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133 results on '"Matarese, Filomena"'

1. Genome-wide modelling of transcription kinetics reveals patterns of RNA production delays

Author

Honkela, Antti, Peltonen, Jaakko, Topa, Hande, Charapitsa, Iryna, Matarese, Filomena, Grote, Korbinian, Stunnenberg, Hendrik G., Reid, George, Lawrence, Neil D., and Rattray, Magnus

Subjects
Quantitative Biology - Genomics, Quantitative Biology - Quantitative Methods, Statistics - Applications
Abstract

Genes with similar transcriptional activation kinetics can display very different temporal mRNA profiles due to differences in transcription time, degradation rate and RNA processing kinetics. Recent studies have shown that a splicing-associated RNA production delay can be significant. We introduce a joint model of transcriptional activation and mRNA accumulation which can be used for inference of transcription rate, RNA production delay and degradation rate given genome-wide data from high-throughput sequencing time course experiments. We combine a mechanistic differential equation model with a non-parametric statistical modelling approach allowing us to capture a broad range of activation kinetics, and use Bayesian parameter estimation to quantify the uncertainty in the estimates of the kinetic parameters. We apply the model to data from estrogen receptor (ER-{\alpha}) activation in the MCF-7 breast cancer cell line. We use RNA polymerase II (pol-II) ChIP-Seq time course data to characterise transcriptional activation and mRNA-Seq time course data to quantify mature transcripts. We find that 11% of genes with a good signal in the data display a delay of more than 20 minutes between completing transcription and mature mRNA production. The genes displaying these long delays are significantly more likely to be short. We also find a statistical association between high delay and late intron retention in pre-mRNA data, indicating significant splicing-associated production delays in many genes., Comment: 42 pages, 17 figures

Published
2015
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2. Inference of RNA Polymerase II Transcription Dynamics from Chromatin Immunoprecipitation Time Course Data

Author

Maina, Ciira wa, Honkela, Antti, Matarese, Filomena, Grote, Korbinian, Stunnenberg, Hendrik G., Reid, George, Lawrence, Neil D., and Rattray, Magnus

Subjects
Quantitative Biology - Quantitative Methods, Quantitative Biology - Molecular Networks
Abstract

Gene transcription mediated by RNA polymerase II (pol-II) is a key step in gene expression. The dynamics of pol-II moving along the transcribed region influence the rate and timing of gene expression. In this work we present a probabilistic model of transcription dynamics which is fitted to pol-II occupancy time course data measured using ChIP-Seq. The model can be used to estimate transcription speed and to infer the temporal pol-II activity profile at the gene promoter. Model parameters are estimated using either maximum likelihood estimation or via Bayesian inference using Markov chain Monte Carlo sampling. The Bayesian approach provides confidence intervals for parameter estimates and allows the use of priors that capture domain knowledge, e.g. the expected range of transcription speeds, based on previous experiments. The model describes the movement of pol-II down the gene body and can be used to identify the time of induction for transcriptionally engaged genes. By clustering the inferred promoter activity time profiles, we are able to determine which genes respond quickly to stimuli and group genes that share activity profiles and may therefore be co-regulated. We apply our methodology to biological data obtained using ChIP-seq to measure pol-II occupancy genome-wide when MCF-7 human breast cancer cells are treated with estradiol (E2). The transcription speeds we obtain agree with those obtained previously for smaller numbers of genes with the advantage that our approach can be applied genome-wide. We validate the biological significance of the pol-II promoter activity clusters by investigating cluster-specific transcription factor binding patterns and determining canonical pathway enrichment. We find that rapidly induced genes are enriched for both estrogen receptor alpha (ER$\alpha$) and FOXA1 binding in their proximal promoter regions., Comment: 40 pages: 21 pages Main text, 19 pages supplementary material

Published
2013

3. Potential impact of celiac disease genetic risk factors on T cell receptor signaling in gluten-specific CD4+ T cells

Author

Bakker, Olivier B., Ramírez-Sánchez, Aarón D., Borek, Zuzanna A., de Klein, Niek, Li, Yang, Modderman, Rutger, Kooy-Winkelaar, Yvonne, Johannesen, Marie K., Matarese, Filomena, Martens, Joost H. A., Kumar, Vinod, van Bergen, Jeroen, Qiao, Shuo-Wang, Lundin, Knut E. A., Sollid, Ludvig M., Koning, Frits, Wijmenga, Cisca, Withoff, Sebo, and Jonkers, Iris H.

