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
If preprints are available, they will be listed here.
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Published
2025
Rossi, F.; Magalhães, A. P.; Buschow, R.; Schubert , T.; Glaser, L. V.; Fontana, A.; Mai , J.; Staege, H.; Grimme, A.; Will, H. et al.; Schriener, .; Hnisz, D.; Vingron, M.; Chiariello, A. M.; Kinkley, S.: Differential oligomerization regulates PHF13 chromatin affinity and function. Nucleic Acids Research
53 (12) (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)
Magalhães, A. P.; Hnisz, D.: Transcription factor condensates: Preventing aggregation by DNA binding. Cell (188), pp. 2831 - 2833 (2025)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
Publications by Dr. Denes Hnisz before 2018
1.
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
2.
Denes Hnisz, Richard A. Young
New Insights into Genome Structure: Genes of a Feather Stick Together
Molecular Cell, Volume 67, Issue 5, 2017
3.
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
4.
Abraham, B., Hnisz, D., Weintraub, A. et al.
Small genomic insertions form enhancers that misregulate oncogenes
Nature Communications volume 8, 2017
5.
James E. Bradner, Denes Hnisz, Richard A. Young
Transcriptional Addiction in Cancer
Cell, Volume 168, Issue 4, 2017
6.
Denes Hnisz, Daniel S. Day, Richard A. Young
Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control
Cell, Volume 167, Issue 5, 2016
7.
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
8.
Denes Hnisz et al.
Activation of proto-oncogenes by disruption of chromosome
Science Vol.351, 2016
9.
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
10.
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