リケラボ論文検索は、全国の大学リポジトリにある学位論文・教授論文を一括検索できる論文検索サービスです。

リケラボ 全国の大学リポジトリにある学位論文・教授論文を一括検索するならリケラボ論文検索大学・研究所にある論文を検索できる

リケラボ 全国の大学リポジトリにある学位論文・教授論文を一括検索するならリケラボ論文検索大学・研究所にある論文を検索できる

大学・研究所にある論文を検索できる 「Genome-wide profiling of histone H3K4me3 and H3K27me3 modifications in individual blastocysts by CUT&Tag without a solid support (NON-TiE-UP CUT&Tag)」の論文概要。リケラボ論文検索は、全国の大学リポジトリにある学位論文・教授論文を一括検索できる論文検索サービスです。

コピーが完了しました

URLをコピーしました

論文の公開元へ論文の公開元へ
書き出し

Genome-wide profiling of histone H3K4me3 and H3K27me3 modifications in individual blastocysts by CUT&Tag without a solid support (NON-TiE-UP CUT&Tag)

Susami, Kazuki Ikeda, Shuntaro Hoshino, Yoichiro Honda, Shinnosuke Minami, Naojiro 京都大学 DOI:10.1038/s41598-022-15417-x

2022

概要

Individual analysis of the epigenome of preimplantation embryos is useful for characterizing each embryo and for investigating the effects of environmental factors on their epigenome. However, it is difficult to analyze genome-wide epigenetic modifications, especially histone modifications, in a large number of single embryos due to the small number of cells and the complexity of the analysis methods. To solve this problem, we further modified the CUT&Tag method, which can analyze histone modifications in a small number of cells, such that the embryo is handled as a cell mass in the reaction solutions in the absence of the solid-phase magnetic beads that are used for antibody and enzyme reactions in the conventional method (NON-TiE-UP CUT&Tag; NTU-CAT). By using bovine blastocysts as a model, we showed that genome-wide profiles of representative histone modifications, H3K4me3 and H3K27me3, could be obtained by NTU-CAT that are in overall agreement with the conventional chromatin immunoprecipitation-sequencing (ChIP-seq) method, even from single embryos. However, this new approach has limitations that require attention, including false positive and negative peaks and lower resolution for broad modifications. Despite these limitations, we consider NTU-CAT a promising replacement for ChIP-seq with the great advantage of being able to analyze individual embryos.

この論文で使われている画像

参考文献

1. Dahl, J. A. et al. Broad histone H3K4me3 domains in mouse oocytes modulate maternal-to-zygotic transition. Nature 537, 548–552.

https://​doi.​org/​10.​1038/​natur​e19360 (2016).

2. Liu, X. et al. Distinct features of H3K4me3 and H3K27me3 chromatin domains in pre-implantation embryos. Nature 537, 558–562.

https://​doi.​org/​10.​1038/​natur​e19362 (2016).

3. Zhang, B. et al. Allelic reprogramming of the histone modification H3K4me3 in early mammalian development. Nature 537,

553–557. https://​doi.​org/​10.​1038/​natur​e19361 (2016).

4. Xia, W. et al. Resetting histone modifications during human parental-to-zygotic transition. Science 365, 353–360. https://​doi.​org/​

10.​1126/​scien​ce.​aaw51​18 (2019).

5. Zhang, W. et al. Maternal-biased H3K27me3 correlates with paternal-specific gene expression in the human morula. Genes Dev.

33, 382–387. https://​doi.​org/​10.​1101/​gad.​323105.​118 (2019).

6. Schmid, M., Durussel, T. & Laemmli, U. K. ChIC and ChEC; genomic mapping of chromatin proteins. Mol. Cell 16, 147–157.

https://​doi.​org/​10.​1016/j.​molcel.​2004.​09.​007 (2004).

7. Skene, P. J. & Henikoff, S. An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites. Elife https://​

doi.​org/​10.​7554/​eLife.​21856 (2017).

8. Skene, P. J., Henikoff, J. G. & Henikoff, S. Targeted in situ genome-wide profiling with high efficiency for low cell numbers. Nat.