Published
2021
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4. Supplementary Table 1 from Death Receptor Pathway Activation and Increase of ROS Production by the Triple Epigenetic Inhibitor UVI5008

Author

Nebbioso, Angela, primary, Pereira, Raquel, primary, Khanwalkar, Harshal, primary, Matarese, Filomena, primary, García-Rodríguez, José, primary, Miceli, Marco, primary, Logie, Colin, primary, Kedinger, Valerie, primary, Ferrara, Felicetto, primary, Stunnenberg, Hendrik G., primary, de Lera, Angel R., primary, Gronemeyer, Hinrich, primary, and Altucci, Lucia, primary

Published
2023
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5. Supplementary Figure 1 from Death Receptor Pathway Activation and Increase of ROS Production by the Triple Epigenetic Inhibitor UVI5008

Author

Nebbioso, Angela, primary, Pereira, Raquel, primary, Khanwalkar, Harshal, primary, Matarese, Filomena, primary, García-Rodríguez, José, primary, Miceli, Marco, primary, Logie, Colin, primary, Kedinger, Valerie, primary, Ferrara, Felicetto, primary, Stunnenberg, Hendrik G., primary, de Lera, Angel R., primary, Gronemeyer, Hinrich, primary, and Altucci, Lucia, primary

Published
2023
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6. Data from Death Receptor Pathway Activation and Increase of ROS Production by the Triple Epigenetic Inhibitor UVI5008

Author

Nebbioso, Angela, primary, Pereira, Raquel, primary, Khanwalkar, Harshal, primary, Matarese, Filomena, primary, García-Rodríguez, José, primary, Miceli, Marco, primary, Logie, Colin, primary, Kedinger, Valerie, primary, Ferrara, Felicetto, primary, Stunnenberg, Hendrik G., primary, de Lera, Angel R., primary, Gronemeyer, Hinrich, primary, and Altucci, Lucia, primary

Published
2023
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7. Supplementary Figure 4 from Death Receptor Pathway Activation and Increase of ROS Production by the Triple Epigenetic Inhibitor UVI5008

Author

Nebbioso, Angela, primary, Pereira, Raquel, primary, Khanwalkar, Harshal, primary, Matarese, Filomena, primary, García-Rodríguez, José, primary, Miceli, Marco, primary, Logie, Colin, primary, Kedinger, Valerie, primary, Ferrara, Felicetto, primary, Stunnenberg, Hendrik G., primary, de Lera, Angel R., primary, Gronemeyer, Hinrich, primary, and Altucci, Lucia, primary

Published
2023
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8. Supplementary Figure 2 from Death Receptor Pathway Activation and Increase of ROS Production by the Triple Epigenetic Inhibitor UVI5008

Author

Nebbioso, Angela, primary, Pereira, Raquel, primary, Khanwalkar, Harshal, primary, Matarese, Filomena, primary, García-Rodríguez, José, primary, Miceli, Marco, primary, Logie, Colin, primary, Kedinger, Valerie, primary, Ferrara, Felicetto, primary, Stunnenberg, Hendrik G., primary, de Lera, Angel R., primary, Gronemeyer, Hinrich, primary, and Altucci, Lucia, primary

Published
2023
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9. Supplementary Methods from Death Receptor Pathway Activation and Increase of ROS Production by the Triple Epigenetic Inhibitor UVI5008

Author

Nebbioso, Angela, primary, Pereira, Raquel, primary, Khanwalkar, Harshal, primary, Matarese, Filomena, primary, García-Rodríguez, José, primary, Miceli, Marco, primary, Logie, Colin, primary, Kedinger, Valerie, primary, Ferrara, Felicetto, primary, Stunnenberg, Hendrik G., primary, de Lera, Angel R., primary, Gronemeyer, Hinrich, primary, and Altucci, Lucia, primary

Published
2023
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10. Supplementary Figure 5 from Death Receptor Pathway Activation and Increase of ROS Production by the Triple Epigenetic Inhibitor UVI5008

Author

Nebbioso, Angela, primary, Pereira, Raquel, primary, Khanwalkar, Harshal, primary, Matarese, Filomena, primary, García-Rodríguez, José, primary, Miceli, Marco, primary, Logie, Colin, primary, Kedinger, Valerie, primary, Ferrara, Felicetto, primary, Stunnenberg, Hendrik G., primary, de Lera, Angel R., primary, Gronemeyer, Hinrich, primary, and Altucci, Lucia, primary

Published
2023
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11. Supplementary Figure 3 from Death Receptor Pathway Activation and Increase of ROS Production by the Triple Epigenetic Inhibitor UVI5008

Author

Nebbioso, Angela, primary, Pereira, Raquel, primary, Khanwalkar, Harshal, primary, Matarese, Filomena, primary, García-Rodríguez, José, primary, Miceli, Marco, primary, Logie, Colin, primary, Kedinger, Valerie, primary, Ferrara, Felicetto, primary, Stunnenberg, Hendrik G., primary, de Lera, Angel R., primary, Gronemeyer, Hinrich, primary, and Altucci, Lucia, primary

Published
2023
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12. Supplementary Figure 1 from Context-Selective Death of Acute Myeloid Leukemia Cells Triggered by the Novel Hybrid Retinoid-HDAC Inhibitor MC2392

Author

De Bellis, Floriana, primary, Carafa, Vincenzo, primary, Conte, Mariarosaria, primary, Rotili, Dante, primary, Petraglia, Francesca, primary, Matarese, Filomena, primary, Françoijs, Kees-Jan, primary, Ablain, Julien, primary, Valente, Sergio, primary, Castellano, Rèmy, primary, Goubard, Armelle, primary, Collette, Yves, primary, Mandoli, Amit, primary, Martens, Joost H.A., primary, de Thé, Hugues, primary, Nebbioso, Angela, primary, Mai, Antonello, primary, Stunnenberg, Hendrik G., primary, and Altucci, Lucia, primary

