Abstract
Oocyte-specific isoforms play crucial roles in oocyte maturation, while current understanding of the oocyte transcriptome is mainly focused on gene level. Here, we utilize single-cell full-length isoform sequencing to detect entire transcripts in human and mouse oocytes. Isoform diversity during oocyte maturation is systematically profiled, including 7154 and 4875 putative novel human and mouse transcripts, respectively. More than half of novel isoforms are categorized as novel-not-in-catalog (NNC) and may serve specific functions in oocytes. For example, ARHGAP18 mainly encoded by novel isoforms colocalizes with microtubules, and targeted knockdown of novel isoforms disrupts oocyte maturation. Moreover, approximately 30% of NNC isoforms are derived from transposable elements, and their incorporation within transcripts could enhance isoform stability during oocyte maturation. Altogether, our findings represent a valuable resource showcasing the complexity and diversity of RNA isoforms in oocytes, as well as transposable element co-option for novel isoform generation and isoform stability enhancement.
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Data availability
All the raw sequencing data generated in this study have been deposited in the Genome Sequence Archive for human (GSA-Human) and Genome Sequence Archive of China National Center for Bioinformation (Human: HRA006583, Mouse: CRA014675). The processed data including assembled transcriptomes (annotated gtf files), new splice junctions and expression tables are publicly available in the OMIX, China National Center for Bioinformation (OMIX012135 [https://ngdc.cncb.ac.cn/omix/release/OMIX012135], OMIX012137). Publicly available oocyte short-read RNA-seq datasets used in this work were retrieved from SRA (SRP011546 [https://www.ncbi.nlm.nih.gov/sra/?term=SRP011546], SRP285893, SRP361878, SRP086707, SRP189718, SRP062106). Publicly available deepCAGE and PAIso-seq datasets used in this work were retrieved from FANTOM5 [https://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/, https://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_latest/basic/human.tissue.hCAGE/], GSA-Human (HRA001288 [https://ngdc.cncb.ac.cn/gsa-human/browse/HRA001288]) and SRA under the accession number PRJNA529588 [https://www.ncbi.nlm.nih.gov/biosample?Db=biosample&DbFrom=bioproject&Cmd=Link&LinkName=bioproject_biosample&LinkReadableName=BioSample&ordinalpos=1&IdsFromResult=529588]. Publicly available multi-tissue short-read RNA-seq data used in this work was retrieved from ENCODE portal (https://www.encodeproject.org/) with the following identifiers: ENCSR278TQR, ENCSR197GCF, ENCSR197GCF, ENCSR344MQK, ENCSR029KNZ, ENCSR000AEU, ENCSR000AFB, ENCSR621PZI, ENCSR096LTX, ENCSR150QJY, ENCSR504NIU, ENCSR759TPN, ENCSR773COB. UCSC genome browser sessions have been created for the human and mouse assembled transcriptomes (https://genome.ucsc.edu/s/kratos12138/Human%20oocyte%20long%2Dread%20transcriptome; https://genome.ucsc.edu/s/kratos12138/Mouse%20oocyte%20long%2Dread%20transcriptome). Source data are provided with this paper.
Code availability
All analyses utilized publicly available algorithms and software. The code used to generate the figures has been deposited on GitHub (https://github.com/Kratos12138/Oocyte-long-read-transcriptome).
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Acknowledgements
We thank the generous donors whose contributions have enabled this research. We thank all the staff in the Center for Reproductive Medicine of Peking University Third Hospital. This project is funded by National Natural Science Foundation of China (82288102 to L.Y., 82125013 to L.Y., 82201838 to P.Y., 82522039 to P.Y.), National Key Research and Development Program (2022YFC2702200 to P.Y., 2023YFA1800300 to L.Y., 2024YFA1802100 to J.Q.), Peking University Third Hospital Fund for Interdisciplinary Research (BYSYJC2023001 to P.Y.), Clinical Medicine Plus X - Young Scholars Project, Peking University, the Fundamental Research Funds for the Central Universities (PKU2024LCXQ005 to P.Y.), and CAMS Innovation Fund for Medical Sciences (2019-I2M-5-001 to J.Q.).
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J.Q., P.Y., L.Y., and Q.L. supervised the project. Y.W., W.W., Yujun Liu, Q.L., P.Y., L.Y., and J.Q. conceived and formulated the concept. Y.W. and Yujun Liu collected the samples and performed all experiments including library construction, single-cell sequencing, siRNA knock down, RNA stability assay, RT-qPCR, western blotting, and immunofluorescence under the supervision of P.Y., L.Y., and J.Q. W.W. and Y.H. conducted bioinformatics analyses and visualization on full-length isoform sequencing and next generation sequencing data under the supervision of P.Y. M.Y., N.W., X.W., L.D., Y.K. and Ying Lian assisted with samples collection and siRNA injection. Y.X., Z.D., and L.C. assisted with ESCs and GCs collection. Y.W., W.W., Yujun Liu, Y.H., and H.S. drafted the initial manuscript. All authors discussed the results and reviewed the manuscript.
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Wang, Y., Wang, W., Liu, Y. et al. Single-oocyte full-length isoform sequencing unveils the impact of transposable elements on RNA diversity and stability. Nat Commun (2026). https://doi.org/10.1038/s41467-026-71425-9
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DOI: https://doi.org/10.1038/s41467-026-71425-9
