Dynamic rRNA methylation regulates translation in the hematopoietic system and is essential for stem cell fitness
Abstract
Abstract Self-renewal and differentiation are at the basis of hematopoiesis. Although it is known that tight regulation of translation is vital for hematopoietic stem cells’ (HSC) biology, the mechanisms underlying translation regulation across the hematopoietic system remain obscure. Here, we reveal a novel mechanism of translation regulation in the hematopoietic hierarchy, which is mediated by rRNA methylation dynamics. Using ultralow-input ribosome profiling, we characterized cell-type–specific translation capacity during erythroid differentiation. We found that translation efficiency (TE) changes progressively with differentiation and can distinguish between discrete cell populations, as well as define differentiation trajectories. To reveal the underlying mechanism, we performed comprehensive mapping of the most abundant rRNA modification, 2ʹ-O-methyl (2ʹOMe). We found that, such as TE, 2ʹOMe dynamics followed a distinct trajectory during erythroid differentiation. Genetic perturbation of individual 2ʹOMe sites demonstrated their distinct roles in modulating proliferation and differentiation. By combining CRISPR screening, molecular, and functional analyses, we identified a specific methylation site, 28S-Gm4588, which is progressively lost during differentiation, as a key regulator of HSC self-renewal. We showed that low methylation at this site led to translational skewing, mediated mainly by codon frequency, which promoted differentiation. Functionally, HSC with diminished 28S-Gm4588 methylation exhibited impaired self-renewal capacity ex vivo, and loss of fitness in vivo in bone marrow transplants. Extending our findings beyond the hematopoietic system, we also found distinct dynamics of 2ʹOMe profiles during differentiation of non-HSC. Our findings reveal rRNA methylation dynamics as a general mechanism for cell-type–specific translation, required for cell function and differentiation.
Article Details
Authors (23)
Ofri Rabany
1Department of Genetics, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
Sivan Ben Dror
Maram Arafat
1Department of Genetics, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
Hadar Aharoni Levitanus
1Department of Genetics, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
Yudit Halperin
1Department of Genetics, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
Virginie Marchand
Nikolai Romanovski
1Department of Genetics, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
Noga Ussishkin
1Department of Genetics, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
Maayan Livneh Golany
1Department of Genetics, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
Adi Reches
1Department of Genetics, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
Judith Wexler
1Department of Genetics, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
Nina Mayorek
3The Concern Foundation Laboratories at The Lautenberg Center for Immunology and Cancer Research, Institute for Medical Research, Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
Galia Monderer-Rothkoff
1Department of Genetics, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
Sagiv Shifman
1Department of Genetics, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
Widad Mâmmer Bouhou
4Oncode Institute, Utrecht, The Netherlands
Michael VanInsberghe
Cornelius Pauli
7Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
Carsten Müller-Tidow
Ola Karmi
Yoav Livneh
10Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
Alexander van Oudenaarden
Yuri Motorin
Daphna Nachmani
1Department of Genetics, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel