1
|
Hu Y, Xu L, Feng B, Wu Q, Wang Y, Gong W, Lv M, Zhao H, Chen J, Li J, Zhang W, Zhan Q. Mutual regulation between cell cycle and transcription termination factor TTF2. SCIENCE CHINA. LIFE SCIENCES 2025:10.1007/s11427-023-2538-2. [PMID: 40410652 DOI: 10.1007/s11427-023-2538-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2024] [Accepted: 12/19/2024] [Indexed: 05/25/2025]
Abstract
Most transcriptional activities are silent during mitosis and reactivated upon mitotic exit; however, the underlying detailed mechanisms are still largely unknown. We revealed that the cell cycle regulatory machinery anaphase-promoting complex/cyclosome (APC/C) and mitotic checkpoint complex (MCC) are coupled with transcription termination to modulate cell cycle progression via the transcription termination factor TTF2. The protein level of TTF2 oscillated during cell cycle progression, and increased in the S and G2/M phases while maintaining a low level in late mitosis and the G1 phase. Knockdown of TTF2 induced G2/M arrest, while overexpression of TTF2 accelerated the M/G1 transition and promoted cell proliferation. Mechanistic studies revealed that TTF2 was ubiquitinated by APC/CCDH1 and targeted for proteasomal degradation. Interestingly, TTF2 bound to CDC20 and prevented MCC formation during normal mitosis. However, TTF2 was degraded by APC/CCDH1 when the cell encountered persistent G2/M arrest, which would release CDC20 and promote the assembly of MCC. Additionally, TTF2 was overexpressed in almost all solid tumors and correlated with poor survival in patients with several kinds of solid tumors. Thus, these findings establish a link between transcription termination and cell cycle regulation, revealing an unexpected mechanism by which TTF2 plays dual roles in mitosis by binding to CDH1 and CDC20 to balance the activation of APC/C and MCC.
Collapse
Affiliation(s)
- Yuying Hu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Lele Xu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, 100142, China
- The Clinical Innovation & Research Center (CIRC), Southern Medical University Shenzhen Hospital, Shenzhen, 518000, China
| | - Bicong Feng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Qingnan Wu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Yan Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Wei Gong
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Mengzhu Lv
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Huihui Zhao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Jie Chen
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Jinting Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Weimin Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, 100142, China.
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, 518107, China.
- Department of Oncology, Cancer Institute, Peking University Shenzhen Hospital, Shenzhen Peking University-Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Shenzhen, 518036, China.
- Research Unit of Molecular Cancer Research, Chinese Academy of Medical Sciences, Beijing, 100021, China.
| | - Qimin Zhan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, 100142, China.
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, 518107, China.
- Department of Oncology, Cancer Institute, Peking University Shenzhen Hospital, Shenzhen Peking University-Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Shenzhen, 518036, China.
- Research Unit of Molecular Cancer Research, Chinese Academy of Medical Sciences, Beijing, 100021, China.
- Peking University International Cancer Institute, Beijing, 100191, China.
| |
Collapse
|
2
|
Lagadec F, Singh PK, Calmels C, Lapaillerie D, Lindemann D, Parissi V, Cherepanov P, Engelman AN, Lesbats P. Timed chromatin invasion during mitosis governs prototype foamy virus integration site selection and infectivity. Nucleic Acids Res 2025; 53:gkaf449. [PMID: 40448500 DOI: 10.1093/nar/gkaf449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2025] [Revised: 05/05/2025] [Accepted: 05/15/2025] [Indexed: 06/02/2025] Open
Abstract
Selection of a suitable chromatin environment during retroviral integration is a tightly regulated process. Most retroviruses, including spumaretroviruses, require mitosis for nuclear entry. However, whether intrinsic chromatin dynamics during mitosis modulates retroviral genome invasion is unknown. Previous work uncovered critical interactions of prototype foamy virus (PFV) Gag with nucleosomes via a highly conserved arginine anchor residue. Yet, the regulation of Gag-chromatin interaction and its functional consequences for spumaretrovirus biology remain obscure. Here, we investigated the kinetics of chromatin binding by Gag during mitosis and proviral integration in synchronized cells. We showed that alteration of Gag affinity for nucleosome binding induced untimely chromatin tethering during mitosis, decreased infectivity, and redistributed viral integration sites to markers associated with late replication timing of chromosomes. Mutant Gag proteins were, moreover, defective in their ability to displace the histone H4 tail from the nucleosome acidic patch of highly condensed chromatin. These data indicate that the chromatin landscape during Gag-nucleosome interactions is important for PFV integration site selection and that spumaretroviruses evolved high-affinity chromatin binding to overcome early mitosis chromatin condensation.
Collapse
Affiliation(s)
- Floriane Lagadec
- Fundamental Microbiology and Pathogenicity Lab (MFP), UMR 5234 CNRS-University of Bordeaux, SBM Department, F-33076 Bordeaux, France
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), F-33076 Bordeaux, France
| | - Parmit K Singh
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, United States
- Department of Medicine, Harvard Medical School, Boston, MA 02115, United States
| | - Christina Calmels
- Fundamental Microbiology and Pathogenicity Lab (MFP), UMR 5234 CNRS-University of Bordeaux, SBM Department, F-33076 Bordeaux, France
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), F-33076 Bordeaux, France
| | - Delphine Lapaillerie
- Fundamental Microbiology and Pathogenicity Lab (MFP), UMR 5234 CNRS-University of Bordeaux, SBM Department, F-33076 Bordeaux, France
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), F-33076 Bordeaux, France
| | - Dirk Lindemann
- Institute of Medical Microbiology and Virology, University Hospital and Medical Faculty "Carl Gustav Carus", Technische Universität Dresden, 01307 Dresden, Germany
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, 01307 Dresden, Germany
| | - Vincent Parissi
- Fundamental Microbiology and Pathogenicity Lab (MFP), UMR 5234 CNRS-University of Bordeaux, SBM Department, F-33076 Bordeaux, France
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), F-33076 Bordeaux, France
| | - Peter Cherepanov
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Alan N Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, United States
- Department of Medicine, Harvard Medical School, Boston, MA 02115, United States
| | - Paul Lesbats
- Fundamental Microbiology and Pathogenicity Lab (MFP), UMR 5234 CNRS-University of Bordeaux, SBM Department, F-33076 Bordeaux, France
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), F-33076 Bordeaux, France
| |
Collapse
|
3
|
Piano V. Multitasking Proteins: Exploring Noncanonical Functions of Proteins during Mitosis. Biochemistry 2025; 64:2123-2137. [PMID: 40315343 DOI: 10.1021/acs.biochem.5c00083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2025]
Abstract
This review provides a comprehensive overview of how mitotic cells drive the repurposing of proteins to fulfill mitosis-specific functions. To ensure the successful completion of cell division, the cell strategically reallocates its "workforce" by assigning additional functions to available proteins. Protein repurposing occurs at multiple levels of cellular organization and involves diverse mechanisms. At the protein level, proteins may gain mitosis-specific functions through post-translational modifications. At the structural level, proteins that typically maintain cellular architecture in interphase are co-opted to participate in mitotic spindle formation, chromosome condensation, and kinetochore assembly. Furthermore, the dynamic reorganization of the nuclear envelope and other organelles relies on the temporary reassignment of enzymes, structural proteins, and motor proteins to facilitate these changes. These adaptive mechanisms underscore the remarkable versatility of the cellular proteome in responding to the stringent requirements of mitosis. By leveraging the existing proteome for dual or multiple specialized roles, cells optimize resource usage while maintaining the precision needed to preserve genomic integrity and ensure the survival of the next generation of cells.
Collapse
Affiliation(s)
- Valentina Piano
- Institute of Human Genetics, University of Cologne, 50931 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital, University of Cologne, 50931 Cologne, Germany
- Cologne Excellence Cluster for Cellular Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| |
Collapse
|
4
|
Chen JK, Liu T, Cai S, Ruan W, Ng CT, Shi J, Surana U, Gan L. Nanoscale analysis of human G1 and metaphase chromatin in situ. EMBO J 2025; 44:2658-2694. [PMID: 40097852 PMCID: PMC12048539 DOI: 10.1038/s44318-025-00407-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Revised: 02/11/2025] [Accepted: 02/21/2025] [Indexed: 03/19/2025] Open
Abstract
The structure of chromatin at the nucleosome level inside cells is still incompletely understood. Here we present in situ electron cryotomography analyses of chromatin in both G1 and metaphase RPE-1 cells. G1 nucleosomes are concentrated in globular chromatin domains, and metaphase nucleosomes are concentrated in the chromatids. Classification analysis reveals that canonical mononucleosomes, and in some conditions ordered stacked dinucleosomes and mononucleosomes with a disordered gyre-proximal density, are abundant in both cell-cycle states. We do not detect class averages that have more than two stacked nucleosomes or side-by-side dinucleosomes, suggesting that groups of more than two nucleosomes are heterogeneous. Large multi-megadalton structures are abundant in G1 nucleoplasm, but not found in G1 chromatin domains and metaphase chromatin. The macromolecular phenotypes studied here represent a starting point for the comparative analysis of compaction in normal vs. unhealthy human cells, in other cell-cycle states, other organisms, and in vitro chromatin assemblies.
Collapse
Affiliation(s)
- Jon Ken Chen
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore, 117543, Singapore
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, 22903, USA
| | - Tingsheng Liu
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore, 117543, Singapore
| | - Shujun Cai
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore, 117543, Singapore
| | - Weimei Ruan
- Institute of Molecular and Cell Biology and Agency for Science Technology and Research, 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Cai Tong Ng
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore, 117543, Singapore
| | - Jian Shi
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore, 117543, Singapore
| | - Uttam Surana
- Institute of Molecular and Cell Biology and Agency for Science Technology and Research, 61 Biopolis Drive, Singapore, 138673, Singapore
- Department of Pharmacology, National University of Singapore, Singapore, 117543, Singapore
| | - Lu Gan
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore, 117543, Singapore.
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, 22903, USA.
| |
Collapse
|
5
|
Placzek S, Vanzan L, Deluz C, Suter DM. Orchestration of pluripotent stem cell genome reactivation during mitotic exit. Cell Rep 2025; 44:115486. [PMID: 40153434 DOI: 10.1016/j.celrep.2025.115486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2025] [Revised: 01/25/2025] [Accepted: 03/07/2025] [Indexed: 03/30/2025] Open
Abstract
Cell identity maintenance faces many challenges during mitosis, as most DNA-binding proteins are evicted from DNA and transcription is virtually abolished. How cells maintain their identity through division and faithfully re-initiate gene expression during mitotic exit is unclear. Here, we develop a novel reporter system enabling cell cycle synchronization-free separation of pluripotent stem cells in temporal bins of <30 min during mitotic exit. This allows us to quantify genome-wide reactivation of transcription, sequential changes in chromatin accessibility and transcription factor footprints, and re-binding of the pluripotency transcription factors OCT4, SOX2, and NANOG (OSN). We find that transcriptional activity progressively ramps up after mitosis and that OSN rapidly reoccupy the genome during the anaphase-telophase transition. We also demonstrate transcription factor-specific, dynamic relocation patterns and a hierarchical reorganization of the OSN binding landscape governed by OCT4 and SOX2. Our study sheds light on the dynamic orchestration of transcriptional reactivation after mitosis.
Collapse
Affiliation(s)
- Silja Placzek
- Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Ludovica Vanzan
- Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Cédric Deluz
- Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - David M Suter
- Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| |
Collapse
|
6
|
Wang NB, Lende-Dorn BA, Beitz AM, Han P, Adewumi HO, O'Shea TM, Galloway KE. Proliferation history and transcription factor levels drive direct conversion to motor neurons. Cell Syst 2025; 16:101205. [PMID: 40086434 PMCID: PMC12006972 DOI: 10.1016/j.cels.2025.101205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 11/07/2024] [Accepted: 02/11/2025] [Indexed: 03/16/2025]
Abstract
The sparse and stochastic nature of conversion has obscured our understanding of how transcription factors (TFs) drive cells to new identities. To overcome this limit, we develop a tailored, high-efficiency conversion system that increases the direct conversion of fibroblasts to motor neurons 100-fold. By tailoring the cocktail to a minimal set of transcripts, we reduce extrinsic variation, allowing us to examine how proliferation and TFs synergistically drive conversion. We show that cell state-as set by proliferation history-defines how cells interpret the levels of TFs. Controlling for proliferation history and titrating each TF, we find that conversion correlates with levels of the pioneer TF Ngn2. By isolating cells by both their proliferation history and Ngn2 levels, we demonstrate that levels of Ngn2 expression alone are insufficient to predict conversion rates. Rather, proliferation history and TF levels combine to drive direct conversion. Finally, increasing the proliferation rate of adult human fibroblasts generates morphologically mature induced human motor neurons at high rates.