Published
2023
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13. Data from Context-Selective Death of Acute Myeloid Leukemia Cells Triggered by the Novel Hybrid Retinoid-HDAC Inhibitor MC2392

Author

De Bellis, Floriana, primary, Carafa, Vincenzo, primary, Conte, Mariarosaria, primary, Rotili, Dante, primary, Petraglia, Francesca, primary, Matarese, Filomena, primary, Françoijs, Kees-Jan, primary, Ablain, Julien, primary, Valente, Sergio, primary, Castellano, Rèmy, primary, Goubard, Armelle, primary, Collette, Yves, primary, Mandoli, Amit, primary, Martens, Joost H.A., primary, de Thé, Hugues, primary, Nebbioso, Angela, primary, Mai, Antonello, primary, Stunnenberg, Hendrik G., primary, and Altucci, Lucia, primary

Published
2023
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14. Supplementary Figure 2 from Context-Selective Death of Acute Myeloid Leukemia Cells Triggered by the Novel Hybrid Retinoid-HDAC Inhibitor MC2392

Author

De Bellis, Floriana, primary, Carafa, Vincenzo, primary, Conte, Mariarosaria, primary, Rotili, Dante, primary, Petraglia, Francesca, primary, Matarese, Filomena, primary, Françoijs, Kees-Jan, primary, Ablain, Julien, primary, Valente, Sergio, primary, Castellano, Rèmy, primary, Goubard, Armelle, primary, Collette, Yves, primary, Mandoli, Amit, primary, Martens, Joost H.A., primary, de Thé, Hugues, primary, Nebbioso, Angela, primary, Mai, Antonello, primary, Stunnenberg, Hendrik G., primary, and Altucci, Lucia, primary

Published
2023
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15. Supplementary Materials and Methods, Tables 1 - 3 from Context-Selective Death of Acute Myeloid Leukemia Cells Triggered by the Novel Hybrid Retinoid-HDAC Inhibitor MC2392

Author

De Bellis, Floriana, primary, Carafa, Vincenzo, primary, Conte, Mariarosaria, primary, Rotili, Dante, primary, Petraglia, Francesca, primary, Matarese, Filomena, primary, Françoijs, Kees-Jan, primary, Ablain, Julien, primary, Valente, Sergio, primary, Castellano, Rèmy, primary, Goubard, Armelle, primary, Collette, Yves, primary, Mandoli, Amit, primary, Martens, Joost H.A., primary, de Thé, Hugues, primary, Nebbioso, Angela, primary, Mai, Antonello, primary, Stunnenberg, Hendrik G., primary, and Altucci, Lucia, primary

Published
2023
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16. Supplementary Figure 4 from Context-Selective Death of Acute Myeloid Leukemia Cells Triggered by the Novel Hybrid Retinoid-HDAC Inhibitor MC2392

Author

De Bellis, Floriana, primary, Carafa, Vincenzo, primary, Conte, Mariarosaria, primary, Rotili, Dante, primary, Petraglia, Francesca, primary, Matarese, Filomena, primary, Françoijs, Kees-Jan, primary, Ablain, Julien, primary, Valente, Sergio, primary, Castellano, Rèmy, primary, Goubard, Armelle, primary, Collette, Yves, primary, Mandoli, Amit, primary, Martens, Joost H.A., primary, de Thé, Hugues, primary, Nebbioso, Angela, primary, Mai, Antonello, primary, Stunnenberg, Hendrik G., primary, and Altucci, Lucia, primary

Published
2023
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17. Supplementary Figure 3 from Context-Selective Death of Acute Myeloid Leukemia Cells Triggered by the Novel Hybrid Retinoid-HDAC Inhibitor MC2392

Author

De Bellis, Floriana, primary, Carafa, Vincenzo, primary, Conte, Mariarosaria, primary, Rotili, Dante, primary, Petraglia, Francesca, primary, Matarese, Filomena, primary, Françoijs, Kees-Jan, primary, Ablain, Julien, primary, Valente, Sergio, primary, Castellano, Rèmy, primary, Goubard, Armelle, primary, Collette, Yves, primary, Mandoli, Amit, primary, Martens, Joost H.A., primary, de Thé, Hugues, primary, Nebbioso, Angela, primary, Mai, Antonello, primary, Stunnenberg, Hendrik G., primary, and Altucci, Lucia, primary

Published
2023
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18. Epigenetic programming of monocyte-to-macrophage differentiation and trained innate immunity

Author

Saeed, Sadia, Quintin, Jessica, Kerstens, Hindrik H. D., Rao, Nagesha A., Aghajanirefah, Ali, Matarese, Filomena, Cheng, Shih-Chin, Ratter, Jacqueline, Berentsen, Kim, van der Ent, Martijn A., Sharifi, Nilofar, Janssen-Megens, Eva M., Ter Huurne, Menno, Mandoli, Amit, van Schaik, Tom, Ng, Aylwin, Burden, Frances, Downes, Kate, Frontini, Mattia, Kumar, Vinod, Giamarellos-Bourboulis, Evangelos J., Ouwehand, Willem H., van der Meer, Jos W. M., Joosten, Leo A. B., Wijmenga, Cisca, Martens, Joost H. A., Xavier, Ramnik J., Logie, Colin, Netea, Mihai G., and Stunnenberg, Hendrik G.

