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.

Publications by the Smith Lab

Preprints

2024

Zagoren, E.; Dias, N.; Smith, Z. D.: A second wave of Notch signaling diversifies the intestinal secretory lineage. bioRxiv (2024)

MPG.PuRe

DOI

pre-print

Published

2025

Smith, Z. D.; Hetzel, S.; Meissner, A.: DNA methylation in mammalian development and disease. Nature Reviews Genetics 26 (1), pp. 7 - 30 (2025)

MPG.PuRe

DOI

publisher-version

2024

Hasenbein, T. P.; Hoelzl, S.; Smith, Z. D.; Gerhardinger, C.; Gonner, M. O. C.; Aguilar-Pimentel, A.; Amarie, O. V.; Becker, L.; Calzada-Wack, J.; Dragano, N. R. V. et al.; da Silva-Buttkus, P.; Garrett, L.; Hölter, S. M.; Kraiger, M.; Östereicher, M. A.; Rathkolb, B.; Sanz-Moreno, A.; Spielmann, N.; Wurst, W.; Gailus-Durner, V.; Fuchs, H.; Hrabě de Angelis, M.; Meissner, A.; Engelhardt, S.; Rinn, J. L.; Andergassen, D.: X-linked deletion of Crossfirre, Firre, and Dxz4 in vivo uncovers diverse phenotypes and combinatorial effects on autosomes. Nature Communications 15 (1), Article 10631 (2024)

MPG.PuRe

DOI

publisher-version

Zagoren, E.; Dias, N.; Smith, Z. D.: A second wave of Notch signaling diversifies the intestinal secretory lineage. bioRxiv (2024)

MPG.PuRe

DOI

pre-print

Bolondi, A.; Law, B. K.; Kretzmer, H.; Gassaloglu, S. I.; Buschow, R.; Riemenschneider, C.; Yang, D.; Walther, M.; Veenvliet, J. V.; Meissner, A. et al.; Smith, Z. D.; Chan, M. M.: Reconstructing axial progenitor field dynamics in mouse stem cell-derived embryoids. Developmental Cell 59 (12), pp. 1489 - 1505 (2024)

MPG.PuRe

DOI

publisher-version

2023

Weigert, R.; Hetzel, S.; Bailly, N.; Haggerty, C.; Ilik, I. A.; Kwong Yung, P. Y.; Navarro, C.; Bolondi, A.; Sampath Kumar, A.; Anania, C. et al.; Brändl, B.; Meierhofer, D.; Lupiáñez, D. G.; Müller, F.-J.; Aktas, T.; Elsässer, S. J.; Kretzmer, H.; Smith, Z. D.; Meissner, A.: Dynamic antagonism between key repressive pathways maintains the placental epigenome. Nature Cell Biology 25 (4), pp. 579 - 591 (2023)

MPG.PuRe

DOI

publisher-version

Publications by Dr. Zachary Smith before 2023

Monique Pedroza, Seher Ipek Gassaloglu, Nicolas Dias, Liangwen Zhong, Tien-Chi Jason Hou, Helene Kretzmer, Zachary D. Smith, Berna Sozen

Self-patterning of human stem cells into post-implantation lineages

Nature volume 622, pages 574–583 (2023)

DOI

Aushaq B Mall, Haoming Yu, Delaney Farris, Srilekha Kadimi, TuKiet T Lam, Andy L Cox, Zachary D Smith, Bluma J Lesch

DOT1L bridges transcription and heterochromatin formation at mammalian pericentromeres

EMBO Rep. 2023 Aug

DOI

Aushaq B Malla, Shannon R Rainsford, Zachary D Smith, Bluma J Lesch

DOT1L promotes spermatid differentiation by regulating expression of genes required for histone-to-protamine replacement

Development. 2023

DOI

Raha Weigert, Sara Hetzel, Nina Bailly, Chuck Haggerty, Ibrahim A. Ilik, Philip Yuk Kwong Yung, Carmen Navarro, Adriano Bolondi, Abhishek Sampath Kumar, Chiara Anania, Björn Brändl, David Meierhofer, Darío G. Lupiáñez, Franz-Josef Müller, Tugce Aktas, Simon J. Elsässer, Helene Kretzmer, Zachary D. Smith, Alexander Meissner

Dynamic antagonism between key repressive pathways maintains the placental epigenome

Nature Cell Biology volume 25 (2023)

DOI

Vahid Asimi, Abhishek Sampath Kumar, Henri Niskanen, Christina Riemenschneider, Sara Hetzel, Julian Naderi, Nina Fasching, Niko Popitsch, Manyu Du, Helene Kretzmer, Zachary D. Smith, Raha Weigert, Maria Walther, Sainath Mamde, David Meierhofer, Lars Wittler, René Buschow, Bernd Timmermann, Ibrahim I. Cisse, Stefan L. Ameres, Alexander Meissner, Denes Hnisz

Hijacking of transcriptional condensates by endogenous retroviruses

Nature Genetics volume 54 (2022)

DOI

Daniel Andergassen, Zachary D Smith, Helene Kretzmer, John L Rinn, Alexander Meissner

Diverse epigenetic mechanisms maintain parental imprints within the embryonic and extraembryonic lineages

Developmental Cell 2021

DOI

Hongcang Gu, Ayush T. Raman, Xiaoxue Wang, Federico Gaiti, Ronan Chaligne, Arman W. Mohammad, Aleksandra Arczewska, Zachary D. Smith, Dan A. Landau, Martin J. Aryee, Alexander Meissner, Andreas Gnirke

Smart-RRBS for single-cell methylome and transcriptome analysis

Nature Protocols volume 16 (2021)

DOI

Stefanie Grosswendt, Helene Kretzmer, Zachary D. Smith, Abhishek Sampath Kumar, Sara Hetzel, Lars Wittler, Sven Klages, Bernd Timmermann, Shankar Mukherji, Alexander Meissner

Epigenetic regulator function through mouse gastrulation

Nature volume 584 (2020)

DOI

Jocelyn Charlton, Eunmi J. Jung, Alexandra L. Mattei, Nina Bailly, Jing Liao, Eric J. Martin, Pay Giesselmann, Björn Brändl, Elena K. Stamenova, Franz-Josef Müller, Evangelos Kiskinis, Andreas Gnirke, Zachary D. Smith, Alexander Meissner

TETs compete with DNMT3 activity in pluripotent cells at thousands of methylated somatic enhancers

Nature Genetics volume 52 (2020)

DOI

Sudhir Thakurela, Camille Sindhu, Evgeny Yurkovsky, Christina Riemenschneider, Zachary D. Smith, Iftach Nachman, Alexander Meissner

Differential regulation of OCT4 targets facilitates reacquisition of pluripotency

Nature Communications volume 10 (2019)

DOI