Transcriptomics in ecotoxicology

Abstract

The emergence of analytical tools for high-throughput screening of biomolecules has revolutionized the way in which toxicologists explore the impact of chemicals or other stressors on organisms. One of the most developed and routinely applied high-throughput analysis approaches is transcriptomics, also often referred to as gene expression profiling. The transcriptome represents all RNA molecules, including the messenger RNA (mRNA), which constitutes the building blocks for translating DNA into amino acids to form proteins. The entirety of mRNA is a mirror of the genes that are actively expressed in a cell or an organism at a given time. This in turn allows one to deduce how organisms respond to changes in the external environment. In this article we explore how transcriptomics is currently applied in ecotoxicology and highlight challenges and trends.FigureThe transcriptome (RNA) is a mirror of the genes that are actively expressed in a cell or organism at a given time, providing information on how organisms respond to chemicals or other stressors in the environment

A New, Sensitive Marine Microalgal Recombinant Biosensor Using Luminescence Monitoring for Toxicity Testing of Antifouling Biocides

“…In the future more sensitive and pollutant-specific biosensors could be developed by using specific target genes fused to luciferase. Such target genes could also be defined using next-generation sequencing of RNA to identify genes that are specifically and rapidly induced or repressed in response to low doses of specific molecules (48)(49)(50). Automated monitoring of these luminescent reporters should allow the development of new platforms for high-throughput screening of the effect of pollutants on marine eukaryotic picophytoplankton.…”

Linking toxicity and adaptive responses across the transcriptome, proteome, and phenotype of Chlamydomonas reinhardtii exposed to silver

“…These parameters, however, reveal neither subtle effects that precede organism level changes nor adaptive responses that allow the organism to recover. Advances in "omics" technologies increasingly facilitate the comprehensive analysis of stressor effects in organisms living in different habitats at different subcellular levels (1,2), including abundance of RNA transcripts (transcriptome) (2) and expression of proteins (proteome). The genome-wide transcriptome and proteome changes should aid in determining the molecular pathways underlying the response of the organism to a stressor.…”

Evolutionary toxicology in an omics world

“…Transcriptomics provides insight into molecular mechanisms that underlie responses and toxicity and can be one of the ways that ecotoxicology aims to understand exposures and their effects on individuals and ultimately populations (Schirmer, Fischer, Madureira, & Pillai, 2010). On the other hand, genetic variation can alter the response of toxin activated genes and pathways (Bozinovic, Sit, Di Giulio, Wills, & Oleksiak, 2013; Reid et al., 2016; Whitehead, Pilcher, Champlin, & Nacci, 2012; Whitehead, Triant, Champlin, & Nacci, 2010).…”

“…Thus, to gain full understanding of the effects of a contaminant on gene expression, a full profile of responsiveness through multiple stages of development needs to be created (Bozinovic et al., 2011). In addition, transcriptomics can often be difficult to replicate and standardize between laboratories (Vidal‐Dorsch et al., 2016) and many transcriptomic responses to contaminants are highly variable in magnitude (Schirmer et al., 2010). Additionally, the level of their responsiveness is not always well translated into downstream effects or implications on organismal health.…”