All Publications

The following publications were published exclusively under the affiliation of the Max Planck Society. For publications by the principal investigator outside of the Max Planck Society, see the links on the lower left.

Publication by Hnisz Lab

Preprints

2022
Basu, S.; Martínez-Cristóbal, P.; Pesarrodona, M.; Frigolé-Vivas, M.; Szulc, E.; Lewis, M.; Bañuelos, C. A.; Sánchez-Zarzalejo, C.; Bielskutė, S.; Zhu, J. et al.; Garcia-Cabau, C.; Batlle, C.; Mateos, B.; Biesaga, M.; Escobedo, A.; Bardia, L.; Verdaguer, X.; Ruffoni, A.; Mawji, N. R.; Wang, J.; Tam, T.; Brun-Heath, I.; Ventura, S.; Meierhofer, D.; García, J.; Robustelli, P.; Stracker, T. H.; Sadar, M. D.; Riera, A.; Hnisz, D.; Salvatella, X.: Androgen receptor condensates as drug targets. bioRxiv (2022)
MPG.PuRe
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pre-print

Published

2025
Zhang, Y.; Stöppelkamp, I.; Fernandez-Pernas, P.; Allram, M.; Charman, M.; Magalhães, A. P.; Piedavent-Salomon, M.; Sommer, G.; Sung, Y.-C.; Meyer, K. et al.; Grams, N.; Halko, E.; Dongre, S.; Meierhofer, D.; Malszycki, M.; Ilik, I. A.; Aktas, T.; Kraushar, M. L.; Vastenhouw, N.; Weitzman, M. D.; Grebien, F.; Niskanen, H.; Hnisz, D.: Probing condensate microenvironments with a micropeptide killswitch. Nature (2025)
MPG.PuRe
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publisher-version
2024
Naderi, J.; Magalhães, A. P.; Kibar, G.; Stik, G.; Zhang, Y.; Mackowiak, S.; Wieler, H. M.; Rossi, F.; Buschow, R.; Christou-Kent, M. et al.; Alcoverro-Bertran, M.; Graf, T.; Vingron, M.; Hnisz, D.: An activity-specificity trade-off encoded in human transcription factors. Nature Cell Biology 26 (8), pp. 1309 - 1321 (2024)
MPG.PuRe
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publisher-version
2023
Basu, S.; Martínez-Cristóbal, P.; Frigolé-Vivas, M.; Pesarrodona, M.; Lewis, M.; Szulc, E.; Bañuelos, C. A.; Sánchez-Zarzalejo, C.; Bielskutė, S.; Zhu, J. et al.; Pombo-García, K.; Garcia-Cabau, C.; Zodi, L.; Dockx, H.; Smak, J.; Kaur, H.; Batlle, C.; Mateos, B.; Biesaga, M.; Escobedo, A.; Bardia, L.; Verdaguer, X.; Ruffoni, A.; Mawji, N. R.; Wang, J.; Obst, J. K.; Tam, T.; Brun-Heath, I.; Ventura, S.; Meierhofer, D.; García, J.; Robustelli, P.; Stracker, T. H.; Sadar, M. D.; Riera, A.; Hnisz, D.; Salvatella, X.: Rational optimization of a transcription factor activation domain inhibitor. Nature Structural & Molecular Biology 30 (12), pp. 1958 - 1969 (2023)
MPG.PuRe
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publisher-version
Bressin, A.; Jasnovidova, O.; Arnold, M.; Altendorfer, E.; Trajkovski , F.; Kratz, T. A.; Handzlik, J. E.; Hnisz, D.; Mayer, A.: High-sensitive nascent transcript sequencing reveals BRD4-specific control of widespread enhancer and target gene transcription. Nature Communications 14 (1), Article 4971 (2023)
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Christou-Kent, M.; Cuartero, S.; Garcia-Cabau, C.; Ruehle, J.; Naderi, J.; Erber, J.; Neguembor, M. V.; Plana-Carmona, M.; Alcoverro-Bertran, M.; De Andres-Aguayo, L. et al.; Klonizakis, A.; Julià-Vilella, E.; Lynch, C.; Serrano, M.; Hnisz, D.; Salvatella, X.; Graf, T.; Stik, G.: CEBPA phase separation links transcriptional activity and 3D chromatin hubs. Cell Reports 42 (8), 112897 (2023)
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publisher-version
Dejosez, M.; Dall’Agnese, A.; Ramamoorthy, M.; Platt, J.; Yin, X.; Hogan, M.; Brosh, R.; Weintraub, A. S.; Hnisz, D.; Abraham, B. J. et al.; Young, R. A.; Zwaka, T. P.: Regulatory architecture of housekeeping genes is driven by promoter assemblies. Cell Reports 42 (5), 112505 (2023)
MPG.PuRe
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publisher-version
