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Studying Promoter and Isoform Diversity with Long-Read Transcriptome Sequencing

C.E. Credits: P.A.C.E. CE Florida CE
Speaker
  • Group leader, Genome Institute of Singapore
    Biography

      Dr. Jonathan Göke is a group leader at the Genome Institute of Singapore. Jonathan's research focuses on computational transcriptomics with a particular interest in third generation RNA-Sequencing and computational methods development. He received his PhD in Computational Biology from the Max Planck Institute for Molecular Genetics in Berlin (Germany). His team has contributed to the Pan-Cancer-Analysis-of-Whole-Genomes consortium (PCAWG) and won the DREAM challenge to predict high risk Multiple Myeloma patients. You can find out more about his research, team, and methods under http://www.jglab.org and https://github.com/GoekeLab


    Abstract

    Most human protein-coding genes are regulated by multiple, distinct promoters, suggesting that the choice of promoter is as important as its level of transcriptional activity. While the role of promoters as driver elements in cancer has been recognized, the contribution of alternative promoters to regulation of the cancer transcriptome remains largely unexplored. Here I will present how active promoters can be identified using RNA-Seq data, enabling the analysis of promoter activity in more than 18,000 samples. In order to study novel promoters, we generated long read RNA-Seq data in 10 different gastric cancer cell lines. Our results show that alternative promoters are frequently used, that they are predictive of patient survival, and that promoters are a major contribution to the diversity of isoforms in cancer.

    Learning Objectives:

    1. Learn about alternative promoters and their role in cancer

    2. Learn how long read RNA-Seq helps to study the transcriptome


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