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

doi:10.1186/s12859-021-04498-6

	Exploring cell-specific miRNA regulation with single-cell miRNA-mRNA co-sequencing data
	Zhang, Junpeng 1,2; Liu, Lin 3; Xu, Taosheng 4; Zhang, Wu 5; Zhao, Chunwen 2; Li, Sijing 2; Li, Jiuyong 3; Rao, Nini 1; Le, Thuc Duy 3
刊名	BMC BIOINFORMATICS
	2021-12-02
卷号	22
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
ISSN号	1471-2105
DOI	10.1186/s12859-021-04498-6
通讯作者	Zhang, Junpeng(zhangjunpeng411@gmail.com) ; Rao, Nini(raonn@uestc.edu.cn) ; Le, Thuc Duy(thuc.le@unisa.edu.au)
英文摘要	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.
资助项目	National Natural Science Foundation of China[61963001] ; National Natural Science Foundation of China[61702069] ; National Natural Science Foundation of China[61902372] ; National Natural Science Foundation of China[61872405] ; National Natural Science Foundation of China[61720106004] ; Yunnan Fundamental Research Projects[202001AT070024] ; Australian Research Council[DP170101306] ; Natural Science Foundation of Anhui Province[2008085QF292] ; NHMRC[1123042]
WOS关键词	CHRONIC MYELOID-LEUKEMIA ; EXPRESSION ; GENOMICS ; CLUSTER
WOS研究方向	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology
语种	英语
出版者	BMC
WOS记录号	WOS:000725531100002
资助机构	National Natural Science Foundation of China ; Yunnan Fundamental Research Projects ; Australian Research Council ; Natural Science Foundation of Anhui Province ; NHMRC
内容类型	期刊论文
源URL	[http://ir.hfcas.ac.cn:8080/handle/334002/126814]
专题	中国科学院合肥物质科学研究院
通讯作者	Zhang, Junpeng; Rao, Nini; Le, Thuc Duy
作者单位	1.Univ Elect Sci & Technol China, Sch Life Sci & Technol, Ctr Informat Biol, Chengdu 610054, Sichuan, Peoples R China 2.Dali Univ, Sch Engn, Dali 671003, Yunnan, Peoples R China 3.Univ South Australia, UniSA STEM, Mawson Lakes, SA 5095, Australia 4.Chinese Acad Sci, Inst Intelligent Machines, Hefei Inst Phys Sci, Hefei 230031, Peoples R China 5.Dali Univ, Sch Agr & Biol Sci, Dali 671003, Yunnan, Peoples R China
推荐引用方式 GB/T 7714	Zhang, Junpeng,Liu, Lin,Xu, Taosheng,et al. Exploring cell-specific miRNA regulation with single-cell miRNA-mRNA co-sequencing data[J]. BMC BIOINFORMATICS,2021,22.
APA	Zhang, Junpeng.,Liu, Lin.,Xu, Taosheng.,Zhang, Wu.,Zhao, Chunwen.,...&Le, Thuc Duy.(2021).Exploring cell-specific miRNA regulation with single-cell miRNA-mRNA co-sequencing data.BMC BIOINFORMATICS,22.
MLA	Zhang, Junpeng,et al."Exploring cell-specific miRNA regulation with single-cell miRNA-mRNA co-sequencing data".BMC BIOINFORMATICS 22(2021).