The landscape of accessible chromatin in bovine oocytes and early embryos
Chromatin reorganization governs the regulation of gene expression during preimplantation development. However, the landscape of chromatin dynamics in this period has not been explored in bovine. In this study, we constructed a genome-wide map of accessible chromatin in bovine oocytes and early embr...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2021-03-01
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| Series: | Epigenetics |
| Subjects: | |
| Online Access: | http://dx.doi.org/10.1080/15592294.2020.1795602 |
| _version_ | 1827811487886868480 |
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| author | Hao Ming Jiangwen Sun Rolando Pasquariello Lauren Gatenby Jason R Herrick Ye Yuan Carlos R Pinto Kenneth R Bondioli Rebecca L Krisher Zongliang Jiang |
| author_facet | Hao Ming Jiangwen Sun Rolando Pasquariello Lauren Gatenby Jason R Herrick Ye Yuan Carlos R Pinto Kenneth R Bondioli Rebecca L Krisher Zongliang Jiang |
| author_sort | Hao Ming |
| collection | DOAJ |
| description | Chromatin reorganization governs the regulation of gene expression during preimplantation development. However, the landscape of chromatin dynamics in this period has not been explored in bovine. In this study, we constructed a genome-wide map of accessible chromatin in bovine oocytes and early embryos using an improved assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) which revealed unique features of the accessible chromatin during bovine early embryo development. We found that chromatin accessibility is low in oocytes and 2-/4-cell embryos, followed by a significant increase in embryos during major embryonic genome activation (EGA), and peaked in elongating day 14 embryos. Genome-wide characteristics of open chromatin showed that ATAC-seq signals in both transcription start sites (TSS) and transcription end sites (TES) were strong. Additionally, the distal ATAC-seq peaks were enriched in repeat elements in a type-specific and stage-specific manner. We further unveiled a series of transcription factor (TF) motifs with distinct variation of enrichment from distal ATAC-seq peaks. By integrated analysis of chromatin accessibility with transcriptomes and DNA methylomes in bovine early embryos, we showed that promoter accessibility was positively correlated with gene expression, especially during major EGA, and was strongly correlated to DNA methylation and CpG density. Finally, we identified the critical chromatin signatures and TFs that differ between in vivo and in vitro derived blastocysts, which provides insights to the potential mechanisms leading to low quality of embryos produced in vitro. Together, this comprehensive analysis revealed critical features of chromatin landscape and epigenetic reprogramming during bovine preimplantation embryo development. |
| first_indexed | 2024-03-11T23:05:45Z |
| format | Article |
| id | doaj.art-a2d65c2e14ac4293bb22320ab2aa6e16 |
| institution | Directory Open Access Journal |
| issn | 1559-2294 1559-2308 |
| language | English |
| last_indexed | 2024-03-11T23:05:45Z |
| publishDate | 2021-03-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | Epigenetics |
| spelling | doaj.art-a2d65c2e14ac4293bb22320ab2aa6e162023-09-21T13:09:24ZengTaylor & Francis GroupEpigenetics1559-22941559-23082021-03-0116330031210.1080/15592294.2020.17956021795602The landscape of accessible chromatin in bovine oocytes and early embryosHao Ming0Jiangwen Sun1Rolando Pasquariello2Lauren Gatenby3Jason R Herrick4Ye Yuan5Carlos R Pinto6Kenneth R Bondioli7Rebecca L Krisher8Zongliang Jiang9AgCenter, Louisiana State UniversityOld Dominion UniversityColorado Center for Reproductive MedicineAgCenter, Louisiana State UniversityColorado Center for Reproductive MedicineColorado Center for Reproductive MedicineSchool of Veterinary Medicine, Louisiana State UniversityAgCenter, Louisiana State UniversityColorado Center for Reproductive MedicineAgCenter, Louisiana State UniversityChromatin reorganization governs the regulation of gene expression during preimplantation development. However, the landscape of chromatin dynamics in this period has not been explored in bovine. In this study, we constructed a genome-wide map of accessible chromatin in bovine oocytes and early embryos using an improved assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) which revealed unique features of the accessible chromatin during bovine early embryo development. We found that chromatin accessibility is low in oocytes and 2-/4-cell embryos, followed by a significant increase in embryos during major embryonic genome activation (EGA), and peaked in elongating day 14 embryos. Genome-wide characteristics of open chromatin showed that ATAC-seq signals in both transcription start sites (TSS) and transcription end sites (TES) were strong. Additionally, the distal ATAC-seq peaks were enriched in repeat elements in a type-specific and stage-specific manner. We further unveiled a series of transcription factor (TF) motifs with distinct variation of enrichment from distal ATAC-seq peaks. By integrated analysis of chromatin accessibility with transcriptomes and DNA methylomes in bovine early embryos, we showed that promoter accessibility was positively correlated with gene expression, especially during major EGA, and was strongly correlated to DNA methylation and CpG density. Finally, we identified the critical chromatin signatures and TFs that differ between in vivo and in vitro derived blastocysts, which provides insights to the potential mechanisms leading to low quality of embryos produced in vitro. Together, this comprehensive analysis revealed critical features of chromatin landscape and epigenetic reprogramming during bovine preimplantation embryo development.http://dx.doi.org/10.1080/15592294.2020.1795602accessible chromatinatac-seqoocytesembryosbovine |
| spellingShingle | Hao Ming Jiangwen Sun Rolando Pasquariello Lauren Gatenby Jason R Herrick Ye Yuan Carlos R Pinto Kenneth R Bondioli Rebecca L Krisher Zongliang Jiang The landscape of accessible chromatin in bovine oocytes and early embryos Epigenetics accessible chromatin atac-seq oocytes embryos bovine |
| title | The landscape of accessible chromatin in bovine oocytes and early embryos |
| title_full | The landscape of accessible chromatin in bovine oocytes and early embryos |
| title_fullStr | The landscape of accessible chromatin in bovine oocytes and early embryos |
| title_full_unstemmed | The landscape of accessible chromatin in bovine oocytes and early embryos |
| title_short | The landscape of accessible chromatin in bovine oocytes and early embryos |
| title_sort | landscape of accessible chromatin in bovine oocytes and early embryos |
| topic | accessible chromatin atac-seq oocytes embryos bovine |
| url | http://dx.doi.org/10.1080/15592294.2020.1795602 |
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