UCL Cancer Institute

Epigenetic Signaling

Group Leader: Dr Steen Ooi



The central dogma of biology is that genes code for proteins, which in turn are responsible for building cells and bodies. Our bodies are composed of diverse cell types, all specialized for specific tasks, which ensure our normal development and survival. This requires the correct expression of all genes present in our genome. One way in which this is controlled is through modifications to our genetic material that, while leaving the underlying sequence information unchanged, affects how it is packaged. Errors in where these modifications occur throughout the genome play an important contributing role in the development of diseases such as cancer. Our group uses genetic, cell and molecular biological approaches to understand how these modifications are controlled and correctly interact.


Within the field of mammalian gene regulation, it is widely accepted that as well as sequence specific transcription factors, modifications to DNA (such as methylation of cytosine residues) and chromatin (through the incorporation of histone variants and post-translation modifications) contribute to gene silencing and activation. These mechanisms/processes underlie epigenetic phenomena, which refer to the transmission of deviations in cellular function and behavior that cannot be explained by genetic differences. Alterations in epigenetic processes are a key contributory aspect of complex, non-infectious diseases such as cancer and understanding how they are regulated will help in the development of more targeted, and therefore effective, therapies.

DNA methylation

The adaptor and regulator of de novo DNA methylation Dnmt3L interacts with active DNMTs as well as nucleosome components. A. Coomassie-stained gel of Dnmt3L interacting factors indentified by mass-spectrometry. B. Crystal structure of human DNMT3L protein after incorporation of the H3 N-terminal tail peptide into the DNMT3L crystal by soaking. Dnmt3L binding requires the absence of methylation at lysine 4 (K4), suggesting that factors regulating this modification are involved in DNA methylation establishment.

Our lab is interested in deciphering how global patterns of DNA methylation, the best-characterized epigenetic modification, are correctly regulated. Although much is known about the enzymes (DNMTs) that mediate this modification, the signals responsible for their recruitment to the correct target loci where DNA methylation normally occurs, remain poorly defined. Using a combination of mouse genetics, tissue culture and molecular biology, we aim to test the hypothesis that the chromatin scaffold itself is an integral feature necessary for targeting DNMTs. We also aim to understand which chromatin-affecting processes are important and their involvement in disease processes.

NDR1 kinase

Correct maintenance of global DNA methylation requires continual recruitment of active DNA methyltransferases. A. Minor satellite repeat sequence-probed Southern blot of genomic DNA digested with the methylation-sensitive enzyme HpaII. Digestion patterns of genomic DNA extracted from three different XY and XX mouse ES cell clones are shown. B. Western blot of whole cell protein extracts from the same XY and XX ES cell using antibodies specific for Dnmt3a and Dnmt3b. Anti-tubulin antibody serves as a loading control. These data demonstrate that disturbances in targeting of DNMTs rather than alterations in their expression are responsible for reductions in the fidelity of global DNA methylation patterns.


Group Members

  • Nancy Stathopoulou (Postdoctoral Research Associate)
  • Gehad Youssef (Postdoctoral Research Associate)
  • Jyoti Bikram Chhetri (Research Technician)



Selected Publications

G.Vlachogiannis, Niederhuth, C.E.,Tuna S., Stathopoulou, A., Viiri, K., de Rooij, D.G., Jenner, R.G., Schmitz R.J., Ooi, S.K.T. “The Dnmt3L ADD controls cytosine methylation establishment during spermatogenesis”. Cell Reports 2015, 10, 944-956

Stathopoulou, A, Lucchiari, G., Ooi, S.K.T., “DNA methylation is dispensable for suppression of the Agouti viable yellow controlling element in murine embryonic stem cells”. PLOS ONE, 2014. 9, e107355

Kao, T.H., Liao, H.F., Wolf, D., Tai, K.Y., Chuang, C.Y., Lee, H.S., Kua, H.C., Hata, K., Zhang, X., Cheng, X., Goff, S.P., Ooi, S.K.T., Bestor, T.H., Lin, S.P. Ectopic DNMT3L triggers assembly of a repressive complex for retroviral silencing in somatic cells. J.Virol., 2014, doi:10.1128/JVI.01176-14

Stadtfeld, M., Apostolou, E., Ferrari, F., Choi, J., Walsh, R.M., Chen, T., Ooi, S.K.T., Kim, S.Y., Bestor, T.H., Shioda, T., et al. (2012). Ascorbic acid prevents loss of Dlk1-Dio3 imprinting and facilitates generation of all-iPS cell mice from terminally differentiated B cells. Nature Genetics, 2012, 44, 831.

Ooi S.K.T., Wolf D, Hartung O, Agarwal S, Daley GQ, Goff SP and Bestor TH. Dynamic instability of genomic methylation patterns in pluripotent stem cells. Epigenetics and Chromatin, 2010, 3, 17

Ooi S.K.T., O’Donnell AH and Bestor TH. Mammalian cytosine methylation at a glance. J. Cell Science, 2009, 122, 2787 PubMed

Ooi S.K.T., Qiu C, Bernstein E, Li K, Jia D, Yang Z, Erdjument-Bromage H, Tempst P, Lin S, Allis CD, Cheng X and Bestor TH. DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. Nature, 2007, 448, 714. PubMed