Mensah, M. A.; Niskanen, H.; Magalhães, A. P.; Basu, S.; Kircher, M.; Sczakiel, H. L.; Reiter, A. M. V.; Elsner, J.; Meinecke, P.; Biskup, S. et al.; Chung, B. H. Y.; Dombrowsky, G.; Eckmann-Scholz, C.; Hitz, M. P.; Hoischen, A.; Holterhus, P.-M.; Hülsemann, W.; Kahrizi, K.; Kalscheuer, V. M.; Kan, A.; Krumbiegel, M.; Kurth, I.; Leubner, J.; Longardt, A. C.; Moritz, J. D.; Najmabadi, H.; Skipalova, K.; Snijders Blok, L.; Tzschach, A.; Wiedersberg, E.; Zenker, M.; Garcia-Cabau, C.; Buschow, R.; Salvatella, X.; Kraushar, M. L.; Mundlos, S.; Caliebe, A.; Spielmann, M.; Horn, D.; Hnisz, D.: Aberrant phase separation and nucleolar dysfunction in rare genetic diseases. Nature 614 (7948), pp. 564 - 571 (2023)
MPG.PuRe
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publisher-version
Landshammer, A.; Bolondi, A.; Kretzmer, H.; Much, C.; Buschow, R.; Rose, A.; Wu, H.-J.; Mackowiak, S. D.; Braendl, B.; Gießelmann, P. et al.; Tornisiello, R.; Mohan Parsi, K.; Huey, J.; Mielke, T.; Meierhofer, D.; Maehr, R.; Hnisz, D.; Michor, F.; Rinn, J. L.; Meissner, A.: T-REX17 is a transiently expressed non-coding RNA essential for human endoderm formation. eLife 12, Article e83077 (2023)
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publisher-version
2022
Asimi, V.; Sampath Kumar, A.; Niskanen, H.; Riemenschneider, C.; Hetzel, S.; Naderi, J.; Fasching, N.; Popitsch, N.; Du, M.; Kretzmer, H. et al.; Smith, Z. D.; Weigert, R.; Walther, M.; Mamde, S.; Meierhofer, D.; Wittler, L.; Buschow, R.; Timmermann, B.; Cisse, I. I.; Ameres, S. L.; Meissner, A.; Hnisz, D.: Hijacking of transcriptional condensates by endogenous retroviruses. Nature Genetics 54 (8), pp. 1238 - 1247 (2022)
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publisher-version
2021
Adane, B.; Alexe, G.; Seong, B. K. A.; Lu, D.; Hwang, E. E.; Hnisz, D.; Lareau, C. A.; Ross, L.; Lin, S.; Dela Cruz, F. S. et al.; Richardson, M.; Weintraub, A. S.; Wang, S.; Balboni Iniguez, A.; Dharia, N. V.; Saur Conway, A.; Robichaud, A. L.; Tanenbaum, B.; Krill-Burger, J. M.; Vazquez, F.; Schenone, M.; Berman, J. N.; Kung, A. L.; Carr, S. A.; Aryee, M. J.; Young, R. A.; Crompton, B. D.; Stegmaier, K.: STAG2 loss rewires oncogenic and developmental programs to promote metastasis in Ewing sarcoma. Cancer Cell 39 (6), pp. 827 - 844 (2021)
MPG.PuRe
publisher-version
ZIP
2020
Jaeger, M. G.; Schwalb, B.; Mackowiak, S. D.; Velychko, T.; Hanzl, A.; Imrichova, H.; Brand, M.; Agerer, B.; Chorn, S.; Nabet, B. et al.; Ferguson, F. M.; Müller, A. C.; Bergthaler, A.; Gray, N. S.; Bradner, J. E.; Bock, C.; Hnisz, D.; Cramer, P.; Winter, G. E.: Selective Mediator dependence of cell-type-specifying transcription. Nature Genetics 52 (7), pp. 719 - 727 (2020)
MPG.PuRe
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Basu, S.; Mackowiak, S.; Niskanen, H.; Knezevic, D.; Asimi, V.; Grosswendt, S.; Geertsema, H.; Ali, S.; Jerković, I.; Ewers, H. et al.; Mundlos, S.; Meissner, A.; Ibrahim, D. M.; Hnisz, D.: Unblending of Transcriptional Condensates in Human Repeat Expansion Disease. Cell 181 (5), pp. 1062 - 1079 (2020)
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publisher-version
2018
Sabari, B. R.; Dall’Agnese, A.; Boija, A.; Klein, I. A.; Coffey, E. L.; Shrinivas, K.; Abraham, B. J.; Hannett, N. M.; Zamudio, A. V.; Manteiga, J. C. et al.; Li, C. H.; Guo, Y. E.; Day, D. S.; Schuijers, J.; Vasile, E.; Malik, S.; Hnisz, D.; Lee, T. I.; Cisse, I. I.; Roeder, R. G.; Sharp, P. A.; Chakraborty, A. K.; Young, R. A.: Coactivator condensation at super-enhancers links phase separation and gene control. Science (6400), eaar3958 (2018)
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Schuijers, J.; Manteiga, J. C.; Weintraub, A. S.; Day, D. S.; Zamudio, A. V.; Hnisz, D.; Lee, T. I.; Young, R. A.: Transcriptional Dysregulation of MYC Reveals Common Enhancer-Docking Mechanism. Cell Reports 23 (2), pp. 349 - 360 (2018)
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Publications by Dr. Denes Hnisz before 2018