Collapse
Affiliation(s)
- Nathan B Wang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Brittany A Lende-Dorn
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Adam M Beitz
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Patrick Han
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Honour O Adewumi
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Timothy M O'Shea
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Kate E Galloway
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| |
Collapse
|
7
|
Arias E, Haynes ME, Nadkarni NA, Lipfert ZK, Muller WA, Batra A, Sullivan DP. EdU tracking of leukocyte recruitment in mouse models of ischemic stroke and sterile lung inflammation. J Cell Sci 2025; 138:jcs263835. [PMID: 40260638 DOI: 10.1242/jcs.263835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2025] [Accepted: 03/17/2025] [Indexed: 04/23/2025] Open
Abstract
The discovery of copper(I)-catalyzed azide-alkyne cycloaddition (click chemistry) has significantly advanced the detection of proliferating cells by utilizing 5-ethynyl-2'-deoxyuridine (EdU). EdU, a thymidine analogue, is incorporated into DNA during replication and detected by the direct reaction with an azide-conjugated fluorophore. Traditionally, dividing cells are labeled using 5-bromodeoxyuridine (BrdU), another nucleotide analogue. However, BrdU detection is a harsh method that requires substantial sample processing, unlike EdU detection. EdU is classically used to identify proliferating cells; however, we report a streamlined methodology that uses EdU to label and track leukocyte recruitment that is compatible with flow cytometry and microscopy and preserves transgenic fluorophores. EdU labeling was performed in two different models of sterile inflammation: ischemic stroke and hydrochloric acid aspiration. EdU injection was timed to differentially label circulating monocytes, neutrophils and T cells. Tissue analysis showed EdU-positive monocytes and T cells were enriched in both inflammatory models. This suggests that recently divided monocytes and T cells are preferentially recruited to these vascular beds during inflammation and highlights the utility of this labeling approach to track leukocyte subtypes longitudinally during inflammation.
Collapse
Affiliation(s)
- Erika Arias
- Department of Pathology, Northwestern University, Chicago, IL 60643, USA
| | - Maureen E Haynes
- Department of Pathology, Northwestern University, Chicago, IL 60643, USA
| | - Neil A Nadkarni
- Department of Neurology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Zoie K Lipfert
- Department of Neurology, Northwestern University, Chicago, IL 60643, USA
| | - William A Muller
- Department of Pathology, Northwestern University, Chicago, IL 60643, USA
| | - Ayush Batra
- Department of Pathology, Northwestern University, Chicago, IL 60643, USA
- Department of Neurology, Northwestern University, Chicago, IL 60643, USA
| | - David P Sullivan
- Department of Pathology, Northwestern University, Chicago, IL 60643, USA
| |
Collapse
|
8
|
Paldi F, Cavalli G. 3D genome folding in epigenetic regulation and cellular memory. Trends Cell Biol 2025:S0962-8924(25)00065-0. [PMID: 40221344 DOI: 10.1016/j.tcb.2025.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2025] [Revised: 03/07/2025] [Accepted: 03/11/2025] [Indexed: 04/14/2025]
Abstract
The 3D folding of the genome is tightly linked to its epigenetic state which maintains gene expression programmes. Although the relationship between gene expression and genome organisation is highly context dependent, 3D genome organisation is emerging as a novel epigenetic layer to reinforce and stabilise transcriptional states. Whether regulatory information carried in genome folding could be transmitted through mitosis is an area of active investigation. In this review, we discuss the relationship between epigenetic state and nuclear organisation, as well as the interplay between transcriptional regulation and epigenetic genome folding. We also consider the architectural remodelling of nuclei as cells enter and exit mitosis, and evaluate the potential of the 3D genome to contribute to cellular memory.
Collapse
Affiliation(s)
- Flora Paldi
- Institute of Human Genetics, CNRS and University of Montpellier, Montpellier, France
| | - Giacomo Cavalli
- Institute of Human Genetics, CNRS and University of Montpellier, Montpellier, France.
| |
Collapse
|
9
|
Hayes LR, Zaepfel B, Duan L, Starner AC, Bartels MD, Rothacher RL, Martin S, French R, Zhang Z, Sinha IR, Ling JP, Sun S, Ayala YM, Coller J, Van Nostrand EL, Florea L, Kalab P. 5-ethynyluridine perturbs nuclear RNA metabolism to promote the nuclear accumulation of TDP-43 and other RNA binding proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.04.02.646885. [PMID: 40236187 PMCID: PMC11996483 DOI: 10.1101/2025.04.02.646885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/17/2025]
Abstract
TDP-43, an essential nucleic acid binding protein and splicing regulator, is broadly disrupted in neurodegeneration. TDP-43 nuclear localization and function depend on the abundance of its nuclear RNA targets and its recruitment into large ribonucleoprotein complexes, which restricts TDP-43 nuclear efflux. To further investigate the interplay between TDP-43 and nascent RNAs, we aimed to employ 5-ethynyluridine (5EU), a widely used uridine analog for 'click chemistry' labeling of newly transcribed RNAs. Surprisingly, 5EU induced the nuclear accumulation of TDP-43 and other RNA-binding proteins and attenuated TDP-43 mislocalization caused by disruption of the nuclear transport apparatus. RNA FISH demonstrated 5EU-induced nuclear accumulation of polyadenylated and GU-repeat-rich RNAs, suggesting increased retention of both processed and intronic RNAs. TDP-43 eCLIP confirmed that 5EU preserved TDP-43 binding at predominantly GU-rich intronic sites. RNAseq revealed significant 5EU-induced changes in alternative splicing, accompanied by an overall reduction in splicing diversity, without any major changes in RNA stability or TDP-43 splicing regulatory function. These data suggest that 5EU may impede RNA splicing efficiency and subsequent nuclear RNA processing and export. Our findings have important implications for studies utilizing 5EU and offer unexpected confirmation that the accumulation of endogenous nuclear RNAs promotes TDP-43 nuclear localization.
Collapse
|
10
|
Jin G, Porello EAL, Zhang J, Lim B. Heterogeneous Sox2 transcriptional dynamics mediate pluripotency maintenance in mESCs in response to LIF signaling perturbations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.17.643751. [PMID: 40166162 PMCID: PMC11957043 DOI: 10.1101/2025.03.17.643751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/02/2025]
Abstract
The LIF signaling pathway and its regulation of internal factors like Sox2 is crucial for maintaining self-renewal and pluripotency in mESCs. However, the direct impact of LIF signaling on Sox2 transcriptional dynamics at the single-cell level remains elusive. Here, we employ PP7/PCP-mediated live imaging to analyze the transcriptional dynamics of Sox2 under perturbation of the LIF signaling pathway at single-cell resolution. Removal of the LIF ligand or addition of a JAK inhibitor heterogeneously affects the cell population, reducing the number of Sox2-active cells, rather than completely abolishing Sox2 expression. Moreover, Sox2-active cells under LIF perturbation exhibit significant reductions in mRNA production per cell. This reduction is characterized by decreased size and frequency of transcriptional bursting, resulting in shorter duration of Sox2 activity. Notably, cells with reduced or absent Sox2 expression demonstrate a significant loss in pluripotency, indicating that a reduction in Sox2 transcription (rather than a complete loss) is sufficient to trigger the transition from embryonic to an early differentiated state. In LIF-perturbed cells with Sox2 expression reduced to about 50% of non-perturbed levels, we observe a binary behavior, with cells either retaining or losing pluripotency-associated traits. Lastly, we find Sox2 expression is transcriptionally inherited across cell cycles, with Sox2-active mother cells more likely to reactivate Sox2 after mitosis compared to Sox2-inactive cells. This robust transcriptional memory is observed independent of LIF signaling perturbation. Our findings provide new insights into the transcriptional regulation of Sox2, advancing our understanding of the quantitative thresholds of gene expression required for pluripotency maintenance and highlighting the power of single-cell approaches to unravel dynamic regulatory mechanisms.
Collapse
|
11
|
Tan ZY, Cai 蔡舒君 S, Paithankar SA, Liu T, Nie X, Shi J, Gan 甘露 L. Macromolecular and cytological changes in fission yeast G0 nuclei. J Cell Sci 2025; 138:jcs263654. [PMID: 40013339 DOI: 10.1242/jcs.263654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 02/19/2025] [Indexed: 02/28/2025] Open
Abstract
When starved of nitrogen, cells of the fission yeast Schizosaccharomyces pombe enter a quiescent 'G0' state with smaller nuclei and transcriptional repression. The genomics of S. pombe G0 cells has been well studied, but much of its nuclear cell biology remains unknown. Here, we use confocal microscopy, immunoblots and electron cryotomography to investigate the cytological, biochemical and ultrastructural differences between S. pombe proliferating, G1-arrested and G0 cell nuclei, with an emphasis on the histone acetylation, RNA polymerase II fates and macromolecular complex packing. Compared to proliferating cells, G0 cells have lower levels of histone acetylation, nuclear RNA polymerase II and active transcription. The G0 nucleus has similar macromolecular crowding yet fewer chromatin-associated multi-megadalton globular complexes. Induced histone hyperacetylation during nitrogen starvation results in cells that have larger nuclei and therefore chromatin that is less compact. However, these histone-hyperacetylated cells remain transcriptionally repressed with similar nuclear crowding. Canonical nucleosomes - those that resemble the crystal structure - are rare in proliferating, G1-arrested and G0 cells. Our study therefore shows that extreme changes in nucleus physiology are possible without extreme reorganization at the macromolecular level.
Collapse
Affiliation(s)
- Zhi Yang Tan
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, 117543Singapore
| | - Shujun Cai 蔡舒君
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, 117543Singapore
| | - Saayli A Paithankar
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, 117543Singapore
| | - Tingsheng Liu
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, 117543Singapore
| | - Xin Nie
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, 117543Singapore
| | - Jian Shi
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, 117543Singapore
| | - Lu Gan 甘露
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, 117543Singapore
| |
Collapse
|
12
|
Ma B, Yang G, Yao J, Wu C, Vega JP, Manske G, Hammoud SS, Sinha S, Singh A, Zhao H, Chen X. Asymmetric Histone Inheritance Regulates Differential Transcription Re-initiation and Cell Fate Decisions in Mouse Olfactory Horizontal Basal Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.02.641101. [PMID: 40093102 PMCID: PMC11908234 DOI: 10.1101/2025.03.02.641101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2025]
Abstract
To understand epigenetic inheritance in mammals, we investigate cell division modes and histone inheritance patterns in the mouse olfactory epithelium using an injury-induced regeneration model. Horizontal basal cells (HBCs), the adult stem cells in this tissue, undergo asymmetric division, coinciding with asymmetric histone H4 inheritance in vivo. Primary HBCs recapitulate both asymmetric cell division and asymmetric histone inheritance for H4, H3, and H3.3, but not H2A-H2B. Upon mitotic exit, asymmetric histone inheritance correlates with differential enrichment of a key 'stemness' transcription factor p63 and asynchronous transcription re-initiation. Single-cell RNA sequencing of paired daughter cells reveals their asymmetric cell fate priming in this multilineage stem cell system. Furthermore, disruption of asymmetric cell division abolishes these asymmetric cellular features, impairing olfactory epithelium regeneration and smell behavior in mice. Together, these findings reveal asymmetric histone inheritance in a mammalian adult stem cell lineage and highlight its biological significance in tissue regeneration and animal behavior.