Protoc. 13, 1006–1019. https://​doi.​org/​10.​1038/​nprot.​2018.​015 (2018).

9. Kaya-Okur, H. S. et al. CUT&Tag for efficient epigenomic profiling of small samples and single cells. Nat. Commun. 10, 1930.

https://​doi.​org/​10.​1038/​s41467-​019-​09982-5 (2019).

10. Kaya-Okur, H. S., Janssens, D. H., Henikoff, J. G., Ahmad, K. & Henikoff, S. Efficient low-cost chromatin profiling with CUT&Tag.

Nat. Protoc. 15, 3264–3283. https://​doi.​org/​10.​1038/​s41596-​020-​0373-x (2020).

11. Ishibashi, M., Ikeda, S. & Minami, N. Comparative analysis of histone H3K4me3 modifications between blastocysts and somatic

tissues in cattle. Sci. Rep. 11, 8253. https://​doi.​org/​10.​1038/​s41598-​021-​87683-0 (2021).

12. Fujiwara, Y. et al. Preparation of optimized concanavalin A-conjugated Dynabeads(R) magnetic beads for CUT&Tag. PLoS ONE

16, e0259846. https://​doi.​org/​10.​1371/​journ​al.​pone.​02598​46 (2021).

13. Berg, D. K. et al. Trophectoderm lineage determination in cattle. Dev. Cell 20, 244–255. https://​doi.​org/​10.​1016/j.​devcel.​2011.​01.​

003 (2011).

14. Kurosaka, S., Eckardt, S. & McLaughlin, K. J. Pluripotent lineage definition in bovine embryos by Oct4 transcript localization.

Biol. Reprod. 71, 1578–1582. https://​doi.​org/​10.​1095/​biolr​eprod.​104.​029322 (2004).

15. Wang, M. & Zhang, Y. Tn5 transposase-based epigenomic profiling methods are prone to open chromatin bias. bioR

xiv:2021.2007.2009.451758. https://​doi.​org/​10.​1101/​2021.​07.​09.​451758 (2021).

16. Halstead, M. M., Ma, X., Zhou, C., Schultz, R. M. & Ross, P. J. Chromatin remodeling in bovine embryos indicates species-specific

regulation of genome activation. Nat. Commun. 11, 4654. https://​doi.​org/​10.​1038/​s41467-​020-​18508-3 (2020).

17. Yamazaki, S., Ikeda, S. & Minami, N. Comparative analysis of histone H3K27me3 modifications between blastocysts and somatic

tissues in cattle. Anim. Sci. J. 93, e13684. https://​doi.​org/​10.​1111/​asj.​13684 (2022).

18. Hu, D. et al. CUT&Tag recovers up to half of ENCODE ChIP-seq peaks. bioRxiv: 2022.2003.2030.486382. https://​doi.​org/​10.​1101/​

2022.​03.​30.​486382 (2022).

19. Li, F. et al. Bivalent histone modifications and development. Curr. Stem Cell Res. Ther. 13, 83–90. https://​doi.​org/​10.​2174/​15748​

88X12​66617​01231​44743 (2018).

20. Xu, R., Li, C., Liu, X. & Gao, S. Insights into epigenetic patterns in mammalian early embryos. Protein Cell 12, 7–28. https://​doi.​

org/​10.​1007/​s13238-​020-​00757-z (2021).

21. Kinkley, S. et al. reChIP-seq reveals widespread bivalency of H3K4me3 and H3K27me3 in CD4(+) memory T cells. Nat. Commun.

7, 12514. https://​doi.​org/​10.​1038/​ncomm​s12514 (2016).

22. Janssens, D. H. et al. CUT&Tag2for1: A modified method for simultaneous profiling of the accessible and silenced regulome in

single cells. Genome Biol. 23, 81. https://​doi.​org/​10.​1186/​s13059-​022-​02642-w (2022).

23. Wu, S. J. et al. Single-cell CUT&Tag analysis of chromatin modifications in differentiation and tumor progression. Nat. Biotechnol.

39, 819–824. https://​doi.​org/​10.​1038/​s41587-​021-​00865-z (2021).

