TY - JOUR T1 - Proteogenomic annotation of the Chinese hamster reveals extensive novel translation events and endogenous retroviral elements JF - bioRxiv DO - 10.1101/468181 SP - 468181 AU - Shangzhong Li AU - Seong Won Cha AU - Kelly Hefner AU - Deniz Baycin Hizal AU - Michael Bowen AU - Raghothama Chaerkady AU - Robert N. Cole AU - Vijay Tejwani AU - Prashant Kaushik AU - Michael Henry AU - Paula Meleady AU - Susan T. Sharfstein AU - Michael J. Betenbaugh AU - Vineet Bafna AU - Nathan E. Lewis Y1 - 2018/01/01 UR - http://biorxiv.org/content/early/2018/11/12/468181.abstract N2 - 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. ER -