Collapse
Affiliation(s)
- Binbin Ma
- Howard Hughes Medical Institute, Department of Biology, Johns Hopkins University, Baltimore, MD
- Department of Biology, Johns Hopkins University, Baltimore, MD
| | - Guanghui Yang
- Howard Hughes Medical Institute, Department of Biology, Johns Hopkins University, Baltimore, MD
- Department of Biology, Johns Hopkins University, Baltimore, MD
| | - Jonathan Yao
- Department of Biology, Johns Hopkins University, Baltimore, MD
| | - Charles Wu
- Department of Biology, Johns Hopkins University, Baltimore, MD
| | | | - Gabriel Manske
- Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, MI
- Department of Human Genetics, University of Michigan, Ann Arbor, MI
| | | | - Satrajit Sinha
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, SUNY at Buffalo, 955 Main St, Buffalo, NY
| | - Abhyudai Singh
- Electrical & Computer Engineering, University of Delaware, Newark, DE
| | - Haiqing Zhao
- Department of Biology, Johns Hopkins University, Baltimore, MD
| | - Xin Chen
- Howard Hughes Medical Institute, Department of Biology, Johns Hopkins University, Baltimore, MD
- Department of Biology, Johns Hopkins University, Baltimore, MD
| |
Collapse
|
13
|
Zippo A, Beyes S. Molecular mechanisms altering cell identity in cancer. Oncogene 2025:10.1038/s41388-025-03314-2. [PMID: 40011573 DOI: 10.1038/s41388-025-03314-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2024] [Revised: 01/28/2025] [Accepted: 02/17/2025] [Indexed: 02/28/2025]
Abstract
Intrinsic and extrinsic factors influence cancer cell identity throughout its lifespan. During tumor progression and metastasis formation, cancer cells are exposed to different environmental stimuli, resulting in a stepwise cellular reprogramming. Similar stepwise changes of cell identity have been shown as a major consequence of cancer treatment, as cells are exposed to extracellular stress that can result in the establishment of subpopulations exhibiting different epigenetic and transcriptional patterns, indicating a rapid adaptation mechanism of cellular identity by extrinsic stress factors. Both mechanisms, tumor progression-mediated changes and therapy response, rely on signaling pathways affecting the epigenetic and subsequent transcriptional landscape, which equip the cells with mechanisms for survival and tumor progression. These non-genetic alterations are propagated to the daughter cells, indicating a need for successful information propagation and transfer to the daughter generations, thereby allowing for a stepwise adaptation to environmental cues. However, the exact mechanisms how these cell identity changes are occurring, which context-specific mechanisms are behind and how this can be exploited for future therapeutic interventions is not yet fully understood and exploited. In this review, we discuss the current knowledge on cell identity maintenance mechanisms intra- and intergenerational in development and disease and how these mechanisms are altered in cancer. We will as well address how cancer treatment might target these properties.
Collapse
Affiliation(s)
- Alessio Zippo
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy.
| | - Sven Beyes
- Robert Bosch Center for Tumor Diseases (RBCT), Stuttgart, Germany.
| |
Collapse
|
14
|
Nichols A, Norman R, Chen Y, Choi Y, Striepen J, Salataj E, Toufektchan E, Koche R, Maciejowski J. Mitotic transcription ensures ecDNA inheritance through chromosomal tethering. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.12.637945. [PMID: 39990406 PMCID: PMC11844496 DOI: 10.1101/2025.02.12.637945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2025]
Abstract
Extrachromosomal DNA (ecDNA) are circular DNA bodies that play critical roles in tumor progression and treatment resistance by amplifying oncogenes across a wide range of cancer types. ecDNA lack centromeres and are thus not constrained by typical Mendelian segregation, enabling their unequal accumulation within daughter cells and associated increases in copy number. Despite intrinsic links to their oncogenic potential, the fidelity and mechanisms of ecDNA inheritance are poorly understood. Here, we show that ecDNA are protected against cytosolic mis-segregation through mitotic clustering and by tethering to the telomeric and subtelomeric regions of mitotic chromosomes. ecDNA-chromosome tethering depends on BRD4 transcriptional co-activation and mitotic transcription of the long non-coding RNA PVT1 , which is co-amplified with MYC in colorectal and prostate cancer cell lines. Disruption of ecDNA-chromosome tethering through BRD4 inhibition, PVT1 depletion, or inhibiting mitotic transcription results in cytosolic mis-segregation, ecDNA reintegration, and the formation of homogeneously staining regions (HSRs). We propose that nuclear inheritance of ecDNA is facilitated by an RNA-mediated physical tether that links ecDNA to mitotic chromosomes and thus protects against cytosolic mis-segregation and chromosomal integration.
Collapse
|
15
|
Shen Z, Adams K, Moreno R, Lera R, Kaufman E, Lang JD, Burkard M. Polo-like kinase 1 maintains transcription and chromosomal accessibility during mitosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.12.637959. [PMID: 39990329 PMCID: PMC11844518 DOI: 10.1101/2025.02.12.637959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2025]
Abstract
Transcription persists at low levels in mitotic cells and plays essential roles in mitotic fidelity and chromosomal dynamics. However, the detailed regulatory network of mitotic transcription remains largely unresolved. Here, we report the novel role of Polo-like kinase 1 (Plk1) in maintaining mitotic transcription. Using 5-ethynyl uridine (5-EU) labeling of nascent RNAs, we found that Plk1 inhibition leads to significant downregulation of nascent transcription in prometaphase cells. Chromatin-localized Plk1 activity is required for transcription regulation and mitotic fidelity. Plk1 sustains global chromosomal accessibility in mitosis, especially at promoter and transcription start site (promoter-TSS) regions, facilitating transcription factor binding and ensuring proper transcriptional activity. We identified SMC4, a common subunit of condensin I and II, as a potential Plk1 substrate. Plk1 activity is fundamental to these processes across non-transformed and transformed cell lines, underscoring its critical role in cell cycle regulation. This study elucidates a novel regulatory mechanism of global mitotic transcription, advancing our understanding of cell cycle control. Significance Statement Cells retain a low level of transcription during mitosis, while the regulatory network and specific contributions of mitotic transcription are not well understood.We identify Polo-like kinase 1 (Plk1) as a novel regulator of mitotic transcription, crucial for chromosome condensation, genome accessibility, and maintaining mitotic fidelity.This study enhances our understanding of Plk1's multifaceted role in mitotic progression, advancing cell cycle regulation knowledge, and informing new cancer therapies' development.
Collapse
|
16
|
Lee U, Laguillo-Diego A, Wong W, Ni Z, Cheng L, Li J, Pelham-Webb B, Pertsinidis A, Leslie C, Apostolou E. Post-mitotic transcriptional activation and 3D regulatory interactions show locus- and differentiation-specific sensitivity to cohesin depletion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.13.638153. [PMID: 40034648 PMCID: PMC11875242 DOI: 10.1101/2025.02.13.638153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 03/05/2025]
Abstract
Prior studies showed that structural loops collapse upon acute cohesin depletion, while regulatory enhancer-promoter (E-P) loops largely persist, consistent with minimal transcriptional changes. However, these studies, conducted in asynchronous cells, could not resolve whether cohesin is required for the establishment of regulatory interactions and transcriptional activation during cell division or cell state transitions. To address this gap, we degraded RAD21, a core cohesin subunit, in naïve mouse embryonic stem cells (ESCs) transitioning from mitosis to G1 either in self-renewal condition or during differentiation toward formative pluripotency. Although most structural loops failed to be re-established without cohesin, about 35% of regulatory loops reformed at normal or higher frequencies. Cohesin-independent loops showed characteristics of strong active enhancers and promoters and a significant association with H3K27ac mitotic bookmarks. However, inhibition of CBP/p300 during mitotic exit did not impact these cohesin-independent interactions, suggesting the presence of complex compensatory mechanisms. At the transcriptional level, cohesin depletion induced only minor changes, supporting that post-mitotic transcriptional reactivation is largely independent of cohesin. The few genes with impaired reactivation were directly bound by RAD21 at their promoters, engaged in many structural loops, and located within strongly insulated TADs with low gene density. Importantly, degrading cohesin during the M-to-G1 transition in the presence of EpiLC differentiation signals revealed a larger group of susceptible genes, including key signature genes and transcription factors. Impaired activation of these genes was partly due to the failure to establish de novo EpiLC-specific interactions in the absence of cohesin. These experiments revealed locus-specific and context-specific dependencies between cohesin, E-P interactions, and transcription.
Collapse
Affiliation(s)
- UkJin Lee
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
- Molecular Biology Program, Graduate School of Medical Sciences, Weill Cornell Medicine, New York, 10065, USA
| | - Alejandra Laguillo-Diego
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - Wilfred Wong
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY 10065, USA
| | - Zhangli Ni
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Lingling Cheng
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jieru Li
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Bobbie Pelham-Webb
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY 10021, USA
| | - Alexandros Pertsinidis
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Christina Leslie
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Effie Apostolou
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| |
Collapse
|
17
|
Flashner S, Azizkhan-Clifford J. Emerging Roles for Transcription Factors During Mitosis. Cells 2025; 14:263. [PMID: 39996736 PMCID: PMC11853531 DOI: 10.3390/cells14040263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2025] [Revised: 02/06/2025] [Accepted: 02/08/2025] [Indexed: 02/26/2025] Open
Abstract
The genome is dynamically reorganized, partitioned, and divided during mitosis. Despite their role in organizing interphase chromatin, transcription factors were largely believed to be mitotic spectators evicted from chromatin during mitosis, only able to reestablish their position on DNA upon entry into G1. However, a panoply of evidence now contradicts this early belief. Numerous transcription factors are now known to remain active during mitosis to achieve diverse purposes, including chromosome condensation, regulation of the centromere/kinetochore function, and control of centrosome homeostasis. Inactivation of transcription factors during mitosis results in chromosome segregation errors, key features of cancer. Moreover, active transcription and the production of centromere-derived transcripts during mitosis are also known to play key roles in maintaining chromosomal stability. Finally, many transcription factors are associated with chromosomal instability through poorly defined mechanisms. Herein, we will review the emerging roles of transcription factors and transcription during mitosis with a focus on their role in promoting the faithful segregation of sister chromatids.
Collapse
Affiliation(s)
| | - Jane Azizkhan-Clifford
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| |
Collapse
|
18
|
Beliveau BJ, Akilesh S. A guide to studying 3D genome structure and dynamics in the kidney. Nat Rev Nephrol 2025; 21:97-114. [PMID: 39406927 PMCID: PMC12023896 DOI: 10.1038/s41581-024-00894-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2024] [Indexed: 10/19/2024]
Abstract
The human genome is tightly packed into the 3D environment of the cell nucleus. Rapidly evolving and sophisticated methods of mapping 3D genome architecture have shed light on fundamental principles of genome organization and gene regulation. The genome is physically organized on different scales, from individual genes to entire chromosomes. Nuclear landmarks such as the nuclear envelope and nucleoli have important roles in compartmentalizing the genome within the nucleus. Genome activity (for example, gene transcription) is also functionally partitioned within this 3D organization. Rather than being static, the 3D organization of the genome is tightly regulated over various time scales. These dynamic changes in genome structure over time represent the fourth dimension of the genome. Innovative methods have been used to map the dynamic regulation of genome structure during important cellular processes including organism development, responses to stimuli, cell division and senescence. Furthermore, disruptions to the 4D genome have been linked to various diseases, including of the kidney. As tools and approaches to studying the 4D genome become more readily available, future studies that apply these methods to study kidney biology will provide insights into kidney function in health and disease.
Collapse
Affiliation(s)
- Brian J Beliveau
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Shreeram Akilesh
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
| |
Collapse
|
19
|
Mao W, Ge X, Chen Q, Li JD. Epigenetic Mechanisms in the Transcriptional Regulation of Circadian Rhythm in Mammals. BIOLOGY 2025; 14:42. [PMID: 39857273 PMCID: PMC11762092 DOI: 10.3390/biology14010042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2024] [Revised: 12/17/2024] [Accepted: 12/19/2024] [Indexed: 01/27/2025]
Abstract
Almost all organisms, from the simplest bacteria to advanced mammals, havea near 24 h circadian rhythm. Circadian rhythms are highly conserved across different life forms and are regulated by circadian genes as well as by related transcription factors. Transcription factors are fundamental to circadian rhythms, influencing gene expression, behavior in plants and animals, and human diseases. This review examines the foundational research on transcriptional regulation of circadian rhythms, emphasizing histone modifications, chromatin remodeling, and Pol II pausing control. These studies have enhanced our understanding of transcriptional regulation within biological circadian rhythms and the importance of circadian biology in human health. Finally, we summarize the progress and challenges in these three areas of regulation to move the field forward.
