The landscape of accessible chromatin in bovine oocytes and early embryos
| Autor: | Lauren Gatenby, Carlos R. F. Pinto, Rebecca L. Krisher, Zongliang Jiang, Jiangwen Sun, Hao Ming, Ye Yuan, K. R. Bondioli, R. Pasquariello, Jason R. Herrick |
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| Rok vydání: | 2020 |
| Předmět: |
0301 basic medicine
Cancer Research Biology Transcriptome 03 medical and health sciences 0302 clinical medicine Pregnancy Transcription (biology) Gene expression Animals Molecular Biology Transcription factor Regulation of gene expression High-Throughput Nucleotide Sequencing DNA Methylation Chromatin Cell biology 030104 developmental biology 030220 oncology & carcinogenesis DNA methylation Oocytes Chromatin Immunoprecipitation Sequencing Cattle Female Reprogramming Research Paper |
| Zdroj: | Epigenetics |
| ISSN: | 1559-2308 1559-2294 |
| DOI: | 10.1080/15592294.2020.1795602 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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