家蚕5龄幼虫精巢和卵巢microRNA芯片及转录组比较分析

【目的】本研究旨在通过对家蚕Bombyx mori 5龄幼虫精巢和卵巢组织微小RNA (microRNA, miRNA)基因芯片及转录组进行分析,找到参与家蚕性腺发育相关的miRNA分子及可能的靶基因。【方法】采用新一代高通量测序平台对家蚕5龄幼虫精巢和卵巢(分别定义为Test和Control)进行miRNA基因芯片检测及转录组测序分析,根据P＜0.05且log₂(fold change, FC)≥2的标准,通过比较筛选出Test vs Control的差异表达miRNA;根据q≤0.05且|log₂(fold change)|≥1的标准,通过比较筛选出Test vs Control的差异表达基因 (differentially expressed genes, DEGs);随机选取8个上调和12个下调差异表达miRNA,对其表达及其预测的5个靶基因进行qRT-PCR验证;对DEGs以及差异表达miRNA的靶基因进行KEGG通路富集分析。【结果】从精巢和卵巢样本中(Test vs Control)分别鉴定出68个差异表达miRNA和3 991个DEGs,其中上调和下调miRNA分别为36和32个,上调和下调DEGs分别为2 033和1 958个。差异表达miRNA的qRT PCR验证结果均与芯片数据一致。KEGG通路富集分析结果显示DEGs在新陈代谢及核糖体的信号通路显著富集。对差异表达miRNA在DEGs中的可能靶基因进行预测,结果找到了4组表达趋势相反的miRNA与靶基因：分别是bmo-miR-2774a与LOC101745556;bmo-miR-92b与LOC101735954以及bmo-miR-3266与LOC733130和LOC778467;1组表达趋势一致的miRNA与靶基因：bmo-miR-3321与LOC101744895。5个靶基因的qRT-PCR验证结果与转录组测序结果一致。【结论】本研究获得了家蚕5龄幼虫精巢和卵巢转录组及miRNA芯片数据,筛选并验证了4组差异表达和1组一致表达miRNA及潜在靶基因,为探究家蚕精巢和卵巢发育差异奠定了基础。     

大鼠颅脑损伤后差异表达基因及miRNA研究

研究背景创伤性脑损伤(Traumatic brain injury, TBI)是致死率和致残率极高的外科疾患,我国在对于TBI的判断、治疗等方面还处于薄弱阶段,因此我们需要在分子层面了解大鼠颅脑损伤后基因及miRNA表达差异,以便更好地对症治疗。目的了解大鼠颅脑损伤后基因及miRNA表达差异,为临床治疗TBI提供新的思路。方法利用GEO2R筛选基因,然后用MiRwalk软件对筛选的miRNA的靶基因进行预测,再用DAVID做基因本体论功能富集分析,最后利用cytoscape做网络关系图。结果发现247个相对明显的差异表达的基因,包括150个上调表达基因和97个下调表达基因;7个差异表达的miRNA,包括2个上调表达miRNA和5个下调表达miRNA。这些差异表达基因在细胞内和细胞外都起作用,并且在炎症反应,药物应答等生物过程中起作用。将差异基因与靶基因对比后,可得到48个重合基因,同时发现这些重合基因与差异表达的miRNA有着一定的联系。     

Mating flight causes genome-wide transcriptional changes in sexually mature honeybee queens

In this study, we analyzed the gene and miRNA expression differences between the courted virgin queen (CVQ) and non-courted virgin queen (NCVQ) of Apis mellifera using a high-throughput sequencing method. Through Digital Gene Expression (DGE) sequencing, 452 genes were differentially expressed, out of which, 90 genes were up-regulated and 362 genes were down-regulated in CVQ compared with NCVQ. Through small RNA sequencing, 27 miRNAs showed significant expression difference between these two samples. Moreover, 9 of the differentially expressed genes are the targets of the 11 differentially expressed miRNAs. Besides, 47 novel miRNA candidates were predicted in these two samples. Our results provided valuable information for understanding the molecular mechanism of the transition to functional queens.     

Global Identification of MicroRNAs and Their Targets in Barley under Salinity Stress

Salinity is a major limiting factor for agricultural production worldwide. A better understanding of the mechanisms of salinity stress response will aid efforts to improve plant salt tolerance. In this study, a combination of small RNA and mRNA degradome sequencing was used to identify salinity responsive-miRNAs and their targets in barley. A total of 152 miRNAs belonging to 126 families were identified, of which 44 were found to be salinity responsive with 30 up-regulated and 25 down-regulated respectively. The majority of the salinity-responsive miRNAs were up-regulated at the 8h time point, while down-regulated at the 3h and 27h time points. The targets of these miRNAs were further detected by degradome sequencing coupled with bioinformatics prediction. Finally, qRT-PCR was used to validate the identified miRNA and their targets. Our study systematically investigated the expression profile of miRNA and their targets in barley during salinity stress phase, which can contribute to understanding how miRNAs respond to salinity stress in barley and other cereal crops.     

