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The genome landscape of the african green monkey kidney-derived vero cell line.

Osada N, Kohara A, Yamaji T, Hirayama N, Kasai F, Sekizuka T, Kuroda M, Hanada K - DNA Res. (2014)

Bottom Line: In addition, an ∼59-Mb loss of heterozygosity around this deleted region suggested that the homozygosity of the deletion was established by a large-scale conversion.Moreover, a genomic analysis of Vero cells revealed a female Chlorocebus sabaeus origin and proviral variations of the endogenous simian type D retrovirus.These results revealed the genomic basis for the non-tumourigenic permanent Vero cell lineage susceptible to various pathogens and will be useful for generating new sub-lines and developing new tools in the quality control of Vero cells.

View Article: PubMed Central - PubMed

Affiliation: Division of Evolutionary Genetics, Department of Population Genetics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.

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Characterization of proviral SRV sequences. DNA-seq short read mapping to the complete SRV-Vero genome sequence. Read depth and mismatch nucleotides are shown in the following colours (Depth: light grey, A: light green, T: red, G: orange, C: dark blue). The high variability of SRV sequences was rarely detected in the 7525–7883 nt region, whereas high variability was observed throughout other regions.
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DSU029F4: Characterization of proviral SRV sequences. DNA-seq short read mapping to the complete SRV-Vero genome sequence. Read depth and mismatch nucleotides are shown in the following colours (Depth: light grey, A: light green, T: red, G: orange, C: dark blue). The high variability of SRV sequences was rarely detected in the 7525–7883 nt region, whereas high variability was observed throughout other regions.

Mentions: Analysis of collected SRV-related short reads from all paired-end short reads of the Vero JCRB0111 cell line, followed by analyses of gene assignment and long terminal repeat (LTR) finding, identified the 8,367 bp complete SRV genome sequence. The medians of variant frequencies were 25.5 and 8.0% in the highly variable and env-deleted region (nucleotide position 7525–7829) of SRV, respectively (Fig. 4). The copy number of SRV with 8.4-kb full length was estimated to be 30%, while that of SRV with the deletion of the 7525–7883 nucleotide (nt) region encompassing the C-terminal part in env and a portion of LTR was 70%. The SRV-Vero of JCRB0111 had 97% of the same nucleotides as those of ATCC CCL81 (Genbank_ID: JN134185). The number of minor alleles was 703 for SNVs and 1 for the insertion among the whole complete consensus SRV sequence in the Vero JCRB0111 genome. Four minor mutation sites caused three nonsense mutations and one frameshift on the pol or env region (Supplementary Table S5). Previous studies suggested a frameshift mutation in pol (position 3726) or frameshift mutation in prt (its position was not reported) on the SRV proviral sequences of Vero E6 or ATCC CCL81 cells.46,47 However, our study did not detect equivalent mutations on the SRV proviral sequences of Vero JCRB0111 cells; however, other notable mutations were instead detected (Supplementary Table S5).Figure 4.


The genome landscape of the african green monkey kidney-derived vero cell line.

Osada N, Kohara A, Yamaji T, Hirayama N, Kasai F, Sekizuka T, Kuroda M, Hanada K - DNA Res. (2014)

Characterization of proviral SRV sequences. DNA-seq short read mapping to the complete SRV-Vero genome sequence. Read depth and mismatch nucleotides are shown in the following colours (Depth: light grey, A: light green, T: red, G: orange, C: dark blue). The high variability of SRV sequences was rarely detected in the 7525–7883 nt region, whereas high variability was observed throughout other regions.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4263300&req=5

DSU029F4: Characterization of proviral SRV sequences. DNA-seq short read mapping to the complete SRV-Vero genome sequence. Read depth and mismatch nucleotides are shown in the following colours (Depth: light grey, A: light green, T: red, G: orange, C: dark blue). The high variability of SRV sequences was rarely detected in the 7525–7883 nt region, whereas high variability was observed throughout other regions.
Mentions: Analysis of collected SRV-related short reads from all paired-end short reads of the Vero JCRB0111 cell line, followed by analyses of gene assignment and long terminal repeat (LTR) finding, identified the 8,367 bp complete SRV genome sequence. The medians of variant frequencies were 25.5 and 8.0% in the highly variable and env-deleted region (nucleotide position 7525–7829) of SRV, respectively (Fig. 4). The copy number of SRV with 8.4-kb full length was estimated to be 30%, while that of SRV with the deletion of the 7525–7883 nucleotide (nt) region encompassing the C-terminal part in env and a portion of LTR was 70%. The SRV-Vero of JCRB0111 had 97% of the same nucleotides as those of ATCC CCL81 (Genbank_ID: JN134185). The number of minor alleles was 703 for SNVs and 1 for the insertion among the whole complete consensus SRV sequence in the Vero JCRB0111 genome. Four minor mutation sites caused three nonsense mutations and one frameshift on the pol or env region (Supplementary Table S5). Previous studies suggested a frameshift mutation in pol (position 3726) or frameshift mutation in prt (its position was not reported) on the SRV proviral sequences of Vero E6 or ATCC CCL81 cells.46,47 However, our study did not detect equivalent mutations on the SRV proviral sequences of Vero JCRB0111 cells; however, other notable mutations were instead detected (Supplementary Table S5).Figure 4.

Bottom Line: In addition, an ∼59-Mb loss of heterozygosity around this deleted region suggested that the homozygosity of the deletion was established by a large-scale conversion.Moreover, a genomic analysis of Vero cells revealed a female Chlorocebus sabaeus origin and proviral variations of the endogenous simian type D retrovirus.These results revealed the genomic basis for the non-tumourigenic permanent Vero cell lineage susceptible to various pathogens and will be useful for generating new sub-lines and developing new tools in the quality control of Vero cells.

View Article: PubMed Central - PubMed

Affiliation: Division of Evolutionary Genetics, Department of Population Genetics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.

Show MeSH