Transcriptome analysis of adherens junction pathway-related genes after peripheral nerve injury

The neural regeneration process is driven by a wide range of molecules and pathways. Adherens junctions are critical cellular junctions for the integrity of peripheral nerves. However, few studies have systematically characterized the transcript changes in the adherens junction pathway following injury. In this study, a rat model of sciatic nerve crush injury was established by forceps. Deep sequencing data were analyzed using comprehensive transcriptome analysis at 0, 1, 4, 7, and 14 days after injury. Results showed that most individual molecules in the adherens junctions were either upregulated or downregulated after nerve injury. The m RNA expression of ARPC1 B, ARPC3, TUBA8, TUBA1 C, CTNNA2, ACTN3, MET, HGF, NME1 and ARF6, which are involved in the adherens junction pathway and in remodeling of adherens junctions, was analyzed using quantitative real-time polymerase chain reaction. Most of these genes were upregulated in the sciatic nerve stump following peripheral nerve injury, except for CTNNA2, which was downregulated. Our findings reveal the dynamic changes of key molecules in adherens junctions and in remodeling of adherens junctions. These key genes provide a reference for the selection of clinical therapeutic targets for peripheral nerve injury.

Transcriptome and Functional Analysis of Fiber-related Gene Expression in Cotton

Fiber cell initiation is a complex process involving many pathways,including phytohormones and components for transcriptional and posttranscriptional regulation.Here we report expression

Global impact of RNA splicing on transcriptome remodeling in the heart

In the eukaryotic transcriptome, both the numbers of genes and different RNA species produced by each gene contribute to the overall complexity. These RNA species are generated by the utilization of different transcriptional initiation or termination sites, or more commonly, from different messenger RNA (mRNA) splicing events. Among the 30 000+ genes in human genome, it is estimated that more than 95% of them can generate more than one gene product via alternative RNA splicing. The protein products generated from different RNA splicing variants can have different intracellular localization, activity, or tissue-distribution. Therefore, alternative RNA splicing is an important molecular process that contributes to the overall complexity of the genome and the functional specificity and diversity among different cell types. In this review, we will discuss current efforts to unravel the full complexity of the cardiac transcriptome using a deep-sequencing approach, and highlight the potential of this technology to uncover the global impact of RNA splicing on the transcriptome during development and diseases of the heart.

Advances in Transcriptomic Studies and Ginsenoside Biosynthesis of American Ginseng

American ginseng（Panax quinquefolius L.）, belonging to the Araliaceae family, is one of the most widely used traditional herbs in the world. Its major bioactive constituents are triterpene saponins known as ginsenosides. Up to date, it is still a big challenge to sequence and assemble the large and repeat-enriched genome of tetraploid American ginseng, using whole genome shotgun（WGS） sequencing strategy. The lack of American ginseng genome information has significantly impeded its genetic and functional genomic studies. With the development of next-generation sequencing（NGS） technologies, sequencing and analysis of transcriptomes have become powerful tools for the discovery of novel genes and elucidation of specific biosynthetic pathways of secondary metabolites. Here we summarized the recent advances in the transcriptomic studies of American ginseng, including high-throughput transcriptome sequencing, assembly, and functional gene annotation and classification. Based on the results of transcriptomic data mining and co-expression analyses, many candidate genes possibly involved in the biosynthetic pathway of ginsenosides have been found, thereby providing an unparalleled opportunity to fully understand the mechanism of ginsenoside biosynthesis and its regulations in American ginseng. Advances in transcriptomic studies will contribute to the molecular breeding and planting management of American ginseng and to the development of novel ginsenoside-type drugs.