Abraham S. Weintraub, Charles H. Li, Alicia V. Zamudio, Alla A. Sigovo, Nancy M. Hannett, Daniel S. Day, Brian J. Abraham, Malkiel A. Cohen, Behnam Nabet, Dennis L. Buckley, Yang Eric Guo, Denes Hnisz, Rudolf Jaenisch, James E. Bradner, Nathanael S. Gray, Richard A. Young
YY1 Is a Structural Regulator of Enhancer-Promoter Loops
Cell, Volume 171, Issue 7, 2017
DOI
Denes Hnisz, Richard A. Young
New Insights into Genome Structure: Genes of a Feather Stick Together
Molecular Cell, Volume 67, Issue 5, 2017
DOI
Denes Hnisz, Krishna Shrinivas, Richard A. Young, Arup K. Chakraborty, Phillip A. Sharp
A Phase Separation Model for Transcriptional Control
Cell, Volume 169, Issue 1, 2017
DOI
Abraham, B., Hnisz, D., Weintraub, A. et al.
Small genomic insertions form enhancers that misregulate oncogenes
Nature Communications volume 8,  2017
DOI
James E. Bradner, Denes Hnisz, Richard A. Young
Transcriptional Addiction in Cancer
Cell, Volume 168, Issue 4, 2017
DOI
Denes Hnisz, Daniel S. Day, Richard A. Young
Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control
Cell, Volume 167, Issue 5, 2016
DOI
Clark, V., Harmancı, A., Bai, H., Hnisz, Denes et al.
Recurrent somatic mutations in POLR2A define a distinct subset of meningiomas
Nature Genetics volume 48, 2016
DOI
Denes Hnisz et al.
Activation of proto-oncogenes by disruption of chromosome
 Science Vol.351, 2016 
DOI
Xiong Ji, Daniel B. Dadon, Benjamin E. Powell, Zi Peng Fan, Diego Borges-Rivera, Sigal Shachar, Abraham S. Weintraub, Denes Hnisz, Gianluca Pegoraro, Tong Ihn Lee, Tom Misteli, Rudolf Jaenisch, Richard A. Young
3D Chromosome Regulatory Landscape of Human Pluripotent Cells
Cell Stem Cell, Volume 18, Issue 2, 2016
DOI
Denes Hnisz, Jurian Schuijers, Charles Y. Lin, Abraham S. Weintraub, Brian J. Abraham, Tong Ihn Lee, James E. Bradner, Richard A. Young
Convergence of Developmental and Oncogenic Signaling Pathways at Transcriptional Super-Enhancers
Molecular Cell, Volume 58, Issue 2, 2015
DOI
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