Resetting H3K4me3, H3K27ac, H3K9me3 and H3K27me3 during the maternal-to-zygotic transition and blastocyst lineage specification in bovine embryos

Zhou, Chuan; Halstead, Michelle M.; Bonnet-Garnier, Amélie; Schultz, Richard M.; Ross, Pablo J.

doi:10.1101/2022.04.07.486777

Cited by 2 publications

(4 citation statements)

References 102 publications

(158 reference statements)

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“…function of H3K4me3 and H3K27ac. The H3K4me3 signals around the TSSs were higher than those of H3K27ac, which is also consistent with the results shown by Zhou et al, who used the same antibodies (30). This is the first simultaneous detection of H3K4me3 and H3K27ac modifications within identical single blastocysts.…”

Section: Discussionsupporting

confidence: 90%

“…Fig. 3a shows the same region as reported in the preprint by Zhou et al (30), who used 1,000-1,500 blastomeres for CUT&Tag for these These analyses clearly demonstrated H3K4me3-or H3K27ac-dominant genes even within the same embryo (e.g., NDUFA3 and GJB3, respectively) (Fig. 3e).…”

Section: Wow-catsupporting

confidence: 73%

“…Fig. 3a shows the same region as reported by Zhou et al (30), who used 1,000-1,500 blastomeres for CUT&Tag to detect these modifications. A high similarity was demonstrated in the common (unshaded), H3K4me3dominant (blue-shaded), and H3K27ac-dominant (red-shaded) areas, indicating a high similarity between conventional CUT&Tag using a group of embryos and WOW-CAT using even a part of single embryos.…”

Section: Discussionmentioning

confidence: 52%

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Diagnostic histone modification analysis of individual preimplantation embryos

Zeng¹,

Hoshino²,

Susami³

et al. 2023

Preprint

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Background: We previously reported a modification of the CUT&Tag method (NTU-CAT) that allows genome-wide histone modification analysis in individual preimplantation embryos. In the present study, NTU-CAT was further simplified by taking advantage of the Well-of-the-Well (WOW) system, which enables the processing of multiple embryos in a shorter time with less reagent and cell loss during the procedure (WOW-CUT&Tag, WOW-CAT). Results: WOW-CAT allowed histone modification profiling from not only a single blastocyst but also from a portion of it. WOW-CAT generated similar H3K4me3 profiles as NTU-CAT, but they were closer to the profiles produced by chromatin immunoprecipitation-sequencing, such as a valley-like trend, indicating that WOW-CAT may attenuate the bias of Tn5 transposase to cut open chromatin regions. Simultaneous WOW-CAT of two halves of single blastocysts was conducted to analyze two different histone modifications (H3K4me3 and H3K27ac) within the same embryo. Furthermore, trophectoderm cells were biopsied and subjected to WOW-CAT in anticipation of preimplantation diagnosis of histone modifications. WOW-CAT allowed the monitoring of epigenetic modifications in the main body of the embryo. For example, analysis of H3K4me3 modifications of XIST and DDX3Y in trophectoderm biopsies could be used to sex embryos in combination with quantitative PCR, but without the need for deep sequencing. Conclusions: These results suggest the applicability of WOW-CAT for flexible epigenetic analysis of individual embryos in preimplantation epigenetic diagnosis.

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Section: Discussionsupporting

confidence: 90%

Section: Wow-catsupporting

confidence: 73%

Section: Discussionmentioning

confidence: 52%

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Diagnostic histone modification analysis of individual preimplantation embryos

Zeng¹,

Hoshino²,

Susami³

et al. 2023

Preprint

View full text Add to dashboard Cite

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“…In particular, using the normalized PTM binding levels of active/inactive genes in the adult head as a baseline ( Supplementary Methods ), we estimate 35% of the total genes, and an excess (66%, P < 0.05, fisher exact test) of the reported maternal genes are bound by one of the H3K4me3, H3K36me3 or H3K79me2 at their TSSs or coding regions; and only 9% of the total genes and 13% of the zygotic genes are bound by H3K27me3. This suggests that consistent with mammals, Drosophila maternal genes are enriched for potentially maternally deposited active histone modifications 28 . 24% of the TEs are bound by H3K9me2/3 ( Supplementary Table S2 ) at the prezygotic stage, although this could be an underestimate because of the TE regions that cannot be uniquely mapped by the sequencing reads.…”

Section: Resultsmentioning

confidence: 65%

Development and Evolution of Drosophila Chromatin Landscape in a 3D genome context

Ali

Younas

Liu

et al. 2022

Preprint

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Chromatin states of genes and transposable elements (TEs) dictated by combinations of various histone modifications comprise key information for understanding the mechanisms of genome organization and regulation. However, little is known about the principles of their dynamic changes during development and evolution in a three-dimensional genome context. To address this, we study Drosophila pseudoobscura, a Drosophila model species that diverged from D. melanogaster about 25 million years ago. We collected 71 epigenomic datasets targeting 11 histone modification marks and 4 Hi-C datasets, and projected 15 chromatin states across four different developmental stages and two adult tissues. We estimate that before zygotic genome activation, 41% of the genome has already been deposited with histone modifications, while 20% of the rest genome switches from a null state to an active/inactive chromatin state after the zygotic genome activation. Over two thirds of the genomic region exhibit at least one transition between different chromatin states during development. And such transitions on cis-regulatory regions are associated with tissue- or stage-specific formation of chromatin loops or topologically associated domain borders (TABs), as well as specific activation of gene expression. We further demonstrate that while evolutionarily young TEs are preferentially targeted by silencing histone modifications, old TEs are more frequently domesticated as TABs or specific enhancers that further contribute to the genome organization or local gene regulation. Interestingly, this trend is reversed on the newly evolved X chromosome in D. pseudoobscura, due to the acquisition of dosage compensation mechanism. Overall we characterize the developmental and evolutionary dynamics of Drosophila epigenomic states, and highlight the roles of certain TEs of different evolutionary ages in genome organization and regulation.

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Resetting H3K4me3, H3K27ac, H3K9me3 and H3K27me3 during the maternal-to-zygotic transition and blastocyst lineage specification in bovine embryos

Cited by 2 publications

References 102 publications

Diagnostic histone modification analysis of individual preimplantation embryos

Diagnostic histone modification analysis of individual preimplantation embryos

Development and Evolution of Drosophila Chromatin Landscape in a 3D genome context

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