Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos

Xiaoying Fan; Xiannian Zhang; Xinglong Wu; Hongshan Guo; Yuqiong Hu; Fuchou Tang; Yanyi Huang

doi:10.1186/s13059-015-0706-1

Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos

Genome Biol. 2015 Jul 23;16(1):148. doi: 10.1186/s13059-015-0706-1.

Authors

Xiaoying Fan^{1

2}, Xiannian Zhang^{3

4}, Xinglong Wu^{5

6

7}, Hongshan Guo^{8

9}, Yuqiong Hu^{10

11

12}, Fuchou Tang^{13

14

15

16

17}, Yanyi Huang^{18

19

20}

Affiliations

¹ Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing, 100871, China. sharryfan100@gmail.com.
² College of Life Sciences, Peking University, Beijing, 100871, China. sharryfan100@gmail.com.
³ Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing, 100871, China. friedpine@gmail.com.
⁴ College of Engineering, Peking University, Beijing, 100871, China. friedpine@gmail.com.
⁵ Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing, 100871, China. wuxinglong11@sina.com.
⁶ Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China. wuxinglong11@sina.com.
⁷ Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China. wuxinglong11@sina.com.
⁸ Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing, 100871, China. guohongshan1024@gmail.com.
⁹ College of Life Sciences, Peking University, Beijing, 100871, China. guohongshan1024@gmail.com.
¹⁰ Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing, 100871, China. yqhu2012@126.com.
¹¹ Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China. yqhu2012@126.com.
¹² Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China. yqhu2012@126.com.
¹³ Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing, 100871, China. tangfuchou@pku.edu.cn.
¹⁴ College of Life Sciences, Peking University, Beijing, 100871, China. tangfuchou@pku.edu.cn.
¹⁵ Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Peking University, Beijing, 100871, China. tangfuchou@pku.edu.cn.
¹⁶ Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China. tangfuchou@pku.edu.cn.
¹⁷ Center for Molecular and Translational Medicine, Peking University Health Science Center, Beijing, 100191, China. tangfuchou@pku.edu.cn.
¹⁸ Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing, 100871, China. yanyi@pku.edu.cn.
¹⁹ College of Engineering, Peking University, Beijing, 100871, China. yanyi@pku.edu.cn.
²⁰ Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China. yanyi@pku.edu.cn.

Abstract

Circular RNAs (circRNAs) are a new class of non-polyadenylated non-coding RNAs that may play important roles in many biological processes. Here we develop a single-cell universal poly(A)-independent RNA sequencing (SUPeR-seq) method to sequence both polyadenylated and non-polyadenylated RNAs from individual cells. This method exhibits robust sensitivity, precision and accuracy. We discover 2891 circRNAs and 913 novel linear transcripts in mouse preimplantation embryos and further analyze the abundance of circRNAs along development, the function of enriched genes, and sequence features of circRNAs. Our work is key to deciphering regulation mechanisms of circRNAs during mammalian early embryonic development.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Blastocyst / metabolism*
Cells, Cultured
Female
Gene Expression Profiling / methods*
HEK293 Cells
Humans
Mice
RNA / chemistry
RNA / metabolism*
RNA, Circular
Sequence Analysis, RNA / methods*
Single-Cell Analysis
Transcriptome

Substances

RNA, Circular
RNA

Associated data

GEO/GSE53386