NUV irradiation. Sequence analysis revealed that 23 out of the 46 sequences (50%) showed significant matches to known fungal genes. The 46 genes were categorized as either BLR1-dependent or BLR1-independent expression groups using the BLR1-deficient mutant, which presumably lacks the blue/UVA-absorbing photoreceptor. This finding demonstrates that NUV irradiation can induce gene regulation, and that this response may be mediated by both a blue/UVA-absorbing photoreceptor and an as-yet-unidentified photoreceptor in B. oryzae.

Gene expression profiling related to powdery mildew resistance in wheat with the method of suppression subtractive hybridization

'Bainong 3217 × Mardler' BC5F4 wheat line at the initial stage of inoculation with powdery mildew pathogen (Erysiphe graminis DC) was used to construct a suppression subtractive hybridization (SSH) cDNA library. Totally 760 ESTs were obtained through sequencing. Similarity analysis of ESTs based on BLASTn and BLASTx with the sequences in GenBank, in combination with macroarray differential screening, revealed that 199 ESTs of 65 kinds were known to be functionally disease resistance related. Based on the gene expression profiling in the present study, it is postulated that salicylic acid (SA) and MAP-related signal transduction pathways were involved in powdery mildew resistance in wheat. System acquired resistance genes were predominant in terms of kinds and quantity. With the initiation of cell defense reaction, the genes conferring anti-oxidation substances were largely expressed and thus cell protection mechanism was activated. Much evidence revealed that phenylpropanes metabolic pathway was

Identification and Cloning of Differentially Expressed Genes Involved in the Interaction Between Potato and Phytophthora infestans using a Subtractive Hybridization and cDNA-AFLP Combinational Approach

Using a subtractive hybridization （SH）/cDNA-AFLP combinational approach, differentially expressed genes involved in the potato-Phytophthora infestans interaction were identified. These included genes potentially controlling pathogenesis or avr genes in P. infestans as well as those potentially involved in potato resistance or susceptibility to this pathogen. Forty-one differentially expressed transcript, derived fragments （TDFs）, resulting from the interaction, were cloned and sequenced. Two TDFs, suggested as potential pathogenicity factors, have sequence similarity to N-succinyl diaminopimelate aminotransferase and a transcriptional regulator, TetR family gene, respectively. Two other TDFs, suggested as potential avr genes, have sequence similarity to an EST sequence from Avr41Cf.41Avr91Cf- 9 and a P. infestans avirulence-associated gene, respectively. Genes＇ expression and origin were confirmed using Southern blots, Northern blots and qRT-PCR, he., potential resistance gene DL81 was induced at 12 hpi in the moderately resistant cultivar, whereas it was down-regulated as early as 6 hpi in the susceptible cultivar. On the other hand, DL21 was induced at 6 hpi （3.38-fold） in response to the highly aggressive isolate （US8） and strongly up-regulated thereafter （25.13-fold at 120 hpi.）, whereas it was only slightly up-regulated in response to the weakly aggressive isolate US11 （3.82-fold at 96 hpi）, suggesting its potential involvement as a susceptibility gene.

Identification of over-expressed genes in human renal cell carcinoma by combining suppression subtractive hybridi-zation and cDNA library array

