TY - JOUR
T1 - Proteogenomic Annotation of Chinese Hamsters Reveals Extensive Novel Translation Events and Endogenous Retroviral Elements
AU - Li, Shangzhong
AU - Cha, Seong Won
AU - Heffner, Kelly
AU - Hizal, Deniz Baycin
AU - Bowen, Michael A.
AU - Chaerkady, Raghothama
AU - Cole, Robert N.
AU - Tejwani, Vijay
AU - Kaushik, Prashant
AU - Henry, Michael
AU - Meleady, Paula
AU - Sharfstein, Susan T.
AU - Betenbaugh, Michael J.
AU - Bafna, Vineet
AU - Lewis, Nathan E.
N1 - Publisher Copyright:
© 2019 American Chemical Society.
PY - 2019/6/7
Y1 - 2019/6/7
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 incorrect predictions of translated sequence, inaccurate 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 3529 new proteins compared to the hamster RefSeq protein annotation and 2256 novel translational events (e.g., alternative splices, mutations, and 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 119 type-C retroviruses, thus enabling future efforts to eliminate retroviruses to reduce the costs incurred with retroviral particle clearance. In summary, the improved annotation provides a more accurate resource for CHO cell line engineering, by facilitating the interpretation of omics data, defining of cellular pathways, and engineering of complex phenotypes.
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 incorrect predictions of translated sequence, inaccurate 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 3529 new proteins compared to the hamster RefSeq protein annotation and 2256 novel translational events (e.g., alternative splices, mutations, and 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 119 type-C retroviruses, thus enabling future efforts to eliminate retroviruses to reduce the costs incurred with retroviral particle clearance. In summary, the improved annotation provides a more accurate resource for CHO cell line engineering, by facilitating the interpretation of omics data, defining of cellular pathways, and engineering of complex phenotypes.
KW - Chinese hamster
KW - endogenous retrovirus
KW - genome annotation
KW - proteogenomics
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U2 - 10.1021/acs.jproteome.8b00935
DO - 10.1021/acs.jproteome.8b00935
M3 - Article
C2 - 31020842
AN - SCOPUS:85066882061
SN - 1535-3893
VL - 18
SP - 2433
EP - 2445
JO - Journal of proteome research
JF - Journal of proteome research
IS - 6
ER -