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Characterization of the long noncoding RNA transcriptome in human preimplantation embryo development

  • Embryo Biology
  • Published:
Journal of Assisted Reproduction and Genetics Aims and scope Submit manuscript

Abstract

Purpose

Infertility remains a human health burden globally. Only a fraction of embryos produced via assisted reproductive technologies (ARTs) develop to the blastocyst stage in vitro. lncRNA abundance changes significantly during human early embryonic development, indicating vital regulatory roles of lncRNAs in this process. The aim of this study is to obtain insights into the transcriptional basis of developmental events.

Methods

scRNA-seq data and SUPeR-seq data were used to investigate the lncRNA profiles of human preimplantation embryos. The top 50 highly expressed unique and shared lncRNAs in each stage of preimplantation development were identified. Comparative analysis of the two datasets was used to verify the consistent expression patterns of the lncRNAs. Differentially expressed lncRNAs were identified and subjected to functional enrichment analysis.

Results

The lncRNA profiles of human preimplantation embryos in the E-MTAB-3929 dataset were similar to those in the GSE71318 dataset. The ratios of overlap among the top 50 highly expressed lncRNAs between two pairs of stages (2-cell stage vs. 4-cell stage and 8-cell stage vs. morula) were aberrantly low compared with those between other stages. Each stage of preimplantation development exhibited unique and shared lncRNAs among the top 50 highly expressed lncRNAs. Among the between-group comparisons, the 2-cell stage vs. 4-cell stage showed the highest number of differentially expressed lncRNAs. Functional enrichment analysis revealed that differentially expressed lncRNAs and their associated super enhancers and RNA binding proteins (RBPs) are closely involved in regulating embryonic development. These lncRNAs could function as important cell markers for distinguishing fetal germ cells.

Conclusions

Our study paves the way for understanding the regulation of developmental events, which might be beneficial for improved reproductive outcomes.

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Data availability

All data generated or analyzed during this study are included in this published article and its supplementary information files.

Abbreviations

ARTs :

Assisted reproductive technologies

RBPs :

RNA binding proteins

2PN :

Two-pronuclear

TE :

Trophectoderm cells

ICM :

The inner cell mass

lncRNAs :

Long noncoding RNAs

MZT :

Maternal-to-zygotic transition

ZGA :

Zygotic gene activation

References

  1. Elhussein OG, Ahmed MA, Suliman SO, Yahya LI, Adam I. Epidemiology of infertility and characteristics of infertile couples requesting assisted reproduction in a low-resource setting in Africa. Sudan Fertil Res Pract. 2019;5:7. https://doi.org/10.1186/s40738-019-0060-1.

    Article  PubMed  Google Scholar 

  2. Vander Borght M, Wyns C. Fertility and infertility: Definition and epidemiology. Clin Biochem. 2018;62:2–10. https://doi.org/10.1016/j.clinbiochem.2018.03.012.

    Article  PubMed  Google Scholar 

  3. Sun H, Gong TT, Jiang YT, Zhang S, Zhao YH, Wu QJ. Global, regional, and national prevalence and disability-adjusted life-years for infertility in 195 countries and territories, 1990–2017: results from a global burden of disease study, 2017. Aging (Albany NY). 2019;11:10952–91. https://doi.org/10.18632/aging.102497.

    Article  PubMed  Google Scholar 

  4. Kobayashi T, Ishikawa H, Ishii K, Sato A, Nakamura N, Saito Y, et al. Time-lapse monitoring of fertilized human oocytes focused on the incidence of 0PN embryos in conventional in vitro fertilization cycles. Sci Rep. 2021;11:18862. https://doi.org/10.1038/s41598-021-98312-1.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Fang H, Luo Z, Lin C. Epigenetic reorganization during early embryonic lineage specification. Genes Genomics. 2022;44:379–87. https://doi.org/10.1007/s13258-021-01213-w.

    Article  CAS  PubMed  Google Scholar 

  6. Liu W, Chen J, Yang C, Lee KF, Lee YL, Chiu PC, et al. Expression of microRNA let-7 in cleavage embryos modulates cell fate determination and formation of mouse blastocystsdagger. Biol Reprod. 2022;107:1452–63. https://doi.org/10.1093/biolre/ioac181.

