KDM3A regulates alternative splicing of cell-cycle genes following DNA damage.

Changes in the cellular environment result in chromatin structure alteration, which in turn regulates gene expression. To learn about the effect of the cellular environment on the transcriptome, we studied the H3K9 demethylase KDM3A. Using RNA-seq, we found that KDM3A regulates the transcription and alternative splicing of genes associated with cell cycle and DNA damage. We showed that KDM3A undergoes phosphorylation by PKA at serine 265 following DNA damage, and that the phosphorylation is important for proper cell-cycle regulation. We demonstrated that SAT1 alternative splicing, regulated by KDM3A, plays a role in cell-cycle regulation. Furthermore we found that KDM3A's demethylase activity is not needed for SAT1 alternative splicing regulation. In addition, we identified KDM3A's protein partner ARID1A, the SWI/SNF subunit, and SRSF3 as regulators of SAT1 alternative splicing and showed that KDM3A is essential for SRSF3 binding to SAT1 pre-mRNA. These results suggest that KDM3A serves as a sensor of the environment and an adaptor for splicing factor binding. Our work reveals chromatin sensing of the environment in the regulation of alternative splicing.

Regulation of alternative splicing by p300-mediated acetylation of splicing factors.

Splicing of precursor mRNA (pre-mRNA) is an important regulatory step in gene expression. Recent evidence points to a regulatory role of chromatin-related proteins in alternative splicing regulation. Using an unbiased approach, we have identified the acetyltransferase p300 as a key chromatin-related regulator of alternative splicing. p300 promotes genome-wide exon inclusion in both a transcription-dependent and -independent manner. Using CD44 as a paradigm, we found that p300 regulates alternative splicing by modulating the binding of splicing factors to pre-mRNA. Using a tethering strategy, we found that binding of p300 to the CD44 promoter region promotes CD44v exon inclusion independently of RNAPII transcriptional elongation rate. Promoter-bound p300 regulates alternative splicing by acetylating splicing factors, leading to exclusion of hnRNP M from CD44 pre-mRNA and activation of Sam68. p300-mediated CD44 alternative splicing reduces cell motility and promotes epithelial features. Our findings reveal a chromatin-related mechanism of alternative splicing regulation and demonstrate its impact on cellular function.

Predictive models for wastewater flow forecasting based on time series analysis and artificial neural network.

Wastewater flow forecasting is key for proper management of wastewater treatment plants (WWTPs). However, to predict the amount of incoming wastewater in WWTPs, wastewater engineers face challenges arising from numerous complexities and uncertainties, such as the nonlinear precipitation-runoff relationships in combined sewer systems, unpredictability due to aging infrastructure, and frequently inconsistent data quality. To address such challenges, a time series analysis model (i.e., the autoregressive integrated moving average, ARIMA) and an artificial neural network model (i.e., the multilayer perceptron neural network, MLPNN) were developed for predicting wastewater inflow. A case study of the Barrie Wastewater Treatment Facility in Barrie, Canada, was carried out to demonstrate the performance of the proposed models. Fifteen-minute flow data over a period of 1 year were collected, and the resampled daily flow data were used to train and validate the developed models. The model performances were examined using root mean square error, mean absolute percentage error, coefficient of determination, and Nash-Sutcliffe efficiency. The results indicate that both models provided reliable forecasts, while ARIMA showed a slightly better performance than MLPNN in this case study. The proposed models can provide useful decision support for the optimization and management of WWTPs.

Analytical description of colloid behavior in single fractures under irreversible deposition.

OBJECTIVES: Irreversible colloid deposition in groundwater-saturated fractures is typically modeled using a lumped deposition coefficient (κ) that reflects the system physiochemical conditions. A mathematical relationship between this coefficient and the physicochemical conditions controlling deposition has not yet been defined in the literature; thus, κ is typically fitted using experimental observations. This research develops, for the first time, an analytical relationship between κ and the fraction of colloids retained in single fractures (Fr). This relationship could be subsequently integrated with available models relating Fr to the system's physicochemical properties to develop an explicit mathematical relationship between κ and these properties. METHOD: The Fr-κ analytical relationship was developed through conceptualizing irreversible deposition as first-order decay, as both lead to permanent mass loss, and coupling this with the advection-dispersion equation. The model estimates of colloid deposition were compared to observations from laboratory-scale colloid tracer experiments. A variance-based global sensitivity analysis was applied to identify the parameters controlling deposition. FINDINGS: The analytical relationship efficiently replicated the experimental observations, and the global sensitivity analysis revealed that colloid deposition variability is controlled by fracture length, aperture size, and deposition coefficient; this supports the accepted understanding that colloid deposition is controlled by the system's physicochemical properties.

VEGFA's distal enhancer regulates its alternative splicing in CML.

Enhancer demethylation in leukemia has been shown to lead to overexpression of genes which promote cancer characteristics. The vascular endothelial growth factor A (VEGFA) enhancer, located 157 Kb downstream of its promoter, is demethylated in chronic myeloid leukemia (CML). VEGFA has several alternative splicing isoforms with different roles in cancer progression. Since transcription and splicing are coupled, we wondered whether VEGFA enhancer activity can also regulate the gene's alternative splicing to contribute to the pathology of CML. Our results show that mutating the VEGFA +157 enhancer promotes exclusion of exons 6a and 7 and activating the enhancer by tethering a chromatin activator has the opposite effect. In line with these results, CML patients present with high expression of +157 eRNA and inclusion of VEGFA exons 6a and 7. In addition, our results show that the positive regulator of RNAPII transcription elongation, CCNT2, binds VEGFA's promoter and enhancer, and its silencing promotes exclusion of exons 6a and 7 as it slows down RNAPII elongation rate. Thus our results suggest that VEGFA's +157 enhancer regulates its alternative splicing by increasing RNAPII elongation rate via CCNT2. Our work demonstrates for the first time a connection between an endogenous enhancer and alternative splicing regulation of its target gene.

A Genetic Programming-Based Model for Colloid Retention in Fractures.

Understanding the behavior of colloids in groundwater is critical as some are pathogenic while others may facilitate or inhibit the transport of dissolved contaminants. Colloid behavior in saturated fractured aquifers is governed by the physical and chemical properties of the groundwater-particle-fracture system. The interaction between these properties is nonlinear, and there is a need for a mathematical model describing the relationship between them to advance the mechanistic understanding of colloid transport in fractures and facilitate modeling in fractured environments. This paper coupled genetic programming and linear regression within a multigene genetic programming framework to develop a robust mathematical model describing the relationship between colloid retention in fractures and the physical and chemical parameters that describe the system. The data employed for model development and validation were collected from a series of 75 laboratory-scale colloid tracer experiments conducted under a range of conditions in three laboratory-induced discrete dolomite fractures and their epoxy replicas. The model sufficiently reproduced the observed data with coefficients of determination (R2 ) of 0.92 and 0.80 for model development and validation, respectively. A cross-validation demonstrated the model generality to 86% of the observed data. A variance-based global sensitivity analysis confirmed that attachment is the primary retention mechanism in the systems employed in this work. The model developed in this study provides a tool describing colloid retention in factures, which furthers the understanding of groundwater-particle-fracture system conditions contributing to the retention of colloids and can aid in the design of groundwater remediation strategies and development of groundwater management plans.