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

Susami, Kazuki; Ikeda, Shuntaro; Hoshino, Yoichiro; Honda, Shinnosuke; Minami, Naojiro

doi:10.1038/s41598-022-15417-x

Cited by 8 publications

(18 citation statements)

References 34 publications

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“…First, 30,257 peaks obtained from the ChIP‐seq data of placenta (Male 1) were designated as placental peaks. The 13,110 common peaks from two single blastocysts (P14 and P15) previously reported from our laboratory (Susami et al., 2022) were designated as the blastocyst peaks. By comparing the placental and blastocyst peaks, we extracted 18,099 placenta‐specific peaks, 12,168 common peaks, and 2921 blastocyst‐specific peaks (Figure 3a).…”

Section: Resultsmentioning

confidence: 99%

Analysis of histone H3K4me3 modifications in bovine placenta derived from different calf‐production methods

Hattori,

Hoshino,

Kachi

et al. 2024

Reprod Domestic Animals

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In ruminants, the overgrowth of offspring produced by in vitro fertilization (IVF) is a common problem. Abnormal epigenetic modifications caused by environmental factors during the early embryonic period are suspected as an aetiology of overgrowth. In this study, we investigated the genome‐wide histone H3K4me3 profiles of bovine placentae that play a pivotal role in foetal development and compared their characteristics between artificial insemination (AI)‐ and IVF‐derived samples. Cotyledons were harvested from the placentae obtained at parturition of 5 AI‐ and 13 IVF‐derived calves, and chromatin immunoprecipitation sequencing was performed for H3K4me3. We confirmed no significant maternal tissue contamination in the samples we used. The revealed H3K4me3 profiles reflected the general characteristics of the H3K4me3 modification, which is abundantly distributed in the promoter region of active genes. By extracting common modifications from multiple samples, the genes involved in placenta‐specific biological processes could be enriched. Comparison with the H3K4me3 modifications of blastocyst samples was also effective for enriching the placenta‐specific features. Principal component analysis suggested the presence of differential H3K4me3 modifications in AI‐ and IVF‐derived samples. The genes contributing to the difference were related to the developmental biological processes. Imprinted genes such as BEGAIN, ZNF215 and DLX5 were among the extracted genes. Principal component and discriminant analyses using only male samples categorized the samples into three groups based on foetal weight and calf‐production methods. To our knowledge, this is the first study to profile the genome‐wide histone modifications of bovine foetal placentae and reveal their differential characteristics between different calf‐production methods.

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Section: Resultsmentioning

confidence: 99%

Analysis of histone H3K4me3 modifications in bovine placenta derived from different calf‐production methods

Hattori,

Hoshino,

Kachi

et al. 2024

Reprod Domestic Animals

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“…In identifying histone modifications associated with embryo quality, genome‐wide analysis using individual embryos rather than cohort analysis would be particularly useful because each individual embryo differs in developmental competence. Based on this idea, we proposed a method to analyze multiple embryos individually using bovine preimplantation embryos 61 . It is anticipated that the identification of useful epigenetic modifications will continue to progress for histone modifications, which will allow for the evaluation of embryo quality.…”

Section: Histone Modificationsmentioning

confidence: 99%

Current status of genome‐wide epigenetic profiling of mammalian preimplantation embryos

Ikeda

2023

Reprod Medicine & Biology

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BackgroundGenome‐wide information on epigenetic modifications in mammalian preimplantation embryos was an unexplored sanctuary of valuable research insights protected by the difficulty of its analysis. However, that is no longer the case, and many epigenome maps are now available for sightseeing there.MethodsThis review overviews the current status of genome‐wide epigenetic profiling in terms of DNA methylome and histone modifications in mammalian preimplantation embryos.Main findingsAs the sensitivity of methods for analyzing epigenetic modifications increased, pioneering work began to explore the genome‐wide epigenetic landscape in the mid‐2010s, first for DNA methylation and then for histone modifications. Since then, a huge amount of data has accumulated, revealing typical epigenetic profiles in preimplantation development and, more recently, changes in response to environmental interventions.ConclusionsThese accumulating data may be used to improve the quality of preimplantation embryos, both in terms of their short‐term developmental competence and their subsequent long‐term health implications.

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“…Sequencing and data processing were performed as previously reported (16). Briefly, paired-end 150-base pair sequencing reads generated by a HiSeqX (Illumina) were quality checked, merged, and aligned to the bovine genome (Bos_taurus_UMD_3.1.1/bosTau8, June 2014) using Bowtie 2 (25).…”

Section: Dna Sequencing and Data Processingmentioning

confidence: 99%

“…Since we had previously validated NTU-CAT and obtained comparable results to ChIP-seq for the H3K4me3 modification (16), we initially targeted this modification for WOW-CAT application. A snapshot of the WOW-CAT peaks for the H3K4me3 modification from four replicates (i.e., four single blastocysts) is shown in Fig.…”

Section: H3k4me3 Profile Of Whole Blastocysts Assessed By Wow-catmentioning

confidence: 99%

“…Then, Cleavage Under Targets and Tagmentation (CUT&Tag) was developed, in which a fusion protein of Tn5 transposase and pA (pA-Tn5) is used instead of pA-micrococcal nuclease, enabling the cutting and adaptor tagmentation of the fragments in situ simultaneously (14,15). Nowadays, CUT&Tag is used to profile representative histone modifications in single blastocysts without binding to a solid phase (NON-TiE-UP CUT&Tag [NTU-CAT]), which has made this method more readily applicable (16). After the successful implementation of NTU-CAT, we hypothesized that this method could be simplified and optimized by using the Well-of-the-Well (WOW) system (17,18), which was named WOW-CUT&Tag (WOW-CAT).…”

Section: Introductionmentioning

confidence: 99%

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

Cited by 8 publications

References 34 publications

Analysis of histone H3K4me3 modifications in bovine placenta derived from different calf‐production methods

Analysis of histone H3K4me3 modifications in bovine placenta derived from different calf‐production methods

Current status of genome‐wide epigenetic profiling of mammalian preimplantation embryos

Diagnostic histone modification analysis of individual preimplantation embryos

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