Beyond the gene: decoding alternative isoforms

It has been well-established that the vast majority of human genes are expressed not as a single mRNA transcript but rather as a series of many distinct mRNAs due to processes including alternative splicing, promoter use, and polyadenylation. When these transcripts differ in their coding sequences, they can be translated into alternative protein isoforms. Despite known examples of alternative isoforms that are functionally important, whether they diversify the human proteome en masse has long been debated. Recent technological advances, including long-read RNA sequencing, more sensitive proteomics, and high-throughput methods to perturb individual isoforms suggest that most alternative isoforms are expressed at the protein level, are biochemically distinct from each other, and can be associated with disease. It is therefore important to move 'beyond the gene' toward more complex, isoform-aware characterization of molecular processes.