This study reflects years of work, a big thanks to everyone involved, including Ricardo De Paoli-Iseppi who co-led the work and the many graduate and undergrad students who took on some of the genes for their projects or worked on IsoLamp including @josiegleeson.bsky.social & @youyupei.bsky.social

Research has shown genetic risk for disease can be imparted at the isoform level, as well as the gene level. Therefore, understanding which isoforms genes express is essential to correctly determining the disease-associated isoforms and the molecular mechanisms behind disease aetiology.

We developed a new analysis pipeline, IsoLamp, to discover and quantify isoforms from long-read amplicon sequencing. While much of the analysis and visualisation used IsoVis.
IsoVis: isomix.org/isovis/
IsoLamp: github.com/ClarkLaborat...

Overall we found more than 300 previously unreported RNA isoforms from 31 genes in brain. Some were highly abundant or even the dominant isoform, and we could show translation of novel RNAs into novel proteoforms, including new isoforms of the depression risk gene ITIH4 (see image).

🔹 What’s inside
• Bulk, single-cell & single-nucleus RNA-seq from 8 lung-cancer cell lines spanning 3 cancer types for realistic DE analysis
• Three long-read protocols (ONT PCR-cDNA, ONT direct RNA, PacBio Kinnex) and Illumina short-read sequencing
• Synthetic spike-in controls for ground truth

If you want to explore the data check out the Shiny App: clarklaboratory.shinyapps.io/human_brain_...

Big thanks to Josie Gleeson and Ric De Paoli-Iseppi for leading this work.

- Different RNA isoforms from the same gene can have different modification rates at the same m6A site. Distance to a splice site, transcript 3' end, and the CDS versus UTR status of a nucleotide all exert influence.

We identified 57,000 m6A sites in 15,000 isoforms.

Some of the key results were:
- highest m6A levels in the cerebellum.
- Pre-frontal cortex had the most unique m6A profile, associated with excitatory neurons and synaptic genes.
- Some RNAs are hyper-modified. The lncRNA TUG1 had 37 m6A sites!

Hi Monica, could you please add me to the science feed.

Link to my lab webpage:
biomedicalsciences.unimelb.edu.au/sbs-research...