MENU

A Chinese hamster transcription start site atlas that enables targeted editing of CHO cells

Presented at: Bioprocessing 2021
C.E. Credits: P.A.C.E. CE Florida CE
Speaker
  • PhD Candidate, Bioinformatics & Systems Biology, University of California, San Diego
    Biography

      I am a 5th year PhD candidate in the Bioinformatics & Systems Biology program at UC San Diego with Dr. Nathan Lewis as my advisor. I received a B.S in Biology with a minor in computational neuroscience at Carnegie Mellon University, working on mu-opioid receptor recycling in Dr. Manoj Puthenveedu's lab. I then worked in Dr. Eric Halgren's lab, using ECog data to understand spatiotemporal patterns in sleep and memory. In the Lewis lab, my dissertation examines different points in the lifecycle of biopharmaceuticals, from production to application, using next-generation sequencing technology. My first project-the topic of my talk today- improves the resolution of the transcription start sites (TSSs) in the Chinese Hamster using comprehensive multi-omics across various tissues. This elucidated regulatory regions such as the TATA box and initiator element, enabled CRISPR activation for the Mgat3 gene, and provided a valuable resource for the CHO community. My second focus is on the application of a novel immuno-therapeutic to the clonal makeup of the hematopoietic CD34+ stem and progenitor cell population. Using a recently published single-cell mitochondrial ATAC-seq methodology for lineage tracing, we tracked clonal population expansions and regressions. I am very interested in genetic engineering in combination with sequencing and modeling techniques, and hope to incorporate these techniques to developing and understanding novel therapeutics.


    Abstract

    Chinese hamster ovary (CHO) cells are the most widely used cells for producing biopharmaceuticals. Engineering gene expression in CHO is key to improving drug quality and affordability. However, engineering gene expression or activating silent genes requires accurate annotation of the underlying regulatory elements and transcription start sites (TSSs). Unfortunately, most TSSs in the Chinese hamster genome were computationally predicted and are frequently inaccurate. Here, we revised TSS annotations for 15,308 Chinese hamster genes and 4,478 non-coding RNAs based on experimental data from CHO-K1 cells and 10 hamster tissues. The experimental realignment and discovery of TSSs now expose previously hidden motifs, such as the TATA box. We further demonstrate, by targeting the glycosyltransferase gene Mgat3, how accurate annotations readily facilitate activating silent genes by CRISPRa to obtain more human-like glycosylation. Together, we envision our annotation and data will provide a rich resource for the CHO community, improve genome engineering efforts and aid comparative and evolutionary studies.

    Learning Objectives:

    1. The mapping of TSSs in Chinese Hamster Ovary cells is improved using nascent capped-RNA sequencing methods combined with samples across multiple hamster tissues.

    2. The experimental TSSs is used for CRISPR activation of the silenced protein Mgat3 in the Chinese Hamster.


    Show Resources
    You May Also Like
    OCT 29, 2020 6:00 AM PDT
    C.E. CREDITS
    OCT 29, 2020 6:00 AM PDT
    Date: October 29, 2020 Time: 6:00am (PDT), 9:00am (EDT), Chronic inflammation can occur as a result of a combination of genetic predispositions and environmental factors. Epigenetic modifica...
    FEB 24, 2021 10:00 AM PST
    C.E. CREDITS
    FEB 24, 2021 10:00 AM PST
    DATE: February 24, 2021 TIME: 10am PST Automated lab instruments such as liquid handlers and cell sorters are increasingly common in all types of laboratories, driving fast results for labor...
    NOV 16, 2020 8:00 AM PST
    C.E. CREDITS
    NOV 16, 2020 8:00 AM PST
    Date: November 16, 2020 Time: 8:00am (PST), 11:00am (EST) CRISPR screening has become the prime discovery tool in modern biomedical research and drug discovery. At the same time, most screen...
    DEC 03, 2020 4:30 PM PST
    C.E. CREDITS
    DEC 03, 2020 4:30 PM PST
    This drug development program is designed to create a family of broad-spectrum, pan-coronaviral drugs that respectively inhibit multiple key enzymes required for viral replication. By target...
    MAR 16, 2021 10:00 AM PDT
    C.E. CREDITS
    MAR 16, 2021 10:00 AM PDT
    Date: March 16, 2021 Time: 10:00am (PST) Scientific progress and breakthroughs today are often too expensive for most institutions to acquire. Each year, the National Institutes of Health (N...
    NOV 18, 2020 8:00 AM PST
    C.E. CREDITS
    NOV 18, 2020 8:00 AM PST
    DATE: November 18, 2020 TIME: 08:00am PDT We develop and implement technologies to solve some of the major bottlenecks in biomedical research. In particular, we establish new imaging approac...
    Loading Comments...
    Show Resources
    Attendees
    • See more