Tracing the expression of circular RNAs in human pre-implantation embryos.
PolyA- RNAs have not been widely analyzed in human pre-implantation embryos due to the scarcity of materials. In particular, circular RNA (circRNA), a novel type of polyA- RNA, has not been characterized during human pre-implantation development.



We systematically analyze polyA+ messenger RNAs (mRNAs) and polyA- RNAs in individual human oocytes and pre-implantation embryos using SUPeR-seq. We de novo identify 10,032 circRNAs from 2974 hosting genes. Most of these circRNAs are developmentally stage-specific and dynamically regulated. Many of them are maternally expressed, implying their potentially important regulatory functions in oogenesis and the formation of totipotent zygotes. Comparison between human and mouse embryos reveals both high conservation and clear distinction between these two species. Human pre-implantation embryos generate more types of circRNA compared with mouse embryos and this is associated with a striking increase of the length of the circRNA flanking introns in humans. We also perform RNA de novo assembly and identify novel transcript units, many of which are potentially novel long non-coding RNAs.



This study reports the first analysis of the whole transcriptome comprising both polyA+ mRNAs and polyA- RNAs including circRNAs during human pre-implantation development. It provides an invaluable resource for analyzing the unique function and complex regulatory mechanisms of circRNAs during this process.
Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China.
Yujiao
Y
Dang
Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China.|Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China.
Liying
L
Yan
Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China.
Boqiang
B
Hu
Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China.
Xiaoying
X
Fan
Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China.|Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China.
Yixin
Y
Ren
Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China.|Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China.
Rong
R
Li
Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China.|Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China.
Ying
Y
Lian
Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China.|Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China.
Jie
J
Yan
Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China.
Qingqing
Q
Li
Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China.|Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China.
Yan
Y
Zhang
Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China.|Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China.
Min
M
Li
Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China.|Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China.
Xiulian
X
Ren
Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China.|Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China.
Jin
J
Huang
Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China.|Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China.
Yuqi
Y
Wu
Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China.|Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China.
Ping
P
Liu
Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China.
Lu
L
Wen
Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China.
Chen
C
Zhang
Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China. yanyi@pku.edu.cn.|Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China. yanyi@pku.edu.cn.|College of Engineering, Peking University, Beijing, 100871, China. yanyi@pku.edu.cn.
Yanyi
Y
Huang
Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China. tangfuchou@pku.edu.cn.|Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, 100871, China. tangfuchou@pku.edu.cn.|Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China. tangfuchou@pku.edu.cn.|Center for Molecular and Translational Medicine, Peking University Health Science Center, Beijing, 100191, China. tangfuchou@pku.edu.cn.
Fuchou
F
Tang
Biodynamic Optical Imaging Center & Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China. jie.qiao@263.net.|Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China. jie.qiao@263.net.|Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China. jie.qiao@263.net.|Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing, China. jie.qiao@263.net.
Jie
J
Qiao
D000818:Animals; D004622:Embryo, Mammalian; D047108:Embryonic Development / Q000235:genetics*; D006801:Humans; D007438:Introns / Q000235:genetics; D051379:Mice; D009866:Oogenesis / Q000235:genetics; D012313:RNA / Q000096:biosynthesis / Q000235:genetics*; D000079962:RNA, Circular; D012333:RNA, Messenger / Q000235:genetics; D017423:Sequence Analysis, RNA; D059467:Transcriptome / Q000235:genetics*; D015053:Zygote / Q000254:growth & development
D000079962:RNA, Circular; D012333:RNA, Messenger; D012313:RNA
RNA de novo assembly; SUPeR-seq; circular RNA; human pre-implantation embryos; mRNA quantification