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DamID to Map Genome-Protein Interactions in Preimplantation Mouse Embryos

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Epigenetic Reprogramming During Mouse Embryogenesis

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2214))

Abstract

Investigating the chromatin landscape of the early mammalian embryo is essential to understand how epigenetic mechanisms may direct reprogramming and cell fate allocation. Genome-wide analyses of the epigenome in preimplantation mouse embryos have recently become available, thanks to the development of low-input protocols. DNA adenine methyltransferase identification (DamID) enables the investigation of genome-wide protein-DNA interactions without the requirement of specific antibodies. Most importantly, DamID can be robustly applied to single cells. Here we describe the protocol for performing DamID in single oocytes and mouse preimplantation embryos, as well as single blastomeres, using a Dam-LaminB1 fusion to generate high-resolution lamina-associated domain (LAD) maps. This low-input method can be adapted for other proteins of interest to faithfully profile their genomic interaction, allowing us to interrogate the chromatin dynamics and nuclear organization during the early mammalian development.

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References

  1. Bonev B, Cavalli G (2016) Organization and function of the 3D genome. Nat Rev Genet 17:661–678. https://doi.org/10.1038/nrg.2016.112

    Article  CAS  PubMed  Google Scholar 

  2. Hug CB, Vaquerizas JM (2018) The birth of the 3D genome during early embryonic development. Trends Genet 34:903–914. https://doi.org/10.1016/j.tig.2018.09.002

    Article  CAS  PubMed  Google Scholar 

  3. Zheng H, Xie W (2019) The role of 3D genome organization in development and cell differentiation. Nat Rev Mol Cell Biol 20:535–550. https://doi.org/10.1038/s41580-019-0132-4

    Article  CAS  PubMed  Google Scholar 

  4. Guelen L, Pagie L, Brasset E, Meuleman W, Faza MB, Talhout W, Eussen BH, de Klein A, Wessels L, de Laat W, van Steensel B (2008) Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature 453:948–951. https://doi.org/10.1038/nature06947

    Article  CAS  PubMed  Google Scholar 

  5. Peric-Hupkes D, Meuleman W, Pagie L, Bruggeman SWM, Solovei I, Brugman W, Gräf S, Flicek P, Kerkhoven RM, van Lohuizen M, Reinders M, Wessels L, van Steensel B (2010) Molecular maps of the reorganization of genome–nuclear lamina interactions during differentiation. Mol Cell 38:603–613. https://doi.org/10.1016/j.molcel.2010.03.016

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Akhtar W, de Jong J, Pindyurin AV, Pagie L, Meuleman W, de Ridder J, Berns A, Wessels LFA, van Lohuizen M, van Steensel B (2013) Chromatin position effects assayed by thousands of reporters integrated in parallel. Cell 154:914–927. https://doi.org/10.1016/j.cell.2013.07.018

    Article  CAS  PubMed  Google Scholar 

  7. Liu X, Wang C, Liu W, Li J, Li C, Kou X, Chen J, Zhao Y, Gao H, Wang H, Zhang Y, Gao Y, Gao S (2016) Distinct features of H3K4me3 and H3K27me3 chromatin domains in pre-implantation embryos. Nature 537:558–562. https://doi.org/10.1038/nature19362

    Article  CAS  PubMed  Google Scholar 

  8. Zhang B, Zheng H, Huang B, Li W, Xiang Y, Peng X, Ming J, Wu X, Zhang Y, Xu Q, Liu W, Kou X, Zhao Y, He W, Li C, Chen B, Li Y, Wang Q, Ma J, Yin Q, Kee K, Meng A, Gao S, Xu F, Na J, Xie W (2016) Allelic reprogramming of the histone modification H3K4me3 in early mammalian development. Nature 537:553–557. https://doi.org/10.1038/nature19361

    Article  CAS  PubMed  Google Scholar 

  9. Ke Y, Xu Y, Chen X, Feng S, Liu Z, Sun Y, Yao X, Li F, Zhu W, Gao L, Chen H, Du Z, Xie W, Xu X, Huang X, Liu J (2017) 3D chromatin structures of mature gametes and structural reprogramming during mammalian embryogenesis. Cell 170:367–381.e20. https://doi.org/10.1016/j.cell.2017.06.029

    Article  CAS  PubMed  Google Scholar 

  10. Flyamer IM, Gassler J, Imakaev M, Brandão HB, Ulianov SV, Abdennur N, Razin SV, Mirny LA, Tachibana-Konwalski K (2017) Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition. Nature 544:110–114. https://doi.org/10.1038/nature21711

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Gassler J, Brandão HB, Imakaev M, Flyamer IM, Ladstätter S, Bickmore WA, Peters J-M, Mirny LA, Tachibana K (2017) A mechanism of cohesin-dependent loop extrusion organizes zygotic genome architecture. EMBO J 36:3600–3618. https://doi.org/10.15252/embj.201798083

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Wu J, Xu J, Liu B, Yao G, Wang P, Lin Z, Huang B, Wang X, Li T, Shi S, Zhang N, Duan F, Ming J, Zhang X, Niu W, Song W, Jin H, Guo Y, Dai S, Hu L, Fang L, Wang Q, Li Y, Li W, Na J, Xie W, Sun Y (2018) Chromatin analysis in human early development reveals epigenetic transition during ZGA. Nature 557:256–260. https://doi.org/10.1038/s41586-018-0080-8

