Splice Isoform Profiling of Ion Channels

Creative Bioarray provides clients with long-read transcript profiling of ion channel splice isoforms using mRNA sequencing methods that combine long-read nanopore sequencing technology with PCR targeting. Our professional scientific services and technical support will contribute to our clients' full understanding of ion channel gene expression and function.

Introduction

Alternative splicing of RNA transcripts is a rich source of regulation of gene expression and a key means of generating functionally diverse voltage-gated ion channels. Alternative splicing of exons encoding key functional regions can have an impact on ion channel gating and downstream signaling. Splicing between different exons in the same transcript can be coordinated to achieve coupling of specific properties of different functional regions. To understand how different functional regions of ion channels regulate each other, it is necessary to characterize the identities of full-length transcript isoforms.

Standard RNA sequencing and the reconstruction of transcripts from short sequencing reads spanning exon junctions may not accurately reflect the identities of the transcript variants present. The advent of long-read nanopore sequencing provides a powerful tool to enable the sequencing of full-length transcripts and to accurately reveal the identity of full-length transcript variants. Based on the characterization of full-length transcript isoforms in a specific sample, predictions of the functional impacts of these splice variants can be made, which are critical to fully understanding the expression and function of ion channel genes.

Fig. 1 Long-read methods for profiling isoforms. (De Paoli-Iseppi, 2021)

Our Services

The report on the identification of the splice isoforms of the voltage-gated calcium channel CACNA1C in the human brain by long-read sequencing confirms the importance of fully characterizing the transcriptional isoforms. In recent years, our researchers have made a lot of efforts to provide clients with the splice isoform profiling of ion channels. Since ion channel transcripts are difficult to detect due to their relatively low abundance in total RNA extracted from tissues and cells, we applied PCR amplification in the strategy to target sequencing to only transcripts of interest. Our workflow is as follows:

Applications

• Research on the expression and function of ion channel genes
• Long read profiling of splicing in channelopathies
• Research on the impact of alternative splicing on protein function and abundance

The excellent research team at Creative Bioarray provides clients with long read transcript profiling of ion channel splicing isoforms and solutions to possible problems in this technology, such as sequencing failed to produce enough reads and failed to generate enough reads. If you are interested in our services, please feel free to contact us for more details.

Reference

1. De Paoli-Iseppi, R.; et al. Isoform age-splice isoform profiling using long-read technologies. Frontiers in Molecular Biosciences, 2021, 8.