IL-13 regulates cilia loss and foxj1 expression in human airway epithelium.

mucociliary clearance is essential to the defense mechanism of the respiratory system. Loss of normal mucociliary clearance contribute to the pathogenesis of lung disease genetic and acquired. Care network differentiated human airway epithelial cultured Equine Clia Kitswith IL-13 resulted in the loss of ciliated epithelial cells and increased mucus-secreting cells. The loss of ciliated cells characterized by basal body mislocation Ezrin and loss of apical cell compartment.

 In addition to the loss of ciliated cells and mucous cells increased after IL-13 treatment, the cells with the characteristics of both ciliated cells, and mucosal epithelium were observed in the airways. In relation to the decrease in ciliated cells after IL-13 treatment, there was recorded a decrease foxj1 expression in airway epithelium, characterized by a decrease in the number of foxj1-expressing cells. 

In foxj1 promoter, STAT-binding element is identified and inhibition of expression foxj1 by STAT-6 and IL-13 are shown. These findings suggest molecular and cellular mechanisms of cilia loss in lung diseases. Inhibition foxj1 results Ezrin expression and loss of apical localization of basal body with the subsequent loss of the structure axonemal. These findings have important implications for the pathogenesis and treatment of respiratory diseases.

CLIP-seq analysis of multi-mapped reads discover new functional RNA regulatory sites in the human transcriptome.

Cross or RNA immunoprecipitation followed by sequencing (CLIP-seq or RIP-seq) allows transcriptome-wide discovery of RNA regulatory sites. As CLIP-Seq / RIP-Seq short beeps, a computational tool that there is a focus on the unique mapped reads, while the reads mapped to multiple loci are discarded. We present CLAM (CLIP-Seq Analysis of Multi-mapped reads). CLAM using expectation-maximization algorithm to assign multi-mapped General Clia Kits reads and incorporates unique peak calls and multi-mapped reads. 

To demonstrate the utility of CLAM, we applied to a variety of public datasets CLIP-Seq / RIP-Seq involves many splicing factors, microRNAs and RNA methylation M6A. CLAM recovered a large number of novel RNA regulatory sites can not be accessed by uniquely mapped reads. The functional significance of these sites indicated by consensus motif patterns and associated with alternative splicing (splicing factor), transcript abundance (AGO2) and mRNA half-life (M6A). CLAM provide a useful tool to discover novel protein-RNA and RNA modification site of CLIP-seq data and RIP-seq, and revealed the significant contribution of recurring elements to landscape RNA regulation of the human transcriptome.