Single-cell CAS-seq reveals a class of short PIWI-interacting RNAs in human oocytes

• Published in: Nature communications Vol. 10; no. 1; pp. 3389 - 15
• Main Authors: Yang, Qiyuan, Li, Ronghong, Lyu, Qifeng, Hou, Li, Liu, Zhen, Sun, Qiang, Liu, Miao, Shi, Huijuan, Xu, Beiying, Yin, Mingru, Yan, Zhiguang, Huang, Ying, Liu, Mofang, Li, Yiping, Wu, Ligang
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 29.07.2019; Nature Publishing Group; Nature Portfolio
• Subjects: 38/91; 45/90; 631/136/1455; 631/208/199; 631/337/384/521; 631/61/514/1949; Animals; Antisense RNA; Argonaute Proteins - genetics; Argonaute Proteins - metabolism; Bias; Biochemistry; Biology; Cumulus Cells - cytology; Cumulus Cells - metabolism; DNA methylation; DNA Transposable Elements; Embryo, Mammalian - cytology; Embryo, Mammalian - metabolism; Embryos; Female; Females; Gametocytes; Gene sequencing; Humanities and Social Sciences; Humans; Laboratories; Male; Methylation; Mice; multidisciplinary; Neurosciences; Oocytes; Oocytes - cytology; Oocytes - metabolism; Proteins; Ribonucleic acid; RNA; RNA, Messenger - genetics; RNA, Messenger - metabolism; RNA, Small Interfering - genetics; RNA, Small Interfering - metabolism; Science; Science (multidisciplinary); Sequence Analysis, RNA - methods; Single-Cell Analysis - methods; Testes; Testis - cytology; Testis - metabolism
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-019-11312-8

Small RNAs have important functions. However, small RNAs in primate oocytes remain unexplored. Herein, we develop CAS-seq, a single-cell small RNA sequencing method, and profile the small RNAs in human oocytes and embryos. We discover a class of ~20-nt small RNAs that are predominantly expressed in human and monkey oocytes, but not in mouse oocytes. They are specifically associated with HIWI3 (PIWIL3), whereas significantly shorter than the commonly known PIWI-interacting RNAs (piRNAs), designated as oocyte short piRNAs (os-piRNAs). Notably, the os-piRNAs in human oocytes lack 2’-O-methylation at the 3’ end, a hallmark of the classic piRNAs. In addition, the os-piRNAs have a strong 1U/10 A bias and are enriched on the antisense strands of recently evolved transposable elements (TEs), indicating the potential function of silencing TEs by cleavage. Therefore, our study has identified an oocyte-specific piRNA family with distinct features and provides valuable resources for studying small RNAs in primate oocytes. PIWI-interacting RNAs (piRNAs) are ~25–33 nt small RNAs expressed in animal germ cells. Here, the authors develop a single-cell small RNA sequencing method and report that a class of ~20-nt piRNAs lacking 3′ end 2′-O-methylation are associated with PIWIL3 protein and predominantly expressed in human and monkey oocytes.