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LINE-1 and Alu retrotransposition exhibit clonal variation.

Streva VA, Faber ZJ, Deininger PL - Mob DNA (2013)

Bottom Line: Observations of the variability of LINE-1 and Alu retrotransposition in different populations of the same cell line are supported by our results that indicate in some cell types, individual cell clones can have dramatically differing capacity for retrotransposition.The mixed populations of cells commonly used in laboratories have often been passaged for many generations and accumulated significant genetic and epigenetic diversity.Our results suggest that the clonal variability observed by our cloning experiments may lead to a homogenization of retrotransposition capacity, with the resulting mixed population of cells being composed of individual variants having either increased or decreased retrotransposition potential compared to the starting population.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Epidemiology, Tulane Cancer Center, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112, USA. pdeinin@tulane.edu.

ABSTRACT

Background: The non-long terminal repeat (non-LTR) retrotransposons, long interspersed element-1 (LINE-1) and Alu are currently active retroelements in humans. We, and others, have observed that different populations of HeLa cells from different laboratories support retrotransposition of LINE-1 and Alu to varying degrees. We therefore tested whether individual cell clones of HeLa and HCT116 cell lines supported different levels of LINE-1 and Alu retrotransposition, and whether these variations were stable upon re-cloning.

Findings: Standard retrotransposition tissue culture assays were used to measure a cell's ability to support LINE-1 and Alu retrotransposition in clonal HeLa and HCT116 cell lines. We observed that both LINE-1 and Alu retrotransposition exhibited clonal variation in HeLa cells, with certain HeLa cell clones supporting high levels of LINE-1 and Alu retrotransposition and other cell clones being essentially retrotransposition-dead. This clonal variation was similarly observed in HCT116 cells, although possibly not to the same extent. These patterns of clonal variation are relatively consistent upon re-cloning.

Conclusions: Observations of the variability of LINE-1 and Alu retrotransposition in different populations of the same cell line are supported by our results that indicate in some cell types, individual cell clones can have dramatically differing capacity for retrotransposition. The mixed populations of cells commonly used in laboratories have often been passaged for many generations and accumulated significant genetic and epigenetic diversity. Our results suggest that the clonal variability observed by our cloning experiments may lead to a homogenization of retrotransposition capacity, with the resulting mixed population of cells being composed of individual variants having either increased or decreased retrotransposition potential compared to the starting population.

No MeSH data available.


LINE-1 and Alu exhibit clonal variation. (A) LINE-1 retrotransposition assays were performed in eight individual HeLa cell clones and parental HeLa population. Different HeLa clones exhibit different potential for LINE-1 retrotransposition, with HeLa clone 1 exhibiting a 140-fold reduction in LINE-1 retrotransposition rate compared to HeLa clone 7. (B) Alu retrotransposition assays were performed in HeLa cell clones and parental HeLa. Differences in Alu retrotransposition between the two HeLa clones were even greater than those observed for LINE-1, with a 252-fold reduction in Alu retrotransposition in HeLa clone 1 compared to HeLa clone 7. (C) LINE-1 retrotransposition assays were also preformed in HCT116 cell clones to examine whether the effect seen in HeLa also occurred in HCT116 cells. The LINE-1 retrotransposition clonal variation was not observed in five HCT116 cell clones. (D) Alu retrotransposition assays were tested in seven HCT116 cell clones and parental HCT116 cell population and no significant differences in rates of Alu retrotransposition were observed between HCT116 clones. Error bars represent SEM. Sample size is four independent experiments (independent transfections) each performed in triplicate (n = 12). Asterisks indicate statistical significance from the parental population of at least P <0.05 by one-way ANOVA with Tukey’s post-test. LINE-1, long interspersed element-1; SEM, standard error of the mean.
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Figure 1: LINE-1 and Alu exhibit clonal variation. (A) LINE-1 retrotransposition assays were performed in eight individual HeLa cell clones and parental HeLa population. Different HeLa clones exhibit different potential for LINE-1 retrotransposition, with HeLa clone 1 exhibiting a 140-fold reduction in LINE-1 retrotransposition rate compared to HeLa clone 7. (B) Alu retrotransposition assays were performed in HeLa cell clones and parental HeLa. Differences in Alu retrotransposition between the two HeLa clones were even greater than those observed for LINE-1, with a 252-fold reduction in Alu retrotransposition in HeLa clone 1 compared to HeLa clone 7. (C) LINE-1 retrotransposition assays were also preformed in HCT116 cell clones to examine whether the effect seen in HeLa also occurred in HCT116 cells. The LINE-1 retrotransposition clonal variation was not observed in five HCT116 cell clones. (D) Alu retrotransposition assays were tested in seven HCT116 cell clones and parental HCT116 cell population and no significant differences in rates of Alu retrotransposition were observed between HCT116 clones. Error bars represent SEM. Sample size is four independent experiments (independent transfections) each performed in triplicate (n = 12). Asterisks indicate statistical significance from the parental population of at least P <0.05 by one-way ANOVA with Tukey’s post-test. LINE-1, long interspersed element-1; SEM, standard error of the mean.

