Single Cell Isoform Expression Across Mouse Brain Regions and Development
Many human and mouse genes are comprised of multiple exons, which are separated by intervening sequences, referred to as “introns”. In a process called “splicing” introns are removed and exons are concatenated to form a complete isoform. Importantly, by leaving out certain exons (“exon skipping”) and other types of “alternative splicing”, a single gene can produce multiple distinct isoforms. Long-standing, well-established examples have shown that pairs of isoforms from a single gene can be functionally distinct and more recent large-scale analysis has shown that the “multiple-isoform-distinct-function” model is widespread among genes.
In the brain, alternative splicing is known to be different between brain regions and between cell types. This applies both to high-level cell types, like the brain’s immune cells (“microglia”) as opposed to neurons and to finer subtypes, as for example distinct types of excitatory neurons. Likewise, during development, a gene can alter the relative abundances of its isoforms and therefore lead to slight or more drastic changes in its function.
However, methods to test this efficiently for thousands of genes across all cell types in a brain sample had been lacking. Thus, much splicing research in the brain has been carried out “in bulk”. Thus, isoform alterations have been looked at in brain regions as well as in development but which (known or novel) cell types are responsible for which isoform changes is usually not determined in detail. We have developed methods to assess full-length isoforms across cell types, using a single-cell approach. Here, we will apply these technologies across brain regions and some developmental time points in order to facilitate an understanding of which precise known or novel cell populations underlie differences in isoform abundance between brain regions and developmental time points. Furthermore, we aim at understanding to which extent the existence of multiple isoforms per gene is a feature explained by many cell types expressing each only few isoforms or whether isoform diversity is a feature present in many precise cell populations.
Project Leadership
Hagen Tilgner (Principal Investigator)
Assistant Professor, Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York, USA
Project Data Types
- Cell-type specific RNA isoform data in all cell types across five mouse brain regions
- Full-length mouse RNA across all hippocampal and cerebellar cell types during postnatal development
Related Resources
- Allen Brain Atlas: https://portal.brain-map.org/
- Isoform Atlas: https://isoformatlas.com/
- scISOr-Seq approach: https://www.nature.com/articles/nbt.4259
- Tilgner Lab page: https://www.tilgnerlab.com/