Max Planck Institute for Molecular Genetics

Selected Publications

Our top publications

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)

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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)

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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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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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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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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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Hnisz D.^*, Shrinivas K^.*, Young R.A., Chakraborty A., Sharp P.A.

A phase separation model for transcriptional control.

Cell. 169( 1), pp. 13-23. (2017)
^*co-first author

Bradner JE, Hnisz D, Young RA.

Transcriptional addiction in cancer.

Cell. 168 (4), pp. 629-643 (2017) Review

Hnisz D^*$, Day DS^*$, Young RA^$.

Insulated neighborhoods: structural and functional units of mammalian gene control.

Cell 167 (5) pp. 1188-1200 (2016 ) Review
^*co-first author, ^$corresponding author

Hnisz D, Weintraub AS, Day DS, Valton AL, Bak RO, Li CH, Goldmann J, Lajoie BR, Fan ZP, Sigova AA, Reddy J, Borges-Rivera D, Lee TI, Jaenisch R, Porteus MH, Dekker J, Young RA.

Activation of proto-oncogenes by disruption of chromosome neighborhoods.

Science 351 (6280) pp. 1454-1458 (2016)

Ji X, Dadon DB, Powell BE, Fan ZP, Borges-Rivera D, Shachar S, Weintraub AS, Hnisz D, Pegoraro G, Lee TI, Misteli T, Jaenisch R, Young RA.

3D chromosome regulatory landscape of human pluripotent cells.

Cell Stem Cell. 18 (2) pp. 262-75

Hnisz D.^*, Schuijers J^.*, Lin C.Y., Weintraub A.S., Abraham B.J., Lee T.I., Bradner J.E., Young R.A.

Convergence of developmental and oncogenic signaling pathways at transcriptional super-enhancers

Mol Cell 58 ( 2) pp. 362-70 (2015)
^*co-first author

Dowen J.M.^*, Fan Z.P^.*, Hnisz D^.*, Ren G.^*, Abraham B.J., Zhang L.N., Weintraub A.S., Schujiers J., Lee T.I., Zhao K., Young R.A.

Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes.

Cell 159 (2) pp. 374-387 (2014)
^*co-first author

Hnisz D.^*, Abraham B.J.^*, Lee T.I^.*, Lau A., Saint-André V., Sigova A.A., Hoke H.A., Young R.A.

Super-enhancers in the control of cell identity and disease.

Cell 155 (4) pp. 934-47 (2013)
^*co-first author

Whyte W.A.^*, Orlando D.A.^*, Hnisz D.^*, Abraham B.J., Lin C.Y., Kagey M.H., Rahl P.B., Lee T.I., Young R.A.

Master transcription factors and mediator establish super-enhancers at key cell identity genes.

Cell 153 (2) pp. 307-19 (2013)
^*co-first author