Abstract
BackgroundmiRNAs are small, non-coding RNA molecules that mainly act as negative regulators of target gene messages. Due to their regulatory functions, they have lately been implicated in several diseases, including malignancies. Roughly half of known miRNA genes are located within previously annotated protein-coding regions ("intragenic miRNAs"). Although a role of intragenic miRNAs as negative feedback regulators has been speculated, to the best of our knowledge there have been no conclusive large-scale studies investigating the relationship between intragenic miRNAs and host genes and their pathways.ResultsmiRNA-containing host genes were three times longer, contained more introns and had longer 5' introns compared to a randomly sampled gene cohort. These results are consistent with the observation that more than 60% of intronic miRNAs are found within the first five 5' introns. Host gene 3'-untranslated regions (3'-UTRs) were 40% longer and contained significantly more adenylate/uridylate-rich elements (AREs) compared to a randomly sampled gene cohort. Coincidentally, recent literature suggests that several components of the miRNA biogenesis pathway are required for the rapid decay of mRNAs containing AREs. A high-confidence set of predicted mRNA targets of intragenic miRNAs also shared many of these features with the host genes. Approximately 20% of intragenic miRNAs were predicted to target their host mRNA transcript. Further, KEGG pathway analysis demonstrated that 22 of the 74 pathways in which host genes were associated showed significant overrepresentation of proteins encoded by the mRNA targets of associated intragenic miRNAs.ConclusionsOur findings suggest that both host genes and intragenic miRNA targets may potentially be subject to multiple layers of regulation. Tight regulatory control of these genes is likely critical for cellular homeostasis and absence of disease. To this end, we examined the potential for negative feedback loops between intragenic miRNAs, host genes, and miRNA target genes. We describe, how higher-order miRNA feedback on hosts' interactomes may at least in part explain correlation patterns observed between expression of host genes and intragenic miRNA targets in healthy and tumor tissue.
Highlights
MiRNAs are small, non-coding RNA molecules that mainly act as negative regulators of target gene messages
Recent findings demonstrate that transcription of a subset of intronic miRNAs in H. sapiens can be initiated from internal promoters within operons independently from the host gene [3], suggesting that utilization of internal promoters must be considered a viable alternative strategy for intronic miRNA gene transcription
Genomic Properties of Target Genes We looked at genomic properties of a high-confidence set of targets for hosts of intronic miRNAs that would give us a set of similar size as the host genes
Summary
MiRNAs are small, non-coding RNA molecules that mainly act as negative regulators of target gene messages Due to their regulatory functions, they have lately been implicated in several diseases, including malignancies. Microarray analyses supports the hypothesis that intronic miRNAs are usually expressed in coordination with the host gene mRNA in human tissues [4,5], strongly suggesting that co-transcription from the host gene promoter is the most common transcriptional mechanism under normal conditions. This assumption has lately successfully been employed to identify new miRNA targets [6]. Recent findings demonstrate that transcription of a subset of intronic miRNAs in H. sapiens can be initiated from internal promoters within operons independently from the host gene [3], suggesting that utilization of internal promoters must be considered a viable alternative strategy for intronic miRNA gene transcription
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