Exploring cell-specific miRNA regulation with single-cell miRNA-mRNA co-sequencing data

BMC Bioinformatics

Nini Rao¹  Junpeng Zhang²  Taosheng Xu³  Wu Zhang⁴  Sijing Li⁵  Chunwen Zhao⁵  Jiuyong Li⁶  Lin Liu⁶  Thuc Duy Le⁶ 

[1] Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, 610054, Chengdu, Sichuan, China;Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, 610054, Chengdu, Sichuan, China;School of Engineering, Dali University, 671003, Dali, Yunnan, China;Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, 230031, Hefei, China;School of Agriculture and Biological Sciences, Dali University, 671003, Dali, Yunnan, China;School of Engineering, Dali University, 671003, Dali, Yunnan, China;UniSA STEM, University of South Australia, 5095, Mawson Lakes, SA, Australia;

关键词: miRNA;    mRNA;    Single-cell miRNA-mRNA co-sequencing;    Pseudo-cell interpolation;    Cell-specific miRNA regulation;    Single-cell clustering analysis;    Cell–cell crosstalk;    Chronic myelogenous leukemia;   

DOI  :  10.1186/s12859-021-04498-6

来源: Springer

【 摘 要 】

BackgroundExisting computational methods for studying miRNA regulation are mostly based on bulk miRNA and mRNA expression data. However, bulk data only allows the analysis of miRNA regulation regarding a group of cells, rather than the miRNA regulation unique to individual cells. Recent advance in single-cell miRNA-mRNA co-sequencing technology has opened a way for investigating miRNA regulation at single-cell level. However, as currently single-cell miRNA-mRNA co-sequencing data is just emerging and only available at small-scale, there is a strong need of novel methods to exploit existing single-cell data for the study of cell-specific miRNA regulation.ResultsIn this work, we propose a new method, CSmiR (Cell-Specific miRNA regulation) to combine single-cell miRNA-mRNA co-sequencing data and putative miRNA-mRNA binding information to identify miRNA regulatory networks at the resolution of individual cells. We apply CSmiR to the miRNA-mRNA co-sequencing data in 19 K562 single-cells to identify cell-specific miRNA-mRNA regulatory networks for understanding miRNA regulation in each K562 single-cell. By analyzing the obtained cell-specific miRNA-mRNA regulatory networks, we observe that the miRNA regulation in each K562 single-cell is unique. Moreover, we conduct detailed analysis on the cell-specific miRNA regulation associated with the miR-17/92 family as a case study. The comparison results indicate that CSmiR is effective in predicting cell-specific miRNA targets. Finally, through exploring cell–cell similarity matrix characterized by cell-specific miRNA regulation, CSmiR provides a novel strategy for clustering single-cells and helps to understand cell–cell crosstalk.ConclusionsTo the best of our knowledge, CSmiR is the first method to explore miRNA regulation at a single-cell resolution level, and we believe that it can be a useful method to enhance the understanding of cell-specific miRNA regulation.

【 授权许可】

CC BY