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The regulatory epicenter of miRNAs

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Abstract

miRNAs are small non-coding RNAs with average length of ~21 bp. miRNA formation seems to be dependent upon multiple factors besides Drosha and Dicer, in a tissue/stage-specific manner, with interplay of several specific binding factors. In the present study, we have investigated transcription factor binding sites in and around the genomic sequences of precursor miRNAs and RNA-binding protein (RBP) sites in miRNA precursor sequences, analysed and tested in comprehensive manner. Here, we report that miRNA precursor regions are positionally enriched for binding of transcription factors as well as RBPs around the 3′ end of mature miRNA region in 5′ arm. The pattern and distribution of such regulatory sites appears to be a characteristic of precursor miRNA sequences when compared with non-miRNA sequences as negative dataset and tested statistically. When compared with 1 kb upstream regions, a sudden sharp peak for binding sites arises in the enriched zone near the mature miRNA region. An expression-data-based correlation analysis was performed between such miRNAs and their corresponding transcription factors and RBPs for this region. Some specific groups of binding factors and associated miRNAs were identified. We also identified some of the over-represented transcription factors and associated miRNAs with high expression correlation values which could be useful in cancer-related studies. The highly correlated groups were found to host experimentally validated composite regulatory modules, in which Lmo2-GATA1 appeared as the predominant one. For many of RBP–miRNAs associations, co-expression similarity was also evident among the associated miRNA common to given RBPs, supporting the Regulon model, suggesting a common role and common control of these miRNAs by the associated RBPs. Based on our findings, we propose that the observed characteristic distribution of regulatory sites in precursor miRNA sequence regions could be critical in miRNA transcription, processing, stability and formation and are important for therapeutic studies. Our findings also support the recently proposed theory of self-sufficient mode of transcription by miRNAs, which states that miRNA transcription can be carried out in host-independent mode too.

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Acknowledgements

We are thankful to Department of Biotechnology for the fellowship to AJ. MM is thankful to Council of Scientific and Industrial Research, India, for her JRF fellowship. We thank Amit Chaurasia and Dr Mitali Mukerji, IGIB, for sharing TFBS data for human.

The present research work was funded by DBT, India, grant number: BT/PR-11098/BID/07/261/2008 and CSIR grant OLP-0037. We are thankful to Dr PS Ahuja, IHBT, for helping us with internal funding MLP0037. The IHBT communication ID for this manuscript is: 3165.

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  1. Studio of Computational Biology & Bioinformatics, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Council of Scientific & Industrial Research, Palampur, 176 061, HP, India

    Ashwani Jha, Mrigaya Mehra & Ravi Shankar

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  1. Ashwani Jha
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  2. Mrigaya Mehra
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  3. Ravi Shankar
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Correspondence to Ravi Shankar.

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Corresponding editor: Reiner A Veitia

[Jha A, Mehra M and Shankar R 2011 The regulatory epicenter of miRNAs. J. Biosci. 36 621–638] DOI 10.1007/s12038-011-9109-y

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Jha, A., Mehra, M. & Shankar, R. The regulatory epicenter of miRNAs. J Biosci 36, 621–638 (2011). https://doi.org/10.1007/s12038-011-9109-y

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