    Article  PubMed  Google Scholar 

  7. Wamaitha SE, Niakan KK. Human Pre-gastrulation Development. Curr Top Dev Biol. 2018;128:295–338. https://doi.org/10.1016/bs.ctdb.2017.11.004.

    Article  CAS  PubMed  Google Scholar 

  8. Niakan KK, Han J, Pedersen RA, Simon C, Pera RA. Human pre-implantation embryo development. Development. 2012;139:829–41. https://doi.org/10.1242/dev.060426.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Mattick JS, Amaral PP, Carninci P, Carpenter S, Chang HY, Chen LL, et al. Long non-coding RNAs: definitions, functions, challenges and recommendations. Nat Rev Mol Cell Biol. 2023. https://doi.org/10.1038/s41580-022-00566-8.

    Article  PubMed  Google Scholar 

  10. Sun W, Yang Y, Xu C, Guo J. Regulatory mechanisms of long noncoding RNAs on gene expression in cancers. Cancer Genet. 2017;216–217:105–10. https://doi.org/10.1016/j.cancergen.2017.06.003.

    Article  CAS  PubMed  Google Scholar 

  11. Han P, Chang CP. Long non-coding RNA and chromatin remodeling. RNA Biol. 2015;12:1094–8. https://doi.org/10.1080/15476286.2015.1063770.

    Article  PubMed  PubMed Central  Google Scholar 

  12. Long Y, Wang X, Youmans DT, Cech TR. How do lncRNAs regulate transcription? Sci Adv. 2017;3:eaao2110. https://doi.org/10.1126/sciadv.aao2110.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Sebastian-delaCruz M, Gonzalez-Moro I, Olazagoitia-Garmendia A, Castellanos-Rubio A, Santin I. The Role of lncRNAs in Gene Expression Regulation through mRNA Stabilization. Noncoding RNA. 2021;7:3. https://doi.org/10.3390/ncrna7010003

  14. Karakas D, Ozpolat B. The Role of LncRNAs in Translation. Noncoding RNA. 2021;7:16. https://doi.org/10.3390/ncrna7010016

  15. Bouckenheimer J, Assou S, Riquier S, Hou C, Philippe N, Sansac C, et al. Long non-coding RNAs in human early embryonic development and their potential in ART. Hum Reprod Update. 2016;23:19–40. https://doi.org/10.1093/humupd/dmw035.

    Article  CAS  PubMed  Google Scholar 

  16. Dang Y, Yan L, Hu B, Fan X, Ren Y, Li R, et al. Tracing the expression of circular RNAs in human pre-implantation embryos. Genome Biol. 2016;17:130. https://doi.org/10.1186/s13059-016-0991-3.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Petropoulos S, Edsgard D, Reinius B, Deng Q, Panula SP, Codeluppi S, et al. Single-cell RNA-Seq reveals lineage and X chromosome dynamics in human preimplantation embryos. Cell. 2016;165:1012–26. https://doi.org/10.1016/j.cell.2016.03.023.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Tesarik J. Control of maternal-to-zygotic transition in human embryos and other animal species (especially mouse): similarities and differences. Int J Mol Sci. 2022;23:8562. https://doi.org/10.3390/ijms23158562

  19. Viegas JO, Meshorer E. the princess and the P: Pluripotent stem cells and P-bodies. Cell Stem Cell. 2019;25:589–91. https://doi.org/10.1016/j.stem.2019.10.008.

