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Consistent isomiR expression patterns and 3′ addition events in miRNA gene clusters and families implicate functional and evolutionary relationships

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Abstract

3′ addition events in miRNAs are widely detected and may contribute to miRNA stability, but little is known about details of the events in miRNA gene clusters and families. Here, we performed a comprehensive analysis of isomiR expression patterns and 3′ additions in miRNA gene clusters and families by analyzing high-throughput sequencing dataset. According to dominant modified isomiRs, miRNA members in many miRNA gene clusters and families showed the same 3′ additional non-template nucleotides. Although clustered miRNAs and homologous miRNAs had consistent or inconsistent expression levels, we found many of them showed consistent expression patterns at isomiR levels. These findings revealed similar processing mechanism and 3′ modification event of miRNAs in gene clusters and families through miRNA maturation process. The consistent maturation mechanism may contribute to co-regulate biological processes, and may originate from ancestral miRNA genes through complex duplication history.

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Acknowledgments

The work was supported by the project 30871393 from National Natural Science Foundation of China and funded by Tsinghua National Laboratory for Information Science and Technology (TNList) Cross-discipline Foundation. The work was also supported by a research Grant from the Innovation Project for Graduate Student of Jiangsu Province (No. CX10B_081Z), the Scientific Research Foundation of Graduate School of Southeast University, Science and Technology Project in Nanjing (201001095) and Pre-Research Project for National Natural Science Foundation supported by Southeast University (KJ2010442).

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Authors and Affiliations

  1. State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China

    Li Guo, Hailing Li, Jiafeng Lu, Qi Yang & Zuhong Lu

  2. Key Lab for Modern Toxicology, Department of Epidemiology and Biostatistics and Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, 210029, China

    Li Guo

  3. Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210046, China

    Tingming Liang

  4. Key Laboratory of Child Development and Learning Science of Ministry of Education, Southeast University, Nanjing, 210096, China

    Qinyu Ge & Zuhong Lu

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  1. Li Guo
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  2. Hailing Li
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  3. Tingming Liang
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  4. Jiafeng Lu
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  5. Qi Yang
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  6. Qinyu Ge
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  7. Zuhong Lu
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Corresponding authors

Correspondence to Li Guo or Zuhong Lu.

Additional information

Li Guo, Hailing Li, and Tingming Liang contributed equally to this work.

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11033_2012_1493_MOESM1_ESM.tif

Fig. S1 The contribution of cross-mapping between homologous miRNAs. The three isomiRs can simultaneously map to hsa-miR-23a and hsa-miR-23b. (TIFF 34 kb)

Supplementary material 2 (DOC 75 kb)

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Guo, L., Li, H., Liang, T. et al. Consistent isomiR expression patterns and 3′ addition events in miRNA gene clusters and families implicate functional and evolutionary relationships. Mol Biol Rep 39, 6699–6706 (2012). https://doi.org/10.1007/s11033-012-1493-3

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  • DOI: https://doi.org/10.1007/s11033-012-1493-3

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