Published
2014

19. IMMUNOGENETICS: Epigenetic programming of monocyte-to-macrophage differentiation and trained innate immunity

Author

Saeed, Sadia, Quintin, Jessica, Kerstens, Hindrik H. D., Rao, Nagesha A., Aghajanirefah, Ali, Matarese, Filomena, Cheng, Shih-Chin, Ratter, Jacqueline, Berentsen, Kim, van der Ent, Martijn A., Sharifi, Nilofar, Janssen-Megens, Eva M., Huurne, Menno Ter, Mandoli, Amit, van Schaik, Tom, Ng, Aylwin, Burden, Frances, Downes, Kate, Frontini, Mattia, Kumar, Vinod, Giamarellos-Bourboulis, Evangelos J., Ouwehand, Willem H., van der Meer, Jos W. M., Joosten, Leo A. B., Wijmenga, Cisca, Martens, Joost H. A., Xavier, Ramnik J., Logie, Colin, Netea, Mihai G., and Stunnenberg, Hendrik G.

Published
2014
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20. Chromatin-Based Classification of Genetically Heterogeneous AMLs into Two Distinct Subtypes with Diverse Stemness Phenotypes

Author

Yi, G., Wierenga, A.T., Petraglia, F., Narang, P., Janssen-Megens, E.M., Mandoli, A., Berentsen, K., Kim, B., Matarese, Filomena, Singh, A.A., Habibi, E., Prange, K.H.M., Jansen, J.H., Reijden, B.A. van der, Stunnenberg, Hendrik G., Martens, J.H.A., Yi, G., Wierenga, A.T., Petraglia, F., Narang, P., Janssen-Megens, E.M., Mandoli, A., Berentsen, K., Kim, B., Matarese, Filomena, Singh, A.A., Habibi, E., Prange, K.H.M., Jansen, J.H., Reijden, B.A. van der, Stunnenberg, Hendrik G., and Martens, J.H.A.

Abstract

Contains fulltext : 200959.pdf (publisher's version ) (Open Access)

Published
2019

22. Chromatin-Based Classification of Genetically Heterogeneous AMLs into Two Distinct Subtypes with Diverse Stemness Phenotypes

Author

Yi, Guoqiang, primary, Wierenga, Albertus T.J., additional, Petraglia, Francesca, additional, Narang, Pankaj, additional, Janssen-Megens, Eva M., additional, Mandoli, Amit, additional, Merkel, Angelika, additional, Berentsen, Kim, additional, Kim, Bowon, additional, Matarese, Filomena, additional, Singh, Abhishek A., additional, Habibi, Ehsan, additional, Prange, Koen H.M., additional, Mulder, André B., additional, Jansen, Joop H., additional, Clarke, Laura, additional, Heath, Simon, additional, van der Reijden, Bert A., additional, Flicek, Paul, additional, Yaspo, Marie-Laure, additional, Gut, Ivo, additional, Bock, Christoph, additional, Schuringa, Jan Jacob, additional, Altucci, Lucia, additional, Vellenga, Edo, additional, Stunnenberg, Hendrik G., additional, and Martens, Joost H.A., additional

Published
2019
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23. Predicting stimulation-dependent 1 enhancer-promoter interactions from 2 ChIP-Seq time course data

Author

Dzida, Tomasz, Iqbal, Mudassar, Charapitsa, Iryna, Stunnenberg, Henk, Matarese, Filomena, Honkela, Antti, and Rattray, Magnus

Abstract

We have developed a machine learning approach to predict stimulation-dependent enhancer-promoter interactions using evidence from changes in genomic protein occupancy over time. The occupancy of estrogen receptor alpha (ERa), RNA polymerase (Pol II) and histone marks H2AZ and H3K4me3 were measured over time using ChIP-Seq experiments in MCF7 cells stimulated with estrogen. A Bayesian classifier was developed which uses the correlation of temporal binding patterns at enhancers and promoters and genomic proximity as features to predict interactions. This method was trained using experimentally determined interactions from the same system and was shown to achieve much higher precision than predictions based on the genomic proximity of nearest ERa binding. We use the method to identify a genome-wide confident set of ERa target genes and their regulatory enhancers genome-wide. Validation with publicly available GRO-Seq data demonstrates that our predicted targets are much more likely to show early nascent transcription than predictions based on genomic ERa binding proximity alone.