Mentions: Because many cancer cell lines have relatively unstable genomes, we hypothesized that their genome variation could lead to altered abilities to support retrotransposition. To determine whether there was clonal variability in the potential for HeLa clones to support LINE-1 retrotransposition, we performed LINE-1 retrotransposition assays using eight individual HeLa cell clones and the parental population of HeLa from which they originated. The results of the LINE-1 retrotransposition assays in HeLa clones confirm that some cell clones are nearly incapable of supporting LINE-1 retrotransposition (HeLa clone 1), while other cell clones are particularly amenable to LINE-1 retrotransposition events (HeLa clone 7). LINE-1 retrotransposition rates in HeLa clone 7 (mean = 699 colonies) were significantly increased compared to those in HeLa clone 1 (mean = 5 colonies) (Figure 1A). Both HeLa clone 1 and HeLa clone 7 differ significantly from the parental HeLa population in their ability to undergo LINE-1 retrotransposition, with the parental population showing a level of LINE-1 retrotransposition intermediate between the two clones (Figure 1A). Representative flask images for HeLa clones are shown in Additional file 1: Figure S1A,B.


LINE-1 and Alu retrotransposition exhibit clonal variation.

Streva VA, Faber ZJ, Deininger PL - Mob DNA (2013)

LINE-1 and Alu exhibit clonal variation. (A) LINE-1 retrotransposition assays were performed in eight individual HeLa cell clones and parental HeLa population. Different HeLa clones exhibit different potential for LINE-1 retrotransposition, with HeLa clone 1 exhibiting a 140-fold reduction in LINE-1 retrotransposition rate compared to HeLa clone 7. (B) Alu retrotransposition assays were performed in HeLa cell clones and parental HeLa. Differences in Alu retrotransposition between the two HeLa clones were even greater than those observed for LINE-1, with a 252-fold reduction in Alu retrotransposition in HeLa clone 1 compared to HeLa clone 7. (C) LINE-1 retrotransposition assays were also preformed in HCT116 cell clones to examine whether the effect seen in HeLa also occurred in HCT116 cells. The LINE-1 retrotransposition clonal variation was not observed in five HCT116 cell clones. (D) Alu retrotransposition assays were tested in seven HCT116 cell clones and parental HCT116 cell population and no significant differences in rates of Alu retrotransposition were observed between HCT116 clones. Error bars represent SEM. Sample size is four independent experiments (independent transfections) each performed in triplicate (n = 12). Asterisks indicate statistical significance from the parental population of at least P <0.05 by one-way ANOVA with Tukey’s post-test. LINE-1, long interspersed element-1; SEM, standard error of the mean.
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Figure 1: LINE-1 and Alu exhibit clonal variation. (A) LINE-1 retrotransposition assays were performed in eight individual HeLa cell clones and parental HeLa population. Different HeLa clones exhibit different potential for LINE-1 retrotransposition, with HeLa clone 1 exhibiting a 140-fold reduction in LINE-1 retrotransposition rate compared to HeLa clone 7. (B) Alu retrotransposition assays were performed in HeLa cell clones and parental HeLa. Differences in Alu retrotransposition between the two HeLa clones were even greater than those observed for LINE-1, with a 252-fold reduction in Alu retrotransposition in HeLa clone 1 compared to HeLa clone 7. (C) LINE-1 retrotransposition assays were also preformed in HCT116 cell clones to examine whether the effect seen in HeLa also occurred in HCT116 cells. The LINE-1 retrotransposition clonal variation was not observed in five HCT116 cell clones. (D) Alu retrotransposition assays were tested in seven HCT116 cell clones and parental HCT116 cell population and no significant differences in rates of Alu retrotransposition were observed between HCT116 clones. Error bars represent SEM. Sample size is four independent experiments (independent transfections) each performed in triplicate (n = 12). Asterisks indicate statistical significance from the parental population of at least P <0.05 by one-way ANOVA with Tukey’s post-test. LINE-1, long interspersed element-1; SEM, standard error of the mean.
Mentions: Because many cancer cell lines have relatively unstable genomes, we hypothesized that their genome variation could lead to altered abilities to support retrotransposition. To determine whether there was clonal variability in the potential for HeLa clones to support LINE-1 retrotransposition, we performed LINE-1 retrotransposition assays using eight individual HeLa cell clones and the parental population of HeLa from which they originated. The results of the LINE-1 retrotransposition assays in HeLa clones confirm that some cell clones are nearly incapable of supporting LINE-1 retrotransposition (HeLa clone 1), while other cell clones are particularly amenable to LINE-1 retrotransposition events (HeLa clone 7). LINE-1 retrotransposition rates in HeLa clone 7 (mean = 699 colonies) were significantly increased compared to those in HeLa clone 1 (mean = 5 colonies) (Figure 1A). Both HeLa clone 1 and HeLa clone 7 differ significantly from the parental HeLa population in their ability to undergo LINE-1 retrotransposition, with the parental population showing a level of LINE-1 retrotransposition intermediate between the two clones (Figure 1A). Representative flask images for HeLa clones are shown in Additional file 1: Figure S1A,B.

