2020 applicants

Dr Patrick Varga Weisz

School of Life Sciences
Dr Patrick Varga Weisz

Research and professional activities

Research interests

Current Research Interests

My team and I explore how the genome, especially in terms of gene expression, is regulated by its dynamic packaging into chromatin and how this allows stem and progenitor cells, e.g., intestinal stem cells, to respond and to adapt to the environment, for example the presence of the microbiota.

Genome regulation by genome packaging

My lab studies how the packing and organization of the genome in the nucleus of each cell affects biological functions. We focus on the intestinal epithelium, a highly dynamics tissues that continuously regenerates itself. It is also the site where a huge number of microbes live (the microbiota or microbiome) and help us in digestion of food matters. Recently, we have shown how the microbiota affect the genome through a novel modification of the packing material of the genome (link to our paper: http://rdcu.be/EntB). An important level of gene regulation occurs at the packaging of genes into the chromatin superstructure. The first building block of chromatin is the nucleosome, composed of histone proteins around which DNA winds. How gene and genome regulation happens dynamically through chromatin remodeling is of fundamental importance, but still requires much illumination. I have a long standing interest in the biochemistry of nucleosome remodelling factors and their role in maintaining specific chromatin states (Yasui et al., Nature 2002, Collins et al., Nature Genetics, 2002; Poot et al., Nature Cell Biology 2004; Rowbotham et al., Mol Cell 2011; Mermoud et al., Cell Cycle 2012, Durand-Dubief et al., PLoS Genetics, 2013; Sun et al., Nature Medicine 2015). In the last ~ 3 years my lab has moved into the field of chromatin dynamics in the intestinal epithelium and the link between chromatin and cellular metabolism/ tissue homeostasis, in part in collaboration with several groups, such as Marc Veldhoen’s (IMM, Lisbon), Marco Vinolo (UNICAMP, Brazil), Matt Zilbauer (Addenbrooke’s hospital, Cambridge). My lab employs mouse genetics (e.g., using CRISPR/Cas9), intestinal organoid culture, genome-wide chromatin analysis (ChIPseq), transcriptomics, proteomics and in vitro biochemistry to obtain insights into molecular mechanisms in intestinal epigenome regulation and how this is affected by microbial products. Furthermore, in the last 4 years my lab has been involved in a collaborative research program (involving the labs of Peter Fraser, Anne Corcoran, Mikhail Spivakov, Sarah Elderkin) investigating changes in genome regulation and nuclear organization in B cell precursor cells upon ageing in the mouse. We will extend these studies on the effect of inflammation and ageing on intestinal stem cells with emphasis on single cell transcriptomics. A major interest is how defects in epigenetic maintenance mechanisms (epigenetic instability) leads to cellular heterogeneity in ageing, with particular focus on intestinal stem cells in the mouse and human. This will reveal insights into the biology of stem cells under stresses, such as those linked to ageing and inflammation. Research Interests • Link between the microbiota and genome regulation • Chromatin dynamics in intestinal epithelial and stem cells • Chromatin remodeling factors and epigenetic stability • Mechanisms of epigenetic inheritance • Epigenetic stability in aging and disease

Key words: chromatin, histone modifications, nucleosome remodeling, intestinal epithelium, microbiota

Teaching and supervision

Current teaching responsibilities

  • Transferable Skills in Life Sciences (BS143)

  • Employability skills for Biomedical Scientists (BS214)

  • Medical Genetics (BS220)

  • Genome Science (BS222)

  • Research Project in Biomedical Science (BS831)

  • Gene Technology and Synthetic Biology (BS934)


Journal articles (28)

Varga Weisz, P. and Fellows, R., (2020). Chromatin dynamics and histone modifications in the intestinal microbiota-host crosstalk. Molecular Metabolism. 38, 100925-100925

Kazakevych, J., Denizot, J., Liebert, A., Portovedo, M., Mosavie, M., Jain, P., Stellato, C., Fraser, C., Corrêa, RO., Célestine, M., Mattiuz, R., Okkenhaug, H., Miller, JR., Vinolo, MAR., Veldhoen, M. and Varga Weisz, P., (2020). Smarcad1 mediates microbiota-induced inflammation in mouse and coordinates gene expression in the intestinal epithelium. Genome Biology. 21 (1)