Collapse
Affiliation(s)
- Wei Mao
- Department of Radiation Oncology, Zhejiang Cancer Hospital, Hangzhou 310000, China; (W.M.); (X.G.)
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310000, China
| | - Xingnan Ge
- Department of Radiation Oncology, Zhejiang Cancer Hospital, Hangzhou 310000, China; (W.M.); (X.G.)
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310000, China
| | - Qianping Chen
- Department of Radiation Oncology, Zhejiang Cancer Hospital, Hangzhou 310000, China; (W.M.); (X.G.)
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310000, China
| | - Jia-Da Li
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China
| |
Collapse
|
20
|
Zierhut C, Villunger A. Mitotic lethality prevents inflammation. Nat Cell Biol 2025; 27:7-8. [PMID: 39809996 DOI: 10.1038/s41556-024-01529-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2025]
Affiliation(s)
- Christian Zierhut
- Division of Cancer Biology, The Institute of Cancer Research, London, UK.
| | - Andreas Villunger
- Institute for Developmental Immunology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria.
- The Research Center for Molecular Medicine (CeMM) of the Austrian Academy of Sciences, Vienna, Austria.
| |
Collapse
|
21
|
Hu HT, Wang UTT, Chen BC, Hsueh YP, Wang TF. Ki-67 and CDK1 control the dynamic association of nuclear lipids with mitotic chromosomes. J Lipid Res 2025; 66:100731. [PMID: 39706365 PMCID: PMC11786767 DOI: 10.1016/j.jlr.2024.100731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2024] [Revised: 12/13/2024] [Accepted: 12/16/2024] [Indexed: 12/23/2024] Open
Abstract
Nuclear lipids play roles in regulatory processes, such as signaling, transcriptional regulation, and DNA repair. In this report, we demonstrate that nuclear lipids may contribute to Ki-67-regulated chromosome integrity during mitosis. In COS-7 cells, nuclear lipids are enriched at the perichromosomal layer and excluded from intrachromosomal regions during early mitosis but are then detected in intrachromosomal regions during late mitosis, as revealed by TT-ExM (expansion microscopy with trypsin digestion and tyramide signal amplification), an improved expansion microscopy technique that enables high-sensitivity and super-resolution imaging of proteins, lipids, and nuclear DNA. The nuclear nonhistone protein Ki-67 acts as a surfactant to form a repulsive molecular brush around fully condensed sister chromatids in early mitosis, preventing the diffusion or penetration of nuclear lipids into intrachromosomal regions. Ki-67 is phosphorylated during mitosis by cyclin-dependent kinase 1 (CDK1), the best-known master regulator of the cell cycle. Both Ki-67 knockdown and reduced Ki-67 phosphorylation by CDK1 inhibitors allow nuclear lipids to penetrate chromosomal regions. Thus, both Ki-67 protein level and phosphorylation status during mitosis appear to influence the perichromosomal distribution of nuclear lipids. Ki-67 knockdown and CDK1 inhibition also lead to uneven chromosome disjunction between daughter cells, highlighting the critical role of this regulatory mechanism in ensuring accurate chromosome segregation. Given that Ki-67 has been proposed to promote chromosome individualization and establish chromosome-cytoplasmic compartmentalization during open mitosis in vertebrates, our results reveal that nuclear lipid enrichment at the perichromosomal layer enhances the ability of Ki-67 to form a protective perichromosomal barrier (chromosome envelope), which is critical for correct chromosome segregation and maintenance of genome integrity during mitosis.
Collapse
Affiliation(s)
- Hsiao-Tang Hu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Ueh-Ting Tim Wang
- Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan; Department of Photonics, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Bi-Chang Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
| | - Yi-Ping Hsueh
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan.
| | - Ting-Fang Wang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan.
| |
Collapse
|
22
|
Beitz A, Teves J, Oakes C, Johnstone C, Wang N, Brickman JM, Galloway KE. Cells transit through a quiescent-like state to convert to neurons at high rates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.11.22.624928. [PMID: 39651159 PMCID: PMC11623504 DOI: 10.1101/2024.11.22.624928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2024]
Abstract
While transcription factors (TFs) provide essential cues for directing and redirecting cell fate, TFs alone are insufficient to drive cells to adopt alternative fates. Rather, transcription factors rely on receptive cell states to induce novel identities. Cell state emerges from and is shaped by cellular history and the activity of diverse processes. Here, we define the cellular and molecular properties of a highly receptive state amenable to transcription factor-mediated direct conversion from fibroblasts to induced motor neurons. Using a well-defined model of direct conversion to a post-mitotic fate, we identify the highly proliferative, receptive state that transiently emerges during conversion. Through examining chromatin accessibility, histone marks, and nuclear features, we find that cells reprogram from a state characterized by global reductions in nuclear size and transcriptional activity. Supported by globally increased levels of H3K27me3, cells enter a quiescent-like state of reduced RNA metabolism and elevated expression of REST and p27, markers of quiescent neural stem cells. From this transient state, cells convert to neurons at high rates. Inhibition of Ezh2, the catalytic subunit of PRC2 that deposits H3K27me3, abolishes conversion. Our work offers a roadmap to identify global changes in cellular processes that define cells with different conversion potentials that may generalize to other cell-fate transitions. Highlights Proliferation drives cells to a compact nuclear state that is receptive to TF-mediated conversion.Increased receptivity to TFs corresponds to reduced nuclear volumes.Reprogrammable cells display global, genome-wide increases in H3K27me3.High levels of H3K27me3 support cells' transits through a state of altered RNA metabolism.Inhibition of Ezh2 increases nuclear size, reduces the expression of the quiescence marker p27.Acute inhibition of Ezh2 abolishes motor neuron conversion. One Sentence Summary Cells transit through a quiescent-like state characterized by global reductions in nuclear size and transcriptional activity to convert to neurons at high rates.
Collapse
|
23
|
Goel VY, Aboreden NG, Jusuf JM, Zhang H, Mori LP, Mirny LA, Blobel GA, Banigan EJ, Hansen AS. Dynamics of microcompartment formation at the mitosis-to-G1 transition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.16.611917. [PMID: 39345388 PMCID: PMC11430094 DOI: 10.1101/2024.09.16.611917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
As cells exit mitosis and enter G1, mitotic chromosomes decompact and transcription is reestablished. Previously, Hi-C studies showed that essentially all interphase 3D genome features including A/B-compartments, TADs, and CTCF loops, are lost during mitosis. However, Hi-C remains insensitive to features such as microcompartments, nested focal interactions between cis-regulatory elements (CREs). We therefore applied Region Capture Micro-C to cells from mitosis to G1. Unexpectedly, we observe microcompartments in prometaphase, which further strengthen in ana/telophase before gradually weakening in G1. Loss of loop extrusion through condensin depletion differentially impacts microcompartments and large A/B-compartments, suggesting that they are partially distinct. Using polymer modeling, we show that microcompartment formation is favored by chromatin compaction and disfavored by loop extrusion activity, explaining why ana/telophase likely provides a particularly favorable environment. Our results suggest that CREs exhibit intrinsic homotypic affinity leading to microcompartment formation, which may explain transient transcriptional spiking observed upon mitotic exit.
Collapse
Affiliation(s)
- Viraat Y. Goel
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard; Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research; Cambridge, MA, 02139, USA
| | - Nicholas G. Aboreden
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Hematology, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - James M. Jusuf
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard; Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research; Cambridge, MA, 02139, USA
| | - Haoyue Zhang
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Luisa P. Mori
- Division of Hematology, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Leonid A. Mirny
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, 02139 MA, USA
| | - Gerd A. Blobel
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Hematology, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Edward J. Banigan
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, 02139 MA, USA
| | - Anders S. Hansen
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard; Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research; Cambridge, MA, 02139, USA
| |
Collapse
|
24
|
Schooley A, Venev SV, Aksenova V, Navarrete E, Dasso M, Dekker J. Interphase chromosome conformation is specified by distinct folding programs inherited via mitotic chromosomes or through the cytoplasm. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.16.613305. [PMID: 39345587 PMCID: PMC11429855 DOI: 10.1101/2024.09.16.613305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Identity-specific interphase chromosome conformation must be re-established each time a cell divides. To understand how interphase folding is inherited, we developed an experimental approach that physically segregates mediators of G1 folding that are intrinsic to mitotic chromosomes from cytoplasmic factors. Proteins essential for nuclear transport, RanGAP1 and Nup93, were degraded in pro-metaphase arrested DLD-1 cells to prevent the establishment of nucleo-cytoplasmic transport during mitotic exit and isolate the decondensing mitotic chromatin of G1 daughter cells from the cytoplasm. Using this approach, we discover a transient folding intermediate entirely driven by chromosome-intrinsic factors. In addition to conventional compartmental segregation, this chromosome-intrinsic folding program leads to prominent genome-scale microcompartmentalization of mitotically bookmarked and cell type-specific cis-regulatory elements. This microcompartment conformation is formed during telophase and subsequently modulated by a second folding program driven by factors inherited through the cytoplasm in G1. This nuclear import-dependent folding program includes cohesin and factors involved in transcription and RNA processing. The combined and inter-dependent action of chromosome-intrinsic and cytoplasmic inherited folding programs determines the interphase chromatin conformation as cells exit mitosis.
Collapse
Affiliation(s)
- Allana Schooley
- Department of Systems Biology, University of Massachusetts Chan Medical School; Worcester, USA
| | - Sergey V. Venev
- Department of Systems Biology, University of Massachusetts Chan Medical School; Worcester, USA
| | - Vasilisa Aksenova
- Division of Molecular and Cellular Biology, National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-4480, USA
| | - Emily Navarrete
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology; Cambridge, USA
| | - Mary Dasso
- Division of Molecular and Cellular Biology, National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-4480, USA
| | - Job Dekker
- Department of Systems Biology, University of Massachusetts Chan Medical School; Worcester, USA
- Howard Hughes Medical Institute; Chevy Chase, USA
| |
Collapse
|
25
|
De S, Ehrlich M. Arrest and Attack: Microtubule-Targeting Agents and Oncolytic Viruses Employ Complementary Mechanisms to Enhance Anti-Tumor Therapy Efficacy. Genes (Basel) 2024; 15:1193. [PMID: 39336785 PMCID: PMC11431212 DOI: 10.3390/genes15091193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 08/25/2024] [Accepted: 09/04/2024] [Indexed: 09/30/2024] Open
Abstract
Oncolytic viruses (OVs) are promising cancer immunotherapy agents that stimulate anti-tumor immunity through the preferential infection and killing of tumor cells. OVs are currently under limited clinical usage, due in part to their restricted efficacy as monotherapies. Current efforts for enhancement of the therapeutic potency of OVs involve their combination with other therapy modalities, aiming at the concomitant exploitation of complementary tumor weaknesses. In this context, microtubule-targeting agents (MTAs) pose as an enticing option, as they perturb microtubule dynamics and function, induce cell-cycle arrest, and cause mitotic cell death. MTAs induce therapeutic benefit through cancer-cell-autonomous and non-cell-autonomous mechanisms and are a main component of the standard of care for different malignancies. However, off-target effects and acquired resistance involving distinct cellular and molecular mechanisms may limit the overall efficacy of MTA-based therapy. When combined, OVs and MTAs may enhance therapeutic efficacy through increases in OV infection and immunogenic cell death and a decreased probability of acquired resistance. In this review, we introduce OVs and MTAs, describe molecular features of their activity in cancer cells, and discuss studies and clinical trials in which the combination has been tested.