24. Menezo, Y. J. & Herubel, F. Mouse and bovine models for human IVF. Reprod. Biomed. Online 4, 170–175. https://d

​ oi.o

​ rg/1​ 0.1​ 016/​

s1472-​6483(10)​61936-0 (2002).

25. Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359. https://​doi.​org/​10.​1038/​

nmeth.​1923 (2012).

26. Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137. https://​doi.​org/​10.​1186/​gb-​2008-9-​9-​r137

(2008).

27. Shin, H., Liu, T., Manrai, A. K. & Liu, X. S. CEAS: cis-regulatory element annotation system. Bioinformatics 25, 2605–2606. https://​

doi.​org/​10.​1093/​bioin​forma​tics/​btp479 (2009).

28. Shen, L., Shao, N., Liu, X. & Nestler, E. ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating

genomic databases. BMC Genomics 15, 284. https://​doi.​org/​10.​1186/​1471-​2164-​15-​284 (2014).

29. Robinson, J. T. et al. Integrative genomics viewer. Nat. Biotechnol. 29, 24–26. https://​doi.​org/​10.​1038/​nbt.​1754 (2011).

30. da Huang, W., Sherman, B. T. & Lempicki, R. A. Bioinformatics enrichment tools: Paths toward the comprehensive functional

analysis of large gene lists. Nucleic Acids Res. 37, 1–13. https://​doi.​org/​10.​1093/​nar/​gkn923 (2009).

31. da Huang, W., Sherman, B. T. & Lempicki, R. A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics

resources. Nat. Protoc. 4, 44–57. https://​doi.​org/​10.​1038/​nprot.​2008.​211 (2009).

32. Graf, A. et al. Fine mapping of genome activation in bovine embryos by RNA sequencing. Proc. Natl. Acad. Sci. U S A 111,

4139–4144. https://​doi.​org/​10.​1073/​pnas.​13215​69111 (2014).

33. Ishitani, H. et al. Embryonic MTHFR contributes to blastocyst development. J. Assist. Reprod. Genet. 37, 1807–1814. https://​doi.​

org/​10.​1007/​s10815-​020-​01898-0 (2020).

Scientific Reports |

(2022) 12:11727 |

https://doi.org/10.1038/s41598-022-15417-x

11

Vol.:(0123456789)

www.nature.com/scientificreports/

A Self-archived copy in

Kyoto University Research Information Repository

https://repository.kulib.kyoto-u.ac.jp

Acknowledgements

This work was supported by the Kyoto University Live Imaging Center. The authors also thank the staff at the

Kyoto-Meat-Market for allowing us access to bovine ovaries. This work was supported in part by a Livestock

Promotional Subsidy from the Japan Racing Association and grants from the Japan Society for the Promotion

of Science (19H03104 to S.I. and 19H03136 to N.M.).

Author contributions

S.I., Y.H., and N.M. conceived the experiments. K.S. and S.I. performed bovine IVF and NTU-CAT library preparation and sequencing. K.S., S.I., H.Y., S.H., and N.M. analyzed the results. K.S. and S.I. drafted the manuscript.

All authors discussed the results and approved the manuscript.

Competing interests The authors declare no competing interests.

Additional information

Supplementary Information The online version contains supplementary material available at https://​doi.​org/​

10.​1038/​s41598-​022-​15417-x.

Correspondence and requests for materials should be addressed to S.I.

Reprints and permissions information is available at www.nature.com/reprints.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and

institutional affiliations.

Open Access This article is licensed under a Creative Commons Attribution 4.0 International

License, which permits use, sharing, adaptation, distribution and reproduction in any medium or

format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the

Creative Commons licence, and indicate if changes were made. The images or other third party material in this

article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the

material. If material is not included in the article’s Creative Commons licence and your intended use is not

permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from

the copyright holder. To view a copy of this licence, visit http://​creat​iveco​mmons.​org/​licen​ses/​by/4.​0/.

© The Author(s) 2022

Scientific Reports |

Vol:.(1234567890)

(2022) 12:11727 |

https://doi.org/10.1038/s41598-022-15417-x

12

...

参考文献をもっと見る

全国の大学の
卒論・修論・学位論文

一発検索!

この論文の関連論文を見る