基于GEO数据库的胎儿发育异常时羊水游离RNA中组织特异性差异表达基因分析

目的通过生物信息学分析发现羊水游离RNA中能够反映胎儿发育异常的组织特性基因。方法从Human Protein Atlas数据库下载基因在正常组织表达数据,从Gene Expression Omnibus数据库下载唐氏综合征及爱德华综合征胎儿羊水游离RNA芯片检测数据。利用R语言统计分析正常组织表达数据中的组织特异性基因。利用limma程序包分析唐氏综合征及爱德华综合征的差异表达基因。取两者交集获取组织特异性差异表达基因。结果与正常胎儿比较,唐氏综合征胎儿有717个差异基因,爱德华综合征胎儿有1038个差异基因,71个基因为共同差异基因。DOK7、ARHGEF39、FAM111B、CCHCR1、R3HDML、WNK3、FIBCD1、SMIM10L2B及SMIM10L2A 9个基因为组织特异性差异表达基因,这些基因参与大脑、甲状腺、睾丸、消化道等多个组织的发育过程。结论差异表达基因分析和组织特异性基因相结合的方法是筛选羊水游离RNA中胎儿发育异常标志物的可行方法。

Isolation of a Genomic DNA for Gastrodia Antifungal Protein and Analyses of Its Promoter in Transgenic Tobacco

A genomic DNA containing 5'-upstream region and complete open reading frame of a Gastrodia antifungal protein was isolated by screening of a genomic library from Gastrodia elata B1. To investigate the promoter activity, the 5'-flanking region - 1 157 lip upstream from the putative transcription start site was fused to the coding sequence of beta-glucuronidase (GUS) gene and transformed into Nicotiana tabacum. The strongest GUS activity was detected in the roots of transgenic tobacco, followed by stems. The leaves only showed a low GUS activity. Furthermore, the promoter established inducible expression pattern in transgenic tobacco upon fungus Trichoderma viride inoculation and jasmonic acid and salicylic acid treatments.

MicroRNAs and cancer

MicroRNAs (miRNAs) belong to a class of noncoding, regulatory RNAs that are involved in oncogenesis and show remarkable tissue specificity.miRNAs are approximately 22 nt non-coding RNAs, which regulate gene expression in a sequence-specific manner via translational inhibition or messenger RNA (mRNA) degradation, thus affecting various cellular processes.Since the discovery of their fundamental mechanisms of action, the field of miRNAs has opened a new era in the understanding of small noncoding RNAs.Recent evidence has shown that miRNA controls cell growth, apoptosis, and differentiation.Cancer is a complex genetic disease caused by abnormalities in gene structure and expression, moreover, miRNA expression correlates with cancers and could have a crucial function in tumor progression.Bioinformatic data indicate that each miRNA can control hundreds of target genes, but identification of the accurate miRNA targets will be crucial to exploit the emerging knowledge of miRNA contribution to cancer process.

Isolation of a pollen-specific promoter in tritordeum

The promoter is a cis-acting element in regulating gene expression. A promoterless plasmid containing UidA gene was transformed into tritordeum by barmbadment. Histochemical analysis of various tissues in transgenic tritordeum was carried to examine tissue-specific expression of GUS(beta-glucuronidase) activity. The pollen-specific promoter was trapped and identified successfully in a transformant line. PCR(polymerase chain reaction) method was used to isolate this pollen-specific promoter. By sequencing and analyzing the amplified fragment from PCR, a part of UidA gene and a flanking sequence were obtained. Some essential elements of plant promoters were found in the sequence. To determine the function of it, the cloned fragment was fused with UidA gene, then cloned and transformed into Triticum durum. The transgenic plant transformed by this vector showed GUS expression only in pollen. Therefore a pollen-specific promoter was isolated successfully.

Temporal and Tissue-Specific Expression of Tomato 14-3-3 Gene Family in Response to Phosphorus Deficiency

Plants adapt to phosphorus （P） deficiency through a complex of biological processes and many genes are involved. Tomato （Solanum lycopersicum L. ＇Hezuo906＇） plants were selected to grown hydroponically to study the temporal and spatial gene expression patterns of the 14-3-3 gene family and their roles in response to P deficiency in tomato plants. Using real-time reverse-transcriptase polymerase chain reaction （RT-PCR）, we investigated the expression profiles in different tissues （root, stem and leaf） at short-term and long-term P-deficient stress phases. Results revealed that i） four members of 14-3-3 gene family （TFT1, TFT4, TFT6 and TFTT） were involved in the adaptation of tomato plants to P deficiency, ii） TFT7 responded quickly to P deficiency in the root, while TFT6 responded slowly to P deficiency in the leaf, iii） expression response of TFT4 to P-deficient stress was widely distributed in different tissues （root, stem and leaf） while TFT8 only displayed stem-specific expression, and iv） temporal and tissues-specific expression patterns to P deficiency suggested that isoform specificity existed in tomato 14-3-3 gene family. We propose that TFT7 （one member of e-like group in tomato 14-3-3 family） is the early responsive gene and may play a role in the adaptation of tomato plants to shortterm P deficiency, while TFT6 （one member of non-e group in tomato 14-3-3 family） is the later responsive gene and may play a role in the adaptation of tomato plants to long-term P deficiency.

Identification and analysis of mouse non-coding RNA using transcriptome data

Transcripts are expressed spatially and temporally and they are very complicated, precise and specific; however, most studies are focused on protein-coding related genes. Recently, massively parallel c DNA sequencing(RNA-seq) has emerged to be a new and promising tool for transcriptome research, and numbers of non-coding RNAs, especially linc RNAs, have been widely identified and well characterized as important regulators of diverse biological processes. In this study, we used ultra-deep RNA-seq data from 15 mouse tissues to study the diversity and dynamic of non-coding RNAs in mouse. Using our own criteria, we identified totally 16,249 non-coding genes(21,569 non-coding RNAs) in mouse. We annotated these non-coding RNAs by diverse properties and found non-coding RNAs are generally shorter, have fewer exons, express in lower level and are more strikingly tissue-specific compared with protein-coding genes. Moreover, these non-coding RNAs show significant enrichment with transcriptional initiation and elongation signals including histone modifications(H3K4me3, H3K27me3 and H3K36me3), RNAPII binding sites and CAGE tags. The gene set enrichment analysis(GSEA) result revealed several sets of linc RNAs associated with diverse biological processes such as immune effector process, muscle development and sexual reproduction. Taken together, this study provides a more comprehensive annotation of mouse non-coding RNAs and gives an opportunity for future functional and evolutionary study of mouse non-coding RNAs.