Collapse
Affiliation(s)
| | - Marcelo Ehrlich
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel;
| |
Collapse
|
26
|
Gordon J, Phizicky D, Schärfen L, Brown C, Arias Escayola D, Kanyo J, Lam T, Simon M, Neugebauer K. Phosphorylation of the nuclear poly(A) binding protein (PABPN1) during mitosis protects mRNA from hyperadenylation and maintains transcriptome dynamics. Nucleic Acids Res 2024; 52:9886-9903. [PMID: 38943343 PMCID: PMC11381358 DOI: 10.1093/nar/gkae562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 05/23/2024] [Accepted: 06/28/2024] [Indexed: 07/01/2024] Open
Abstract
Polyadenylation controls mRNA biogenesis, nucleo-cytoplasmic export, translation and decay. These processes are interdependent and coordinately regulated by poly(A)-binding proteins (PABPs), yet how PABPs are themselves regulated is not fully understood. Here, we report the discovery that human nuclear PABPN1 is phosphorylated by mitotic kinases at four specific sites during mitosis, a time when nucleoplasm and cytoplasm mix. To understand the functional consequences of phosphorylation, we generated a panel of stable cell lines inducibly over-expressing PABPN1 with point mutations at these sites. Phospho-inhibitory mutations decreased cell proliferation, highlighting the importance of PABPN1 phosphorylation in cycling cells. Dynamic regulation of poly(A) tail length and RNA stability have emerged as important modes of gene regulation. We therefore employed long-read sequencing to determine how PABPN1 phospho-site mutants affected poly(A) tails lengths and TimeLapse-seq to monitor mRNA synthesis and decay. Widespread poly(A) tail lengthening was observed for phospho-inhibitory PABPN1 mutants. In contrast, expression of phospho-mimetic PABPN1 resulted in shorter poly(A) tails with increased non-A nucleotides, in addition to increased transcription and reduced stability of a distinct cohort of mRNAs. Taken together, PABPN1 phosphorylation remodels poly(A) tails and increases mRNA turnover, supporting the model that enhanced transcriptome dynamics reset gene expression programs across the cell cycle.
Collapse
Affiliation(s)
- Jackson M Gordon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - David V Phizicky
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Leonard Schärfen
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Courtney L Brown
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Dahyana Arias Escayola
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Jean Kanyo
- Keck MS & Proteomics Resource, Yale School of Medicine, New Haven, CT 06520, USA
| | - TuKiet T Lam
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
- Keck MS & Proteomics Resource, Yale School of Medicine, New Haven, CT 06520, USA
| | - Matthew D Simon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| |
Collapse
|
27
|
LaFoya B, Penkert RR, Prehoda KE. The cytokinetic midbody mediates asymmetric fate specification at mitotic exit during neural stem cell division. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.27.609974. [PMID: 39253494 PMCID: PMC11383292 DOI: 10.1101/2024.08.27.609974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Asymmetric cell division (ACD) is a broadly used mechanism for generating cellular diversity. Molecules known as fate determinants are segregated during ACD to generate distinct sibling cell fates, but determinants should not be activated until fate can be specified asymmetrically. Determinants could be activated after cell division but many animal cells complete division long after mitosis ends, raising the question of how activation could occur at mitotic exit taking advantage of the unique state plasticity at this time point. Here we show that the midbody, a microtubule-rich structure that forms in the intercellular bridge connecting nascent siblings, mediates fate determinant activation at mitotic exit in neural stem cells (NSCs) of the Drosophila larval brain. The fate determinants Prospero (Pros) and Brain tumor (Brat) are sequestered at the NSC membrane at metaphase but are released immediately following nuclear division when the midbody forms, well before cell division completes. The midbody isolates nascent sibling cytoplasms, allowing determinant release from the membrane via the cell cycle phosphatase String, without influencing the fate of the incorrect sibling. Our results identify the midbody as a key facilitator of ACD that allows asymmetric fate determinant activation to be initiated before division.
Collapse
Affiliation(s)
- Bryce LaFoya
- Institute of Molecular Biology, Department of Chemistry and Biochemistry, 1229 University of Oregon, Eugene, OR 97403
| | - Rhiannon R Penkert
- Institute of Molecular Biology, Department of Chemistry and Biochemistry, 1229 University of Oregon, Eugene, OR 97403
| | - Kenneth E. Prehoda
- Institute of Molecular Biology, Department of Chemistry and Biochemistry, 1229 University of Oregon, Eugene, OR 97403
| |
Collapse
|
28
|
Mouery RD, Lukasik K, Hsu C, Bonacci T, Bolhuis DL, Wang X, Mills CA, Toomer ED, Canterbury OG, Robertson KC, Branigan TB, Brown NG, Herring LE, Gupton SL, Emanuele MJ. Proteomic analysis reveals a PLK1-dependent G2/M degradation program and a role for AKAP2 in coordinating the mitotic cytoskeleton. Cell Rep 2024; 43:114510. [PMID: 39018246 PMCID: PMC11403584 DOI: 10.1016/j.celrep.2024.114510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 04/24/2024] [Accepted: 06/28/2024] [Indexed: 07/19/2024] Open
Abstract
Ubiquitination is an essential regulator of cell division. The kinase Polo-like kinase 1 (PLK1) promotes protein degradation at G2/M phase through the E3 ubiquitin ligase Skp1-Cul1-F box (SCF)βTrCP. However, the magnitude to which PLK1 shapes the mitotic proteome is uncharacterized. Combining quantitative proteomics with pharmacologic PLK1 inhibition revealed a widespread, PLK1-dependent program of protein breakdown at G2/M. We validated many PLK1-regulated proteins, including substrates of the cell-cycle E3 SCFCyclin F, demonstrating that PLK1 promotes proteolysis through at least two distinct E3 ligases. We show that the protein-kinase-A-anchoring protein A-kinase anchor protein 2 (AKAP2) is cell-cycle regulated and that its mitotic degradation is dependent on the PLK1/βTrCP signaling axis. Expression of a non-degradable AKAP2 mutant resulted in actin defects and aberrant mitotic spindles, suggesting that AKAP2 degradation coordinates cytoskeletal organization during mitosis. These findings uncover PLK1's far-reaching role in shaping the mitotic proteome post-translationally and have potential implications in malignancies where PLK1 is upregulated.
Collapse
Affiliation(s)
- Ryan D Mouery
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kimberly Lukasik
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Carolyn Hsu
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Thomas Bonacci
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Derek L Bolhuis
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Xianxi Wang
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - C Allie Mills
- UNC Proteomics Core Facility, Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - E Drew Toomer
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Owen G Canterbury
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kevin C Robertson
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Timothy B Branigan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Nicholas G Brown
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Laura E Herring
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; UNC Proteomics Core Facility, Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Stephanie L Gupton
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Michael J Emanuele
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| |
Collapse
|
29
|
Chen ZL, Xie C, Zeng W, Huang RQ, Yang JE, Liu JY, Chen YJ, Zhuang SM. Synergistic induction of mitotic pyroptosis and tumor remission by inhibiting proteasome and WEE family kinases. Signal Transduct Target Ther 2024; 9:181. [PMID: 38992067 PMCID: PMC11239683 DOI: 10.1038/s41392-024-01896-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 05/26/2024] [Accepted: 06/13/2024] [Indexed: 07/13/2024] Open
Abstract
Mitotic catastrophe (MC), which occurs under dysregulated mitosis, represents a fascinating tactic to specifically eradicate tumor cells. Whether pyroptosis can be a death form of MC remains unknown. Proteasome-mediated protein degradation is crucial for M-phase. Bortezomib (BTZ), which inhibits the 20S catalytic particle of proteasome, is approved to treat multiple myeloma and mantle cell lymphoma, but not solid tumors due to primary resistance. To date, whether and how proteasome inhibitor affected the fates of cells in M-phase remains unexplored. Here, we show that BTZ treatment, or silencing of PSMC5, a subunit of 19S regulatory particle of proteasome, causes G2- and M-phase arrest, multi-polar spindle formation, and consequent caspase-3/GSDME-mediated pyroptosis in M-phase (designated as mitotic pyroptosis). Further investigations reveal that inhibitor of WEE1/PKMYT1 (PD0166285), but not inhibitor of ATR, CHK1 or CHK2, abrogates the BTZ-induced G2-phase arrest, thus exacerbates the BTZ-induced mitotic arrest and pyroptosis. Combined BTZ and PD0166285 treatment (named BP-Combo) selectively kills various types of solid tumor cells, and significantly lessens the IC50 of both BTZ and PD0166285 compared to BTZ or PD0166285 monotreatment. Studies using various mouse models show that BP-Combo has much stronger inhibition on tumor growth and metastasis than BTZ or PD0166285 monotreatment, and no obvious toxicity is observed in BP-Combo-treated mice. These findings disclose the effect of proteasome inhibitors in inducing pyroptosis in M-phase, characterize pyroptosis as a new death form of mitotic catastrophe, and identify dual inhibition of proteasome and WEE family kinases as a promising anti-cancer strategy to selectively kill solid tumor cells.
Collapse
Affiliation(s)
- Zhan-Li Chen
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, State Key Laboratory of Oncology in Southern China, Sun Yat-sen University, Guangzhou, PR China
| | - Chen Xie
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, State Key Laboratory of Oncology in Southern China, Sun Yat-sen University, Guangzhou, PR China
| | - Wei Zeng
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, State Key Laboratory of Oncology in Southern China, Sun Yat-sen University, Guangzhou, PR China
| | - Rui-Qi Huang
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, State Key Laboratory of Oncology in Southern China, Sun Yat-sen University, Guangzhou, PR China
| | - Jin-E Yang
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, State Key Laboratory of Oncology in Southern China, Sun Yat-sen University, Guangzhou, PR China
| | - Jin-Yu Liu
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, State Key Laboratory of Oncology in Southern China, Sun Yat-sen University, Guangzhou, PR China
| | - Ya-Jing Chen
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, State Key Laboratory of Oncology in Southern China, Sun Yat-sen University, Guangzhou, PR China
| | - Shi-Mei Zhuang
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, State Key Laboratory of Oncology in Southern China, Sun Yat-sen University, Guangzhou, PR China.
- Key Laboratory of Liver Disease of Guangdong Province, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, PR China.
| |
Collapse
|
30
|
Bohrer C, Varon E, Peretz E, Reinitz G, Kinor N, Halle D, Nissan A, Shav-Tal Y. CCAT1 lncRNA is chromatin-retained and post-transcriptionally spliced. Histochem Cell Biol 2024; 162:91-107. [PMID: 38763947 PMCID: PMC11227459 DOI: 10.1007/s00418-024-02294-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/22/2024] [Indexed: 05/21/2024]
Abstract
Super-enhancers are unique gene expression regulators widely involved in cancer development. Spread over large DNA segments, they tend to be found next to oncogenes. The super-enhancer c-MYC locus forms long-range chromatin looping with nearby genes, which brings the enhancer and the genes into proximity, to promote gene activation. The colon cancer-associated transcript 1 (CCAT1) gene, which is part of the MYC locus, transcribes a lncRNA that is overexpressed in colon cancer cells through activation by MYC. Comparing different types of cancer cell lines using RNA fluorescence in situ hybridization (RNA FISH), we detected very prominent CCAT1 expression in HeLa cells, observed as several large CCAT1 nuclear foci. We found that dozens of CCAT1 transcripts accumulate on the gene locus, in addition to active transcription occurring from the gene. The accumulating transcripts are released from the chromatin during cell division. Examination of CCAT1 lncRNA expression patterns on the single-RNA level showed that unspliced CCAT1 transcripts are released from the gene into the nucleoplasm. Most of these unspliced transcripts were observed in proximity to the active gene but were not associated with nuclear speckles in which unspliced RNAs usually accumulate. At larger distances from the gene, the CCAT1 transcripts appeared spliced, implying that most CCAT1 transcripts undergo post-transcriptional splicing in the zone of the active gene. Finally, we show that unspliced CCAT1 transcripts can be detected in the cytoplasm during splicing inhibition, which suggests that there are several CCAT1 variants, spliced and unspliced, that the cell can recognize as suitable for export.
Collapse
Affiliation(s)
- Chaya Bohrer
- The Mina and Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - Eli Varon
- The Mina and Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - Eldar Peretz
- The Mina and Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - Gita Reinitz
- The Mina and Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - Noa Kinor
- The Mina and Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - David Halle
- Biochemistry Laboratory, Samson Assuta Ashdod University Hospital, Ashdod, Israel
| | - Aviram Nissan
- Ziv Medical Center, Safed, Israel
- Surgical Innovation Laboratory, The Chaim Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Yaron Shav-Tal
- The Mina and Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel.
| |
Collapse
|
31
|
Gillis A, Berry S. Global control of RNA polymerase II. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195024. [PMID: 38552781 DOI: 10.1016/j.bbagrm.2024.195024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 04/11/2024]
Abstract
RNA polymerase II (Pol II) is the multi-protein complex responsible for transcribing all protein-coding messenger RNA (mRNA). Most research on gene regulation is focused on the mechanisms controlling which genes are transcribed when, or on the mechanics of transcription. How global Pol II activity is determined receives comparatively less attention. Here, we follow the life of a Pol II molecule from 'assembly of the complex' to nuclear import, enzymatic activity, and degradation. We focus on how Pol II spends its time in the nucleus, and on the two-way relationship between Pol II abundance and activity in the context of homeostasis and global transcriptional changes.
