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Malzl D, Peycheva M, Rahjouei A, Gnan S, Klein KN, Nazarova M, Schoeberl UE, Gilbert DM, Buonomo SCB, Di Virgilio M, Neumann T, Pavri R. RIF1 regulates early replication timing in murine B cells. Nat Commun 2023; 14:8049. [PMID: 38081811 PMCID: PMC10713614 DOI: 10.1038/s41467-023-43778-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
The mammalian DNA replication timing (RT) program is crucial for the proper functioning and integrity of the genome. The best-known mechanism for controlling RT is the suppression of late origins of replication in heterochromatin by RIF1. Here, we report that in antigen-activated, hypermutating murine B lymphocytes, RIF1 binds predominantly to early-replicating active chromatin and promotes early replication, but plays a minor role in regulating replication origin activity, gene expression and genome organization in B cells. Furthermore, we find that RIF1 functions in a complementary and non-epistatic manner with minichromosome maintenance (MCM) proteins to establish early RT signatures genome-wide and, specifically, to ensure the early replication of highly transcribed genes. These findings reveal additional layers of regulation within the B cell RT program, driven by the coordinated activity of RIF1 and MCM proteins.
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Affiliation(s)
- Daniel Malzl
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030, Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Lazarettgasse 14, Vienna, Austria
| | - Mihaela Peycheva
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030, Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Lazarettgasse 14, Vienna, Austria
| | - Ali Rahjouei
- Max-Delbruck Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Stefano Gnan
- School of Biological Sciences, Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3FF, UK
| | - Kyle N Klein
- San Diego Biomedical Research Institute, San Diego, CA, 92121, USA
| | - Mariia Nazarova
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030, Vienna, Austria
| | - Ursula E Schoeberl
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030, Vienna, Austria
| | - David M Gilbert
- San Diego Biomedical Research Institute, San Diego, CA, 92121, USA
| | - Sara C B Buonomo
- School of Biological Sciences, Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3FF, UK
| | - Michela Di Virgilio
- Max-Delbruck Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Tobias Neumann
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030, Vienna, Austria.
- Quantro Therapeutics, Vienna Biocenter, 1030, Vienna, Austria.
| | - Rushad Pavri
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030, Vienna, Austria.
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Peycheva M, Neumann T, Malzl D, Nazarova M, Schoeberl UE, Pavri R. DNA replication timing directly regulates the frequency of oncogenic chromosomal translocations. Science 2022; 377:eabj5502. [DOI: 10.1126/science.abj5502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Chromosomal translocations result from the joining of DNA double-strand breaks (DSBs) and frequently cause cancer. However, the steps linking DSB formation to DSB ligation remain undeciphered. We report that DNA replication timing (RT) directly regulates lymphomagenic
Myc
translocations during antibody maturation in B cells downstream of DSBs and independently of DSB frequency. Depletion of minichromosome maintenance complexes alters replication origin activity, decreases translocations, and deregulates global RT. Ablating a single origin at
Myc
causes an early-to-late RT switch, loss of translocations, and reduced proximity with the immunoglobulin heavy chain (
Igh
) gene, its major translocation partner. These phenotypes were reversed by restoring early RT. Disruption of early RT also reduced tumorigenic translocations in human leukemic cells. Thus, RT constitutes a general mechanism in translocation biogenesis linking DSB formation to DSB ligation.
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Affiliation(s)
- Mihaela Peycheva
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030 Vienna, Austria
| | - Tobias Neumann
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030 Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna Biocenter, 1030 Vienna, Austria
| | - Daniel Malzl
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030 Vienna, Austria
| | - Mariia Nazarova
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030 Vienna, Austria
| | - Ursula E. Schoeberl
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030 Vienna, Austria
| | - Rushad Pavri
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter, 1030 Vienna, Austria
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Appel LM, Franke V, Bruno M, Grishkovskaya I, Kasiliauskaite A, Kaufmann T, Schoeberl UE, Puchinger MG, Kostrhon S, Ebenwaldner C, Sebesta M, Beltzung E, Mechtler K, Lin G, Vlasova A, Leeb M, Pavri R, Stark A, Akalin A, Stefl R, Bernecky C, Djinovic-Carugo K, Slade D. PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. Nat Commun 2021; 12:6078. [PMID: 34667177 PMCID: PMC8526623 DOI: 10.1038/s41467-021-26360-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 09/29/2021] [Indexed: 12/16/2022] Open
Abstract
The C-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) is a regulatory hub for transcription and RNA processing. Here, we identify PHD-finger protein 3 (PHF3) as a regulator of transcription and mRNA stability that docks onto Pol II CTD through its SPOC domain. We characterize SPOC as a CTD reader domain that preferentially binds two phosphorylated Serine-2 marks in adjacent CTD repeats. PHF3 drives liquid-liquid phase separation of phosphorylated Pol II, colocalizes with Pol II clusters and tracks with Pol II across the length of genes. PHF3 knock-out or SPOC deletion in human cells results in increased Pol II stalling, reduced elongation rate and an increase in mRNA stability, with marked derepression of neuronal genes. Key neuronal genes are aberrantly expressed in Phf3 knock-out mouse embryonic stem cells, resulting in impaired neuronal differentiation. Our data suggest that PHF3 acts as a prominent effector of neuronal gene regulation by bridging transcription with mRNA decay.
