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

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 in...

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Autores principales: Fan, Xiaoying, Zhang, Xiannian, Wu, Xinglong, Guo, Hongshan, Hu, Yuqiong, Tang, Fuchou, Huang, Yanyi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4511241/
https://www.ncbi.nlm.nih.gov/pubmed/26201400
http://dx.doi.org/10.1186/s13059-015-0706-1
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author Fan, Xiaoying
Zhang, Xiannian
Wu, Xinglong
Guo, Hongshan
Hu, Yuqiong
Tang, Fuchou
Huang, Yanyi
author_facet Fan, Xiaoying
Zhang, Xiannian
Wu, Xinglong
Guo, Hongshan
Hu, Yuqiong
Tang, Fuchou
Huang, Yanyi
author_sort Fan, Xiaoying
collection PubMed
description 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-015-0706-1) contains supplementary material, which is available to authorized users.
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spelling pubmed-45112412015-07-23 Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos Fan, Xiaoying Zhang, Xiannian Wu, Xinglong Guo, Hongshan Hu, Yuqiong Tang, Fuchou Huang, Yanyi Genome Biol Method 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-015-0706-1) contains supplementary material, which is available to authorized users. BioMed Central 2015-07-23 2015 /pmc/articles/PMC4511241/ /pubmed/26201400 http://dx.doi.org/10.1186/s13059-015-0706-1 Text en © Fan et al. 2015 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Method
Fan, Xiaoying
Zhang, Xiannian
Wu, Xinglong
Guo, Hongshan
Hu, Yuqiong
Tang, Fuchou
Huang, Yanyi
Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos
title Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos
title_full Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos
title_fullStr Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos
title_full_unstemmed Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos
title_short Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos
title_sort single-cell rna-seq transcriptome analysis of linear and circular rnas in mouse preimplantation embryos
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4511241/
https://www.ncbi.nlm.nih.gov/pubmed/26201400
http://dx.doi.org/10.1186/s13059-015-0706-1
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