Collapse
Affiliation(s)
- Alexander Gillis
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Sydney, Australia; UNSW RNA Institute, University of New South Wales, Sydney, Australia; Department of Molecular Medicine, School of Biomedical Sciences, University of New South Wales, Sydney, Australia
| | - Scott Berry
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Sydney, Australia; UNSW RNA Institute, University of New South Wales, Sydney, Australia; Department of Molecular Medicine, School of Biomedical Sciences, University of New South Wales, Sydney, Australia
| |
Collapse
|
32
|
Harris HL, Rowley MJ. Mechanistic drivers of chromatin organization into compartments. Curr Opin Genet Dev 2024; 86:102193. [PMID: 38626581 PMCID: PMC11898215 DOI: 10.1016/j.gde.2024.102193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 03/11/2024] [Accepted: 03/26/2024] [Indexed: 04/18/2024]
Abstract
The human genome is not just a simple string of DNA, it is a complex and dynamic entity intricately folded within the cell's nucleus. This three-dimensional organization of chromatin, the combination of DNA and proteins in the nucleus, is crucial for many biological processes and has been prominently studied for its intricate relationship to gene expression. Indeed, the transcriptional machinery does not operate in isolation but interacts intimately with the folded chromatin structure. Techniques for chromatin conformation capture, including genome-wide sequencing approaches, have revealed key organizational features of chromatin, such as the formation of loops by CCCTC-binding factor (CTCF) and the division of loci into chromatin compartments. While much of the recent research and reviews have focused on CTCF loops, we discuss several new revelations that have emerged concerning chromatin compartments, with a particular focus on what is known about mechanistic drivers of compartmentalization. These insights challenge the traditional views of chromatin organization and reveal the complexity behind the formation and maintenance of chromatin compartments.
Collapse
Affiliation(s)
- Hannah L Harris
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Emile St, Omaha 68198, NE, USA
| | - M Jordan Rowley
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Emile St, Omaha 68198, NE, USA.
| |
Collapse
|
33
|
Ly J, Xiang K, Su KC, Sissoko GB, Bartel DP, Cheeseman IM. Nuclear release of eIF1 globally increases stringency of start-codon selection to preserve mitotic arrest physiology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.06.588385. [PMID: 38617206 PMCID: PMC11014515 DOI: 10.1101/2024.04.06.588385] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Regulated start-codon selection has the potential to reshape the proteome through the differential production of uORFs, canonical proteins, and alternative translational isoforms. However, conditions under which start-codon selection is altered remain poorly defined. Here, using transcriptome-wide translation initiation site profiling, we reveal a global increase in the stringency of start-codon selection during mammalian mitosis. Low-efficiency initiation sites are preferentially repressed in mitosis, resulting in pervasive changes in the translation of thousands of start sites and their corresponding protein products. This increased stringency of start-codon selection during mitosis results from increased interactions between the key regulator of start-codon selection, eIF1, and the 40S ribosome. We find that increased eIF1-40S ribosome interactions during mitosis are mediated by the release of a nuclear pool of eIF1 upon nuclear envelope breakdown. Selectively depleting the nuclear pool of eIF1 eliminates the changes to translational stringency during mitosis, resulting in altered mitotic proteome composition. In addition, preventing mitotic translational rewiring results in substantially increased cell death and decreased mitotic slippage following treatment with anti-mitotic chemotherapeutics. Thus, cells globally control translation initiation stringency with critical roles during the mammalian cell cycle to preserve mitotic cell physiology.
Collapse
|
34
|
Budzyński MA, Wong AK, Faghihi A, Teves SS. A dynamic role for transcription factors in restoring transcription through mitosis. Biochem Soc Trans 2024; 52:821-830. [PMID: 38526206 PMCID: PMC11088908 DOI: 10.1042/bst20231022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 03/01/2024] [Accepted: 03/06/2024] [Indexed: 03/26/2024]
Abstract
Mitosis involves intricate steps, such as DNA condensation, nuclear membrane disassembly, and phosphorylation cascades that temporarily halt gene transcription. Despite this disruption, daughter cells remarkably retain the parent cell's gene expression pattern, allowing for efficient transcriptional memory after division. Early studies in mammalian cells suggested that transcription factors (TFs) mark genes for swift reactivation, a phenomenon termed 'mitotic bookmarking', but conflicting data emerged regarding TF presence on mitotic chromosomes. Recent advancements in live-cell imaging and fixation-free genomics challenge the conventional belief in universal formaldehyde fixation, revealing dynamic TF interactions during mitosis. Here, we review recent studies that provide examples of at least four modes of TF-DNA interaction during mitosis and the molecular mechanisms that govern these interactions. Additionally, we explore the impact of these interactions on transcription initiation post-mitosis. Taken together, these recent studies call for a paradigm shift toward a dynamic model of TF behavior during mitosis, underscoring the need for incorporating dynamics in mechanistic models for re-establishing transcription post-mitosis.
Collapse
Affiliation(s)
- Marek A. Budzyński
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Alexander K.L. Wong
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Armin Faghihi
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Sheila S. Teves
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| |
Collapse
|
35
|
Watson S, Porter H, Sudbery I, Thompson R. Modification of Seurat v4 for the Development of a Phase Assignment Tool Able to Distinguish between G2 and Mitotic Cells. Int J Mol Sci 2024; 25:4589. [PMID: 38731808 PMCID: PMC11083997 DOI: 10.3390/ijms25094589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/02/2024] [Accepted: 04/12/2024] [Indexed: 05/13/2024] Open
Abstract
Single-cell RNA sequencing (scRNAseq) is a rapidly advancing field enabling the characterisation of heterogeneous gene expression profiles within a population. The cell cycle phase is a major contributor to gene expression variance between cells and computational analysis tools have been developed to assign cell cycle phases to cells within scRNAseq datasets. Whilst these tools can be extremely useful, all have the drawback that they classify cells as only G1, S or G2/M. Existing discrete cell phase assignment tools are unable to differentiate between G2 and M and continuous-phase-assignment tools are unable to identify a region corresponding specifically to mitosis in a pseudo-timeline for continuous assignment along the cell cycle. In this study, bulk RNA sequencing was used to identify differentially expressed genes between mitotic and interphase cells isolated based on phospho-histone H3 expression using fluorescence-activated cell sorting. These gene lists were used to develop a methodology which can distinguish G2 and M phase cells in scRNAseq datasets. The phase assignment tools present in Seurat were modified to allow for cell cycle phase assignment of all stages of the cell cycle to identify a mitotic-specific cell population.
Collapse
Affiliation(s)
- Steven Watson
- School of Medicine and Population Health, University of Sheffield, Sheffield S10 2TN, UK
| | - Harry Porter
- School of Medicine, University of Nottingham, Nottingham NG5 1PB, UK
| | - Ian Sudbery
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
- Sheffield Institute for Nucleic Acid Research (SInFoNiA), Sheffield S10 2TN, UK
| | - Ruth Thompson
- School of Medicine and Population Health, University of Sheffield, Sheffield S10 2TN, UK
- Sheffield Institute for Nucleic Acid Research (SInFoNiA), Sheffield S10 2TN, UK
| |
Collapse
|
36
|
Kao YR, Chen J, Kumari R, Ng A, Zintiridou A, Tatiparthy M, Ma Y, Aivalioti MM, Moulik D, Sundaravel S, Sun D, Reisz JA, Grimm J, Martinez-Lopez N, Stransky S, Sidoli S, Steidl U, Singh R, D'Alessandro A, Will B. An iron rheostat controls hematopoietic stem cell fate. Cell Stem Cell 2024; 31:378-397.e12. [PMID: 38402617 PMCID: PMC10939794 DOI: 10.1016/j.stem.2024.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 12/20/2023] [Accepted: 01/30/2024] [Indexed: 02/27/2024]
Abstract
Mechanisms governing the maintenance of blood-producing hematopoietic stem and multipotent progenitor cells (HSPCs) are incompletely understood, particularly those regulating fate, ensuring long-term maintenance, and preventing aging-associated stem cell dysfunction. We uncovered a role for transitory free cytoplasmic iron as a rheostat for adult stem cell fate control. We found that HSPCs harbor comparatively small amounts of free iron and show the activation of a conserved molecular response to limited iron-particularly during mitosis. To study the functional and molecular consequences of iron restriction, we developed models allowing for transient iron bioavailability limitation and combined single-molecule RNA quantification, metabolomics, and single-cell transcriptomic analyses with functional studies. Our data reveal that the activation of the limited iron response triggers coordinated metabolic and epigenetic events, establishing stemness-conferring gene regulation. Notably, we find that aging-associated cytoplasmic iron loading reversibly attenuates iron-dependent cell fate control, explicating intervention strategies for dysfunctional aged stem cells.
Collapse
Affiliation(s)
- Yun-Ruei Kao
- Department of Oncology, Albert Einstein College of Medicine, New York, NY, USA.
| | - Jiahao Chen
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Rajni Kumari
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Anita Ng
- Karches Center for Oncology Research, the Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Aliona Zintiridou
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Madhuri Tatiparthy
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Yuhong Ma
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Maria M Aivalioti
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Deeposree Moulik
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Sriram Sundaravel
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Daqian Sun
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Julie A Reisz
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Juliane Grimm
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Nuria Martinez-Lopez
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Vatche and Tamar Manoukian Division of Digestive Diseases, University of California, Los Angeles, Los Angeles, CA, USA; Comprehensive Liver Research Center at University of California Los Angeles, CA, USA
| | - Stephanie Stransky
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, USA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, USA
| | - Ulrich Steidl
- Department of Oncology, Albert Einstein College of Medicine, New York, NY, USA; Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA; Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Albert Einstein College of Medicine, New York, NY, USA; Blood Cancer Institute, Montefiore Einstein Comprehensive Cancer Center, Albert Einstein College of Medicine, Bronx, NY, USA; Cancer Dormancy and Tumor Microenvironment Institute, Montefiore Einstein Comprehensive Cancer Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Rajat Singh
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Vatche and Tamar Manoukian Division of Digestive Diseases, University of California, Los Angeles, Los Angeles, CA, USA; Comprehensive Liver Research Center at University of California Los Angeles, CA, USA
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Britta Will
- Department of Oncology, Albert Einstein College of Medicine, New York, NY, USA; Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA; Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Albert Einstein College of Medicine, New York, NY, USA; Blood Cancer Institute, Montefiore Einstein Comprehensive Cancer Center, Albert Einstein College of Medicine, Bronx, NY, USA; Cancer Dormancy and Tumor Microenvironment Institute, Montefiore Einstein Comprehensive Cancer Center, Albert Einstein College of Medicine, Bronx, NY, USA; Institute for Aging Studies, Albert Einstein College of Medicine, New York, NY, USA.
| |
Collapse
|
37
|
Espinosa-Martínez M, Alcázar-Fabra M, Landeira D. The molecular basis of cell memory in mammals: The epigenetic cycle. SCIENCE ADVANCES 2024; 10:eadl3188. [PMID: 38416817 PMCID: PMC10901381 DOI: 10.1126/sciadv.adl3188] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 01/26/2024] [Indexed: 03/01/2024]
Abstract
Cell memory refers to the capacity of cells to maintain their gene expression program once the initiating environmental signal has ceased. This exceptional feature is key during the formation of mammalian organisms, and it is believed to be in part mediated by epigenetic factors that can endorse cells with the landmarks required to maintain transcriptional programs upon cell duplication. Here, we review current literature analyzing the molecular basis of epigenetic memory in mammals, with a focus on the mechanisms by which transcriptionally repressive chromatin modifications such as methylation of DNA and histone H3 are propagated through mitotic cell divisions. The emerging picture suggests that cellular memory is supported by an epigenetic cycle in which reversible activities carried out by epigenetic regulators in coordination with cell cycle transition create a multiphasic system that can accommodate both maintenance of cell identity and cell differentiation in proliferating stem cell populations.
