Time: 5:00 pm (UK time)/ 9:00 am (PST)
Please join us for the next seminar in this series in which you will first hear from Daniel Garalde, Market Development Manager, Oxford Nanopore Technologies Ltd., who will give an overview of the platform before we are joined by guest speakers, Susan Carpenter from the University of California Santa Cruz, and Simon Hardwick, from Weill Cornell Medicine, who will present their latest research using nanopore sequencing.
Participants of this webinar will learn about:
There will also be an opportunity to submit questions throughout the talks which will be answered in the live Q&A session following the presentations.
Please register below to attend this webinar. You will receive a confirmation of your place from events@nanoporetech.com.
Daniel Garalde, Market Development Manager, Oxford Nanopore Technologies
Daniel Garalde used nanopores to study single-molecule functional complexes of DNA polymerases in one of the pioneering nanopore research groups at University of California Santa Cruz. Daniel consulted Oxford Nanopore on strand-sequencing technology in 2010 and joined Oxford Nanopore full-time in 2011. He has driven forward-looking research projects including cDNA and Direct RNA sequencing, drawing on his experience with electrical engineering, biochemistry and nanopores. Daniel is currently supporting key customer projects and research collaborators in North America and globally.
Dr. Susan Carpenter is an Assistant Professor of MCD Biology at the University of California, Santa Cruz, USA. She graduated from Trinity College Dublin, Ireland with a Ph.D in Biochemistry and Immunology and completed a post-doc with Prof. Kate Fitzgerald at UMASS, focusing on the role of long noncoding RNA (lncRNA) in inflammatory signaling pathways. Susan then moved to UCSF where she worked on developing high throughput genomic approaches to study lncRNA important for human innate immune signaling. Dr. Carpenter’s group at UCSC continues to work on understanding the roles novel genes and their isoforms play in controlling inflammation, with the ultimate goal to identify novel drug targets leading to improved therapeutics for infections and inflammatory diseases.
Determining the layers of gene regulation within the innate immune response is critical to our understanding of the cellular responses to infection and dysregulation in disease. We identified a conserved mechanism of gene regulation in human and mouse via changes in alternative first exon (AFE) usage following inflammation, resulting in changes to isoform usage. Of these AFE events, we identified 50 unannotated transcription start sites (TSS) in mice using Oxford Nanopore native RNA sequencing, one of which is the cytosolic receptor for dsDNA and known inflammatory inducible gene, Aim2. We show that this unannotated AFE isoform of Aim2 is the predominant isoform transcribed during inflammation and contains an iron-responsive element in its 5′UTR enabling mRNA translation to be regulated by iron levels. This work highlights the importance of examining alternative isoform changes and translational regulation in the innate immune response and uncovers novel regulatory mechanisms of Aim2.
Dr. Simon Hardwick is a postdoctoral researcher at Weill Cornell Medicine in New York City. The primary focus of his research is studying RNA isoform usage and splicing in the brain, with a view to better understand neurodevelopment and neurodegeneration. His research involves a combination of new genomic technologies, including single-cell RNA-seq, long-read sequencing and targeted RNA capture, as well as the development of accompanying bioinformatic tools. He is the recipient of an Australian NHMRC Early Career Fellowship. He received his Ph.D. in Genomics from UNSW Sydney in 2018.
In this online seminar, I will start with a general overview of isoform detection with nanopore sequencing, including the potential benefits compared to short-read sequencing and some of the challenges involved. I will then present some of my recent work involving the use of nanopore isoform sequencing to profile non-coding genomic regions associated with neuropsychiatric functions in human brain samples. This work includes a detailed benchmarking of nanopore isoform sequencing using synthetic RNA controls. Finally, I will end with a discussion of some recent bioinformatic tools that have been developed for isoform detection.