MicroRNA Networks in Mouse Lung Organogenesis

Abstract

BackgroundMicroRNAs (miRNAs) are known to be important regulators of both organ development and tumorigenesis. MiRNA networks and their regulation of messenger RNA (mRNA) translation and protein expression in specific biological processes are poorly understood.MethodsWe explored the dynamic regulation of miRNAs in mouse lung organogenesis. Comprehensive miRNA and mRNA profiling was performed encompassing all recognized stages of lung development beginning at embryonic day 12 and continuing to adulthood. We analyzed the expression patterns of dynamically regulated miRNAs and mRNAs using a number of statistical and computational approaches, and in an integrated manner with protein levels from an existing mass-spectrometry derived protein database for lung development.ResultsIn total, 117 statistically significant miRNAs were dynamically regulated during mouse lung organogenesis and clustered into distinct temporal expression patterns. 11,220 mRNA probes were also shown to be dynamically regulated and clustered into distinct temporal expression patterns, with 3 major patterns accounting for 75% of all probes. 3,067 direct miRNA-mRNA correlation pairs were identified involving 37 miRNAs. Two defined correlation patterns were observed upon integration with protein data: 1) increased levels of specific miRNAs directly correlating with downregulation of predicted mRNA targets; and 2) increased levels of specific miRNAs directly correlating with downregulation of translated target proteins without detectable changes in mRNA levels. Of 1345 proteins analyzed, 55% appeared to be regulated in this manner with a direct correlation between miRNA and protein level, but without detectable change in mRNA levels.ConclusionSystematic analysis of microRNA, mRNA, and protein levels over the time course of lung organogenesis demonstrates dynamic regulation and reveals 2 distinct patterns of miRNA-mRNA interaction. The translation of target proteins affected by miRNAs independent of changes in mRNA level appears to be a prominent mechanism of developmental regulation in lung organogenesis.

Regulation of lung endoderm progenitor cell behavior by miR302/367

“…S1 in the supplementary material). Q-PCR confirms the downregulated expression of all members of the miR302/367 cluster, whereas the expression of another miRNA expressed in the lung, miR200b (Gregory et al, 2008;Dong et al, 2010), is not significantly affected (Fig. 6H).…”

Reconstructing dynamic microRNA-regulated interaction networks

“…Because miRNAs often inhibit their direct targets, integrating sequence, mRNA and miRNA expression data are one way to improve such an analysis (6)(7)(8). Several methods, mostly based on (anti-) correlation or regression analysis, have been developed to use expression data when predicting targets of miRNAs (8)(9)(10). A representative example is GenMIR++ (5,6), one of the first methods to integrate miRNA and mRNA expression profiles in a unified probabilistic model.…”

“…GenMIR++ employs a generative model in which miRNA expression profiles are used to explain the expression of a putative target inferred from sequence analysis. Other methods search for anticorrelation (8,9).…”

Toward a Systematic Understanding of mRNA 3' Untranslated Regions

“…Levels of many miRNAs change substantially during development of the lung (27,28) and other organs (29,30). Mice with targeted deletions of specific miRNAs are beginning to reveal the functions of these miRNAs in vivo.…”

“…For example, deletion of the muscle-specific miRNA miR1-2, which recognizes targets in the 39 UTR of the cardiac transcription factor Irx5 mRNA and other cardiac mRNAs, showed a role for this miRNA in cardiac morphogenesis, electrical conduction, and cell cycle control (31). Although little is known about the in vivo effects of specific miRNAs in lung cells, miRNA overexpression experiments together with analyses of effects of concurrent changes in miRNA and mRNA levels suggest that miRNA interactions with miRNA targets in 39 UTRs also play important regulatory roles in lung development (27,28).…”