Collapse
Affiliation(s)
- Mencía Espinosa-Martínez
- Centre for Genomics and Oncological Research (GENYO), Avenue de la Ilustración 114, 18016 Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
| | - María Alcázar-Fabra
- Centre for Genomics and Oncological Research (GENYO), Avenue de la Ilustración 114, 18016 Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
| | - David Landeira
- Centre for Genomics and Oncological Research (GENYO), Avenue de la Ilustración 114, 18016 Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
| |
Collapse
|
38
|
Bandau S, Alvarez V, Jiang H, Graff S, Sundaramoorthy R, Gierlinski M, Toman M, Owen-Hughes T, Sidoli S, Lamond A, Alabert C. RNA polymerase II promotes the organization of chromatin following DNA replication. EMBO Rep 2024; 25:1387-1414. [PMID: 38347224 PMCID: PMC10933433 DOI: 10.1038/s44319-024-00085-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 01/17/2024] [Accepted: 01/23/2024] [Indexed: 02/18/2024] Open
Abstract
Understanding how chromatin organisation is duplicated on the two daughter strands is a central question in epigenetics. In mammals, following the passage of the replisome, nucleosomes lose their defined positioning and transcription contributes to their re-organisation. However, whether transcription plays a greater role in the organization of chromatin following DNA replication remains unclear. Here we analysed protein re-association with newly replicated DNA upon inhibition of transcription using iPOND coupled to quantitative mass spectrometry. We show that nucleosome assembly and the re-establishment of most histone modifications are uncoupled from transcription. However, RNAPII acts to promote the re-association of hundreds of proteins with newly replicated chromatin via pathways that are not observed in steady-state chromatin. These include ATP-dependent remodellers, transcription factors and histone methyltransferases. We also identify a set of DNA repair factors that may handle transcription-replication conflicts during normal transcription in human non-transformed cells. Our study reveals that transcription plays a greater role in the organization of chromatin post-replication than previously anticipated.
Collapse
Affiliation(s)
- Susanne Bandau
- MCDB, School of Life Sciences, University of Dundee, DD15EH, Dundee, UK
| | - Vanesa Alvarez
- MCDB, School of Life Sciences, University of Dundee, DD15EH, Dundee, UK
| | - Hao Jiang
- Laboratory of Quantitative Proteomics, MCDB, School of Life Sciences, University of Dundee, DD15EH, Dundee, UK
| | - Sarah Graff
- Department of Biochemistry at the Albert Einstein College of Medicine, New York, NY, USA
| | | | - Marek Gierlinski
- Data Analysis Group, Division of Computational Biology, School of Life Sciences, University of Dundee, Dow Street, DD1 5EH, Dundee, UK
| | - Matt Toman
- Laboratory of Chromatin Structure and Function, MCDB, School of Life Sciences, University of Dundee, DD15EH, Dundee, UK
| | - Tom Owen-Hughes
- Laboratory of Chromatin Structure and Function, MCDB, School of Life Sciences, University of Dundee, DD15EH, Dundee, UK
| | - Simone Sidoli
- Department of Biochemistry at the Albert Einstein College of Medicine, New York, NY, USA
| | - Angus Lamond
- Laboratory of Quantitative Proteomics, MCDB, School of Life Sciences, University of Dundee, DD15EH, Dundee, UK
| | - Constance Alabert
- MCDB, School of Life Sciences, University of Dundee, DD15EH, Dundee, UK.
| |
Collapse
|
39
|
Janissen R, Barth R, Polinder M, van der Torre J, Dekker C. Single-molecule visualization of twin-supercoiled domains generated during transcription. Nucleic Acids Res 2024; 52:1677-1687. [PMID: 38084930 PMCID: PMC10899792 DOI: 10.1093/nar/gkad1181] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 11/13/2023] [Accepted: 11/30/2023] [Indexed: 02/29/2024] Open
Abstract
Transcription-coupled supercoiling of DNA is a key factor in chromosome compaction and the regulation of genetic processes in all domains of life. It has become common knowledge that, during transcription, the DNA-dependent RNA polymerase (RNAP) induces positive supercoiling ahead of it (downstream) and negative supercoils in its wake (upstream), as rotation of RNAP around the DNA axis upon tracking its helical groove gets constrained due to drag on its RNA transcript. Here, we experimentally validate this so-called twin-supercoiled-domain model with in vitro real-time visualization at the single-molecule scale. Upon binding to the promoter site on a supercoiled DNA molecule, RNAP merges all DNA supercoils into one large pinned plectoneme with RNAP residing at its apex. Transcription by RNAP in real time demonstrates that up- and downstream supercoils are generated simultaneously and in equal portions, in agreement with the twin-supercoiled-domain model. Experiments carried out in the presence of RNases A and H, revealed that an additional viscous drag of the RNA transcript is not necessary for the RNAP to induce supercoils. The latter results contrast the current consensus and simulations on the origin of the twin-supercoiled domains, pointing at an additional mechanistic cause underlying supercoil generation by RNAP in transcription.
Collapse
Affiliation(s)
- Richard Janissen
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, South-Holland 2629HZ, The Netherlands
| | - Roman Barth
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, South-Holland 2629HZ, The Netherlands
| | - Minco Polinder
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, South-Holland 2629HZ, The Netherlands
| | - Jaco van der Torre
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, South-Holland 2629HZ, The Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, South-Holland 2629HZ, The Netherlands
| |
Collapse
|
40
|
Contreras A, Perea-Resa C. Transcriptional repression across mitosis: mechanisms and functions. Biochem Soc Trans 2024; 52:455-464. [PMID: 38372373 PMCID: PMC10903446 DOI: 10.1042/bst20231071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/20/2024]
Abstract
Transcription represents a central aspect of gene expression with RNA polymerase machineries (RNA Pol) driving the synthesis of RNA from DNA template molecules. In eukaryotes, a total of three RNA Pol enzymes generate the plethora of RNA species and RNA Pol II is the one transcribing all protein-coding genes. A high number of cis- and trans-acting factors orchestrates RNA Pol II-mediated transcription by influencing the chromatin recruitment, activation, elongation, and/or termination steps. The levels of DNA accessibility, defining open-euchromatin versus close-heterochromatin, delimits RNA Pol II activity as well as the encounter with other factors acting on chromatin such as the DNA replication or DNA repair machineries. The stage of the cell cycle highly influences RNA Pol II activity with mitosis representing the major challenge. In fact, there is a massive inhibition of transcription during the mitotic entry coupled with chromatin dissociation of most of the components of the transcriptional machinery. Mitosis, as a consequence, highly compromises the transcriptional memory and the perpetuation of cellular identity. Once mitosis ends, transcription levels immediately recover to define the cell fate and to safeguard the proper progression of daughter cells through the cell cycle. In this review, we evaluate our current understanding of the transcriptional repression associated with mitosis with a special focus on the molecular mechanisms involved, on the potential function behind the general repression, and on the transmission of the transcriptional machinery into the daughter cells. We finally discuss the contribution that errors in the inheritance of the transcriptional machinery across mitosis might play in stem cell aging.
Collapse
Affiliation(s)
- A. Contreras
- Centro de Biología Molecular Severo Ochoa (CBMSO-CSIC), C/Nicolas Cabrera 1, 28049 Madrid, Spain
| | - C. Perea-Resa
- Centro de Biología Molecular Severo Ochoa (CBMSO-CSIC), C/Nicolas Cabrera 1, 28049 Madrid, Spain
| |
Collapse
|
41
|
Zhang Q, Chen Y, Teng Z, Lin Z, Liu H. CDK11 facilitates centromeric transcription to maintain centromeric cohesion during mitosis. Mol Biol Cell 2024; 35:ar18. [PMID: 38019613 PMCID: PMC10881149 DOI: 10.1091/mbc.e23-08-0303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 12/01/2023] Open
Abstract
Actively-transcribing RNA polymerase (RNAP)II is remained on centromeres to maintain centromeric cohesion during mitosis, although it is largely released from chromosome arms. This pool of RNAPII plays an important role in centromere functions. However, the mechanism of RNAPII retention on mitotic centromeres is poorly understood. We here demonstrate that Cyclin-dependent kinase (Cdk)11 is involved in RNAPII regulation on mitotic centromeres. Consistently, we show that Cdk11 knockdown induces centromeric cohesion defects and decreases Bub1 on kinetochores, but the centromeric cohesion defects are partially attributed to Bub1. Furthermore, Cdk11 knockdown and the expression of its kinase-dead version significantly reduce both RNAPII and elongating RNAPII (pSer2) levels on centromeres and decrease centromeric transcription. Importantly, the overexpression of centromeric α-satellite RNAs fully rescues Cdk11-knockdown defects. These results suggest that the maintenance of centromeric cohesion requires Cdk11-facilitated centromeric transcription. Mechanistically, Cdk11 localizes on centromeres where it binds and phosphorylates RNAPII to promote transcription. Remarkably, mitosis-specific degradation of G2/M Cdk11-p58 recapitulates Cdk11-knockdown defects. Altogether, our findings establish Cdk11 as an important regulator of centromeric transcription and as part of the mechanism for retaining RNAPII on centromeres during mitosis.
Collapse
Affiliation(s)
- Qian Zhang
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112
| | - Yujue Chen
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112
| | - Zhen Teng
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112
| | - Zhen Lin
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA 70112
| | - Hong Liu
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112
- Tulane Aging Center, Tulane University School of Medicine, New Orleans, LA 70112
| |
Collapse
|
42
|
Fenstermaker TK, Petruk S, Mazo A. An emerging paradigm in epigenetic marking: coordination of transcription and replication. Transcription 2024; 15:22-37. [PMID: 38378467 PMCID: PMC11093037 DOI: 10.1080/21541264.2024.2316965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/22/2024] Open
Abstract
DNA replication and RNA transcription both utilize DNA as a template and therefore need to coordinate their activities. The predominant theory in the field is that in order for the replication fork to proceed, transcription machinery has to be evicted from DNA until replication is complete. If that does not occur, these machineries collide, and these collisions elicit various repair mechanisms which require displacement of one of the enzymes, often RNA polymerase, in order for replication to proceed. This model is also at the heart of the epigenetic bookmarking theory, which implies that displacement of RNA polymerase during replication requires gradual re-building of chromatin structure, which guides recruitment of transcriptional proteins and resumption of transcription. We discuss these theories but also bring to light newer data that suggest that these two processes may not be as detrimental to one another as previously thought. This includes findings suggesting that these processes can occur without fork collapse and that RNA polymerase may only be transiently displaced during DNA replication. We discuss potential mechanisms by which RNA polymerase may be retained at the replication fork and quickly rebind to DNA post-replication. These discoveries are important, not only as new evidence as to how these two processes are able to occur harmoniously but also because they have implications on how transcriptional programs are maintained through DNA replication. To this end, we also discuss the coordination of replication and transcription in light of revising the current epigenetic bookmarking theory of how the active gene status can be transmitted through S phase.
Collapse
Affiliation(s)
- Tyler K. Fenstermaker
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Svetlana Petruk
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Alexander Mazo
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| |
Collapse
|
43
|
Ramos-Alonso L, Chymkowitch P. Maintaining transcriptional homeostasis during cell cycle. Transcription 2024; 15:1-21. [PMID: 37655806 PMCID: PMC11093055 DOI: 10.1080/21541264.2023.2246868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 09/02/2023] Open
Abstract
The preservation of gene expression patterns that define cellular identity throughout the cell division cycle is essential to perpetuate cellular lineages. However, the progression of cells through different phases of the cell cycle severely disrupts chromatin accessibility, epigenetic marks, and the recruitment of transcriptional regulators. Notably, chromatin is transiently disassembled during S-phase and undergoes drastic condensation during mitosis, which is a significant challenge to the preservation of gene expression patterns between cell generations. This article delves into the specific gene expression and chromatin regulatory mechanisms that facilitate the preservation of transcriptional identity during replication and mitosis. Furthermore, we emphasize our recent findings revealing the unconventional role of yeast centromeres and mitotic chromosomes in maintaining transcriptional fidelity beyond mitosis.
