Functional consequences of developmentally regulated alternative splicing

By Auinash Kalsotra, T. Cooper. Nature reviews genetics, 2011

690 citations recorded by the source corpus.

Genome-wide analyses of metazoan transcriptomes have revealed an unexpected level of mRNA diversity that is generated by alternative splicing. Recently, regulatory networks have been identified through which splicing promotes dynamic remodelling of the transcriptome to promote physiological changes, which involve robust and coordinated alternative splicing transitions. The regulation of splicing in yeast, worms, flies and vertebrates affects a variety of biological processes. The functional classes of genes that are regulated by alternative splicing include both those with widespread homeostatic activities and those with cell-type-specific functions. Alternative splicing can drive determinative physiological change or can have a permissive role by providing mRNA variability that is used by other regulatory mechanisms.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/99594b83714f9ff581fba5685a2d65694342b165

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Citations in the corpus

Alternative Splicing Regulatory Networks: Functions, Mechanisms, and Evolution. (2019, background): “To date, dynamic alternative splicing networks have been detected in embryonic stem and precursor cells, during the differentiation or reprogramming of various cell lineages as well as epithelial-mesenchymal transitions, and in adult organs such as the brain, heart, skeletal muscle, liver, kidney, a”
The RNA binding protein quaking regulates formation of circRNAs. (2015, neutral): “On the other hand, regulated alternative splicing plays amajor role in expanding the transcriptome is critical in development and in physiological responses (Kalsotra and Cooper, 2011), making it likely that splicing factors may participate in regulating circRNA biogenesis.”
rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data (2014, background): “Changes in alternative splicing underlie gene regulation in diverse biological and disease processes (5 – 7).”
A highly conserved program of neuronal microexons is misregulated in autistic brains (2014, background): “of Neuronal Microexons Is”
The Third Revolution in Sequencing Technology. (2018, background): “This is a major limitation given the importance of alternative splicing in many physiological and developmental processes [49].”
A census of human RNA-binding proteins (2014, background): “example, the abundance of various splicing factors can influence mRNA splicing patterns (Chen and Manley, 2009; Kalsotra and Cooper, 2011; Kornblihtt et al., 2013; Smith and Valcarcel, 2000; Wahl et al., 2009), while U1 snRNP levels control alternative polyadenylation sites (Berg”
Complexity of the Alternative Splicing Landscape in Plants[C][W][OPEN] (2013, background): “New tools based on recent technological advances are allowing genome-wide analysis of RNA elements in transcripts and of chromatin modifications that regulate AS. Application of these tools in plants will provide significant new insights into AS regulation and crosstalk between AS and other layers…”
MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data (2012, background): “This is important considering the prevalence of tissueand condition-specific alternative splicing (32).”