    Article  CAS  PubMed  Google Scholar 

  20. Viegas JO, Azad GK, Lv Y, Fishman L, Paltiel T, Pattabiraman S, et al. RNA degradation eliminates developmental transcripts during murine embryonic stem cell differentiation via CAPRIN1-XRN2. Dev Cell. 2022;57:2731-2744e2735. https://doi.org/10.1016/j.devcel.2022.11.014.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Ma X, Renda MJ, Wang L, Cheng EC, Niu C, Morris SW, et al. Rbm15 modulates Notch-induced transcriptional activation and affects myeloid differentiation. Mol Cell Biol. 2007;27:3056–64. https://doi.org/10.1128/MCB.01339-06.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Neumann DP, Goodall GJ, Gregory PA. The Quaking RNA-binding proteins as regulators of cell differentiation. Wiley Interdiscip Rev RNA. 2022;13:e1724. https://doi.org/10.1002/wrna.1724.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Li J, Yang Y, Fan J, Xu H, Fan L, Li H, Zhao RC. Long noncoding RNA ANCR inhibits the differentiation of mesenchymal stem cells toward definitive endoderm by facilitating the association of PTBP1 with ID2. Cell Death Dis. 2019;10:492. https://doi.org/10.1038/s41419-019-1738-3.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Chembazhi UV, Tung WS, Hwang H, Wang Y, Lalwani A, Nguyen KL, et al. PTBP1 controls intestinal epithelial regeneration through post-transcriptional regulation of gene expression. Nucleic Acids Res. 2023. https://doi.org/10.1093/nar/gkad042.

    Article  PubMed  PubMed Central  Google Scholar 

  25. Kim J, Muraoka M, Okada H, Toyoda A, Ajima R, Saga Y. The RNA helicase DDX6 controls early mouse embryogenesis by repressing aberrant inhibition of BMP signaling through miRNA-mediated gene silencing. PLoS Genet. 2022;18:e1009967. https://doi.org/10.1371/journal.pgen.1009967.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Cirera-Salinas D, Yu J, Bodak M, Ngondo RP, Herbert KM, Ciaudo C. Noncanonical function of DGCR8 controls mESC exit from pluripotency. J Cell Biol. 2017;216:355–66. https://doi.org/10.1083/jcb.201606073.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Yamaji M, Tanaka T, Shigeta M, Chuma S, Saga Y, Saitou M. Functional reconstruction of NANOS3 expression in the germ cell lineage by a novel transgenic reporter reveals distinct subcellular localizations of NANOS3. Reproduction. 2010;139:381–93. https://doi.org/10.1530/REP-09-0373.

    Article  CAS  PubMed  Google Scholar 

  28. You KT, Park J, Kim VN. Role of the small subunit processome in the maintenance of pluripotent stem cells. Genes Dev. 2015;29:2004–9. https://doi.org/10.1101/gad.267112.115.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Zhang J, Ratanasirintrawoot S, Chandrasekaran S, Wu Z, Ficarro SB, Yu C, et al. LIN28 regulates stem cell metabolism and conversion to primed pluripotency. Cell Stem Cell. 2016;19:66–80. https://doi.org/10.1016/j.stem.2016.05.009.

    Article  CAS  PubMed  Google Scholar 

  30. Adachi K, Suemori H, Yasuda SY, Nakatsuji N, Kawase E. Role of SOX2 in maintaining pluripotency of human embryonic stem cells. Genes Cells. 2010;15:455–70. https://doi.org/10.1111/j.1365-2443.2010.01400.x.

    Article  CAS  PubMed  Google Scholar 

  31. Pan G, Thomson JA. Nanog and transcriptional networks in embryonic stem cell pluripotency. Cell Res. 2007;17:42–9. https://doi.org/10.1038/sj.cr.7310125.

    Article  CAS  PubMed  Google Scholar 

  32. Xu C, Zhang Y, Wang Q, Xu Z, Jiang J, Gao Y, et al. Long non-coding RNA GAS5 controls human embryonic stem cell self-renewal by maintaining NODAL signalling. Nat Commun. 2016;7:13287. https://doi.org/10.1038/ncomms13287.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Zhu Y, Liu Q, Liao M, Diao L, Wu T, Liao W, et al. Overexpression of lncRNA EPB41L4A-AS1 induces metabolic reprogramming in trophoblast cells and placenta tissue of miscarriage. Mol Ther Nucleic Acids. 2019;18:518–32. https://doi.org/10.1016/j.omtn.2019.09.017.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Hupalowska A, Jedrusik A, Zhu M, Bedford MT, Glover DM, Zernicka-Goetz M. CARM1 and paraspeckles regulate pre-implantation mouse embryo development. Cell. 2018;175:1902-1916e1913. https://doi.org/10.1016/j.cell.2018.11.027.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Nakagawa S, Shimada M, Yanaka K, Mito M, Arai T, Takahashi E, et al. The lncRNA Neat1 is required for corpus luteum formation and the establishment of pregnancy in a subpopulation of mice. Development. 2014;141:4618–27. https://doi.org/10.1242/dev.110544.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Peyny M, Jarrier-Gaillard P, Boulanger L, Daniel N, Lavillatte S, Cadoret V, et al. Investigating the role of BCAR4 in ovarian physiology and female fertility by genome editing in rabbit. Sci Rep. 2020;10:4992. https://doi.org/10.1038/s41598-020-61689-6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Lu W, Yu J, Shi F, Zhang J, Huang R, Yin S, et al. The long non-coding RNA Snhg3 is essential for mouse embryonic stem cell self-renewal and pluripotency. Stem Cell Res Ther. 2019;10:157. https://doi.org/10.1186/s13287-019-1270-5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Aoki F. Zygotic gene activation in mice: profile and regulation. J Reprod Dev. 2022;68:79–84. https://doi.org/10.1262/jrd.2021-129.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Ko MS. Zygotic genome activation revisited: Looking through the expression and function of Zscan4. Curr Top Dev Biol. 2016;120:103–24. https://doi.org/10.1016/bs.ctdb.2016.04.004.

