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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.


Spiophanes tcherniai maximum catalytic rates of citrate synthase normalized to protein mass in worms maintained for 4 weeks at −1.5°C and +4°C.
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Figure 2: Spiophanes tcherniai maximum catalytic rates of citrate synthase normalized to protein mass in worms maintained for 4 weeks at −1.5°C and +4°C.

Mentions: The maximum specific activity for citrate synthase (CS) reveals a wide inter-individual variance at the onset of the experiment. Within the first 2 weeks of culturing, this variance decreases (Figure 2). There is a noticeable decrease in the mean citrate Vmax at day 14 in the −1.5°C control cultures, in contrast to a maintenance of the same mean levels between day 0 and 14 in the +4°C cultures. This represents a temporal pattern in shifting means and variances suggestive of a temperature induced response between −1.5°C and +4°C cultures on day 14. However, CS Vmax treatment means were not statistically different at day 28 (ANOVA, n = 29).


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

Marsh AG, Pasqualone AA - Front Physiol (2014)

Spiophanes tcherniai maximum catalytic rates of citrate synthase normalized to protein mass in worms maintained for 4 weeks at −1.5°C and +4°C.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Spiophanes tcherniai maximum catalytic rates of citrate synthase normalized to protein mass in worms maintained for 4 weeks at −1.5°C and +4°C.
Mentions: The maximum specific activity for citrate synthase (CS) reveals a wide inter-individual variance at the onset of the experiment. Within the first 2 weeks of culturing, this variance decreases (Figure 2). There is a noticeable decrease in the mean citrate Vmax at day 14 in the −1.5°C control cultures, in contrast to a maintenance of the same mean levels between day 0 and 14 in the +4°C cultures. This represents a temporal pattern in shifting means and variances suggestive of a temperature induced response between −1.5°C and +4°C cultures on day 14. However, CS Vmax treatment means were not statistically different at day 28 (ANOVA, n = 29).

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.