517
RNASeq, is that they allow for non-biased assessments of all gene expression in an
organism, which is important for fully understanding the range of subcellular
responses an organism may have under a variety of conditions, including exposure
to toxins. Consistent improvements in cost, versatility, and analysis methods have
made RNASeq the current choice for transcriptomics studies.
For species with sequenced genomes, RNASeq reads can be aligned or “mapped”
to an annotated genome to identify expressed transcripts. For non-model species
without fully sequenced genomes, de novo assembly of reads can be used to create
a transcriptome in a species of interest (methods reviewed in Conesa et al. 2016 and
Chen et al. 2017), and/or a comparative genomics approach can be used to map
reads to the genomes of several closely related taxa (O’Leary et al. 2018). After
mapping, transcripts can be quantified and annotated using a variety of methods
(e.g., Li and Dewey 2011; Anders et al. 2014; Patro et al. 2015) to identify log-fold
changes and differentially expressed genes at a user-defined p-value (Robinson
et al. 2010; Love et al. 2014). The characterization of differential gene expression
and the processes/pathways they are involved in among experimental treatments
can be used to identify and understand aspects of subcellular response to xenobiotic
compounds such as oil.
Following the Deepwater Horizon (DWH) oil spill in the Gulf of Mexico, several
whole-transcriptome studies assessed the biological response of native fish species
to oil exposure. Impacts on early developmental stages have been studied in fish
including mahi-mahi, Coryphaena hippurus; red drum, Sciaenops ocellatus; and
haddock, Melanogrammus aeglefinus (Xu et al. 2016a, 2017; Sørhus et al. 2017).
Most studies in adult fish used the Gulf killifish, Fundulus grandis, or mummichog,
Fundulus heteroclitus (Whitehead et al. 2010, 2012a). The results of these studies
confirmed previously identified response mechanisms to oil but in addition have
identified novel changes in gene expression. First, this section will focus on the
transcriptomic effects of oil on activation of aryl-hydrocarbon receptor (AHR)mediated pathways. The AHR pathway is a well-characterized response mechanism
of oil exposure that contributes to cardiac malformations, including poor looping,
arrhythmia, and reduced contractility (Incardona 2017). Secondly, this section will
discuss emerging evidence that non-AHR-pathway gene expression changes also
are a prevalent component of oil-induced organismal response.
One of the primary transcriptional responses to oil exposure is polycyclic aromatic hydrocarbon (PAH)-induced activation of aryl-hydrocarbon receptors (AHR)
and their downstream response genes, known as the AHR pathway (Wirgin and
Waldman 2004; Oleksiak et al. 2011). The AHR pathway regulates detoxification of
planar aromatic hydrocarbons such as PAHs via activation of xenobiotic metabolism
and stress-response pathways. Binding of PAHs to AHRs induces transcriptional
changes in the AHR pathway. For example, activation of phase I enzymes such as
cytochrome p450s (CYP) converts PAHs to intermediates, which are further processed by phase II enzymes into compounds that can be safely and easily eliminated
from the body. Persistent overactivation of genes in the AHR pathway during prolonged oil exposure is related to developmental abnormalities, decreased hatching
30 Genetics and Oil: Transcriptomics, Epigenetics, and Population Genomics as Tools…
RNASeq, is that they allow for non-biased assessments of all gene expression in an
organism, which is important for fully understanding the range of subcellular
responses an organism may have under a variety of conditions, including exposure
to toxins. Consistent improvements in cost, versatility, and analysis methods have
made RNASeq the current choice for transcriptomics studies.
For species with sequenced genomes, RNASeq reads can be aligned or “mapped”
to an annotated genome to identify expressed transcripts. For non-model species
without fully sequenced genomes, de novo assembly of reads can be used to create
a transcriptome in a species of interest (methods reviewed in Conesa et al. 2016 and
Chen et al. 2017), and/or a comparative genomics approach can be used to map
reads to the genomes of several closely related taxa (O’Leary et al. 2018). After
mapping, transcripts can be quantified and annotated using a variety of methods
(e.g., Li and Dewey 2011; Anders et al. 2014; Patro et al. 2015) to identify log-fold
changes and differentially expressed genes at a user-defined p-value (Robinson
et al. 2010; Love et al. 2014). The characterization of differential gene expression
and the processes/pathways they are involved in among experimental treatments
can be used to identify and understand aspects of subcellular response to xenobiotic
compounds such as oil.
Following the Deepwater Horizon (DWH) oil spill in the Gulf of Mexico, several
whole-transcriptome studies assessed the biological response of native fish species
to oil exposure. Impacts on early developmental stages have been studied in fish
including mahi-mahi, Coryphaena hippurus; red drum, Sciaenops ocellatus; and
haddock, Melanogrammus aeglefinus (Xu et al. 2016a, 2017; Sørhus et al. 2017).
Most studies in adult fish used the Gulf killifish, Fundulus grandis, or mummichog,
Fundulus heteroclitus (Whitehead et al. 2010, 2012a). The results of these studies
confirmed previously identified response mechanisms to oil but in addition have
identified novel changes in gene expression. First, this section will focus on the
transcriptomic effects of oil on activation of aryl-hydrocarbon receptor (AHR)mediated pathways. The AHR pathway is a well-characterized response mechanism
of oil exposure that contributes to cardiac malformations, including poor looping,
arrhythmia, and reduced contractility (Incardona 2017). Secondly, this section will
discuss emerging evidence that non-AHR-pathway gene expression changes also
are a prevalent component of oil-induced organismal response.
One of the primary transcriptional responses to oil exposure is polycyclic aromatic hydrocarbon (PAH)-induced activation of aryl-hydrocarbon receptors (AHR)
and their downstream response genes, known as the AHR pathway (Wirgin and
Waldman 2004; Oleksiak et al. 2011). The AHR pathway regulates detoxification of
planar aromatic hydrocarbons such as PAHs via activation of xenobiotic metabolism
and stress-response pathways. Binding of PAHs to AHRs induces transcriptional
changes in the AHR pathway. For example, activation of phase I enzymes such as
cytochrome p450s (CYP) converts PAHs to intermediates, which are further processed by phase II enzymes into compounds that can be safely and easily eliminated
from the body. Persistent overactivation of genes in the AHR pathway during prolonged oil exposure is related to developmental abnormalities, decreased hatching
30 Genetics and Oil: Transcriptomics, Epigenetics, and Population Genomics as Tools…