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1. A simple method to visualize pre-mRNA splicing with the naked eye using a genetically encoded visual splicing reporter

   https://doi.org/10.1093/plphys/kiae396  

   Prasad, Kasavajhala_V_S_K; Cheema, Amandeep; Scanlon, William; Matthews, Allison; Sharifova, Saida; Huq, Enamul; Reddy, Anireddy_S_N (July 2024, Plant Physiology)

   A genetically encoded splicing reporter allows naked-eye visualization of pre-mRNA splicing and requires no expensive equipment or substrate. 

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2. Instanton L-spaces and splicing

   https://doi.org/10.5802/ahl.148  

   Baldwin, John A; Sivek, Steven (January 2022, Annales Henri Lebesgue)
3. SWAP1-SFPS-RRC1 splicing factor complex modulates pre-mRNA splicing to promote photomorphogenesis in Arabidopsis.

   Kathare, P.K. (January 2022, Proceedings of the National Academy of Sciences of the United States of America)
4. The effects of mutations on gene expression and alternative splicing

   https://doi.org/10.1098/rspb.2023.0565  

   Snyman, Marelize; Xu, Sen (July 2023, Proceedings of the Royal Society B: Biological Sciences)

   Understanding the relationship between mutations and their genomic and phenotypic consequences has been a longstanding goal of evolutionary biology. However, few studies have investigated the impact of mutations on gene expression and alternative splicing on the genome-wide scale. In this study, we aim to bridge this knowledge gap by utilizing whole-genome sequencing data and RNA sequencing data from 16 obligately parthenogeneticDaphniamutant lines to investigate the effects of ethyl methanesulfonate-induced mutations on gene expression and alternative splicing. Using rigorous analyses of mutations, expression changes and alternative splicing, we show that trans-effects are the major contributor to the variance in gene expression and alternative splicing between the wild-type and mutant lines, whereas cis mutations only affected a limited number of genes and do not always alter gene expression. Moreover, we show that there is a significant association between differentially expressed genes and exonic mutations, indicating that exonic mutations are an important driver of altered gene expression. 

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5. SWAP1-SFPS-RRC1 splicing factor complex modulates pre-mRNA splicing to promote photomorphogenesis in Arabidopsis

   https://doi.org/10.1073/pnas.2214565119  

   Kathare, Praveen Kumar; Xin, Ruijiao; Ganesan, Abirama Sundari; June, Viviana M.; Reddy, Anireddy S.; Huq, Enamul (November 2022, Proceedings of the National Academy of Sciences)

   Light signals perceived by a group of photoreceptors have profound effects on the physiology, growth, and development of plants. The red/far-red light–absorbing phytochromes (phys) modulate these aspects by intricately regulating gene expression at multiple levels. Here, we report the identification and functional characterization of an RNA-binding splicing factor, SWAP1 (SUPPRESSOR-OF-WHITE-APRICOT/SURP RNA-BINDING DOMAIN-CONTAINING PROTEIN1). Loss-of-function swap1-1 mutant is hyposensitive to red light and exhibits a day length–independent early flowering phenotype. SWAP1 physically interacts with two other splicing factors, (SFPS) SPLICING FACTOR FOR PHYTOCHROME SIGNALING and (RRC1) REDUCED RED LIGHT RESPONSES IN CRY1CRY2 BACKGROUND 1 in a light-independent manner and forms a ternary complex. In addition, SWAP1 physically interacts with photoactivated phyB and colocalizes with nuclear phyB photobodies. Phenotypic analyses show that the swap1sfps , swap1rrc1, and sfpsrrc1 double mutants display hypocotyl lengths similar to that of the respective single mutants under red light, suggesting that they function in the same genetic pathway. The swap1sfps double and swap1sfpsrrc1 triple mutants display pleiotropic phenotypes, including sterility at the adult stage. Deep RNA sequencing (RNA-seq) analyses show that SWAP1 regulates the gene expression and pre–messenger RNA (mRNA) alternative splicing of a large number of genes, including those involved in plant responses to light signaling. A comparative analysis of alternative splicing among single, double, and triple mutants showed that all three splicing factors coordinately regulate the alternative splicing of a subset of genes. Our study uncovered the function of a splicing factor that modulates light-regulated alternative splicing by interacting with photoactivated phyB and other splicing factors. 

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