Erase and start againResearchers at the Babraham Institute have provided the most comprehensive analysis so far of how sperm DNA is reprogrammed after fertilisation to contribute to the start of a new life.
The fertilisation of an egg by a sperm is the start of a whole new life built on the inherited genetic information from the parents. However, this information needs to be modified before it can be used. Fertilisation triggers the erasure of marks on the paternal (sperm) genome. These marks are the result of a process called DNA methylation which is where one of the four bases of the genetic code (the ‘C’ - cytosine) is chemically modified. This modification generally represses the expression of genes and contributes to how our cells, which mostly share the same genetic information, become specialised into different cell types. The removal of these marks is called demethylation and it is suggested that this happens after fertilisation in order for the inherited DNA to be used as a clean slate to create new life.
The most powerful technique developed to study DNA methylation – whole-genome bisulfite sequencing – can look at every cytosine in the genome. However, because this approach has traditionally required many cells to be effective, it couldn’t be used to analyse cells that can only be obtained in small numbers – such as zygotes, the initial cell created by the fusion of an egg and a sperm. Instead, alternative methods were used which limited the analysis to a small fraction of the genome. This means that the great majority of methylation changes occurring just after fertilisation have been left unexplored. By optimising a novel strategy for whole-genome bisulfite sequencing to allow it to be applied to far fewer cells, researchers from the Babraham Institute, working with collaborators from the EMBL-European Bioinformatics Institute and the Wellcome Trust Sanger Institute, were able to describe methylation across the entire genome of zygotes for the first time.
The study, reported in the journal Cell Reports, presents a global view of extensive loss of methylation across the genome and generated some important new insights. In particular, it revealed that methylation located within genes is widely stripped from the sperm genome in the zygote. Most research into methylation has focused on the areas next to genes that control their expression; in contrast, the function of methylation within the gene itself is poorly understood. The discovery that removal of this methylation is an important part of the reprogramming at fertilisation opens up new avenues for understanding the functional impact of these changes. The authors’ analysis suggests the possibility that demethylation within genes is linked both to turning on the genome of the new embryo, and creating different cell types as development progresses.
Dr Julian Peat, lead author on the paper, said ”The reprogramming that occurs at fertilisation is profound: the specialised identities of the sperm and egg need to be transformed into a cell that can generate an entire organism. Our genome-wide approach adds new breadth to the picture of methylation trajectories during this reprogramming window – allowing us to better understand how the genome is remodelled and what role this plays in the development of the newly formed embryo.”
To investigate the cellular pathways responsible for removing methylation from the sperm genome in the zygote, the team also examined genetically modified zygotes which lack a known demethylation protein called TET3. As predicted, this showed that methylation is not removed as effectively in the absence of TET3. However, these zygotes were still able to demethylate most of the sperm genome – meaning that there are pathways other than TET3 that can do the job. This redundant network may be in place to make sure reprogramming is achieved even if mutations disrupt a particular pathway.
Image description:The image shows a stylised representation of a zygote created by the fertilisation of an egg by a sperm. In the course of this process DNA methylation is lost from the paternal genome (coloured dark brown) and not the maternal genome (coloured salmon).
Animal research statement:As a publicly funded research institute, the Babraham Institute is committed to engagement and transparency in all aspects of its research. The research presented here involved the use of mice for generating zygotes.
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Publication reference:Peat et al. (2014). Genome-wide Bisulfite Sequencing in Zygotes Identifies Demethylation Targets and Maps the Contribution of TET3 Oxidation. Cell Reports.
Associated researchers (in author order):Julian Peat, postdoc researcher (Reik lab)
Wendy Dean, Senior research scientist (Reik lab)
Stephen Clark, Research assistant (Kelsey and Reik labs)
Felix Krueger, Bioinformatician
Sébastien Smallwood, postdoc researcher (Kelsey lab)
Gabriella Ficz, previous postdoc researcher (Reik lab)
Jong Kim, EMBL-EBI
John Marioni, EMBL-EBI and associated faculty at the Wellcome Trust Sanger Institute
Timothy Hore, postdoc researcher (Reik lab)
Wolf Reik (Head of Epigenetics programme and group leader at the Babraham Institute, and associated faculty at the Wellcome Trust Sanger Institute)
12 December, 2014