Fachi, JL., Felipe, JDS., Pral, LP., da Silva, BK., Corrêa, RO., de Andrade, MCP., da Fonseca, DM., Basso, PJ., Câmara, NOS., de Sales e Souza, ÉL., dos Santos Martins, F., Guima, SES., Thomas, AM., Setubal, JC., Magalhães, YT., Forti, FL., Candreva, T., Rodrigues, HG., de Jesus, MB., Consonni, SR., Farias, ADS., Varga Weisz, P. and Vinolo, MAR., (2019). Butyrate Protects Mice from Clostridium difficile-Induced Colitis through an HIF-1-Dependent Mechanism. Cell Reports. 27 (3), 750-761.e7

Kazakevych, J., Stoyanova, E., Liebert, A. and Varga Weisz, P., (2019). Transcriptome analysis identifies a robust gene expression program in the mouse intestinal epithelium on aging. Scientific Reports. 9 (1)

Fellows, R., Denizot, J., Stellato, C., Cuomo, A., Jain, P., Stoyanova, E., Balázsi, S., Hajnády, Z., Liebert, A., Kazakevych, J., Blackburn, H., Corrêa, RO., Fachi, JL., Sato, FT., Ribeiro, WR., Ferreira, CM., Perée, H., Spagnuolo, M., Mattiuz, R., Matolcsi, C., Guedes, J., Clark, J., Veldhoen, M., Bonaldi, T., Vinolo, MAR. and Varga Weisz, PD., (2018). Microbiota derived short chain fatty acids promote histone crotonylation in the colon through histone deacetylases. Nature Communications. 9 (1)

Koohy, H., Bolland, DJ., Matheson, LS., Schoenfelder, S., Stellato, C., Dimond, A., Várnai, C., Chovanec, P., Chessa, T., Denizot, J., Garcia, RM., Wingett, SW., Freire-Pritchett, P., Nagano, T., Hawkins, P., Stephens, L., Elderkin, S., Spivakov, M., Fraser, P., Corcoran, AE. and Varga-Weisz, PD., (2018). Genome organization and chromatin analysis identify transcriptional downregulation of insulin-like growth factor signaling as a hallmark of aging in developing B cells. Genome Biology. 19 (1), 126-

Fellows, R. and Varga Weisz, P., (2018). In vitro Enzymatic Assays of Histone Decrotonylation on Recombinant Histones. Bio-protocol. 8 (14)

Sun, H., Damez-Werno, DM., Scobie, KN., Shao, N-Y., Dias, C., Rabkin, J., Koo, JW., Korb, E., Bagot, RC., Ahn, FH., Cahill, ME., Labonté, B., Mouzon, E., Heller, EA., Cates, H., Golden, SA., Gleason, K., Russo, SJ., Andrews, S., Neve, R., Kennedy, PJ., Maze, I., Dietz, DM., Allis, CD., Turecki, G., Varga-Weisz, P., Tamminga, C., Shen, L. and Nestler, EJ., (2015). ACF chromatin-remodeling complex mediates stress-induced depressive-like behavior. Nature Medicine. 21 (10), 1146-1153

Petrini, E., Baillet, V., Cridge, J., Hogan, CJ., Guillaume, C., Ke, H., Brandetti, E., Walker, S., Koohy, H., Spivakov, M. and Varga-Weisz, P., (2015). A new phosphate-starvation response in fission yeast requires the endocytic function of myosin I. Journal of Cell Science. 128 (20), 3707-3713

Varga-Weisz, PD., (2014). Chromatin remodeling: a collaborative effort. Nature Structural & Molecular Biology. 21 (1), 14-16

Mermoud, JE., Rowbotham, SP. and Varga-Weisz, PD., (2011). Keeping chromatin quiet. Cell Cycle. 10 (23), 4017-4025

Varga-Weisz, PD., (2010). Insights into how chromatin remodeling factors find their target in the nucleus. Proceedings of the National Academy of Sciences. 107 (46), 19611-19612

