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

Abstract Background Existing 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 ad...

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Autores principales:	Junpeng Zhang, Lin Liu, Taosheng Xu, Wu Zhang, Chunwen Zhao, Sijing Li, Jiuyong Li, Nini Rao, Thuc Duy Le
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	miRNA mRNA Single-cell miRNA-mRNA co-sequencing Pseudo-cell interpolation Cell-specific miRNA regulation Single-cell clustering analysis Computer applications to medicine. Medical informatics R858-859.7 Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/b77154efc5954fb7be9a514def7e611a
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spelling	oai:doaj.org-article:b77154efc5954fb7be9a514def7e611a2021-12-05T12:08:40ZExploring cell-specific miRNA regulation with single-cell miRNA-mRNA co-sequencing data10.1186/s12859-021-04498-61471-2105https://doaj.org/article/b77154efc5954fb7be9a514def7e611a2021-12-01T00:00:00Zhttps://doi.org/10.1186/s12859-021-04498-6https://doaj.org/toc/1471-2105Abstract Background Existing 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. Results In 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. Conclusions To 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.Junpeng ZhangLin LiuTaosheng XuWu ZhangChunwen ZhaoSijing LiJiuyong LiNini RaoThuc Duy LeBMCarticlemiRNAmRNASingle-cell miRNA-mRNA co-sequencingPseudo-cell interpolationCell-specific miRNA regulationSingle-cell clustering analysisComputer applications to medicine. Medical informaticsR858-859.7Biology (General)QH301-705.5ENBMC Bioinformatics, Vol 22, Iss 1, Pp 1-19 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	miRNA mRNA Single-cell miRNA-mRNA co-sequencing Pseudo-cell interpolation Cell-specific miRNA regulation Single-cell clustering analysis Computer applications to medicine. Medical informatics R858-859.7 Biology (General) QH301-705.5
spellingShingle	miRNA mRNA Single-cell miRNA-mRNA co-sequencing Pseudo-cell interpolation Cell-specific miRNA regulation Single-cell clustering analysis Computer applications to medicine. Medical informatics R858-859.7 Biology (General) QH301-705.5 Junpeng Zhang Lin Liu Taosheng Xu Wu Zhang Chunwen Zhao Sijing Li Jiuyong Li Nini Rao Thuc Duy Le Exploring cell-specific miRNA regulation with single-cell miRNA-mRNA co-sequencing data
description	Abstract Background Existing 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. Results In 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. Conclusions To 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.
format	article
author	Junpeng Zhang Lin Liu Taosheng Xu Wu Zhang Chunwen Zhao Sijing Li Jiuyong Li Nini Rao Thuc Duy Le
author_facet	Junpeng Zhang Lin Liu Taosheng Xu Wu Zhang Chunwen Zhao Sijing Li Jiuyong Li Nini Rao Thuc Duy Le
author_sort	Junpeng Zhang
title	Exploring cell-specific miRNA regulation with single-cell miRNA-mRNA co-sequencing data
title_short	Exploring cell-specific miRNA regulation with single-cell miRNA-mRNA co-sequencing data
title_full	Exploring cell-specific miRNA regulation with single-cell miRNA-mRNA co-sequencing data
title_fullStr	Exploring cell-specific miRNA regulation with single-cell miRNA-mRNA co-sequencing data
title_full_unstemmed	Exploring cell-specific miRNA regulation with single-cell miRNA-mRNA co-sequencing data
title_sort	exploring cell-specific mirna regulation with single-cell mirna-mrna co-sequencing data
publisher	BMC
publishDate	2021
url	https://doaj.org/article/b77154efc5954fb7be9a514def7e611a
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Exploring cell-specific miRNA regulation with single-cell miRNA-mRNA co-sequencing data

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