Hagen Tilgner

Brain and Mind Research Institute and Center for Neurogenetics, Weill Cornell Medicine, New York, USA.

Hagen Tilgner studied computer science in Germany and France, and after a brief stint in the UK, did his doctoral studies with Roderic Guigo at Centre for Genomic Regulation in Barcelona. There he focused on RNA and the co-transcriptionality of splicing (see Tilgner et al, Genome Res, 2012 for example). His postdoctoral work at Stanford with Michael Snyder focused on technology development, specifically for long-read transcriptomics (see for example Sharon*, Tilgner*, Grubert, Snyder, Nature Biotechnology, 2013 or Tilgner*, Jahanbani*, Nature Biotechnology, 2015). He started his lab at Weill Cornell in New York City in 2016 focusing on technologies to decipher the actions of RNA isoforms in the brain. The lab is a multi-disciplinary lab, including wet-lab technology development (see for example single-cell isoform RNA sequencing, ScISOr-Seq, Gupta*, Collier*, Nature Biotechnology, 2018 as well as single-nuclei isoform RNA sequencing, Hardwick*, Hu*, Joglekar* et al, Nature Biotechnology, 2022) and dry-lab approaches (see for example Joglekar et al, Nature Communications, 2021), where Maths/CS, molecular biology and neuroscience backgrounds interact to further our understanding of isoforms in healthy and diseased brain of humans and model organisms. 

Title

Brain isoforms in space and time

Abstract

Most mammalian genes encode multiple distinct RNA isoforms and the brain harbors especially diverse isoforms. Complex tissue, including the brain, often include highly divergent cell types and these cell types employ distinct isoforms for many genes. To untangle the distinct cell-type specific isoform profiles of the brain, we developed Single-cell isoform RNA sequencing (ScISOr-Seq¹) for fresh tissues as well Single-nuclei isoform RNA sequencing (SnISOr-Seq²). To add spatial resolution, we developed Slide-isoform sequencing³. Collectively, these long-read approaches reveal a striking difference between coordinated pairs of exons with in-between exons (“Distant coordinated exons”) and without in-between exons (“Adjacent coordinated exons”): The former show strong enrichment for cell-type specific usage of exons, whereas the latter do not in mouse¹ and human brain². Of note, coordinated TSS-exon pairs and exon-polyA-site pairs follow the same trend as distant coordinated exon pairs². Simultaneously, autism-associated exons are among the most highly variably used exons across cell types². Differences in isoform expression between hippocampus and prefrontal cortex are most often explained by differences arising between the two regions in one specific cell type (e.g., excitatory neurons), but for a smaller program of genes brain regions can override cell-type identity³. Spatially barcoded isoform sequencing revealed that often region-specific isoform differences correlate with precise boundaries of brain structures (e.g., from the choroid plexus to the hippocampus). However, genes including Snap²⁵ go against this trend, using a steady gradient of exon inclusion as one traverses the brain³. Moreover, choroid plexus epithelial cells show a dramatically distinct isoform profile, which originates from distinct exon and poly(A) site usage, but most strongly from distinct TSS usage³. Most recently, we have made advances in understanding the error sources of Pacific Biosciences and Oxford Nanopore long-read sequencing technologies⁴ and have implemented a highly accurate long-read interpretation pipeline⁵. 

1. Gupta*, Collier* et al, Nature Biotechnology, 2018 
2. Hardwick*, Hu*, Joglekar* et al, Nature Biotechnology, 2022 
3. Joglekar et al, Nature Communications, 2021 
4. Mikheenko*, Prjibelski*, Genome Research, 2022 
5. Prjibelski et al, https://assets.researchsquare.com/files/rs-1571850/v1_covered.pdf