Gene Regulation, Stems Cells and Cancer


Chromatin and Gene Expression

Miguel Beato
Guillermo Vicent
Ivan Junier (since April), François Le Dily, Priyanka Sharma (Marie Curie Fellow), Gaetano Verde (Marie Curie Fellow), Roni Wright
Gireesh Bogu (La Caixa Fellow, until June), Roberto Ferrari (since October), Alexandra Leopoldi (Severo Ochoa Fellow, since Septeber), Antonios Lioutas (since July), Andy Pohl
Jofre Font Mateu, A. Silvina Nacht, Daniel Soronellas (bioinformatics)
Maria Florencia Ogara (EMBO Short Term Fellow, University of Buenos Aires), Caroline Wiggers (Erasmus Fellow, University of Amsterdam)


Figure 1. Changes in TAD topology in response to Progestins (Pg).

The group explores how eukaryotic cells respond to external cues, in particular how signals are transduced to the nucleus to modulate chromatin structure and gene expression. Steroid hormones signal to chromatin via binding of their intracellular receptors. A fraction of these receptors is attached to the cell membrane where they crosstalk with kinase signalling pathways, which ultimately facilitate the interaction of receptors with the target sites in nucleosomes and the subsequent chromatin remodelling. The hormone initiates two consecutive cycles of remodelling involving kinases; PARP1, histone modifying enzymes and ATP-dependent complexes lead to sequential displacement of histones H1 and H2A/H2B. We found that large topological chromatin domains (~1 Mb long) behave as units of hormone response that undergo structural changes in cells exposed to hormone, ultimately leading to cell proliferation. The ATP required for this extensive chromatin remodelling is generated in the nucleus from ADP-Ribose and PPi. We are now using antibody arrays and phosphoproteomics to explore the time kinetics of the complete signalling network. Our final aim is to integrate this network with the changes in the topological organization of chromatin that modulate the transcriptional response to generate a dynamic vision of the cell response in 3D. Nodes of this hormonal signalling network controlling cell proliferation would be potential targets for the combinatorial control of cancer cell proliferation.

Research Projects

  • Global analysis of chromatin structure and dynamics during hormonal gene regulation  
    G. Bogu, R. Ferrari, F. Le Dily, A. Lioutas, S. Nacht, A. Pohl, P. Sharma, D. Soronellas, G. Verde, G. Vicent, R. Wright.
    Progestin (Pg) addition to T47D breast cancer cells activates the Progesterone Receptor (PR) that binds to nucleosomaly organised promoter/enhancer regions of target genes along with kinases, histone modifying enzymes and chromatin remodeller, leading to coordinate activation or repression of genes clustered in topological associating domains (TADs) (Le Dily et al. Genes Dev 2014) (Figure 1). Depletion or inhibition of MSK1 compromises hormonal gene regulation and blocks proliferation of breast cancer cells in vitro and in mouse xenografts (Reyes et al. Oncogene 2014). The PR associated factors lead to opening of chromatin and the ATP required for this remodeling is synthesized by NUDIX5 from ADPR (Wright et al. bioRxiv 2014). In collaboration with the group of Thomas Graf we found that C/EBPa also contributes to iPS generation from B cells by favouring chromatin opening of the relevant enhancers (Di Sefano et al. Nature 2014)
  • Signalling by progesterone to chromatin via kinase cascades
    J. Font Mateu, R. Wright
    We have discovered a number of protein kinases that participate in the response of breast cancer cells to oestrogens and progesterone, acting as co-activator of their respective receptors. In endometrial stromal cells the effect of hormones on the kinases can activate cell proliferation in the absence of a transcriptional action of the hormones (Vallejo et al. PLoS One 2014). We are completing these studies with an analysis of changes in the whole cell phosphoproteome, different times after hormone treatment. The goal is to integrate these results in a dynamic network (collaboration with J. Saez-Rodriguez, EBI, UK), which should help identifying relevant nodes connecting various signaling pathways to regulation of different gene cohorts.

Selected Publications

Le Dily F, Baù D, Pohl A, Vicent G, Serra F, Soronellas D, Castellano G, Wright RHG, Ballare C, Filion G, Marti-Renom MA, Beato M.
“Distinct structural transitions of chromatin topological domains correlate with hormone-induced gene regulation”
Genes Dev, 28:2151-62. doi:10.1101/003293 (2014).

Reyes D, Ballare C, Castellano G, Soronellas D, Bago JR, Blanco J, Beato M.
“Activation of Mitogen- and Stress-activated Kinase 1 is required for proliferation of breast cancer cells in response to estrogens and progesterone.”
Oncogene, 33:1570-1580 (2014).

Di Stefano B, Sardina JL, van Oevelen C, Kallin EM, Collombet S, Kalin EM, Vicent GP, Lu J, Thieffry D, Beato M, Graf T.
“Overcoming the stochastic phase of iPS cells reprogramming by a pulse of C/EBPα.”
Nature, 506:235-239 (2014).

Vallejo G, La Greca AD, Tarifa-Reischle IC, Mestre-Citrinovitz AC, Ballare C, Beato M, Saragüeta P.
“CDC2 mediates Progestin initiated endometrial stromal cell proliferation: PR signaling to gene expression independently of its binding to chromatin.”
PLoS One, 9:e97311.doi: 10.1371 (2014).

Wright RHG, LeDily F, Soronellas D, Pohl A, Bonet J, Nacht AS, Vicent GP, Wierer M, Oliva B, Beato M.
“ADP-ribose derived nuclear ATP is required for chromatin remodelling and hormonal gene regulation in breast cancer cells.”
bioRxiv, 25 June 2014. doi:10.1101/006593.