Bottom Line: Observations of the variability of LINE-1 and Alu retrotransposition in different populations of the same cell line are supported by our results that indicate in some cell types, individual cell clones can have dramatically differing capacity for retrotransposition.The mixed populations of cells commonly used in laboratories have often been passaged for many generations and accumulated significant genetic and epigenetic diversity.Our results suggest that the clonal variability observed by our cloning experiments may lead to a homogenization of retrotransposition capacity, with the resulting mixed population of cells being composed of individual variants having either increased or decreased retrotransposition potential compared to the starting population.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Epidemiology, Tulane Cancer Center, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112, USA. pdeinin@tulane.edu.

ABSTRACT

Background: The non-long terminal repeat (non-LTR) retrotransposons, long interspersed element-1 (LINE-1) and Alu are currently active retroelements in humans. We, and others, have observed that different populations of HeLa cells from different laboratories support retrotransposition of LINE-1 and Alu to varying degrees. We therefore tested whether individual cell clones of HeLa and HCT116 cell lines supported different levels of LINE-1 and Alu retrotransposition, and whether these variations were stable upon re-cloning.

Findings: Standard retrotransposition tissue culture assays were used to measure a cell's ability to support LINE-1 and Alu retrotransposition in clonal HeLa and HCT116 cell lines. We observed that both LINE-1 and Alu retrotransposition exhibited clonal variation in HeLa cells, with certain HeLa cell clones supporting high levels of LINE-1 and Alu retrotransposition and other cell clones being essentially retrotransposition-dead. This clonal variation was similarly observed in HCT116 cells, although possibly not to the same extent. These patterns of clonal variation are relatively consistent upon re-cloning.

Conclusions: Observations of the variability of LINE-1 and Alu retrotransposition in different populations of the same cell line are supported by our results that indicate in some cell types, individual cell clones can have dramatically differing capacity for retrotransposition. The mixed populations of cells commonly used in laboratories have often been passaged for many generations and accumulated significant genetic and epigenetic diversity. Our results suggest that the clonal variability observed by our cloning experiments may lead to a homogenization of retrotransposition capacity, with the resulting mixed population of cells being composed of individual variants having either increased or decreased retrotransposition potential compared to the starting population.

No MeSH data available.