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The composition dynamics of transposable elements in human blastocysts

Journal of Human Genetics volume 68, pages 681–688 (2023)Cite this article

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Abstract

Transposable elements (TEs) are mobile DNA sequences that can replicate themselves and play significant roles in embryo development and chromosomal structure remodeling. In this study, we investigated the variation of TEs in blastocysts with different parental genetic backgrounds. We analyzed the proportions of 1137 TEs subfamilies from six classes at the DNA level using Bowtie2 and PopoolationTE2 in 196 blastocysts with abnormal parental chromosomal diseases. Our findings revealed that the parental karyotype was the dominant factor influencing TEs frequencies. Out of the 1116 subfamilies, different frequencies were observed in blastocysts with varying parental karyotypes. The development stage of blastocysts was the second most crucial factor influencing TEs proportions. A total of 614 subfamilies exhibited different proportions at distinct blastocyst stages. Notably, subfamily members belonging to the Alu family showed a high proportion at stage 6, while those from the LINE class exhibited a high proportion at stage 3 and a low proportion at stage 6. Moreover, the proportions of some TEs subfamilies also varied depending on blastocyst karyotype, inner cell mass status, and outer trophectoderm status. We found that 48 subfamilies displayed different proportions between balanced and unbalanced blastocysts. Additionally, 19 subfamilies demonstrated varying proportions among different inner cell mass scores, and 43 subfamilies exhibited different proportions among outer trophectoderm scores. This study suggests that the composition of TEs subfamilies may be influenced by various factors and undergoes dynamic modulation during embryo development.

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Data availability

The raw sequence data reported in this paper have been deposited in the Genome Sequence Archive in National Genomics Data Center, China National Center for Bioinformation/Beijing Institute of Genomics, Chinese Academy of Sciences (GSA-Human: HRA003662) that are publicly accessible at https://ngdc.cncb.ac.cn/gsa-human.

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Acknowledgements

This work was supported by grants from the National Natural Science Foundation of China (32170641 and 81872295 to YG), Guangdong Science and Technology Department (2021A1515011183 to YG and 2020B1212060018).

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Author notes

  1. These authors contributed equally: Jian Li, Ping Yuan.

Authors and Affiliations

  1. Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China

    Jian Li

  2. IVF Center, Department of Obstetrics and Gynecology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China

    Ping Yuan, Qingxue Zhang & Wenjun Wang

  3. IVF Center, The First People’s Hospital of Kashi Prefecture, Kashi, China

    Ping Yuan

  4. Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China

    Guangwei Ma

  5. Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China

    Ying Liu & Yabin Guo

  6. Reproductive Medical Center, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou, Henan, China

    Ying Liu

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Contributions

JL and YG designed the project. JL and PY collected and arranged the sequencing and clinical data. JL, GM, YL, QZ and YG analyzed the data. JL, PY and YG wrote the manuscript. WW and YG supervised the study and edited the manuscript.

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Correspondence to Wenjun Wang or Yabin Guo.

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Li, J., Yuan, P., Ma, G. et al. The composition dynamics of transposable elements in human blastocysts. J Hum Genet 68, 681–688 (2023). https://doi.org/10.1038/s10038-023-01169-7

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