Max Planck Institute for Molecular Genetics

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.

2025

Stark, H.; Faltings, F.; Choi, M.; Xie, Y.; Hur, E.; O’Donnell, T.; Bushuiev, A.; Uçar, T.; Passaro, S.; Mao, W. et al.; Reveiz, M.; Bushuiev, R.; Pluskal, T.; Sivic, J.; Kreis, K.; Vahdat, A.; Ray, S.; Goldstein, J. T.; Savinov, A.; Hambalek, J. A.; Gupta, A.; Taquiri-Diaz, D. A.; Zhang, Y.; Hatstat, A. K.; Arada, A.; Kim, N. H.; Tackie-Yarboi, E.; Boselli, D.; Schnaider, L.; Liu, C. C.; Li, G.-W.; Hnisz, D.; Sabatini, D. M.; DeGrado, W. F.; Wohlwend, J.; Corso, G.; Barzilay, R.; Jaakkola, T.: BoltzGen: Toward Universal Binder Design. bioRxiv: the preprint server for biology (2025)

MPG.PuRe

Llombart, V.; O’Connor, D.; Demeulemeester, J.; Bhamra, A.; Surinova, S.; Turna, A.; Fung, K.; Wang, L.; Li, Y.; Rapoz-D’Silva, T. et al.; Ahmed, F.; Niskanen, H.; Stöppelkamp, I.; Hnisz, D.; Bottaro, S.; Fisicaro, C.; He, S.; Look, A. T.; Mansour, M. R.: MYC-induced oncogenesis is dependent on acidic patches within its N-terminal intrinsically disordered domain. bioRxiv: the preprint server for biology (2025)

MPG.PuRe

Bielskutė, S.; Mateos, B.; Awawdy, M.; Garcia-Cabau, C.; Niskanen, H.; Sánchez-Zarzalejo, C.; Bracaglia, L.; Pierattelli, R.; Felli, I. C.; Frigolé-Vivas, M. et al.; García, J.; Riera, A.; Hnisz, D.; Salvatella, X.: Oligomerization enables the selective targeting of intrinsically disordered regions by small molecules. bioRxiv: the preprint server for biology (2025)

MPG.PuRe

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)

MPG.PuRe

publisher-version

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

publisher-version

Magalhães, A. P.; Hnisz, D.: Transcription factor condensates: Preventing aggregation by DNA binding. Cell (188), pp. 2831 - 2833 (2025)

MPG.PuRe

Taguchi, A.; Magalhães, A. P.; Bolondi, A.; Lee, M.-K.; Kretzmer, H.; Wittler, L.; Hnisz, D.; Meissner, A.: Single-cell activation screen identifies hepatic maturation regulators with zonal resolution. Developmental Cell (2025)

MPG.PuRe

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

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)

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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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publisher-version

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)

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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)

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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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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)

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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)

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publisher-version

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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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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publisher-version

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

Denes Hnisz, Richard A. Young

New Insights into Genome Structure: Genes of a Feather Stick Together

Molecular Cell, Volume 67, Issue 5, 2017

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

Abraham, B., Hnisz, D., Weintraub, A. et al.

Small genomic insertions form enhancers that misregulate oncogenes

Nature Communications volume 8, 2017

James E. Bradner, Denes Hnisz, Richard A. Young

Transcriptional Addiction in Cancer

Cell, Volume 168, Issue 4, 2017

Denes Hnisz, Daniel S. Day, Richard A. Young

Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control

Cell, Volume 167, Issue 5, 2016

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

Denes Hnisz et al.

Activation of proto-oncogenes by disruption of chromosome

Science Vol.351, 2016

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

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