520
which supports the usage of them as biomarkers, though they are not specific to oil
exposure (Nilsen et al. 1998; Hilscherova et al. 2000). Transcription of genes not
related to the AHR pathway, such as those involved in cardiac and eye development, as well as nervous system function, has been found to change in oil-exposed
individuals, leading to adverse outcomes. The summation of these changes in gene
expression can lead to phenotypic defects and increased mortality of fishes
exposed to oil.
30.3 Epigenetics
Epigenetics is the study of heritable modifications to the DNA molecule that affect
the DNA’s availability, but are not base changes, and as such are reversible. These
changes, passed from mother cells to daughter cells, alter gene expression by inhibiting protein binding but also may reduce DNA damage by reducing availability of
the DNA strand to things like reactive oxidative species (Ljungman and Hanawalt
1992; Takata et al. 2013) and ionizing radiation (Takata et al. 2013). Epigenetic
changes include chromatin remodeling, such as histone modification, removal,
replacement, or addition; DNA modifications, such as the addition of a methyl
group to the carbon ring of cytosine; and non-coding RNA-mediated gene silencing.
These modifications are often called epigenetic “tags” and serve important roles in
cell line differentiation during development and phenotype-environment interactions, and are not only heritable down cell lines but can be passed from parent to
offspring (Reik 2007; Labbé et al. 2017).
Many methods have been developed to assess and characterize epigenetic alterations. Patterns of DNA methylation are assessed by determining the methylation
state of cytosines either in specific targeted areas of interest or on genome-wide
scales. Instrumentation used for analyses ranges from high-performance liquid
chromatography with an ultraviolet visible absorbance detector (HPLC-UV), to
methylome sequencing, to enzyme-linked immunosorbent assay (ELISA; see
Kurdyukov and Bullock 2016 for a review). The location of chromatin remodeling
can be assessed through chromatin immunoprecipitation (ChIP) assays and can be
complimented with DNA analysis methods such as quantitative PCR (qPCR),
microarray, or bisulfite treatment of DNA followed by sequencing (see Das et al.
2004 and DeAngelis et al. 2008 for reviews).
When an organism is exposed to an environmental stimulus, cells may alter gene
expression to account for the altered environment. During this process, epigenetic
mechanisms can be used to modify gene expression (Kanherkar et al. 2014).
Changes in epigenetic tags in one or a few cells can lead to rapid cascading effects
when these changed cells export products that enter other cells and alter their epigenetic profile (Peschansky and Wahlestedt 2014). In this way, large-scale epigenetic changes can occur in hours (e.g., embryo reprogramming; see Jiang et al. 2013;
Potok et al. 2013), but the results can last for a lifetime (e.g., Knecht et al. 2017).
D. S. Portnoy et al.
which supports the usage of them as biomarkers, though they are not specific to oil
exposure (Nilsen et al. 1998; Hilscherova et al. 2000). Transcription of genes not
related to the AHR pathway, such as those involved in cardiac and eye development, as well as nervous system function, has been found to change in oil-exposed
individuals, leading to adverse outcomes. The summation of these changes in gene
expression can lead to phenotypic defects and increased mortality of fishes
exposed to oil.
30.3 Epigenetics
Epigenetics is the study of heritable modifications to the DNA molecule that affect
the DNA’s availability, but are not base changes, and as such are reversible. These
changes, passed from mother cells to daughter cells, alter gene expression by inhibiting protein binding but also may reduce DNA damage by reducing availability of
the DNA strand to things like reactive oxidative species (Ljungman and Hanawalt
1992; Takata et al. 2013) and ionizing radiation (Takata et al. 2013). Epigenetic
changes include chromatin remodeling, such as histone modification, removal,
replacement, or addition; DNA modifications, such as the addition of a methyl
group to the carbon ring of cytosine; and non-coding RNA-mediated gene silencing.
These modifications are often called epigenetic “tags” and serve important roles in
cell line differentiation during development and phenotype-environment interactions, and are not only heritable down cell lines but can be passed from parent to
offspring (Reik 2007; Labbé et al. 2017).
Many methods have been developed to assess and characterize epigenetic alterations. Patterns of DNA methylation are assessed by determining the methylation
state of cytosines either in specific targeted areas of interest or on genome-wide
scales. Instrumentation used for analyses ranges from high-performance liquid
chromatography with an ultraviolet visible absorbance detector (HPLC-UV), to
methylome sequencing, to enzyme-linked immunosorbent assay (ELISA; see
Kurdyukov and Bullock 2016 for a review). The location of chromatin remodeling
can be assessed through chromatin immunoprecipitation (ChIP) assays and can be
complimented with DNA analysis methods such as quantitative PCR (qPCR),
microarray, or bisulfite treatment of DNA followed by sequencing (see Das et al.
2004 and DeAngelis et al. 2008 for reviews).
When an organism is exposed to an environmental stimulus, cells may alter gene
expression to account for the altered environment. During this process, epigenetic
mechanisms can be used to modify gene expression (Kanherkar et al. 2014).
Changes in epigenetic tags in one or a few cells can lead to rapid cascading effects
when these changed cells export products that enter other cells and alter their epigenetic profile (Peschansky and Wahlestedt 2014). In this way, large-scale epigenetic changes can occur in hours (e.g., embryo reprogramming; see Jiang et al. 2013;
Potok et al. 2013), but the results can last for a lifetime (e.g., Knecht et al. 2017).
D. S. Portnoy et al.