A potential role for intragenic miRNAs on their hosts' interactome

BMC Genomics, Oct 2010

Background 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. Results 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. Conclusions 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.

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A potential role for intragenic miRNAs on their hosts' interactome

BMC Genomics A potential role for intragenic miRNAs on their hosts' interactome Ludwig Christian G Hinske 0 2 Pedro AF Galante 1 Winston P Kuo 3 4 Lucila Ohno-Machado 2 0 Department of Anaesthesiology, Clinic of the University of Munich , Marchioninistrasse 15, 81377 Munich , Germany 1 Ludwig Institute for Cancer Research, Hospital Alemão Oswaldo Cruz , Rua João Julião, São Paulo 01323-903 , Brazil 2 Division of Biomedical Informatics, University of California San Diego , 9500 Gilman Dr, La Jolla, California 92093 , USA 3 Harvard Catalyst - Laboratory for Innovative Translational Technologies, Harvard Medical School , 77 Avenue Louis Pasteur, Boston, Massachusetts 02115 , USA 4 Harvard School of Dental Medicine , 188 Longwood Avenue, Boston, Massachusetts 02115 , USA Background: 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. Results: 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. Conclusions: 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. Background microRNAs (miRNAs) are small (~22-nt) functional RNA species that provide a newly appreciated layer of gene regulation with an important role in development, cellular homeostasis and pathophysiology. miRNAs are encoded in the genome and transcribed primarily in a Pol II-dependent manner [ 1 ], although Pol III-dependent transcription has also been reported [ 2,3 ]. Roughly half of the known human microRNAs are found in intergenic regions of the genome, suggesting production of unique primary transcripts (pri-miRNAs) containing one or more miRNA hairpins under the control of independent promoter elements. The overwhelming majority of the other ~50% map to previously annotated intronic regions of protein coding genes, while a small number are even found within exons. The relationship between intragenic miRNAs and their host genes presents many unique questions regarding genomic organization, transcriptional regulation, processing and function. The genomic organization of intragenic miRNAs exhibits a strong directional bias, such that these species are predominantly oriented on the same strand of the DNA as that of the host gene. The directional bias may prevent steric interference between RNA polymerases transcribing the host gene and the miRNA gene(s) [ 4 ]; however, the existence of individual antisense miRNA genes and miRNA gene clusters argues that the primary evolutionary pressure for the positional bias is coregulation of the intronic miRNA and the host gene. Indeed, 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]. However, recent findings demonstrate that t (...truncated)


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Ludwig Hinske, Pedro AF Galante, Winston P Kuo, Lucila Ohno-Machado. A potential role for intragenic miRNAs on their hosts' interactome, BMC Genomics, 2010, pp. 533, 11, DOI: 10.1186/1471-2164-11-533