To isolate the over-expressed genes in human renal cell carcinoma (RCC) and analyze its molecular basis of carcinogenesis, we used the mRNA from human RCC tissues as tester and that from the matched normal kidney tissues as driver to construct the suppression subtractive hybridization library. 379 of the subtracted clones were arrayed onto a nylon mem-brane and the over-expressed genes were then screened by hybridizing the filter with radioac-tively labeled cDNA from RCC and matched normal kidney tissues. 67 clones over-expressed in RCC by a factor of 6 or more were sequenced and its identities were analyzed in GenBank da-tabase. 4 clones were previously unknown fragments and 2 clones represent KIAA genes. The rest clones were the known genes and some of them were RCC-related, including vascular en-dothelial growth factor, vimentin and tissue factor. Most of the known genes were the RCC-related genes previously unknown, including zinc ribbon domain-containing 1 protein (ZNRD1), pituitary tumor transforming gene1 (PTTG1). Northern blot and semi-quantitative RT-PCR confirmed that the mRNA levels of the 3 novel fragments and 1 KIAA and 3 known genes were significantly higher in RCC than in the matched normal kidney tissues. Immunohis-tochemical and Western blot analysis for PTTG1 and ZNRD1 revealed increased protein level in RCC. The over-expressed genes in RCC are the potential molecular targets for diagnosis and therapy and it is very important to understand the molecular mechanism of RCC through the profile of over-expressed genes.

Identification of differentially expressed genes in esophageal cancer through SSH in combination with high throughput reverse Northern screening

To understand the molecular mechanisms of carcinogenesis of esophagus and to isolate genes with different expression levels in esophageal cancer, suppression sub-tractive hybridization (SSH) was combined with PCR-based cDNA synthesis and reverse Northern on the cancer tissues and matched almost normal mucosa using 5 microgram of total RNA as starting marterial. Eight genes were found expressed differentially in esophageal cancer, in which 5 were known genes and 3 were novel ones; and 6 were down-regulated in cancer tissues, while 2 were up-regulated; 6 were of mid-high abundance and 2 were of low abundance in esophagus. The results revealed that alteration in expression level of multiple genes underlied the initiation and development of esophageal cancer. The differentially expressed genes identified in this study such as liporcotin I, cystatin A, cystatin B, cytokeratin 13 may play roles in dedifferentiation, transformation and malignant proliferation of esophageal cancer. The combination of SSH with

Screening of differentially expressed genes in the hypothalamus of a rat neuropathic pain model following sciatic nerve injury

Background Neuropathic pain is induced by injury or disease of the nervous system. Most studies have so far focused only on a few known molecules and signaling pathways among neurons. However, all signal transmissions involved in neuropathic pain appear to be an integral system at different molecular levels. This study was designed to screen the differentially expressed genes of the hypothalamus in chronic constriction injury （CCI） rats and analyze their functions in developing neuropathic pain. Methods Ten adult female Sprague-Dawley rats （（200±10） g） were used in experimental group and sham group （n=-5 in each group）. Mechanical allodynia tests were performed to ensure that the CCI rat model was constructed successfully. Total hypothalamus RNAs were isolated from each group. Forward suppression subtractive hybridization （SSH） library of rat hypothalamus was constructed and up-regulated cDNA clones at neuropathic pain states were obtained via suppressed subtractive hybridization technique and the functions of these genes were analyzed bioinformatically. Results Mechanical allodynia tests showed that the experimental rats had a significantly reduced mechanical allodynia threshold 3 to 13 days after CCI vs sham surgery rats （P 〈0.01）, indicating that the model was successful. Forward SSH library of the rat hypothalamus was constructed successfully and 26 over-expressed expression sequence tags （ESTs） were obtained from these up-regulated cDNA clones. Conclusion Twenty-six up-regulated genes, involved in the regulation of cell cycle and apoptosis, signal transduction, and neuroprotection, may play key roles in decreasing mechanical withdraw thresholds in CCI rats, which implicates a multidimensional and integrated molecular mechanism at gene level in developing neuropathic pain with the supraspinal contributions.

