Open Access Highly Accessed Research article

A potential role for intragenic miRNAs on their hosts' interactome

Ludwig Christian G Hinske12*, Pedro AF Galante3, Winston P Kuo45 and Lucila Ohno-Machado2

Author Affiliations

1 Department of Anaesthesiology, Clinic of the University of Munich, Marchioninistrasse 15, 81377 Munich, Germany

2 Division of Biomedical Informatics, University of California San Diego, 9500 Gilman Dr, La Jolla, California 92093, USA

3 Ludwig Institute for Cancer Research, Hospital Alemão Oswaldo Cruz, Rua João Julião, São Paulo 01323-903, Brazil

4 Harvard School of Dental Medicine, 188 Longwood Avenue, Boston, Massachusetts 02115, USA

5 Harvard Catalyst - Laboratory for Innovative Translational Technologies, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA

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BMC Genomics 2010, 11:533  doi:10.1186/1471-2164-11-533

Published: 1 October 2010



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. 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.


miRNA-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.


Our 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.