Published
2017
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25. Time-resolved analysis of DNA-protein interactions in living cells by UV laser pulses

Author

Nebbioso, Angela, primary, Benedetti, Rosaria, additional, Conte, Mariarosaria, additional, Carafa, Vincenzo, additional, De Bellis, Floriana, additional, Shaik, Jani, additional, Matarese, Filomena, additional, Della Ventura, Bartolomeo, additional, Gesuele, Felice, additional, Velotta, Raffaele, additional, Martens, Joost H. A., additional, Stunnenberg, Hendrik G., additional, Altucci, Carlo, additional, and Altucci, Lucia, additional

Published
2017
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27. Recruitment of the mammalian histone-modifying EMSY complex to target genes is regulated by ZNF131

Author

Varier, Radhika A., De Santa Pau, Enrique Carrillo, van der Groep, Petra, Lindeboom, Rik G H, Matarese, Filomena, Mensinga, Anneloes, Smits, Arne H., Edupuganti, Raghu Ram, Baltissen, Marijke P., Jansen, Pascal W T C, Hoeve, Natalie Ter, Van Weely, Danny R., Poser, Ina, Van Diest, Paul J., Stunnenberg, Hendrik G., Vermeulen, Michiel, Varier, Radhika A., De Santa Pau, Enrique Carrillo, van der Groep, Petra, Lindeboom, Rik G H, Matarese, Filomena, Mensinga, Anneloes, Smits, Arne H., Edupuganti, Raghu Ram, Baltissen, Marijke P., Jansen, Pascal W T C, Hoeve, Natalie Ter, Van Weely, Danny R., Poser, Ina, Van Diest, Paul J., Stunnenberg, Hendrik G., and Vermeulen, Michiel

Published
2016

28. Recruitment of the mammalian histone-modifying EMSY complex to target genes is regulated by ZNF131

Author

Projecten, Cancer, Groep Timmers, Pathologie Laboratorium diagnostiek, Pathologie, Groep Vermeulen, Varier, Radhika A., De Santa Pau, Enrique Carrillo, van der Groep, Petra, Lindeboom, Rik G H, Matarese, Filomena, Mensinga, Anneloes, Smits, Arne H., Edupuganti, Raghu Ram, Baltissen, Marijke P., Jansen, Pascal W T C, Hoeve, Natalie Ter, Van Weely, Danny R., Poser, Ina, Van Diest, Paul J., Stunnenberg, Hendrik G., Vermeulen, Michiel, Projecten, Cancer, Groep Timmers, Pathologie Laboratorium diagnostiek, Pathologie, Groep Vermeulen, Varier, Radhika A., De Santa Pau, Enrique Carrillo, van der Groep, Petra, Lindeboom, Rik G H, Matarese, Filomena, Mensinga, Anneloes, Smits, Arne H., Edupuganti, Raghu Ram, Baltissen, Marijke P., Jansen, Pascal W T C, Hoeve, Natalie Ter, Van Weely, Danny R., Poser, Ina, Van Diest, Paul J., Stunnenberg, Hendrik G., and Vermeulen, Michiel

Published
2016

29. Epigenetic programming of monocyte-to-macrophage differentiation and trained innate immunity

Author

Saeed, Sadia Quintin, Jessica Kerstens, Hindrik H. D. Rao, Nagesha A. Aghajanirefah, Ali Matarese, Filomena Cheng, Shih-Chin Ratter, Jacqueline Berentsen, Kim van der Ent, Martijn A. Sharifi, Nilofar Janssen-Megens, Eva M. Ter Huurne, Menno Mandoli, Amit van Schaik, Tom Ng, Aylwin and Burden, Frances Downes, Kate Frontini, Mattia Kumar, Vinod and Giamarellos-Bourboulis, Evangelos J. Ouwehand, Willem H. van der Meer, Jos W. M. Joosten, Leo A. B. Wijmenga, Cisca and Martens, Joost H. A. Xavier, Ramnik J. Logie, Colin Netea, Mihai G. Stunnenberg, Hendrik G.

Abstract

Monocyte differentiation into macrophages represents a cornerstone process for host defense. Concomitantly, immunological imprinting of either tolerance or trained immunity determines the functional fate of macrophages and susceptibility to secondary infections. We characterized the transcriptomes and epigenomes in four primary cell types: monocytes and in vitro-differentiated naive, tolerized, and trained macrophages. Inflammatory and metabolic pathways were modulated in macrophages, including decreased inflammasome activation, and we identified pathways functionally implicated in trained immunity. beta-glucan training elicits an exclusive epigenetic signature, revealing a complex network of enhancers and promoters. Analysis of transcription factor motifs in deoxyribonuclease I hypersensitive sites at cell-type-specific epigenetic loci unveiled differentiation and treatment-specific repertoires. Altogether, we provide a resource to understand the epigenetic changes that underlie innate immunity in humans.

