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Ming H, Sun J, Pasquariello R, Gatenby L, Herrick JR, Yuan Y, Pinto CR, Bondioli KR, Krisher RL, Jiang Z. The landscape of accessible chromatin in bovine oocytes and early embryos. Epigenetics 2021; 16:300-312. [PMID: 32663104 PMCID: PMC7901547 DOI: 10.1080/15592294.2020.1795602] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/24/2020] [Accepted: 06/29/2020] [Indexed: 12/14/2022] Open
Abstract
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.
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Affiliation(s)
- Hao Ming
- School of Animal Sciences, AgCenter, Louisiana State University, Baton Rouge, LA, USA
| | - Jiangwen Sun
- Department of Computer Science, Old Dominion University, Norfolk, VA, USA
| | | | - Lauren Gatenby
- School of Animal Sciences, AgCenter, Louisiana State University, Baton Rouge, LA, USA
| | - Jason R Herrick
- Colorado Center for Reproductive Medicine, Lone Tree, CO, USA
| | - Ye Yuan
- Colorado Center for Reproductive Medicine, Lone Tree, CO, USA
| | - Carlos R Pinto
- Department of Theriogenology, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA
| | - Kenneth R Bondioli
- School of Animal Sciences, AgCenter, Louisiana State University, Baton Rouge, LA, USA
| | | | - Zongliang Jiang
- School of Animal Sciences, AgCenter, Louisiana State University, Baton Rouge, LA, USA
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The landscape of accessible chromatin in mammalian preimplantation embryos. Nature 2016; 534:652-7. [DOI: 10.1038/nature18606] [Citation(s) in RCA: 424] [Impact Index Per Article: 47.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Accepted: 05/27/2016] [Indexed: 12/28/2022]
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Razin SV, Gavrilov AA, Ulyanov SV. Transcription-controlling regulatory elements of the eukaryotic genome. Mol Biol 2015. [DOI: 10.1134/s0026893315020119] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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