Environmental contaminants and microRNA regulation: Transcription factors as regulators of toxicant-altered microRNA expression.
MicroRNAs (miRNAs) regulate gene expression by binding mRNA and inhibiting translation and/or inducing degradation of the associated transcripts. Expression levels of miRNAs have been shown to be altered in response to environmental toxicants, thus impacting cellular function and influencing disease risk. Transcription factors (TFs) are known to be altered in response to environmental toxicants and play a critical role in the regulation of miRNA expression. To date, environmentally-responsive TFs that are important for regulating miRNAs remain understudied. In a state-of-the-art analysis, we utilized an in silico bioinformatic approach to characterize potential transcriptional regulators of environmentally-responsive miRNAs. Using the miRStart database, genomic sequences of promoter regions for all available human miRNAs (n=847) were identified and promoter regions were defined as -1000/+500 base pairs from the transcription start site. Subsequently, the promoter region sequences of environmentally-responsive miRNAs (n=128) were analyzed using enrichment analysis to determine overrepresented TF binding sites (TFBS). While most (56/73) TFs differed across environmental contaminants, a set of 17 TFs was enriched for promoter binding among miRNAs responsive to numerous environmental contaminants. Of these, one TF was common to miRNAs altered by the majority of environmental contaminants, namely SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily A, member 3 (SMARCA3). These identified TFs represent candidate common transcriptional regulators of miRNAs perturbed by environmental toxicants.
Department of Environmental Science & Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, USA.
James
J
Sollome
Department of Environmental Science & Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, USA.
Elizabeth
E
Martin
Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, NC, USA.
Praveen
P
Sethupathy
Department of Environmental Science & Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, USA; Curriculum in Toxicology, School of Medicine, University of North Carolina, Chapel Hill, NC, USA. Electronic address: rfry@unc.edu.
Rebecca C
RC
Fry
D004785:Environmental Pollutants / Q000633:toxicity*; D006801:Humans; D035683:MicroRNAs / Q000378:metabolism*; D011401:Promoter Regions, Genetic; D014157:Transcription Factors / Q000378:metabolism*; D014158:Transcription, Genetic
D004785:Environmental Pollutants; D035683:MicroRNAs; D014157:Transcription Factors
Environmental toxicants; Promoters; Transcription factors; miRNA; microRNA