    Article  CAS  PubMed  Google Scholar 

  40. Chen X, Liu Y, Xu C, Ba L, Liu Z, Li X, et al. QKI is a critical pre-mRNA alternative splicing regulator of cardiac myofibrillogenesis and contractile function. Nat Commun. 2021;12:89. https://doi.org/10.1038/s41467-020-20327-5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Paz S, Ritchie A, Mauer C, Caputi M. The RNA binding protein SRSF1 is a master switch of gene expression and regulation in the immune system. Cytokine Growth Factor Rev. 2021;57:19–26. https://doi.org/10.1016/j.cytogfr.2020.10.008.

    Article  CAS  PubMed  Google Scholar 

  42. Chen CY, Chan CH, Chen CM, Tsai YS, Tsai TY, Wu Lee YH, You LR. Targeted inactivation of murine Ddx3x: essential roles of Ddx3x in placentation and embryogenesis. Hum Mol Genet. 2016;25:2905–22. https://doi.org/10.1093/hmg/ddw143.

    Article  CAS  PubMed  Google Scholar 

  43. Pan H, Schultz RM. Sox2 modulates reprogramming of gene expression in two-cell mouse embryos. Biol Reprod. 2011;85:409–16. https://doi.org/10.1095/biolreprod.111.090886.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Grubelnik G, Bostjancic E, Pavlic A, Kos M, Zidar N. NANOG expression in human development and cancerogenesis. Exp Biol Med (Maywood). 2020;245:456–64. https://doi.org/10.1177/1535370220905560.

    Article  CAS  PubMed  Google Scholar 

  45. Onichtchouk D, Driever W. Zygotic genome activators, Developmental timing, and pluripotency. Curr Top Dev Biol. 2016;116:273–97. https://doi.org/10.1016/bs.ctdb.2015.12.004.

    Article  CAS  PubMed  Google Scholar 

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Funding

This work was supported by the Natural Science Foundation of Inner Mongolia (2020BS08002); Startup Foundation for Advanced Talents of Inner Mongolia; Program for Young Talents of Science and Technology in Universities of Inner Mongolia Autonomous Region (NJYT22014); and the Doctoral Scientific Research Foundation of the Affiliated Hospital of Inner Mongolia Medical University (NYFY BS 202111).

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Author notes

  1. Le Zhang and Hailong Sun contributed equally.

Authors and Affiliations

  1. Center for Reproductive Medicine, the Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010050, Inner Mongolia, China

    Le Zhang, Hailong Sun & Xiujuan Chen

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  1. Le Zhang
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Contributions

XC and LZ generated the hypothesis and designed the study. LZ and HS interpreted data and prepared figures. LZ and HS prepared the first draft of the manuscript. LZ edited and prepared the final draft of the manuscript. LZ supervised the secured funding. XC supervised the overall research and interpreted results. All authors read and approved the final manuscript.

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Correspondence to Xiujuan Chen.

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Zhang, L., Sun, H. & Chen, X. Characterization of the long noncoding RNA transcriptome in human preimplantation embryo development. J Assist Reprod Genet 40, 2913–2923 (2023). https://doi.org/10.1007/s10815-023-02951-4

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