Application of RNA subcellular fraction estimation method to explore RNA localization regulation

doi:10.1093/g3journal/jkab371

	Application of RNA subcellular fraction estimation method to explore RNA localization regulation
	Dai, Xiaomin1,2,3 ; Li, Yangmengjie 4; Liu, Weizhen1 ; Pan, Xiuqi1 ; Guo, Chenyue1 ; Zhao, Xiaojing1 ; Lv, Jingwen1,2,3 ; Lei, Haixin 4; Zhang, Liye1
	2022-01
发表期刊	G3-GENES GENOMES GENETICS (IF:2.1[JCR-2023],2.5[5-Year])
ISSN	2160-1836
卷号	12 期号:1
发表状态	已发表
DOI	10.1093/g3journal/jkab371
摘要	RNA localization is involved in multiple biological processes. Recent advances in subcellular fractionation-based sequencing approaches uncovered localization pattern on a global scale. Most of existing methods adopt relative localization ratios (such as ratios of separately normalized transcripts per millions of different subcellular fractions without considering the difference in total RNA abundances in different fractions), however, absolute ratios may yield different results on the preference to different cellular compartment. Experimentally, adding external Spike-in RNAs to different fractionation can be used to obtain absolute ratios. In addition, a spike-in independent computational approach based on multiple linear regression model can also be used. However, currently, no custom tool is available. To solve this problem, we developed a method called subcellular fraction abundance estimator to correctly estimate relative RNA abundances of different subcellular fractionations. The ratios estimated by our method were consistent with existing reports. By applying the estimated ratios for different fractions, we explored the RNA localization pattern in cell lines and also predicted RBP motifs that were associated with different localization patterns. In addition, we showed that different isoforms of same genes could exhibit distinct localization patterns. To conclude, we believed our tool will facilitate future subcellular fractionation-related sequencing study to explore the function of RNA localization in various biological problems.
关键词	RNA localization nuclear retention RBP subcellular RNA abundance cis-elements isoform
URL	查看原文
收录类别	SCI ; SCIE
语种	英语
资助项目	National Natural Science Foundation of China[31871332,31670823]
WOS研究方向	Genetics & Heredity
WOS类目	Genetics & Heredity
WOS记录号	WOS:000743786100022
出版者	OXFORD UNIV PRESS INC
引用统计	正在获取...
文献类型	期刊论文
条目标识符	https://kms.shanghaitech.edu.cn/handle/2MSLDSTB/135521
专题	生命科学与技术学院_博士生生命科学与技术学院_PI研究组_张力烨组生命科学与技术学院_硕士生生命科学与技术学院_本科生信息科学与技术学院_硕士生
通讯作者	Lei, Haixin; Zhang, Liye
作者单位	1.ShanghaiTech Univ, Sch Life Sci & Technol, Shanghai 201210, Peoples R China 2.Chinese Acad Sci, CAS Ctr Excellence Mol Cell Sci, Shanghai Inst Biochem & Cell Biol, Shanghai 200031, Peoples R China 3.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 4.Dalian Med Univ, Canc Ctr, Inst Canc Stem Cell, Dalian 116044, Peoples R China
第一作者单位	生命科学与技术学院
通讯作者单位	生命科学与技术学院
第一作者的第一单位	生命科学与技术学院
推荐引用方式 GB/T 7714	Dai, Xiaomin,Li, Yangmengjie,Liu, Weizhen,et al. Application of RNA subcellular fraction estimation method to explore RNA localization regulation[J]. G3-GENES GENOMES GENETICS,2022,12(1).
APA	Dai, Xiaomin.,Li, Yangmengjie.,Liu, Weizhen.,Pan, Xiuqi.,Guo, Chenyue.,...&Zhang, Liye.(2022).Application of RNA subcellular fraction estimation method to explore RNA localization regulation.G3-GENES GENOMES GENETICS,12(1).
MLA	Dai, Xiaomin,et al."Application of RNA subcellular fraction estimation method to explore RNA localization regulation".G3-GENES GENOMES GENETICS 12.1(2022).