Tracks through the genome to physiological events

Abstract

New Findings What is the topic of this review? We discuss tools available to access genome‐wide data sets that harbour cell‐specific, brain region‐specific and tissue‐specific information on exon usage for several species, including humans. In this Review, we demonstrate how to access this information in genome databases and its enormous value to physiology. What advances does it highlight? The sheer scale of protein diversity that is possible from complex genes, including those that encode voltage‐gated ion channels, is vast. But this choice is critical for a complete understanding of protein function in the most physiologically relevant context. Many proteins of great interest to physiologists and neuroscientists are structurally complex and located in specialized subcellular domains, such as neuronal synapses and transverse tubules of muscle. Genes that encode these critical signalling molecules (receptors, ion channels, transporters, enzymes, cell adhesion molecules, cell–cell interaction proteins and cytoskeletal proteins) are similarly complex. Typically, these genes are large; human Dystrophin (DMD) encodes a cytoskeletal protein of muscle and it is the largest naturally occurring gene at a staggering 2.3 Mb. Large genes contain many non‐coding introns and coding exons; human Titin (TTN), which encodes a protein essential for the assembly and functioning of vertebrate striated muscles, has over 350 exons and consequently has an enormous capacity to generate different forms of Titin mRNAs that have unique exon combinations. Functional and pharmacological differences among protein isoforms originating from the same gene may be subtle but nonetheless of critical physiological significance. Standard functional, immunological and pharmacological approaches, so useful for characterizing proteins encoded by different genes, typically fail to discriminate among splice isoforms of individual genes. Tools are now available to access genome‐wide data sets that harbour cell‐specific, brain region‐specific and tissue‐specific information on exon usage for several species, including humans. In this Review, we demonstrate how to access this information in genome databases and its enormous value to physiology.

Cell-Specific RNA Binding Protein Rbfox2 Regulates CaV2.2 mRNA Exon Composition and CaV2.2 Current Size

“…1 B ) but it (and other conserved cell-specific alternatively spliced exons) can be resolved as a region of high conservation in multiple species alignments and conservation tracks (100 Vert Cons; Fig. 1 B ), and validated by analyses of mRNAs in specific cells and tissues (see below; Lipscombe et al, 2015 ).…”

“…1 B ). E18a is an alternatively spliced cassette exon present in all mammalian Cacna1b genes but mRNAs containing this exon are frequently overlooked because e18a-Ca V 2.2 mRNAs are most abundant in regions of the nervous system that have poor representation in the RefSeq database ( Lipscombe et al, 2015 ; e.g., SCG ( Fig. 1 C ) and spinal cord; Gray et al, 2007 ), and they are found in low abundance in regions with strong representation in the RefSeq database (e.g., cortex, CT; Fig.…”

“…This form of cell-specific pre-mRNA processing greatly expands the coding capacity of genes without increasing genetic load. The resulting pool of mRNA splice isoforms in specific tissues carries a rich source of information about the function and the state of the cell ( Lipscombe and Andrade, 2015 ; Lipscombe et al, 2015 ). Cell-specific inclusion or exclusion of alternative exons in the nervous system is essential for development, axon targeting, neuronal excitability, circuit formation, G protein signaling, and drug action ( Grabowski and Black, 2001 ; Xie and Black, 2001 ; Gray et al, 2007 ; Asadi et al, 2009 ; Jepson et al, 2013 ; Lipscombe et al, 2013a ; Lipscombe et al, 2013b ; Saito et al, 2016 ).…”

Major advances in physiology: celebrating a centenary of contributions by women

“…The tools available to access the genome-wide data sets containing cell-specific information on exon usage that allow discrimination of proteins generated as splice isoforms are reviewed by Diana Lipscombe and colleagues. They show how such information has helped to establish the physiological significance of isoforms of genes encoding voltage-operated Ca 2+ channels and neuronal Na + channels, and discuss the potential of strategies to normalize splicing events associated with various diseases (Lipscombe et al 2015).…”

“…They show how such information has helped to establish the physiological significance of isoforms of genes encoding voltage‐operated Ca 2+ channels and neuronal Na + channels, and discuss the potential of strategies to normalize splicing events associated with various diseases (Lipscombe et al . ).…”