rMATS-turbo: an efficient and flexible computational tool for alternative splicing analysis of large-scale RNA-seq data.

Pre-mRNA alternative splicing is a prevalent mechanism for diversifying eukaryotic transcriptomes and proteomes. Regulated alternative splicing plays a role in many biological processes, and dysregulated alternative splicing is a feature of many human diseases. Short-read RNA sequencing (RNA-seq) is now the standard approach for transcriptome-wide analysis of alternative splicing. Since 2011, our laboratory has developed and maintained Replicate Multivariate Analysis of Transcript Splicing (rMATS), a computational tool for discovering and quantifying alternative splicing events from RNA-seq data. Here we provide a protocol for the contemporary version of rMATS, rMATS-turbo, a fast and scalable re-implementation that maintains the statistical framework and user interface of the original rMATS software, while incorporating a revamped computational workflow with a substantial improvement in speed and data storage efficiency. The rMATS-turbo software scales up to massive RNA-seq datasets with tens of thousands of samples. To illustrate the utility of rMATS-turbo, we describe two representative application scenarios. First, we describe a broadly applicable two-group comparison to identify differential alternative splicing events between two sample groups, including both annotated and novel alternative splicing events. Second, we describe a quantitative analysis of alternative splicing in a large-scale RNA-seq dataset (~1,000 samples), including the discovery of alternative splicing events associated with distinct cell states. We detail the workflow and features of rMATS-turbo that enable efficient parallel processing and analysis of large-scale RNA-seq datasets on a compute cluster. We anticipate that this protocol will help the broad user base of rMATS-turbo make the best use of this software for studying alternative splicing in diverse biological systems.

Influence of circadian rhythm on effects induced by mechanical strain in periodontal ligament cells.

PURPOSE: The aim of this study was to investigate the influence of mechanical strain on clock gene function in periodontal ligament (PDL) cells. Furthermore, we wanted to analyze whether effects induced by mechanical stress vary in relation to the circadian rhythm. METHODS: Human PDL fibroblasts were synchronized in their circadian rhythm with dexamethasone and stretched over 24 h. Unstretched cells served as controls. Gene expression of the core clock genes were analyzed at 4 h intervals by quantitative real-time polymerase chain reaction (qRT-PCR). Time points 0 h (group SI1) and 12 h (group SI2) after synchronization served as starting points of a 4 h force application period. Collagen-1α (COL-1α/Col-1α), interleukin-1ß (IL1-ß), and runt-related transcription factor 2 (RUNX2/Runx2) were assessed by qRT-PCR and enzyme-linked immunosorbent assay (ELISA) after 2 and 4 h. Statistical analysis comprised one-way analysis of variance (ANOVA) and post hoc tests. RESULTS: After synchronization, the typical pattern for clock genes was visible in control cells over the 24 h period. This pattern was significantly altered by mechanical strain. Under tensile stress, ARNTL gene expression was reduced, while Per1 and 2 gene expression were upregulated. In addition, mechanical stress had a differential effect on the expression of Col-1α and IL1­ß depending on its initiation within the circadian rhythm (group SI1 vs group SI2). For RUNX2, no significant differences in the two groups were observed. CONCLUSION: Our results suggest that mechanical stress affects the molecular peripheral oscillator of PDL cells. Vice versa, the circadian rhythm also seems to partially influence the effects that mechanical stress exerts on PDL cells.

Functional analysis of ESRP1/2 gene variants and CTNND1 isoforms in orofacial cleft pathogenesis.

Orofacial cleft (OFC) is a common human congenital anomaly. Epithelial-specific RNA splicing regulators ESRP1 and ESRP2 regulate craniofacial morphogenesis and their disruption result in OFC in zebrafish, mouse and humans. Using esrp1/2 mutant zebrafish and murine Py2T cell line models, we functionally tested the pathogenicity of human ESRP1/2 gene variants. We found that many variants predicted by in silico methods to be pathogenic were functionally benign. Esrp1 also regulates the alternative splicing of Ctnnd1 and these genes are co-expressed in the embryonic and oral epithelium. In fact, over-expression of ctnnd1 is sufficient to rescue morphogenesis of epithelial-derived structures in esrp1/2 zebrafish mutants. Additionally, we identified 13 CTNND1 variants from genome sequencing of OFC cohorts, confirming CTNND1 as a key gene in human OFC. This work highlights the importance of functional assessment of human gene variants and demonstrates the critical requirement of Esrp-Ctnnd1 acting in the embryonic epithelium to regulate palatogenesis.