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DNA methylation and temperature stress in an Antarctic polychaete, Spiophanes tcherniai.

Marsh AG, Pasqualone AA - Front Physiol (2014)

Bottom Line: In comparing these aligned sites between treatments, only 3000 (11%) evidenced a change in methylation state, but over 85% of changes involved a gain of a 5-methyl group on a CpG site (net increase in methyation).The ability to score CpG sites as partially methylated among gDNA copies in a sample opens up a new avenue for assessing DNA methylation responses to changing environments.By quantitatively distinguishing a "mixed" population of copies of one CpG site, we can begin to identify dynamic, non-binary, continuous-response reactions in DNA methylation intensity or density that previously may have been overlooked as noise.

View Article: PubMed Central - PubMed

Affiliation: Center for Bioinformatics and Computational Biology, School of Marine Science and Policy, University of Delaware Lewes, DE, USA.

ABSTRACT
Epigenetic modifications of DNA and histones are a primary mechanism by which gene expression activities may be modified in response to environmental stimuli. Here we characterize patterns of methyl-cytosine composition in the marine polychaete Spiophanes tcherniai from McMurdo Sound, Antarctica. We cultured adult worms at two temperatures, -1.5°C (ambient control) and +4°C (warm treatment), for 4 weeks. We observed a rapid capacity for S. tcherniai organismal respiration rates and underlying catalytic rates of citrate synthase at +4°C to return to control levels in less than 4 weeks. We profiled changes in the methylation states of CpG sites in these treatments using an NGS strategy to computationally reconstruct and quantify methylation status across the genome. In our analysis we recovered 120,000 CpG sites in assembled contigs from both treatments. Of those, we were able to align 28,000 CpG sites in common between the two sample groups. In comparing these aligned sites between treatments, only 3000 (11%) evidenced a change in methylation state, but over 85% of changes involved a gain of a 5-methyl group on a CpG site (net increase in methyation). The ability to score CpG sites as partially methylated among gDNA copies in a sample opens up a new avenue for assessing DNA methylation responses to changing environments. By quantitatively distinguishing a "mixed" population of copies of one CpG site, we can begin to identify dynamic, non-binary, continuous-response reactions in DNA methylation intensity or density that previously may have been overlooked as noise.

No MeSH data available.


Total methylation dynamics. Data for each CpG site in Figures 3, 4 are now linked by a line and separated into six shifts (each panel) to reveal the pattern of shifts identified in the experiment. Each point on the plot represents a single CpG site that has evidenced a change in methylation state during the experiment (n = 3067 matched CpG sites). The circle symbols plot the quantitative state in the +4°C treatment while the line extending from each circle connects to the methylation state of the same CpG site in the comparative −1.5°C control treatment.
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Figure 5: Total methylation dynamics. Data for each CpG site in Figures 3, 4 are now linked by a line and separated into six shifts (each panel) to reveal the pattern of shifts identified in the experiment. Each point on the plot represents a single CpG site that has evidenced a change in methylation state during the experiment (n = 3067 matched CpG sites). The circle symbols plot the quantitative state in the +4°C treatment while the line extending from each circle connects to the methylation state of the same CpG site in the comparative −1.5°C control treatment.

Mentions: If one were to overlay the two Figures 3, 4 and draw lines to connect the same CpG site in both treatments, the comparative idea would be clear, but the resulting graph would be indecipherable. In Figure 5, this idea of overlaying the +4°C and −1.5°C data with a line for each CpG site connecting its methylation state in each treatment has been simplified by pulling the data apart into six panels, one for each potential shift. These shifts are (read x-to-y): MET:MIX (partial methylation loss), MET:UMT (full methylation loss), MIX:MET (partial methylation gain), MIX:UMT (partial methylation loss), UMT:MET (full methylation gain), UMT:MIX (partial methylation gain).


DNA methylation and temperature stress in an Antarctic polychaete, Spiophanes tcherniai.

Marsh AG, Pasqualone AA - Front Physiol (2014)

Total methylation dynamics. Data for each CpG site in Figures 3, 4 are now linked by a line and separated into six shifts (each panel) to reveal the pattern of shifts identified in the experiment. Each point on the plot represents a single CpG site that has evidenced a change in methylation state during the experiment (n = 3067 matched CpG sites). The circle symbols plot the quantitative state in the +4°C treatment while the line extending from each circle connects to the methylation state of the same CpG site in the comparative −1.5°C control treatment.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4017131&req=5

Figure 5: Total methylation dynamics. Data for each CpG site in Figures 3, 4 are now linked by a line and separated into six shifts (each panel) to reveal the pattern of shifts identified in the experiment. Each point on the plot represents a single CpG site that has evidenced a change in methylation state during the experiment (n = 3067 matched CpG sites). The circle symbols plot the quantitative state in the +4°C treatment while the line extending from each circle connects to the methylation state of the same CpG site in the comparative −1.5°C control treatment.
Mentions: If one were to overlay the two Figures 3, 4 and draw lines to connect the same CpG site in both treatments, the comparative idea would be clear, but the resulting graph would be indecipherable. In Figure 5, this idea of overlaying the +4°C and −1.5°C data with a line for each CpG site connecting its methylation state in each treatment has been simplified by pulling the data apart into six panels, one for each potential shift. These shifts are (read x-to-y): MET:MIX (partial methylation loss), MET:UMT (full methylation loss), MIX:MET (partial methylation gain), MIX:UMT (partial methylation loss), UMT:MET (full methylation gain), UMT:MIX (partial methylation gain).

Bottom Line: In comparing these aligned sites between treatments, only 3000 (11%) evidenced a change in methylation state, but over 85% of changes involved a gain of a 5-methyl group on a CpG site (net increase in methyation).The ability to score CpG sites as partially methylated among gDNA copies in a sample opens up a new avenue for assessing DNA methylation responses to changing environments.By quantitatively distinguishing a "mixed" population of copies of one CpG site, we can begin to identify dynamic, non-binary, continuous-response reactions in DNA methylation intensity or density that previously may have been overlooked as noise.

View Article: PubMed Central - PubMed

Affiliation: Center for Bioinformatics and Computational Biology, School of Marine Science and Policy, University of Delaware Lewes, DE, USA.

ABSTRACT
Epigenetic modifications of DNA and histones are a primary mechanism by which gene expression activities may be modified in response to environmental stimuli. Here we characterize patterns of methyl-cytosine composition in the marine polychaete Spiophanes tcherniai from McMurdo Sound, Antarctica. We cultured adult worms at two temperatures, -1.5°C (ambient control) and +4°C (warm treatment), for 4 weeks. We observed a rapid capacity for S. tcherniai organismal respiration rates and underlying catalytic rates of citrate synthase at +4°C to return to control levels in less than 4 weeks. We profiled changes in the methylation states of CpG sites in these treatments using an NGS strategy to computationally reconstruct and quantify methylation status across the genome. In our analysis we recovered 120,000 CpG sites in assembled contigs from both treatments. Of those, we were able to align 28,000 CpG sites in common between the two sample groups. In comparing these aligned sites between treatments, only 3000 (11%) evidenced a change in methylation state, but over 85% of changes involved a gain of a 5-methyl group on a CpG site (net increase in methyation). The ability to score CpG sites as partially methylated among gDNA copies in a sample opens up a new avenue for assessing DNA methylation responses to changing environments. By quantitatively distinguishing a "mixed" population of copies of one CpG site, we can begin to identify dynamic, non-binary, continuous-response reactions in DNA methylation intensity or density that previously may have been overlooked as noise.

No MeSH data available.