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

• Published in: Genome Biology Vol. 16; no. 1; p. 148
• Main Authors: Fan, Xiaoying, Zhang, Xiannian, Wu, Xinglong, Guo, Hongshan, Hu, Yuqiong, Tang, Fuchou, Huang, Yanyi
• Format: Journal Article
• Language: English
• Published: England BioMed Central 23.07.2015
• Subjects: Animals; Blastocyst - metabolism; Cells, Cultured; class; Embryogenesis; Female; Gene expression; Gene Expression Profiling - methods; genome; Genomes; HEK293 Cells; Humans; Method; Mice; Nucleotide sequence; Poly(A); Polyadenylation; Protocol; Ribonucleic acid; RNA; RNA - chemistry; RNA - metabolism; RNA polymerase; sequence analysis; Sequence Analysis, RNA - methods; Single-Cell Analysis; Stem cells; Transcriptome; transcriptomics
• ISSN: 1465-6906; 1474-7596; 1465-6906; 1474-760X; 1465-6914
• DOI: 10.1186/s13059-015-0706-1

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.