Published
2014

30. β-Glucan Reverses the Epigenetic State of LPS-Induced Immunological Tolerance

Author

Novakovic, Boris, primary, Habibi, Ehsan, additional, Wang, Shuang-Yin, additional, Arts, Rob J.W., additional, Davar, Robab, additional, Megchelenbrink, Wout, additional, Kim, Bowon, additional, Kuznetsova, Tatyana, additional, Kox, Matthijs, additional, Zwaag, Jelle, additional, Matarese, Filomena, additional, van Heeringen, Simon J., additional, Janssen-Megens, Eva M., additional, Sharifi, Nilofar, additional, Wang, Cheng, additional, Keramati, Farid, additional, Schoonenberg, Vivien, additional, Flicek, Paul, additional, Clarke, Laura, additional, Pickkers, Peter, additional, Heath, Simon, additional, Gut, Ivo, additional, Netea, Mihai G., additional, Martens, Joost H.A., additional, Logie, Colin, additional, and Stunnenberg, Hendrik G., additional

Published
2016
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31. Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells

Author

Chen, Lu, primary, Ge, Bing, additional, Casale, Francesco Paolo, additional, Vasquez, Louella, additional, Kwan, Tony, additional, Garrido-Martín, Diego, additional, Watt, Stephen, additional, Yan, Ying, additional, Kundu, Kousik, additional, Ecker, Simone, additional, Datta, Avik, additional, Richardson, David, additional, Burden, Frances, additional, Mead, Daniel, additional, Mann, Alice L., additional, Fernandez, Jose Maria, additional, Rowlston, Sophia, additional, Wilder, Steven P., additional, Farrow, Samantha, additional, Shao, Xiaojian, additional, Lambourne, John J., additional, Redensek, Adriana, additional, Albers, Cornelis A., additional, Amstislavskiy, Vyacheslav, additional, Ashford, Sofie, additional, Berentsen, Kim, additional, Bomba, Lorenzo, additional, Bourque, Guillaume, additional, Bujold, David, additional, Busche, Stephan, additional, Caron, Maxime, additional, Chen, Shu-Huang, additional, Cheung, Warren, additional, Delaneau, Oliver, additional, Dermitzakis, Emmanouil T., additional, Elding, Heather, additional, Colgiu, Irina, additional, Bagger, Frederik O., additional, Flicek, Paul, additional, Habibi, Ehsan, additional, Iotchkova, Valentina, additional, Janssen-Megens, Eva, additional, Kim, Bowon, additional, Lehrach, Hans, additional, Lowy, Ernesto, additional, Mandoli, Amit, additional, Matarese, Filomena, additional, Maurano, Matthew T., additional, Morris, John A., additional, Pancaldi, Vera, additional, Pourfarzad, Farzin, additional, Rehnstrom, Karola, additional, Rendon, Augusto, additional, Risch, Thomas, additional, Sharifi, Nilofar, additional, Simon, Marie-Michelle, additional, Sultan, Marc, additional, Valencia, Alfonso, additional, Walter, Klaudia, additional, Wang, Shuang-Yin, additional, Frontini, Mattia, additional, Antonarakis, Stylianos E., additional, Clarke, Laura, additional, Yaspo, Marie-Laure, additional, Beck, Stephan, additional, Guigo, Roderic, additional, Rico, Daniel, additional, Martens, Joost H.A., additional, Ouwehand, Willem H., additional, Kuijpers, Taco W., additional, Paul, Dirk S., additional, Stunnenberg, Hendrik G., additional, Stegle, Oliver, additional, Downes, Kate, additional, Pastinen, Tomi, additional, and Soranzo, Nicole, additional

Published
2016
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32. eFORGE: A Tool for Identifying Cell Type-Specific Signal in Epigenomic Data

Author

Breeze, Charles E., primary, Paul, Dirk S., additional, van Dongen, Jenny, additional, Butcher, Lee M., additional, Ambrose, John C., additional, Barrett, James E., additional, Lowe, Robert, additional, Rakyan, Vardhman K., additional, Iotchkova, Valentina, additional, Frontini, Mattia, additional, Downes, Kate, additional, Ouwehand, Willem H., additional, Laperle, Jonathan, additional, Jacques, Pierre-Étienne, additional, Bourque, Guillaume, additional, Bergmann, Anke K., additional, Siebert, Reiner, additional, Vellenga, Edo, additional, Saeed, Sadia, additional, Matarese, Filomena, additional, Martens, Joost H.A., additional, Stunnenberg, Hendrik G., additional, Teschendorff, Andrew E., additional, Herrero, Javier, additional, Birney, Ewan, additional, Dunham, Ian, additional, and Beck, Stephan, additional

Published
2016
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33. The Hematopoietic Transcription Factors RUNX1 and ERG Prevent AML1-ETO Oncogene Overexpression and Onset of the Apoptosis Program in t(8;21) AMLs

Author

Mandoli, Amit, primary, Singh, Abhishek A., additional, Prange, Koen H.M., additional, Tijchon, Esther, additional, Oerlemans, Marjolein, additional, Dirks, Rene, additional, Ter Huurne, Menno, additional, Wierenga, Albertus T.J., additional, Janssen-Megens, Eva M., additional, Berentsen, Kim, additional, Sharifi, Nilofar, additional, Kim, Bowon, additional, Matarese, Filomena, additional, Nguyen, Luan N., additional, Hubner, Nina C., additional, Rao, Nagesha A., additional, van den Akker, Emile, additional, Altucci, Lucia, additional, Vellenga, Edo, additional, Stunnenberg, Hendrik G., additional, and Martens, Joost H.A., additional

