Poster abstracts

Poster number 68 submitted by Jason Underwood

Putting the gene in genomes: long read transcriptomics from gene annotation to single cell biology

Jason G. Underwood (Pacific Biosciences), Elizabeth Tseng (Pacific Biosciences), Ting Hon (Pacific Biosciences), Vijay Ramani (Biochem and Biophysics, UCSF), Evan Eichler (Genome Sciences, University of Washington)

Abstract:
Long read mRNA sequencing methods such as PacBio’s Iso-Seq method offers high-throughput transcriptome profiling in prokaryotic and eukaryotic cells. By avoiding the transcript assembly problem and instead sequencing full-length cDNA, Iso-Seq has emerged as the most accurate technology for annotating isoforms and, in turn, improving proteome predictions in a wide variety of organisms. Improvements in library preparation, sequencing throughput, and bioinformatics has enabled the Iso-Seq method to be complete solution to apply to a variety of difficult biological questions.

We demonstrate how highly accurate transcript reads can annotate human genomes and distinguish paralogs that are over 99% identical. We show recent cases where the Iso-Seq data was instrumental in generating quality annotations for tricky genomic regions including some that for the last 20 years have remained gaps in human reference assemblies. (1-4)

We further show recent data from multiple single cell platforms where the workflows have been adapted for the PacBio platform with cell barcode and UMI information directly accessible in the long read data. This enables isoform-resolution at the single cell level and we use this to explore isoforms expressed during the human and mouse cell cycle.

References:
1. Adaptive archaic introgression of copy number variants and the discovery of previously unknown human genes.
Hsieh P et al.
Science. 2019 Oct 18;366(6463) doi: 10.1126/science.aax2083.

2. Transcriptional fates of human-specific segmental duplications in brain.
Dougherty ML, Underwood JG et al.
Genome Res. 2018 Sep 18. doi: 10.1101/gr.237610.118.

3. High-resolution comparative analysis of great ape genomes
Kronenberg ZN et al.
Science 2018, DOI: 10.1126/science.aar6343

4. The structure, function, and evolution of a complete human chromosome 8
Logsdon et al.
biorxiv DOI:10.1101/2020.09.08.285395

Keywords: transcriptomics, isoforms, single cell