At VUGENE, we have integrated alternative splicing analysis into our RNA-seq pipeline and strongly recommend its use in every experiment as studying alternative splicing will significantly advance our understanding of mRNA complexity and regulation, providing valuable insights into disease etiology.
The importance of alternative splicing
The alternative removal of introns during mRNA maturation is essential for major biological processes in eukaryotes, such as cellular differentiation, response to environmental stress, and proper gene regulation. However, the ability to gain novel insights into the regulation and function of splicing is often hindered by the challenge of estimating transcript abundances from short-read RNA-seq data.
Alternative splicing can produce isoforms with distinct, and sometimes antagonistic, activities. Changes in mRNA through differential inclusion of sequences can alter transcript localization, longevity, or protein sequences.
Furthermore, approximately 15% of human hereditary diseases and cancers are associated with alternative splicing. For general RNA-seq experimentsaimed at identifying differentially expressed genes, alternative splicing analysis can provide a broader understanding of the changes occurring between conditions of interest.
It is important to note that standard differential expression analyses may yield incomplete results, as alternatively spliced isoforms are counted together. This means that differential expression might not appear significant even when the expression originates from different transcript variants.
Incorporating alternative splicing analysis in RNA-seq experiments is not merely an added bonus, it is essential for capturing the full spectrum of transcriptomic variation.
Written by: Milda Milčiūtė, Miglė Gabrielaitė, PhD
Cover image credits: Olena / Adobe Stock