用抑制性差减杂交构建新疆Kaposi肉瘤差异表达基因文库

目的:分离卡波氏肉瘤(Kaposi's sarcoma,KS)差异表达基因,并建立相应的cDNA文库,为从分子水平揭示KS发病机制打下良好基础.方法:采集KS肉瘤及来源于同一患者的正常皮肤组织,抽提总RNA,逆转录酶合成dscDNA,经Rsa I酶切,与2种不同的接头衔接,分别以正常组织和肿瘤组织作为tester和driver,进行双向抑制性差减杂交(suppression subtractive hybridization,SSH),初步筛选KS肉瘤与正常皮肤差异表达基因,将差异基因PCR扩增,产物与pGEM-Teasy克隆载体连接,转化DH5α大肠杆菌,采用蓝白斑筛选,获得白色阳性克隆菌落,并煮沸破菌,PCR扩增出未知基因片段.结果:差减得到差异基因片段多位于200～500bp,成功构建了2个分别代表在KS肿瘤组织中表达上调和下调的基因文库.结论:经双向抑制性差减杂交获得了KS差异表达基因文库.抑制性差减杂交是一种快速、方便、有效的建立差异基因文库的方法.

大鼠心肌缺血预适应诱导表达上调基因的筛选和鉴定

采用反复短时间结扎及松解左冠状动脉前降支构建大鼠心肌缺血预适应动物模型 ,运用抑制消减杂交技术建立大鼠心肌缺血预适应诱导表达上调基因的消减cDNA文库 ,通过反向RNA点杂交对部分文库基因进行差异表达初筛 ,选取表达差异最明显的 85个基因进行测序 ,获得了 3 1个核编码基因和 18个新基因 (EST) ,核编码基因中有相当一部分与细胞保护或信号转导有关 ,新基因已被GenBank收录 .从已测序基因中任选 5个进行RT PCR检测 ,并任选 2个进行RNA印迹检测 ,均证实在缺血预适应时表达增高 .

黏类小麦育性相关基因SSH文库的构建

为了深入研究黏类小麦雄性不育的分子遗传机制,利用抑制差减杂交技术构建了黏类小麦育性相关基因的cDNA文库。文库质量检测表明,差减杂交效率较高,质量较好。在不育和可育cDNA文库中随机挑选120个阳性克隆进行测序,获得100余条高质量的表达序列标签(EST)。对序列进行BLAST比对及功能注释,比较了不育和可育cDNA文库的基因表达谱,发现在可育cDNA文库中参与能量代谢的基因出现频率较高,在不育cDNA文库中检测到了与花发育调控相关的MADS-box转录因子、细胞凋亡相关的泛素结合酶及阻遏淀粉合成的腺苷二磷酸葡萄糖磷酸化酶等相关基因。这些基因很可能与育性相关。

人参植物与皂苷生物合成相关的差减cDNA文库构建及基因差异表达分析

应用抑制差减杂交技术,分别以源于4年和1年生人参根组织cDNA群体作为检测子(tester)与驱赶子(driver),成功构建了与人参植物皂苷生物合成相关的差减cDNA文库,并对从中筛选的阳性cDNA克隆进行DNA测序及其序列分析、PCR及Northern印迹杂交鉴定.结果显示,获得的13个克隆为新基因序列.其中6个差减克隆系人参植物根生长发育阶段差异表达基因.目前,6个差异表达新基因的结构与功能仍在进一步研究中.

籽鹅卵巢组织差异表达基因的研究

本研究旨在筛选产蛋前期和产蛋期籽鹅卵巢组织差异表达的基因,并进行功能分析,从而探讨鹅产蛋的分子调控机理。利用抑制性消减杂交技术筛选籽鹅卵巢组织中的差异表达基因,用GOTM软件将所得ESTs从分子功能水平进行GO分类。结果表明,所构建的籽鹅卵巢组织消减cDNA文库的削减效率在20倍以上,片段大小主要在300～750bp;挑选86个阳性克隆测序,获得15个ESTs,其中有11个为已知的ESTs,4个未知的ESTs;11个已知的ESTs被分成结合功能、催化活性、酶调节活性、转运蛋白活性和其它功能。本研究成功构建了籽鹅卵巢组织消减cDNA文库,并筛选得到了15个可能在产蛋前期和产蛋期籽鹅卵巢组织中差异表达的ESTs,它们可能在鹅产蛋过程中起着重要的调控作用。