Methylome Dynamics of Bovine Gametes and in vivo Early Embryos.
Jingyue Duan,Zongliang Carl Jiang,Fahad Alqahtani,Ion I. Mandoiu,Dong Hong,Zheng Xinbao,Sadie L. Marjani,Jingbo Chen,Xiuchun Cindy Tian +8 more
Reads0
Chats0
TLDR
This comprehensive analysis provides insight into the critical features of the bovine embryo methylome, and serves as an important reference for embryos produced in vitro, such as by in vitro fertilization and cloning.Abstract:
DNA methylation undergoes drastic fluctuation during early mammalian embryogenesis. The dynamics of global DNA methylation in bovine embryos, however, have mostly been studied by immunostaining. We adopted the whole genome bisulfite sequencing (WGBS) method to characterize stage-specific genome-wide DNA methylation in bovine sperm, immature oocytes, oocytes matured in vivo and in vitro, as well as in vivo developed single embryos at the 2-, 4-, 8-, and 16-cell stages. We found that the major wave of genome-wide DNA demethylation was complete by the 8-cell stage when de novo methylation became prominent. Sperm and oocytes were differentially methylated in numerous regions (DMRs), which were primarily intergenic, suggesting that these non-coding regions may play important roles in gamete specification. DMRs were also identified between in vivo and in vitro matured oocytes, suggesting environmental effects on epigenetic modifications. In addition, virtually no (less than 1.5%) DNA methylation was found in mitochondrial DNA. Finally, by using RNA-seq data generated from embryos at the same developmental stages, we revealed a weak inverse correlation between gene expression and promoter methylation. This comprehensive analysis provides insight into the critical features of the bovine embryo methylome, and serves as an important reference for embryos produced in vitro, such as by in vitro fertilization and cloning. Lastly, these data can also provide a model for the epigenetic dynamics in human early embryos.read more
Citations
More filters
Journal ArticleDOI
DNA methylation changes during preimplantation development reveal inter-species differences and reprogramming events at imprinted genes.
Elena Ivanova,Sebastian Canovas,Soledad García-Martínez,Raquel Romar,Jordana S. Lopes,Dimitrios Rizos,María Jesús Sánchez-Calabuig,Felix Krueger,Simon Andrews,Fernando Perez-Sanz,Gavin Kelsey,Gavin Kelsey,Pilar Coy +12 more
TL;DR: In this article, the authors extended the analysis to two key livestock species, the pig and the cow, and revealed species differences in DNA methylation reprogramming and revealed that porcine or bovine models may be closer to human in key aspects than in the mouse model.
Journal ArticleDOI
Comparative whole genome DNA methylation profiling across cattle tissues reveals global and tissue-specific methylation patterns
Yang Zhou,Shuli Liu,Shuli Liu,Yan Hu,Lingzhao Fang,Yahui Gao,Han Xia,Steven G. Schroeder,Benjamin D. Rosen,Erin E. Connor,Congjun Li,Ransom L. Baldwin,John B. Cole,Curtis P. Van Tassell,Liguo Yang,Li Ma,George E. Liu +16 more
TL;DR: This study provides a comprehensive resource for bovine epigenomic research and enables new discoveries about DNA methylation and its role in complex traits.
Journal ArticleDOI
The landscape of accessible chromatin in bovine oocytes and early embryos.
Hao Ming,Jiangwen Sun,R. Pasquariello,Lauren Gatenby,Jason R. Herrick,Ye Yuan,Carlos R. F. Pinto,K. R. Bondioli,Rebecca L. Krisher,Zongliang Jiang +9 more
TL;DR: It is 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.
Journal ArticleDOI
Impacts of Epigenetic Processes on the Health and Productivity of Livestock.
TL;DR: In this article, a review examines the recent discoveries on epigenetic processes due to DNA methylation, histone modification and chromatin remodeling and their impacts on health and production traits in farm animals, including bovine, swine, sheep, goat, and poultry species.
Journal ArticleDOI
The Epigenetics of Gametes and Early Embryos and Potential Long-Range Consequences in Livestock Species-Filling in the Picture With Epigenomic Analyses.
TL;DR: In this article, the effects of parental environmental exposures on the epigenetics of gametes and the early embryo, and evidence for transgenerational inheritance in livestock species was discussed.
References
More filters
Journal ArticleDOI
Trimmomatic: a flexible trimmer for Illumina sequence data
TL;DR: Timmomatic is developed as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data and is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested.
Journal ArticleDOI
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.
TL;DR: By following this protocol, investigators are able to gain an in-depth understanding of the biological themes in lists of genes that are enriched in genome-scale studies.
Journal ArticleDOI
BEDTools: a flexible suite of utilities for comparing genomic features
Aaron R. Quinlan,Ira M. Hall +1 more
TL;DR: A new software suite for the comparison, manipulation and annotation of genomic features in Browser Extensible Data (BED) and General Feature Format (GFF) format, which allows the user to compare large datasets (e.g. next-generation sequencing data) with both public and custom genome annotation tracks.
Journal ArticleDOI
Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists
TL;DR: The survey will help tool designers/developers and experienced end users understand the underlying algorithms and pertinent details of particular tool categories/tools, enabling them to make the best choices for their particular research interests.
Journal ArticleDOI
Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown
TL;DR: This protocol describes all the steps necessary to process a large set of raw sequencing reads and create lists of gene transcripts, expression levels, and differentially expressed genes and transcripts.
Related Papers (5)
Genome-wide DNA methylation patterns of bovine blastocysts derived from in vivo embryos subjected to in vitro culture before, during or after embryonic genome activation
Dessie Salilew-Wondim,Mohammed Saeed-Zidane,Michael Hoelker,Samuel Gebremedhn,Mikhael Poirier,H. O. Pandey,Ernst Tholen,Christiane Neuhoff,Eva Held,Urban Besenfelder,Vita Havlicek,Franca Rings,Eric Fournier,Dominic Gagné,Marc-André Sirard,Claude Robert,Ahmed Gad,Karl Schellander,Dawit Tesfaye +18 more