结肠癌中核内miRNA的激活调控作用研究

为了探究增强子介导的核内miRNA在结肠癌发生中的作用,本研究筛选了结肠癌中的差异表达的miRNA数据、结肠的特异性增强子数据、结肠癌中差异表达基因数据,利用细胞核内miRNA靶向增强子预测算法,筛选miRNA调控的结肠特异性增强子;利用增强子靶基因预测数据,筛选核内miRNA调控的差异表达靶基因,并且构建核内miRNA-靶基因网络,并通过网络的分析和筛选获得结肠癌中关键的致病基因,同时对网络中的靶基因进行GO的功能注释。结果表明,我们所构建的核内miRNA-激活调控靶基因网络包含miRNA-靶基因关系对2 121个,259个节点,其中包含34个下调基因、183个上调的基因,7个下调的miRNA,35个上调的miRNA。而后我们分析了网络进行的节点度的整体分布情况,发现网络中大部分的节点的度都是小于10的,仅有少量miRNA结合和部分的差异表达基因节点的度大于10。核内miRNA主要通过激活调控了一些应激反应相关的功能和,同时,抑制调控了细胞周期、细胞凋亡、细胞死亡巨噬细胞代谢等相关功能,通过激活和抑制相关功能诱发结肠癌的发生。从核内miRNA的激活调控角度研究结肠癌的发病机制,是对原有细胞浆中miRNA抑制调控机制的补充,也为结肠癌的系统研究提供了新的视野。     

星形细胞瘤生存预后相关miRNA-mRNA调控关系对筛选

利用GEO数据库中的芯片数据,筛选与星形细胞瘤生存预后相关的miRNA-mRNA调控关系对,为后续研究提供理论支持.下载芯片数据利用R语言进行差异表达分析,得到星形细胞瘤较正常组织表达显著改变的miRNA与mRNA;通过miRNA靶基因预测,将靶基因与差异表达mRNA取交集,明确mRNA与miRNA之间的关系;利用GE...     

High-Throughput MicroRNA and mRNA Sequencing Reveals that MicroRNAs May Be Involved in Pectinesterase-Mediated Cold Resistance in Potato

Since potato cultivars are sensitive to low temperature, cold injury severely affects the geographical distribution and yield of potato. Although some miRNAs have been identified in response to cold stress in plants, there is no report about the role of miRNAs in the response to cold stress in potato. Here, via high throughput sequencing, we described the profiling of cold stress response to miRNA and mRNA in potato. Two small RNA and six mRNA libraries were constructed and sequenced. 296 known and 211 novel miRNAs were identified, in which 34 miRNAs in Cold Group (CG) had the higher expression quantity than which in Normal Group (NG) and 32 in CG had lower expression quantity than which in NG. 3068 differentially expressed genes were detected between NG and CG, in which 1400 genes were up-regulated and 1668 genes were down-regulated. The metabolism pathway of starch and sucrose (ko00500) is the common KEGG pathway in differentially expressed miRNA and mRNA. In this pathway, StuPME21575 and StuPME42971 are pectinesterase which mainly catalyzes the pectin-forming pectate, which are controlled by stu-miR6023 and stu-novel-miR42365. As the potato suffering cold stress, these two miRNAs expression levels became higher, but their target genes expression levels were just opposite and this result is the same with qRT-PCR.     

Expression patterns of conserved microRNAs in the male gametophyte of loblolly pine (Pinus taeda)

MicroRNAs (miRNAs) are small RNAs that regulate genes involved in various aspects of plant development, but their presence and expression patterns in the male gametophytes of gymnosperms have not yet been established. Therefore, this study identified and compared the expression patterns of conserved miRNAs from two stages of the male gametophyte of loblolly pine (Pinus taeda), which are the mature (ungerminated) and germinated pollen. Microarray was used to identify conserved miRNAs that varied in expression between these two stages of the loblolly pine male gametophyte. Forty-seven conserved miRNAs showed significantly different expression levels between mature and germinated loblolly pine pollen. In particular, miRNAs representing 14 and 8 families were up- and down-regulated in germinated loblolly pine pollen, respectively. qRT-PCR was used to validate their expression patterns using representative miRNAs. Target genes and proteins were identified using psRNATarget program. Predicted targets of the 22 miRNA families belong mostly to classes of genes involved in defense/stress response, metabolism, regulation, and signaling. qRT-PCR was also used to validate the expression patterns of representative target genes. This study shows that conserved miRNAs are expressed in mature and germinated loblolly pine pollen. Many of these miRNAs are differentially expressed, which indicates that the two stages of the male gametophyte examined are regulated at the miRNA level. This study also expands our knowledge of the male gametophytes of seed plants by providing insights on some similarities and differences in the types and expression patterns of conserved miRNAs between loblolly pine with those of rice and Arabidopsis.     

Identification of novel MiRNAs and MiRNA expression profiling during grain development in indica rice

ABSTRACT: BACKGROUND: MicroRNAs (miRNAs) modulate gene expression in different tissues and at diverse developmental stages, including grain development in japonica rice. To identify novel miRNAs in indica rice and to study their expression patterns during the entire grain filling process, small RNAs from all stages of grain development were sequenced and their expression patterns were studied using customized miRNA chips. RESULTS: A total of 21 conserved and 91 non-conserved miRNA families were found in developing indica grains. We also discovered 11 potential novel miRNAs based on the presence of their miRNA*s. Expression patterns of these identified miRNAs were analyzed using customized miRNA chips. The results showed that during the filling phase about half of the detected miRNAs were up-regulated, whereas the remainder were down-regulated. Predicted targets of differentially expressed miRNAs may participate in carbohydrate metabolism, hormone signaling and pathways associated with seed maturity, suggesting potentially important roles in rice grain development. CONCLUSIONS: This study is the first genome-wide investigation of miRNAs during the grain-filling phase of an indica variety of rice. The novel miRNAs identified might be involved in new miRNA regulatory pathways for grain development. The complexity of these miRNAs and their targets and interactions require further study to obtain a better understanding of the molecular mechanisms underlying grain development. Key words: miRNA, grain filling, indica rice.