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30.1 Introduction
When organisms are exposed to oil, a number of subcellular responses occur to
facilitate excretion of toxins and ensure maintenance of homeostasis. Metabolic
pathways are induced to make xenobiotic compounds water soluble, facilitating
excretion, but in the process often produce more bioactive toxic species (Schlenk
et al. 2008a). Therefore, organisms may also mount responses meant to protect
basic functioning and minimize direct DNA damage (Shimada 2006). These mechanisms are well suited to handle short-term response to low levels of contaminants;
however, long-term (chronic) exposure and/or high concentrations of oil may overburden pathways leading to the accumulation of bioactive species in tissues (Wills
et al. 2009). Additionally, transcription factors involved in xenobiotic metabolism
may disrupt processes important for normal cellular functioning (Androutsopoulos
et al. 2009). Chronically exposed organisms, therefore, may differ in response to oil
exposure due to heritable changes in gene regulation, population-level changes in
gene frequencies, or a combination of these changes to genes that are involved in
xenobiotic metabolism.
Because both immediate- and long-term responses to oil are a function of gene
expression, gene regulation, and ultimately gene content, modern molecular techniques offer a set of tools for detecting exposure, understanding causes of lethal and
sublethal responses, and assessing population-level effects. These techniques can be
used to predict the long-term resilience of populations and the potential for residual
oil in the system following a spill to cause permanent change in the genetic make-up
of organisms, a phenomenon called anthropogenic evolution. In this chapter, we
discuss three fields of molecular study, transcriptomics (gene expression), epigenetics (gene regulation), and population genomics (gene content within species),
highlighting the latest advancements in the field, discussing what we have learned
from the application of these techniques to exposure research, and suggesting future
directions for research.
30.2 Transcriptomics
Transcriptomic studies use molecular technology to characterize gene expression in
whole organisms and/or specific tissues and can be used to assess changes in gene
expression among organisms in different experimental treatments or naturally
occurring environments (Conesa et al. 2016). Early transcriptomic studies in the
mid-1990s utilized microarrays to measure the abundance of several thousand targeted transcripts of interest at once via hybridization to complementary probes
(Schena et al. 1995). In recent years, high-throughput transcriptome sequencing
(RNASeq) has allowed researchers to identify gene expression changes without
having to target specific genes. An advantage of non-targeted approaches, such as
D. S. Portnoy et al.
30.1 Introduction
When organisms are exposed to oil, a number of subcellular responses occur to
facilitate excretion of toxins and ensure maintenance of homeostasis. Metabolic
pathways are induced to make xenobiotic compounds water soluble, facilitating
excretion, but in the process often produce more bioactive toxic species (Schlenk
et al. 2008a). Therefore, organisms may also mount responses meant to protect
basic functioning and minimize direct DNA damage (Shimada 2006). These mechanisms are well suited to handle short-term response to low levels of contaminants;
however, long-term (chronic) exposure and/or high concentrations of oil may overburden pathways leading to the accumulation of bioactive species in tissues (Wills
et al. 2009). Additionally, transcription factors involved in xenobiotic metabolism
may disrupt processes important for normal cellular functioning (Androutsopoulos
et al. 2009). Chronically exposed organisms, therefore, may differ in response to oil
exposure due to heritable changes in gene regulation, population-level changes in
gene frequencies, or a combination of these changes to genes that are involved in
xenobiotic metabolism.
Because both immediate- and long-term responses to oil are a function of gene
expression, gene regulation, and ultimately gene content, modern molecular techniques offer a set of tools for detecting exposure, understanding causes of lethal and
sublethal responses, and assessing population-level effects. These techniques can be
used to predict the long-term resilience of populations and the potential for residual
oil in the system following a spill to cause permanent change in the genetic make-up
of organisms, a phenomenon called anthropogenic evolution. In this chapter, we
discuss three fields of molecular study, transcriptomics (gene expression), epigenetics (gene regulation), and population genomics (gene content within species),
highlighting the latest advancements in the field, discussing what we have learned
from the application of these techniques to exposure research, and suggesting future
directions for research.
30.2 Transcriptomics
Transcriptomic studies use molecular technology to characterize gene expression in
whole organisms and/or specific tissues and can be used to assess changes in gene
expression among organisms in different experimental treatments or naturally
occurring environments (Conesa et al. 2016). Early transcriptomic studies in the
mid-1990s utilized microarrays to measure the abundance of several thousand targeted transcripts of interest at once via hybridization to complementary probes
(Schena et al. 1995). In recent years, high-throughput transcriptome sequencing
(RNASeq) has allowed researchers to identify gene expression changes without
having to target specific genes. An advantage of non-targeted approaches, such as
D. S. Portnoy et al.