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Centre for Trophoblast Research


Uncovering epigenetic regulation in the human placenta


This project will involve the computational analysis of next-generation sequencing methylation data and the development of novel computational methods to accurately determine the genomic locations of the two most abundant epigenetic marks, methyl-cytosine (mC) and hydroxymethyl-cytosine (hmC). Cytosine methylation has a long-established role as a regulatory mechanism, hmC the oxidised form of mC, has recently been discovered to be a stable epigenetic mark in its own right. See Prater & Hamilton, 2017 for a review of cytosine modifications and their computational analyses.


Human placental tissue has been shown to display differential localization of mC, hmC and the H3K9me3 and H3K27me3 histone marks across different cell types in the trophoblast giving clues to the non-canonical influence of these key epigenetic marks on cell specific functions (Fogarty, Burton & Ferguson-Smith, 2015).


This project will utilize high quality bisulfite/oxidative bisulfite treated samples from mouse models as a gold standard to develop novel computational methods, with a focus on machine learning. The samples also benefit from matched RNA-Seq, CHIP-Seq and proteomic data. The developed computational methods will then be applied to human placental tissue to unravel the epigenetic regulation underlying the observed placental cell type differences.


For further information, please do not hesitate to contact us:
Email:  Dr. Russell Hamilton ( or Prof. Anne Ferguson-Smith (


Prater M & Hamilton RS (2017) Epigenetics: Analysis of cytosine modifications at single base resolution. In "Encyclopedia of Bioinformatics and Computational Biology", Ed. S. Ranganathan, Elsevier


Fogarty NM, Burton GJ & Ferguson-Smith AC (2015) Different epigenetic states define syncytiotrophoblast and cytotrophoblast nuclei in the trophoblast of the human placenta. Placenta, 796-802