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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.


Distributions of the magnitude of the methylation changes for each CpG site divided into gain and loss components.
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Figure 6: Distributions of the magnitude of the methylation changes for each CpG site divided into gain and loss components.

Mentions: The length of the lines plotted for each CpG site in Figure 5 are essentially a representation of the magnitude of a methylation change across all copies of a CpG site in a sample. In Figure 6, frequency distribution plots are shown for these magnitude vectors divided into “Gain” and “Loss” processes. Overall, there is a striking difference in the “Gain” and “Loss” distributions in terms of both the numerical number of events and their magnitude. The observed counts here reveal the degree to which points and lines are plotted over one another in Figures 3, 4, and 5. The “Gain” distribution is clearly bimodal as a result of the strong Full methylation increases (Figure 5, panel UMT:MET) and the strong Partial methylation increases (Figure 5, panel MIX:MET).


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

Marsh AG, Pasqualone AA - Front Physiol (2014)

Distributions of the magnitude of the methylation changes for each CpG site divided into gain and loss components.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 6: Distributions of the magnitude of the methylation changes for each CpG site divided into gain and loss components.
Mentions: The length of the lines plotted for each CpG site in Figure 5 are essentially a representation of the magnitude of a methylation change across all copies of a CpG site in a sample. In Figure 6, frequency distribution plots are shown for these magnitude vectors divided into “Gain” and “Loss” processes. Overall, there is a striking difference in the “Gain” and “Loss” distributions in terms of both the numerical number of events and their magnitude. The observed counts here reveal the degree to which points and lines are plotted over one another in Figures 3, 4, and 5. The “Gain” distribution is clearly bimodal as a result of the strong Full methylation increases (Figure 5, panel UMT:MET) and the strong Partial methylation increases (Figure 5, panel MIX:MET).

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.