Published
2016
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34. ZMYND8 Co-localizes with NuRD on Target Genes and Regulates Poly(ADP-Ribose)-Dependent Recruitment of GATAD2A/NuRD to Sites of DNA Damage

Author

Spruijt, Cornelia G., primary, Luijsterburg, Martijn S., additional, Menafra, Roberta, additional, Lindeboom, Rik G.H., additional, Jansen, Pascal W.T.C., additional, Edupuganti, Raghu Ram, additional, Baltissen, Marijke P., additional, Wiegant, Wouter W., additional, Voelker-Albert, Moritz C., additional, Matarese, Filomena, additional, Mensinga, Anneloes, additional, Poser, Ina, additional, Vos, Harmjan R., additional, Stunnenberg, Hendrik G., additional, van Attikum, Haico, additional, and Vermeulen, Michiel, additional

Published
2016
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35. Recruitment of the Mammalian Histone-modifying EMSY Complex to Target Genes Is Regulated by ZNF131

Author

Varier, Radhika A., primary, de Santa Pau, Enrique Carrillo, additional, van der Groep, Petra, additional, Lindeboom, Rik G.H., additional, Matarese, Filomena, additional, Mensinga, Anneloes, additional, Smits, Arne H., additional, Edupuganti, Raghu Ram, additional, Baltissen, Marijke P., additional, Jansen, Pascal W.T.C., additional, ter Hoeve, Natalie, additional, van Weely, Danny R., additional, Poser, Ina, additional, van Diest, Paul J., additional, Stunnenberg, Hendrik G., additional, and Vermeulen, Michiel, additional

Published
2016
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39. Context-Selective Death of Acute Myeloid Leukemia Cells Triggered by the Novel Hybrid Retinoid-HDAC Inhibitor MC2392

Author

De Bellis, Floriana, primary, Carafa, Vincenzo, additional, Conte, Mariarosaria, additional, Rotili, Dante, additional, Petraglia, Francesca, additional, Matarese, Filomena, additional, Françoijs, Kees-Jan, additional, Ablain, Julien, additional, Valente, Sergio, additional, Castellano, Rèmy, additional, Goubard, Armelle, additional, Collette, Yves, additional, Mandoli, Amit, additional, Martens, Joost H.A., additional, de Thé, Hugues, additional, Nebbioso, Angela, additional, Mai, Antonello, additional, Stunnenberg, Hendrik G., additional, and Altucci, Lucia, additional

Published
2014
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40. RAD21 Cooperates with Pluripotency Transcription Factors in the Maintenance of Embryonic Stem Cell Identity

Author

Buchholz, Frank, Nitzsche, Anja, Paszkowski-Rogacz, Maciej, Matarese, Filomena, Janssen-Megens, Eva M., Hubner, Nina C., Schulz, Herbert, de Vries, Ingrid, Ding, Li, Huebner, Norbert, Mann, Matthias, Stunnenberg, Hendrik G., Buchholz, Frank, Nitzsche, Anja, Paszkowski-Rogacz, Maciej, Matarese, Filomena, Janssen-Megens, Eva M., Hubner, Nina C., Schulz, Herbert, de Vries, Ingrid, Ding, Li, Huebner, Norbert, Mann, Matthias, and Stunnenberg, Hendrik G.

Abstract

For self-renewal, embryonic stem cells (ESCs) require the expression of specific transcription factors accompanied by a particular chromosome organization to maintain a balance between pluripotency and the capacity for rapid differentiation. However, how transcriptional regulation is linked to chromosome organization in ESCs is not well understood. Here we show that the cohesin component RAD21 exhibits a functional role in maintaining ESC identity through association with the pluripotency transcriptional network. ChIP-seq analyses of RAD21 reveal an ESC specific cohesin binding pattern that is characterized by CTCF independent co-localization of cohesin with pluripotency related transcription factors Oct4, Nanog, Sox2, Esrrb and Klf4. Upon ESC differentiation, most of these binding sites disappear and instead new CTCF independent RAD21 binding sites emerge, which are enriched for binding sites of transcription factors implicated in early differentiation. Furthermore, knock-down of RAD21 causes expression changes that are similar to expression changes after Nanog depletion, demonstrating the functional relevance of the RAD21 - pluripotency transcriptional network association. Finally, we show that Nanog physically interacts with the cohesin or cohesin interacting proteins STAG1 and WAPL further substantiating this association. Based on these findings we propose that a dynamic placement of cohesin by pluripotency transcription factors contributes to a chromosome organization supporting the ESC expression program.

