PCB126 exposure revealed alterations in m6A RNA modifications in transcripts associated with AHR activation

Chemical modifications of proteins, DNA and RNA moieties play critical
roles in regulating gene expression. Emerging evidence suggests
the RNA modifications (epitranscriptomics) have substantive roles in basic
biological processes. One of the most common modifications in mRNA and
noncoding RNAs is N6-methyladenosine (m6A). In a subset of mRNAs, m6A
sites are preferentially enriched near stop codons, in 3′ UTRs, and within
exons, suggesting an important role in the regulation of mRNA processing
and function including alternative splicing and gene expression. Very
little is known about the effect of environmental chemical exposure on m6A
modifications. As many of the commonly occurring environmental
contaminants alter gene expression profiles and have detrimental effects
on physiological processes, it is important to understand the effects of
exposure on this important layer of gene regulation. Hence, the objective
of this study was to characterize the acute effects of developmental
exposure to PCB126, an environmentally relevant dioxin-like PCB, on m6A
methylation patterns. We exposed zebrafish embryos to PCB126 for 6 hours
starting from 72 hours post-fertilization and profiled m6A RNA using
methylated RNA immunoprecipitation followed by sequencing (MeRIP-seq). Our
analysis revealed 117 and 217 m6A peaks in the DMSO and PCB126 samples
(FDR 5%), respectively. The majority of the peaks were preferentially
located around the 3’UTR and stop codons. Statistical analysis revealed 15
m6A marked transcripts to be differentially methylated by PCB126 exposure.
These include transcripts that are known to be activated by AHR agonists
(e.g., ahrra, tiparp, nfe2l2b) as well as others that are important for
normal development (vgf, cebpd, sned1). These results suggest that
environmental chemicals such as dioxin-like PCBs could affect
developmental gene expression patterns by altering m6A levels. Further
studies are necessary to understand the functional consequences of
exposure-associated alterations in m6A levels.