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ARS Home » Southeast Area » Stoneville, Mississippi » Genomics and Bioinformatics Research » Research » Publications at this Location » Publication #315090
Title: Transcriptomic changes in zebrafish embryos and larvae following benzo[a]pyrene exposure

Author
item FANG, XIEFAN
item CORRALES, JONES
item THORNTON, CAMMI
item CLERK, TRACY
item Scheffler, Brian
item WILLETT, KRISTINE

Submitted to: Toxicological Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/19/2015
Publication Date: 8/1/2015
Citation: Fang, X., Corrales, J., Thornton, C., Clerk, T., Scheffler, B.E., Willett, K.L. 2015. Transcriptomic changes in zebrafish embryos and larvae following benzo[a]pyrene exposure. Toxicological Sciences. 146(2):395-411. doi: 10.1093/toxsci/kfv105..

Interpretive Summary: Benzo[a]pyrene (BaP) is an environmentally relevant contaminant and can be found in water systems thus impacting fish. The compound can cause immediate or long-term health issues and this is influenced by the amount of the compound, length of exposure, and stage of fish development. In this study, zebrafish were used as a model system due to the availability of extensive genomic data. Early developmental stages were examined, 3.3 and 96 hours after fertilization. Using ILACUC approved procedures, the impact of BaP was determined by a technique called RNASeq which measures the amount of mRNA produced by each gene for any given treatment. Bioinformatic tools were then used to assign each mRNA to a gene in zebrafish and then a total was calculated for each gene. These values were then compared by statistical means to determine the difference of gene expression between BaP treatments. In this study, the number of genes significantly altered at the 3.3 hour stage with and without BaP was limited to eight genes. At 96 hours the number of changes were much higher with 1153 genes being impacted. Genes impacted by BaP were categorized by their potential function. Many genes that were impacted by BaP are in known disease related pathways. Many genes were not previously associated with response to BaP and this novel discovery could be helpful in future studies in trying to understand the full impact of BaP.

Technical Abstract: Benzo[a]pyrene (BaP) is an environmentally relevant carcinogenic and endocrine disrupting compound that causes immediate, long-term, and multigenerational health deficits in mammals and fish. Previously, we found that BaP alters DNA methylation patterns in developing zebrafish, which may affect gene expression. Herein, we performed a genome-wide transcriptional analysis and discovered differential gene expression and splicing in developing zebrafish. Adult zebrafish were exposed to control or 42.0 ± 1.9 µg/L BaP for 7 days. Eggs were collected and raised in control conditions or continuously exposed to BaP until 3.3 and 96 hours post fertilization (hpf). RNA sequencing (RNA-Seq) was conducted on zebrafish embryos and larvae. Data were analyzed to identify differentially expressed (DE) genes (changed at the gene or transcript variant level) and genes with differential exon usage (DEU; changed at the exon level). At 3.3 hpf, BaP exposure resulted in 8 DE genes and 51 DEU genes. At 96 hpf, BaP exposure altered expression in 1153 DE genes and 159 DEU genes. Functional ontology analysis by Ingenuity Pathway Analysis revealed that many disease pathways, including organismal death, growth failure, abnormal morphology of embryonic tissue, congenital heart disease, and adverse neuritogenesis, were significantly enriched for the DE and DEU genes, providing novel insights on the mechanisms of action of BaP-induced developmental toxicities. Collectively, we discovered substantial transcriptomic changes at the gene, transcript variant, and exon levels in developing zebrafish after early life BaP waterborne exposure, and these changes may lead to adverse consequences on health.