Published
2011

41. Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers

Author

Vermeulen, Michiel, Eberl, H Christian, Matarese, Filomena, Marks, Hendrik, Denissov, Sergei, Butter, Falk, Lee, Kenneth K, Olsen, Jesper Velgaard, Hyman, Anthony A, Stunnenberg, Henk G, Mann, Matthias, Vermeulen, Michiel, Eberl, H Christian, Matarese, Filomena, Marks, Hendrik, Denissov, Sergei, Butter, Falk, Lee, Kenneth K, Olsen, Jesper Velgaard, Hyman, Anthony A, Stunnenberg, Henk G, and Mann, Matthias

Abstract

Trimethyl-lysine (me3) modifications on histones are the most stable epigenetic marks and they control chromatin-mediated regulation of gene expression. Here, we determine proteins that bind these marks by high-accuracy, quantitative mass spectrometry. These chromatin "readers" are assigned to complexes by interaction proteomics of full-length BAC-GFP-tagged proteins. ChIP-Seq profiling identifies their genomic binding sites, revealing functional properties. Among the main findings, the human SAGA complex binds to H3K4me3 via a double Tudor-domain in the C terminus of Sgf29, and the PWWP domain is identified as a putative H3K36me3 binding motif. The ORC complex, including LRWD1, binds to the three most prominent transcriptional repressive lysine methylation sites. Our data reveal a highly adapted interplay between chromatin marks and their associated protein complexes. Reading specific trimethyl-lysine sites by specialized complexes appears to be a widespread mechanism to mediate gene expression.

Published
2010

42. Whole-Genome Bisulfite Sequencing of Two Distinct Interconvertible DNA Methylomes of Mouse Embryonic Stem Cells

Author

Habibi, Ehsan, primary, Brinkman, Arie B., additional, Arand, Julia, additional, Kroeze, Leonie I., additional, Kerstens, Hindrik H.D., additional, Matarese, Filomena, additional, Lepikhov, Konstantin, additional, Gut, Marta, additional, Brun-Heath, Isabelle, additional, Hubner, Nina C., additional, Benedetti, Rosaria, additional, Altucci, Lucia, additional, Jansen, Joop H., additional, Walter, Jörn, additional, Gut, Ivo G., additional, Marks, Hendrik, additional, and Stunnenberg, Hendrik G., additional

Published
2013
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44. Integrative Analysis of Deep Sequencing Data Identifies Estrogen Receptor Early Response Genes and Links ATAD3B to Poor Survival in Breast Cancer

Author

Ovaska, Kristian, primary, Matarese, Filomena, additional, Grote, Korbinian, additional, Charapitsa, Iryna, additional, Cervera, Alejandra, additional, Liu, Chengyu, additional, Reid, George, additional, Seifert, Martin, additional, Stunnenberg, Hendrik G., additional, and Hautaniemi, Sampsa, additional

Published
2013
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45. Comparative genome-wide DNA methylation analysis of colorectal tumor and matched normal tissues

Author

Simmer, Femke, primary, Brinkman, Arie B., additional, Assenov, Yassen, additional, Matarese, Filomena, additional, Kaan, Anita, additional, Sabatino, Lina, additional, Villanueva, Alberto, additional, Huertas, Dori, additional, Esteller, Manel, additional, Lengauer, Thomas, additional, Bock, Christoph, additional, Colantuoni, Vittorio, additional, Altucci, Lucia, additional, and Stunnenberg, Hendrik G., additional

Published
2012
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46. Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk

Author

Brinkman, Arie B., primary, Gu, Hongcang, additional, Bartels, Stefanie J.J., additional, Zhang, Yingying, additional, Matarese, Filomena, additional, Simmer, Femke, additional, Marks, Hendrik, additional, Bock, Christoph, additional, Gnirke, Andreas, additional, Meissner, Alexander, additional, and Stunnenberg, Hendrik G., additional

Published
2012
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47. Death Receptor Pathway Activation and Increase of ROS Production by the Triple Epigenetic Inhibitor UVI5008

Author

Nebbioso, Angela, primary, Pereira, Raquel, additional, Khanwalkar, Harshal, additional, Matarese, Filomena, additional, García-Rodríguez, José, additional, Miceli, Marco, additional, Logie, Colin, additional, Kedinger, Valerie, additional, Ferrara, Felicetto, additional, Stunnenberg, Hendrik G., additional, de Lera, Angel R., additional, Gronemeyer, Hinrich, additional, and Altucci, Lucia, additional

Published
2011
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48. RAD21 Cooperates with Pluripotency Transcription Factors in the Maintenance of Embryonic Stem Cell Identity

Author

Nitzsche, Anja, primary, Paszkowski-Rogacz, Maciej, additional, Matarese, Filomena, additional, Janssen-Megens, Eva M., additional, Hubner, Nina C., additional, Schulz, Herbert, additional, de Vries, Ingrid, additional, Ding, Li, additional, Huebner, Norbert, additional, Mann, Matthias, additional, Stunnenberg, Hendrik G., additional, and Buchholz, Frank, additional

Published
2011
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50. Distinct Signaling Pathways Mediate Stimulation of Cell Cycle Progression and Prevention of Apoptotic Cell Death by Estrogen in Rat Pituitary Tumor PR1 Cells

Author

Caporali, Simona, primary, Imai, Manami, additional, Altucci, Lucia, additional, Cancemi, Massimo, additional, Caristi, Silvana, additional, Cicatiello, Luigi, additional, Matarese, Filomena, additional, Penta, Roberta, additional, Sarkar, Dipak K., additional, Bresciani, Francesco, additional, and Weisz, Alessandro, additional

Published
2003
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