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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 oxygen consumption rates normalized to DNA mass in maintained for 4 weeks at −1.5C°C and +4°C.
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Figure 1: Spiophanes tcherniai oxygen consumption rates normalized to DNA mass in maintained for 4 weeks at −1.5C°C and +4°C.

Mentions: Field collection of adult worms requires scooping sediment up into buckets while SCUBA diving, returning the buckets to the lab, sieving the sediment to isolate adult worm tubes, and then transferring those tubes into fresh culture trays in running seawater. In Figure 1, the mechanical agitation from the collection and handling may be apparent in the wide variance in respiration rates that were measured on the 1st day that the experimental culture trays were setup. During the 4 week time course of the study, respiration rates in the control and the +4 treatment group were lower with reduced inter individual variance. Individual oxygen consumption rates were not statistically different at the 4 week sampling point (ANOVA, n = 23).


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

Marsh AG, Pasqualone AA - Front Physiol (2014)

Spiophanes tcherniai oxygen consumption rates normalized to DNA mass in maintained for 4 weeks at −1.5C°C and +4°C.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Spiophanes tcherniai oxygen consumption rates normalized to DNA mass in maintained for 4 weeks at −1.5C°C and +4°C.
Mentions: Field collection of adult worms requires scooping sediment up into buckets while SCUBA diving, returning the buckets to the lab, sieving the sediment to isolate adult worm tubes, and then transferring those tubes into fresh culture trays in running seawater. In Figure 1, the mechanical agitation from the collection and handling may be apparent in the wide variance in respiration rates that were measured on the 1st day that the experimental culture trays were setup. During the 4 week time course of the study, respiration rates in the control and the +4 treatment group were lower with reduced inter individual variance. Individual oxygen consumption rates were not statistically different at the 4 week sampling point (ANOVA, n = 23).

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.