Creyghton: Epigenomics

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The Creyghton group uses comparative epigenomics to study changes in gene regulation during linked to human evolution, development and disease.

Deciphering how cells can exist in the diverse cellular states that make up a functional organism while carrying the same genomic information is a major challenge in biology. Transcription factors are responsible for the deposition of epigenomic modifications upon the genome that serve as instructions as to how the genome is being read in each different cell type, thus allowing the cell to adopt a specialized state. Furthermore, these instructions are highly dynamic and can change under the influence of extracellular cues presenting the cells with the ability to respond to changes in their environment.

Key publications

Epigenomic annotation of gene regulatory alterations during evolution of the primate brain.

Vermunt, M.W., Tan S.C., Castelijns B., Geeven, G., Reinink, P., de Bruijn, E., Kondova I., Persengiev S., Netherlands Brain Bank; Bontrop R., Cuppen, E., de Laat, W. and Creyghton M.P.

Nature Neurosci. 3: 494-503


Large scale identification of co-regulated enhancer networks in the adult human brain.

Vermunt, M.W., Reinink, P., Korving J., de Bruijn, E., Creyghton, P.M., Basak, O., Geeven, G., Toonen, P.W., Lansu, N., Meunier, C., Heesch, S., Netherlands Brain Bank; Clevers, H., de Laat, W., Cuppen, E. and Creyghton M.P.

Cell Rep. 9: 1-13


Histone H3K27ac separates active from poised enhancers and predicts developmental state.

Creyghton, M.P., Cheng, A., Welstead, G.G., Kooistra, T., Carey, B.W., Steine, E.J., Hanna, J., Lodato, M.A., Frampton ,G.M., Sharp, P.A., Boyer, L.A., Young, R.A., Jaenisch, R.

Proc. Natl. Acad. Sci. 107: 21931-21936


Other publications

Local compartment changes and regulatory landscape alterations in histone H1-depleted cells

Geeven G., Zhu Y., Kim B.J., Bartholdy B.A., Yang S.M., Macfarlan T.S., Gifford W.D., Pfaff S.L., Verstegen M.J., Pinto H., Vermunt M.W., Creyghton M.P., Wijchers P.J., Stamatoyannopoulos J.A., Skoultchi A.I., de Laat W.

Genome Biol 16(1):289


Inhibition of Super-Enhancer Activity in Autoinflammatory Site-Derived T Cells Reduces Disease-Associated Gene Expression

Peeters J.G., Vervoort S.J., Tan S.C., Mijnheer G., de Roock S., Vastert S.J., Nieuwenhuis E.E., van Wijk F., Prakken B.J., Creyghton M.P., Coffer P.J., Mokry M., van Loosdregt J.

Cell Rep 12(12):1986-96


Histone acetylation in astrocytes suppresses GFAP and stimulates a re-organization of the intermediate filament network

Kanski, R., Sneeboer, M., van Bodegraven, E., Sluijs, J.A., Kropff, W.W., Vermunt, M.W., Creyghton, M.P., De Filippis, L., Vescovi, A., Aronica, E., van Tijn, P., van Strien, M and Hol, E.

J Cell Sci 127(Pt 20):4368-80


X-linked H3K27me3 demethylase Utx is required for embryonic development in a sex-specific manner

Welstead G.G., Creyghton, M.P., Bilodeau S., Cheng A.W., Markoulaki S., Young R.A., Jaenisch R.

PNAS USA 109(32):13004-9


Reprogramming factor stoichiometry influences the epigenetic state and biological properties of induced pluripotent stem cells

Carey B.W., Markoulaki S., Hanna, J., Faddah D.A., Buganim Y, Kim J, Ganz K, Steine E.J., Cassady J.P., Creyghton, M.P., Welstead G.G., Gao Q, Jaenisch R.

Cell Stem Cell 9(6):588-98


Direct reprogramming is a stochastic process amenable to acceleration

Hanna, J., Saha, K., Pando, B., van Zon, B., Lengner, C.J., Creyghton, M.P., van Oudenaarden, A., Jaenisch, R.

Nature 462: 595-601


H2AZ if enriched at polycomb complex target genes in ES cells and is necessary for lineage commitment

Creyghton, M.P., Markoulaki, S., Levine, S., Hanna, J., Lodato, M.A., Sha, K., Young, R.A., Jaenisch, R., Boyer, L.A.

Cell 135: 649-661


Direct reprogramming of terminally differentiated mature B lymphocytes to pluripotency

Hanna, J., Markoulaki, S., Schorderet, P., Carey, B.W., Beard, C., Wernig, M., Creyghton, M.P., Steine, E.J., Cassady, J.P., Foreman, R., Lengner, C.J., Dausman, J.A. & Jaenisch, R.

Cell 133, 250-264


PR130 is a modulator of the Wnt-signaling cascade that counters repression of the antagonist Naked cuticle

Creyghton, M.P., Roël G, Eichhorn P.J., Vredeveld L.C., Destrée O., Bernards R.

PNAS USA 103(14):5397-402


PR72, a novel regulator of Wnt signaling is required for Naked cuticle function

Creyghton, M.P., Roël G, Eichhorn P.J., Hijmans E.M., Maurer I., Destrée O., Bernards R.

Genes Dev 19(3): 376-86


Group leader

Menno Creyghton

Menno Creyghton is group leader at the Hubrecht Institute. His group studies in the complex epigenomic landscape of the brain using large scale ChIP-sequencing experiments on human brain tissue. These experiments are combined with functional assays in stem cells and model organisms in order to understand the cell state changes that underlie development and evolution of the human brain, and also its susceptibility to disease, such as neurodegenerative diseases and cancer.

Scientific training and positions

Group members

Menno Creyghton

Group Leader

Mirna Baak


Ilia Timpanaro


Bas Castelijns

PhD Student

Caroline Wiggers

PhD Student

Jessica Schlachter


Twan de Winter


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