Hogan, CJ., Aligianni, S., Durand-Dubief, M., Persson, J., Will, WR., Webster, J., Wheeler, L., Mathews, CK., Elderkin, S., Oxley, D., Ekwall, K. and Varga-Weisz, PD., (2010). Fission Yeast Iec1-Ino80-Mediated Nucleosome Eviction Regulates Nucleotide and Phosphate Metabolism. Molecular and Cellular Biology. 30 (3), 657-674

Varga-Weisz, PD. and Becker, PB., (2006). Regulation of higher-order chromatin structures by nucleosome-remodelling factors. Current Opinion in Genetics & Development. 16 (2), 151-156

Poot, RA., Bozhenok, L., Berg, DLCVD., Hawkes, N. and Varga-Weisz, PD., (2005). Chromatin Remodelling by WSTF-ISWI at the Replication Site: Opening a Window of Opportunity for Epigenetic Inheritance?. Cell Cycle. 4 (4), 543-546

Kukimoto, I., Elderkin, S., Grimaldi, M., Oelgeschläger, T. and Varga-Weisz, PD., (2004). The Histone-Fold Protein Complex CHRAC-15/17 Enhances Nucleosome Sliding and Assembly Mediated by ACF. Molecular Cell. 13 (2), 265-277

Poot, RA., Bozhenok, L., van den Berg, DLC., Steffensen, S., Ferreira, F., Grimaldi, M., Gilbert, N., Ferreira, J. and Varga-Weisz, PD., (2004). The Williams syndrome transcription factor interacts with PCNA to target chromatin remodelling by ISWI to replication foci. Nature Cell Biology. 6 (12), 1236-1244

Varga-Weisz, PD. and Dalgaard, JZ., (2002). A Mark in the Core. Molecular Cell. 9 (6), 1154-1156

Collins, N., Poot, RA., Kukimoto, I., García-Jiménez, C., Dellaire, G. and Varga-Weisz, PD., (2002). An ACF1–ISWI chromatin-remodeling complex is required for DNA replication through heterochromatin. Nature Genetics. 32 (4), 627-632

Poot, RA., (2000). HuCHRAC, a human ISWI chromatin remodelling complex contains hACF1 and two novel histone-fold proteins. The EMBO Journal. 19 (13), 3377-3387

Varga-Weisz, PD., Bonte, EJ. and Becker, PB., (1999). Analysis of modulators of chromatin structure in Drosophila. Methods in Enzymology. 304, 742-757

Alexiadis, V., (1998). In vitro chromatin remodelling by chromatin accessibility complex (CHRAC) at the SV40 origin of DNA replication. The EMBO Journal. 17 (12), 3428-3438

Varga-Weisz, PD. and Becker, PB., (1998). Chromatin-remodeling factors: machines that regulate?. Current Opinion in Cell Biology. 10 (3), 346-353

Varga-Weisz, PD., Wilm, M., Bonte, E., Dumas, K., Mann, M. and Becker, PB., (1997). Erratum: Chromatin-remodelling factor CHRAC contains the ATPases ISWI and topoisomerase II. Nature. 389 (6654), 1003-1003

Varga-Weisz, PD., Wilm, M., Bonte, E., Dumas, K., Mann, M. and Becker, PB., (1997). Chromatin-remodelling factor CHRAC contains the ATPases ISWI and topoisomerase II. Nature. 388 (6642), 598-602

Varga-Weisz, PD., Blank, TA. and Becker, PB., (1995). Energy-dependent chromatin accessibility and nucleosome mobility in a cell-free system.. The EMBO Journal. 14 (10), 2209-2216

Varga-Weisz, PD. and Becker, PB., (1995). Transcription factor-mediated chromatin remodelling: mechanisms and models. FEBS Letters. 369 (1), 118-121

Wall, G., Varga-Weisz, PD., Sandaltzopoulos, R. and Becker, PB., (1995). Chromatin remodeling by GAGA factor and heat shock factor at the hypersensitive Drosophila hsp26 promoter in vitro.. The EMBO Journal. 14 (8), 1727-1736

Grants and funding


Role of histone acylations in intestinal epithelium homeostasis

The Royal Society

Addressing the Inflammatory Bowel Disease Challenge in Vietnam by Bridging the Basic-Clinical Science Divide in Gastroenterology: A Vietnam-UK Collaborative Network

Academy of Medical Sciences


+44 (0) 1206 872318


3SW.3.04, Colchester Campus