RT Journal Article
SR Electronic
T1 Proteogenomic annotation of the Chinese hamster reveals extensive novel translation events and endogenous retroviral elements
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 468181
DO 10.1101/468181
A1 Shangzhong Li
A1 Seong Won Cha
A1 Kelly Hefner
A1 Deniz Baycin Hizal
A1 Michael Bowen
A1 Raghothama Chaerkady
A1 Robert N. Cole
A1 Vijay Tejwani
A1 Prashant Kaushik
A1 Michael Henry
A1 Paula Meleady
A1 Susan T. Sharfstein
A1 Michael J. Betenbaugh
A1 Vineet Bafna
A1 Nathan E. Lewis
YR 2018
UL http://biorxiv.org/content/early/2018/11/12/468181.abstract
AB A high quality genome annotation greatly facilitates successful cell line engineering. Standard draft genome annotation pipelines are based largely on de novo gene prediction, homology, and RNA-Seq data. However, draft annotations can suffer from incorrectly predictions of translated sequence, incorrect splice isoforms and missing genes. Here we generated a draft annotation for the newly assembled Chinese hamster genome and used RNA-Seq, proteomics, and Ribo-Seq to experimentally annotate the genome. We identified 4,333 new proteins compared to the hamster RefSeq protein annotation and 2,503 novel translational events (e.g., alternative splices, mutations, novel splices). Finally, we used this pipeline to identify the source of translated retroviruses contaminating recombinant products from Chinese hamster ovary (CHO) cell lines, including 131 type-C retroviruses, thus enabling future efforts to eliminate retroviruses by reducing the costs incurred with retroviral particle clearance. In summary, the improved annotation provides a more accurate platform for guiding CHO cell line engineering, including facilitating the interpretation of omics data, defining of cellular pathways, and engineering of complex phenotypes.