Mechanisms of physiological plasticity in early stage marine invertebrates in response to multiple stressors - epigenomic perspective in a global change context

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National Science Foundation
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Ecology and Evolution

The goal of this project is to investigate mechanisms that contribute to rapid shifts in organismal physiological plasticity in response to environmental change, processes that would operate on ecological rather than evolutionary time scales. Our model system is the early life stages of the purple sea urchin, Strongylocentrotus purpuratus, and we will focus on two processes: intragenerational plasticity and trans-generational plasticity. Here, we will specifically interrogate epigenetic mechanisms that may that alter physiological plasticity in early stage urchins. For the environment-organism interaction, we will focus on co-occurring multiple abiotic factors (pCO2, oxygen and temperature) that are ecologically relevant, and are projected to change drastically in future climate change scenarios.

Along with physiological metrics of performance, we propose to use next-generation sequencing to conduct comparative transcriptomics, and will assess changes in global DNA methylation patterns that may drive observed changes in gene expression. We hypothesize that DNA methylation as a form of epigenomic mechanism is driving plasticity in sea urchins embryos in response to variable pCO2/ temperature conditions in the environment.

The project has three Specific Aims:

Specific Aim 1: To investigate intragenerational plasticity in S. purpuratus embryos and larvae in response to changes in temperature, pCO2 and dissolved oxygen.

Specific Aim 2: To examine the role of trans-generational plasticity in altering the physiological tolerance and resistance of S. purpuratus embryos and larvae in response to variable temperature and pCO2 conditions.

Specific Aim 3: To perform simultaneous profiling of the transcriptome and the DNA methylome in S. purpuratus larvae raised under variable temperature and pCO2 conditions.

Methods to be employed are: (1) raising cultures of sea urchins at variable pCO2 and temperature conditions, 2) measuring growth, metabolic rate and lipid content on 4 development stages, (2) measuring patterns of DNA methylation using 2 assays: an ELISA-based method that measures levels of 5-methylcytosine (5-mC) in samples of genomic DNA, and the methylation-sensitive amplification polymorphism assay, (4) RNA-Seq to profile gene expression, and (5) concurrent profiling of the larval transcriptome and methylome using Illumina sequencing technology, in this case, RNA-Seq combined with whole genome bisulfite sequencing.