    Article  CAS  PubMed  Google Scholar 

  13. Wang C, Liu X, Gao Y, Yang L, Li C, Liu W, Chen C, Kou X, Zhao Y, Chen J, Wang Y, Le R, Wang H, Duan T, Zhang Y, Gao S (2018) Reprogramming of H3K9me3-dependent heterochromatin during mammalian embryo development. Nat Cell Biol 20:620–631. https://doi.org/10.1038/s41556-018-0093-4

    Article  CAS  PubMed  Google Scholar 

  14. Kind J, Pagie L, de Vries SS, Nahidiazar L, Dey SS, Bienko M, Zhan Y, Lajoie B, de Graaf CA, Amendola M, Fudenberg G, Imakaev M, Mirny LA, Jalink K, Dekker J, van Oudenaarden A, van Steensel B (2015) Genome-wide maps of nuclear lamina interactions in single human cells. Cell 163:134–147. https://doi.org/10.1016/j.cell.2015.08.040

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. van Steensel B, Henikoff S (2000) Identification of in vivo DNA targets of chromatin proteins using tethered Dam methyltransferase. Nat Biotechnol 18:424–428. https://doi.org/10.1038/74487

    Article  CAS  PubMed  Google Scholar 

  16. Ikegami K, Egelhofer TA, Strome S, Lieb JD (2010) Caenorhabditis elegans chromosome arms are anchored to the nuclear membrane via discontinuous association with LEM-2. Genome Biol 11:R120. https://doi.org/10.1186/gb-2010-11-12-r120

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Pickersgill H, Kalverda B, de Wit E, Talhout W, Fornerod M, van Steensel B (2006) Characterization of the Drosophila melanogaster genome at the nuclear lamina. Nat Genet 38:1005–1014. https://doi.org/10.1038/ng1852

    Article  CAS  PubMed  Google Scholar 

  18. Kind J, Pagie L, Ortabozkoyun H, Boyle S, de Vries SS, Janssen H, Amendola M, Nolen LD, Bickmore WA, van Steensel B (2013) Single-cell dynamics of genome-nuclear lamina interactions. Cell 153:178–192. https://doi.org/10.1016/j.cell.2013.02.028

    Article  CAS  PubMed  Google Scholar 

  19. Borsos M, Perricone SM, Schauer T, Pontabry J, de Luca KL, de Vries SS, Ruiz-Morales ER, Torres-Padilla M-E, Kind J (2019) Genome–lamina interactions are established de novo in the early mouse embryo. Nature 569:729–733. https://doi.org/10.1038/s41586-019-1233-0

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Rooijers K, Markodimitraki CM, Rang FJ, de Vries SS, Chialastri A, de Luca KL, Mooijman D, Dey SS, Kind J (2019) Simultaneous quantification of protein–DNA contacts and transcriptomes in single cells. Nat Biotechnol 37:766–772. https://doi.org/10.1038/s41587-019-0150-y

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Nishimura K, Fukagawa T, Takisawa H, Kakimoto T, Kanemaki M (2009) An auxin-based degron system for the rapid depletion of proteins in nonplant cells. Nat Methods 6:917–922. https://doi.org/10.1038/nmeth.1401

    Article  CAS  PubMed  Google Scholar 

  22. Marshall OJ, Brand AH (2015) damidseq_pipeline: an automated pipeline for processing DamID sequencing datasets. Bioinformatics 31:3371–3373. https://doi.org/10.1093/bioinformatics/btv386

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Szczesnik T, Ho JWK, Sherwood R (2019) Dam mutants provide improved sensitivity and spatial resolution for profiling transcription factor binding. Epigenetics Chromatin 12:36. https://doi.org/10.1186/s13072-019-0273-x

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgments

Work in the Torres-Padilla lab is funded by the Helmholtz Association, the German Research Council (CRC 1064), and H2020 Marie-Curie Actions ITN EpiSystem and ChromDesign. M.P. is funded through the ChromDesign ITN under the Marie Skłodowska-Curie grant agreement No 813327. J.K. is funded through ERC-Stg EpiID. The Oncode Institute is supported by KWF Dutch Cancer Society. We thank Adam Burton for providing the images shown in Fig. 2.

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Authors and Affiliations

  1. Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, Munich, Germany

    Mrinmoy Pal & Maria-Elena Torres-Padilla

  2. Oncode Institute, Hubrecht Institute–KNAW and University Medical Center Utrecht, Utrecht, The Netherlands

    Jop Kind

  3. Faculty of Biology, Ludwig-Maximilians Universität, Munich, Germany

    Maria-Elena Torres-Padilla

Authors
  1. Mrinmoy Pal
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  2. Jop Kind
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  3. Maria-Elena Torres-Padilla
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Corresponding author

Correspondence to Maria-Elena Torres-Padilla .

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Editors and Affiliations

  1. Institut Curie, CNRS UMR3215/ INSERM U934, Paris Sciences & Lettres Research University (PSL), Paris, France

    Katia Ancelin

  2. Institut Curie, CNRS UMR3215/ INSERM U934, Paris Sciences & Lettres Research University (PSL), Institut de Ge´ne´tique Mole´culaire de Montpellier, Univ Montpellier, CNRS Montpellier, France, Paris, France

    Maud Borensztein

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Pal, M., Kind, J., Torres-Padilla, ME. (2021). DamID to Map Genome-Protein Interactions in Preimplantation Mouse Embryos. In: Ancelin, K., Borensztein, M. (eds) Epigenetic Reprogramming During Mouse Embryogenesis. Methods in Molecular Biology, vol 2214. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0958-3_18

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  • DOI: https://doi.org/10.1007/978-1-0716-0958-3_18

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0957-6

  • Online ISBN: 978-1-0716-0958-3

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