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Affiliation(s)
- Lisa-Marie Appel
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Vedran Franke
- The Berlin Institute for Medical Systems Biology, Max Delbrück Center, Berlin, Germany
| | - Melania Bruno
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Irina Grishkovskaya
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Aiste Kasiliauskaite
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Tanja Kaufmann
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Ursula E Schoeberl
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Martin G Puchinger
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Sebastian Kostrhon
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Carmen Ebenwaldner
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Marek Sebesta
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Etienne Beltzung
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Karl Mechtler
- Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, Vienna Biocenter (VBC), Vienna, Austria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Gen Lin
- Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, Vienna Biocenter (VBC), Vienna, Austria
| | - Anna Vlasova
- Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, Vienna Biocenter (VBC), Vienna, Austria
| | - Martin Leeb
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Rushad Pavri
- Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, Vienna Biocenter (VBC), Vienna, Austria
| | - Alexander Stark
- Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, Vienna Biocenter (VBC), Vienna, Austria
| | - Altuna Akalin
- The Berlin Institute for Medical Systems Biology, Max Delbrück Center, Berlin, Germany
| | - Richard Stefl
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Carrie Bernecky
- Institute of Science and Technology Austria (IST Austria), Am Campus 1, Klosterneuburg, Austria
| | - Kristina Djinovic-Carugo
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
- Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Dea Slade
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria.
- Department of Radiation Oncology, Medical University of Vienna, Vienna, Austria.
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria.
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Fitz J, Neumann T, Steininger M, Wiedemann EM, Garcia AC, Athanasiadis A, Schoeberl UE, Pavri R. Spt5-mediated enhancer transcription directly couples enhancer activation with physical promoter interaction. Nat Genet 2020; 52:505-515. [PMID: 32251373 DOI: 10.1038/s41588-020-0605-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 02/28/2020] [Indexed: 12/19/2022]
Abstract
Active enhancers are frequently transcribed, yet the regulatory role of enhancer transcription remains debated. Here, we depleted the RNA polymerase II pausing and elongation factor Spt5 in activated mouse B cells and found that approximately 50% of enhancer-gene pairs showed co-regulated transcription, consistent with a potential functional requirement for enhancer transcription. In particular, Spt5 depletion led to loss of super-enhancer-promoter physical interaction and gene expression at the immunoglobulin heavy-chain locus (Igh), abrogating antibody class switch recombination. This defect correlated strictly with loss of enhancer transcription but did not affect acetylation of histone H3 at lysine 27, chromatin accessibility and occupancy of Mediator and cohesin at the enhancer. Strikingly, CRISPRa-mediated rescue of enhancer transcription in Spt5-depleted cells restored Igh gene expression. Our work suggests that Spt5-mediated enhancer transcription underlies the physical and functional interaction between a subset of active enhancers and their target promoters.
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Affiliation(s)
- Johanna Fitz
- Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | - Tobias Neumann
- Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | | | | | | | | | | | - Rushad Pavri
- Research Institute of Molecular Pathology (IMP), Vienna, Austria.
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Schoeberl UE, Kurth HM, Noto T, Mochizuki K. Biased transcription and selective degradation of small RNAs shape the pattern of DNA elimination in Tetrahymena. Genes Dev 2012; 26:1729-42. [PMID: 22855833 PMCID: PMC3418590 DOI: 10.1101/gad.196493.112] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 06/21/2012] [Indexed: 01/05/2023]
Abstract
The ciliated protozoan Tetrahymena undergoes extensive programmed DNA elimination when the germline micronucleus produces the new macronucleus during sexual reproduction. DNA elimination is epigenetically controlled by DNA sequences of the parental macronuclear genome, and this epigenetic regulation is mediated by small RNAs (scan RNAs [scnRNAs]) of ∼28-30 nucleotides that are produced and function by an RNAi-related mechanism. Here, we examine scnRNA production and turnover by deep sequencing. scnRNAs are produced exclusively from the micronucleus and nonhomogeneously from a variety of chromosomal locations. scnRNAs are preferentially derived from the eliminated sequences, and this preference is mainly determined at the level of transcription. Despite this bias, a significant fraction of scnRNAs is also derived from the macronuclear-destined sequences, and these scnRNAs are degraded during the course of sexual reproduction. These results indicate that the pattern of DNA elimination in the new macronucleus is shaped by the biased transcription in the micronucleus and the selective degradation of scnRNAs in the parental macronucleus.
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Affiliation(s)
| | | | | | - Kazufumi Mochizuki
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), A-1030 Vienna, Austria
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Abstract
Many transposon-related sequences are removed from the somatic macronucleus of ciliates during sexual reproduction. In the ciliate Tetrahymena, an RNAi-related mechanism produces small noncoding RNAs that induce heterochromatin formation, which is followed by DNA elimination. Because RNAi-related mechanisms repress transposon activities in a variety of eukaryotes, the DNA elimination mechanism of ciliates might have evolved from these types of transposon-silencing mechanisms. Nuclear dimorphism allows ciliates to identify any DNA that has invaded the germ-line micronucleus using small RNAs and a whole genome comparison of the micronucleus and the somatic macronucleus.
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Affiliation(s)
- Ursula E Schoeberl
- Institute of Molecular Biotechnology, Austrian Academy of Sciences (IMBA), A-1030 Vienna, Austria
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