Cargando…
Genome-wide profiling of histone H3K4me3 and H3K27me3 modifications in individual blastocysts by CUT&Tag without a solid support (NON-TiE-UP CUT&Tag)
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 lar...
Autores principales: | , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2022
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9276795/ https://www.ncbi.nlm.nih.gov/pubmed/35821505 http://dx.doi.org/10.1038/s41598-022-15417-x |
_version_ | 1784745806801141760 |
---|---|
author | Susami, Kazuki Ikeda, Shuntaro Hoshino, Yoichiro Honda, Shinnosuke Minami, Naojiro |
author_facet | Susami, Kazuki Ikeda, Shuntaro Hoshino, Yoichiro Honda, Shinnosuke Minami, Naojiro |
author_sort | Susami, Kazuki |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-9276795 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-92767952022-07-14 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 Sci Rep Article 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. Nature Publishing Group UK 2022-07-11 /pmc/articles/PMC9276795/ /pubmed/35821505 http://dx.doi.org/10.1038/s41598-022-15417-x Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/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://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Susami, Kazuki Ikeda, Shuntaro Hoshino, Yoichiro Honda, Shinnosuke Minami, Naojiro Genome-wide profiling of histone H3K4me3 and H3K27me3 modifications in individual blastocysts by CUT&Tag without a solid support (NON-TiE-UP CUT&Tag) |
title | Genome-wide profiling of histone H3K4me3 and H3K27me3 modifications in individual blastocysts by CUT&Tag without a solid support (NON-TiE-UP CUT&Tag) |
title_full | Genome-wide profiling of histone H3K4me3 and H3K27me3 modifications in individual blastocysts by CUT&Tag without a solid support (NON-TiE-UP CUT&Tag) |
title_fullStr | Genome-wide profiling of histone H3K4me3 and H3K27me3 modifications in individual blastocysts by CUT&Tag without a solid support (NON-TiE-UP CUT&Tag) |
title_full_unstemmed | Genome-wide profiling of histone H3K4me3 and H3K27me3 modifications in individual blastocysts by CUT&Tag without a solid support (NON-TiE-UP CUT&Tag) |
title_short | Genome-wide profiling of histone H3K4me3 and H3K27me3 modifications in individual blastocysts by CUT&Tag without a solid support (NON-TiE-UP CUT&Tag) |
title_sort | genome-wide profiling of histone h3k4me3 and h3k27me3 modifications in individual blastocysts by cut&tag without a solid support (non-tie-up cut&tag) |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9276795/ https://www.ncbi.nlm.nih.gov/pubmed/35821505 http://dx.doi.org/10.1038/s41598-022-15417-x |
work_keys_str_mv | AT susamikazuki genomewideprofilingofhistoneh3k4me3andh3k27me3modificationsinindividualblastocystsbycuttagwithoutasolidsupportnontieupcuttag AT ikedashuntaro genomewideprofilingofhistoneh3k4me3andh3k27me3modificationsinindividualblastocystsbycuttagwithoutasolidsupportnontieupcuttag AT hoshinoyoichiro genomewideprofilingofhistoneh3k4me3andh3k27me3modificationsinindividualblastocystsbycuttagwithoutasolidsupportnontieupcuttag AT hondashinnosuke genomewideprofilingofhistoneh3k4me3andh3k27me3modificationsinindividualblastocystsbycuttagwithoutasolidsupportnontieupcuttag AT minaminaojiro genomewideprofilingofhistoneh3k4me3andh3k27me3modificationsinindividualblastocystsbycuttagwithoutasolidsupportnontieupcuttag |