Virtual methylome dissection facilitated by single-cell analyses

	Virtual methylome dissection facilitated by single-cell analyses
	Yin, LD; Luo, YT; Xu, XG; Wen, SY; Wu, XW; Lu, XM; Xie, HH
	2019
发表期刊	EPIGENETICS & CHROMATIN
卷号	12 期号:1
摘要	BackgroundNumerous cell types can be identified within plant tissues and animal organs, and the epigenetic modifications underlying such enormous cellular heterogeneity are just beginning to be understood. It remains a challenge to infer cellular composition using DNA methylomes generated for mixed cell populations. Here, we propose a semi-reference-free procedure to perform virtual methylome dissection using the nonnegative matrix factorization (NMF) algorithm.ResultsIn the pipeline that we implemented to predict cell-subtype percentages, putative cell-type-specific methylated (pCSM) loci were first determined according to their DNA methylation patterns in bulk methylomes and clustered into groups based on their correlations in methylation profiles. A representative set of pCSM loci was then chosen to decompose target methylomes into multiple latent DNA methylation components (LMCs). To test the performance of this pipeline, we made use of single-cell brain methylomes to create synthetic methylomes of known cell composition. Compared with highly variable CpG sites, pCSM loci achieved a higher prediction accuracy in the virtual methylome dissection of synthetic methylomes. In addition, pCSM loci were shown to be good predictors of the cell type of the sorted brain cells. The software package developed in this study is available in the GitHub repository (https://github.com/Gavin-Yinld).ConclusionsWe anticipate that the pipeline implemented in this study will be an innovative and valuable tool for the decoding of cellular heterogeneity.
收录类别	sci
语种	英语
文献类型	期刊论文
条目标识符	http://ir.kiz.ac.cn/handle/152453/13148
专题	科研部门_适应性进化与进化医学（吕雪梅）昆明动物研究所
推荐引用方式 GB/T 7714	Yin, LD,Luo, YT,Xu, XG,et al. Virtual methylome dissection facilitated by single-cell analyses[J]. EPIGENETICS & CHROMATIN,2019,12(1).
APA	Yin, LD.,Luo, YT.,Xu, XG.,Wen, SY.,Wu, XW.,...&Xie, HH.(2019).Virtual methylome dissection facilitated by single-cell analyses.EPIGENETICS & CHROMATIN,12(1).
MLA	Yin, LD,et al."Virtual methylome dissection facilitated by single-cell analyses".EPIGENETICS & CHROMATIN 12.1(2019).

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2023022116.pdf（5034KB）	期刊论文	出版稿	开放获取	CC BY-NC-SA	请求全文