Collapse
Affiliation(s)
- Lucía Ramos-Alonso
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Pierre Chymkowitch
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| |
Collapse
|
44
|
Zhang L, Hu C, Xu Z, Li H, Ye B, Li X, Czajkowsky DM, Shao Z. Quantitative catalogue of mammalian mitotic chromosome-associated RNAs. Sci Data 2024; 11:43. [PMID: 38184632 PMCID: PMC10771512 DOI: 10.1038/s41597-023-02884-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 12/27/2023] [Indexed: 01/08/2024] Open
Abstract
The faithful transmission of a cell's identity and functionality to its daughters during mitosis requires the proper assembly of mitotic chromosomes from interphase chromatin in a process that involves significant changes in the genome-bound material, including the RNA. However, our understanding of the RNA that is associated with the mitotic chromosome is presently limited. Here, we present complete and quantitative characterizations of the full-length mitotic chromosome-associated RNAs (mCARs) for 3 human cell lines, a monkey cell line, and a mouse cell line derived from high-depth RNA sequencing (3 replicates, 47 M mapped read pairs for each replicate). Overall, we identify, on average, more than 20,400 mCAR species per cell-type (including isoforms), more than 5,200 of which are enriched on the chromosome. Notably, overall, more than 2,700 of these mCARs were previously unknown, which thus also expands the annotated genome of these species. We anticipate that these datasets will provide an essential resource for future studies to better understand the functioning of mCARs on the mitotic chromosome and in the cell.
Collapse
Affiliation(s)
- Le Zhang
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chuansheng Hu
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zeqian Xu
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hua Li
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Bishan Ye
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xinhui Li
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Daniel M Czajkowsky
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Zhifeng Shao
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.
| |
Collapse
|
45
|
Rizvi S, Chhabra A, Tripathi A, Tyagi RK. Mitotic genome-bookmarking by nuclear hormone receptors: A novel dimension in epigenetic reprogramming and disease assessment. Mol Cell Endocrinol 2023; 578:112069. [PMID: 37730146 DOI: 10.1016/j.mce.2023.112069] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 09/07/2023] [Accepted: 09/12/2023] [Indexed: 09/22/2023]
Abstract
Arrival of multi-colored fluorescent proteins and advances in live cell imaging has immensely contributed to our understanding of intracellular trafficking of nuclear receptors and their roles in gene regulatory functions. These regulatory events need to be faithfully propagated from progenitor to progeny cells. This is corroborated by multiple converging mechanisms that include histone modifications and lately, the phenomenon of 'mitotic genome-bookmarking' by specific transcription factors. This phenomenon refers to the retention and feed-forward transmission of progenitor's architectural blueprint of active transcription status which is silenced and preserved during mitosis. Upon mitotic exit, this phenomenon ensures accurate reactivation of transcriptome, proteome, cellular traits and phenotypes in the progeny cells. In addition to diverse modes of genome-bookmarking by nuclear receptors, a correlation between disease-associated receptor polymorphism and disruption of this phenomenon is apparent. However, breakthrough technologies shall reveal finer details of this phenomenon to help achieve normalcy in receptor-specific diseases.
Collapse
Affiliation(s)
- Sheeba Rizvi
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Ayushi Chhabra
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Anjali Tripathi
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Rakesh K Tyagi
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India.
| |
Collapse
|
46
|
Wang NB, Lende-Dorn BA, Adewumi HO, Beitz AM, Han P, O'Shea TM, Galloway KE. Proliferation history and transcription factor levels drive direct conversion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.26.568736. [PMID: 38077004 PMCID: PMC10705288 DOI: 10.1101/2023.11.26.568736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
The sparse and stochastic nature of reprogramming has obscured our understanding of how transcription factors drive cells to new identities. To overcome this limit, we developed a compact, portable reprogramming system that increases direct conversion of fibroblasts to motor neurons by two orders of magnitude. We show that subpopulations with different reprogramming potentials are distinguishable by proliferation history. By controlling for proliferation history and titrating each transcription factor, we find that conversion correlates with levels of the pioneer transcription factor Ngn2, whereas conversion shows a biphasic response to Lhx3. Increasing the proliferation rate of adult human fibroblasts generates morphologically mature, induced motor neurons at high rates. Using compact, optimized, polycistronic cassettes, we generate motor neurons that graft with the murine central nervous system, demonstrating the potential for in vivo therapies.
Collapse
Affiliation(s)
- Nathan B Wang
- Department of Chemical Engineering, MIT, Cambridge, MA 02139, USA
| | | | - Honour O Adewumi
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Adam M Beitz
- Department of Chemical Engineering, MIT, Cambridge, MA 02139, USA
| | - Patrick Han
- Department of Chemical Engineering, MIT, Cambridge, MA 02139, USA
| | - Timothy M O'Shea
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Kate E Galloway
- Department of Chemical Engineering, MIT, Cambridge, MA 02139, USA
| |
Collapse
|
47
|
Zhang L, Ye B, Xu Z, Li X, D M C, Shao Z. Genome-wide identification of mammalian cell-cycle invariant and mitotic-specific macroH2A1 domains. Biosci Trends 2023; 17:393-400. [PMID: 37778979 DOI: 10.5582/bst.2023.01214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
The histone variant macroH2A has been found to play important regulatory roles in genomic processes, especially in regulating transcriptomes. However, whether macroH2A nucleosomes are retained on mitotic chromosomes to enable maintenance of cell-specific transcriptomes is not known. Here, examining mouse embryonic fibroblast cells (NIH-3T3) with native chromatin immunoprecipitation and sequencing (nChIP-seq), we show that the overwhelming majority (~90%) of macroH2A1 domains identified at the G1/S stage are indeed stably retained on mitotic chromosomes. Unexpectedly though, we also find that there are a number of macroH2A domains that are specific for either mitotic or G1/S cells. Notably, more than 7,000 interphase expressed genes flanked by macroH2A1 domains are loaded with macroH2A1 nucleosomes on the mitotic chromosome to form extended domains. Overall, these results reveal that, while the majority of macroH2A1 domains are indeed faithfully transmitted through the mitotic chromosomes, there is a previously unknown cell-cycle dependent exchange of macroH2A1 nucleosomes at numerous genomic loci, indicating the existence of molecular machineries for this dynamically regulated process. We anticipate that these findings will prove to be essential for the integrity of mitotic progression and the maintenance of cellular identity.
Collapse
Affiliation(s)
- Le Zhang
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University, Shanghai, China
- Bio-ID Center, Shanghai Jiao Tong University, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Bishan Ye
- Bio-ID Center, Shanghai Jiao Tong University, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Zeqian Xu
- Bio-ID Center, Shanghai Jiao Tong University, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Xinhui Li
- Bio-ID Center, Shanghai Jiao Tong University, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Czajkowsky D M
- Bio-ID Center, Shanghai Jiao Tong University, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Zhifeng Shao
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University, Shanghai, China
- Bio-ID Center, Shanghai Jiao Tong University, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| |
Collapse
|
48
|
Harris RJ, Heer M, Levasseur MD, Cartwright TN, Weston B, Mitchell JL, Coxhead JM, Gaughan L, Prendergast L, Rico D, Higgins JMG. Release of Histone H3K4-reading transcription factors from chromosomes in mitosis is independent of adjacent H3 phosphorylation. Nat Commun 2023; 14:7243. [PMID: 37945563 PMCID: PMC10636195 DOI: 10.1038/s41467-023-43115-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 10/31/2023] [Indexed: 11/12/2023] Open
Abstract
Histone modifications influence the recruitment of reader proteins to chromosomes to regulate events including transcription and cell division. The idea of a histone code, where combinations of modifications specify unique downstream functions, is widely accepted and can be demonstrated in vitro. For example, on synthetic peptides, phosphorylation of Histone H3 at threonine-3 (H3T3ph) prevents the binding of reader proteins that recognize trimethylation of the adjacent lysine-4 (H3K4me3), including the TAF3 component of TFIID. To study these combinatorial effects in cells, we analyzed the genome-wide distribution of H3T3ph and H3K4me2/3 during mitosis. We find that H3T3ph anti-correlates with adjacent H3K4me2/3 in cells, and that the PHD domain of TAF3 can bind H3K4me2/3 in isolated mitotic chromatin despite the presence of H3T3ph. Unlike in vitro, H3K4 readers are still displaced from chromosomes in mitosis in Haspin-depleted cells lacking H3T3ph. H3T3ph is therefore unlikely to be responsible for transcriptional downregulation during cell division.
Collapse
Affiliation(s)
- Rebecca J Harris
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Maninder Heer
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Mark D Levasseur
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Tyrell N Cartwright
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Bethany Weston
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Jennifer L Mitchell
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Jonathan M Coxhead
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Luke Gaughan
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
- Newcastle University Centre for Cancer, Faculty of Medical Sciences, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Lisa Prendergast
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Daniel Rico
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK.
- Newcastle University Centre for Cancer, Faculty of Medical Sciences, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK.
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), CSIC-Universidad Sevilla-Universidad Pablo de Olavide-Junta de Andalucía, 41092, Seville, Spain.
| | - Jonathan M G Higgins
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK.
- Newcastle University Centre for Cancer, Faculty of Medical Sciences, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK.
| |
Collapse
|
49
|
Massacci G, Perfetto L, Sacco F. The Cyclin-dependent kinase 1: more than a cell cycle regulator. Br J Cancer 2023; 129:1707-1716. [PMID: 37898722 PMCID: PMC10667339 DOI: 10.1038/s41416-023-02468-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/26/2023] [Accepted: 10/13/2023] [Indexed: 10/30/2023] Open
Abstract
The Cyclin-dependent kinase 1, as a serine/threonine protein kinase, is more than a cell cycle regulator as it was originally identified. During the last decade, it has been shown to carry out versatile functions during the last decade. From cell cycle control to gene expression regulation and apoptosis, CDK1 is intimately involved in many cellular events that are vital for cell survival. Here, we provide a comprehensive catalogue of the CDK1 upstream regulators and substrates, describing how this kinase is implicated in the control of key 'cell cycle-unrelated' biological processes. Finally, we describe how deregulation of CDK1 expression and activation has been closely associated with cancer progression and drug resistance.
Collapse
Affiliation(s)
- Giorgia Massacci
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Livia Perfetto
- Department of Biology and Biotechnologies "Charles Darwin", University of Rome La Sapienza, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Francesca Sacco
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133, Rome, Italy.
| |
Collapse
|
50
|
Mouery RD, Hsu C, Bonacci T, Bolhuis DL, Wang X, Mills CA, Toomer ED, Canterbury OG, Robertson KC, Branigan TB, Brown NG, Herring LE, Emanuele MJ. Proteomic Analysis Reveals a PLK1-Dependent G2/M Degradation Program and Links PKA-AKAP2 to Cell Cycle Control. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.11.561963. [PMID: 37873169 PMCID: PMC10592729 DOI: 10.1101/2023.10.11.561963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Targeted protein degradation by the ubiquitin-proteasome system is an essential mechanism regulating cellular division. The kinase PLK1 coordinates protein degradation at the G2/M phase of the cell cycle by promoting the binding of substrates to the E3 ubiquitin ligase SCFβTrCP. However, the magnitude to which PLK1 shapes the mitotic proteome has not been characterized. Combining deep, quantitative proteomics with pharmacologic PLK1 inhibition (PLK1i), we identified more than 200 proteins whose abundances were increased by PLK1i at G2/M. We validate many new PLK1-regulated proteins, including several substrates of the cell cycle E3 SCFCyclin F, demonstrating that PLK1 promotes proteolysis through at least two distinct SCF-family E3 ligases. Further, we found that the protein kinase A anchoring protein AKAP2 is cell cycle regulated and that its mitotic degradation is dependent on the PLK1/βTrCP-signaling axis. Interactome analysis revealed that the strongest interactors of AKAP2 function in signaling networks regulating proliferation, including MAPK, AKT, and Hippo. Altogether, our data demonstrate that PLK1 coordinates a widespread program of protein breakdown at G2/M. We propose that dynamic proteolytic changes mediated by PLK1 integrate proliferative signals with the core cell cycle machinery during cell division. This has potential implications in malignancies where PLK1 is aberrantly regulated.
Collapse
Affiliation(s)
- Ryan D Mouery
- Curriculum in Genetics and Molecular Biology. The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center. The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599, USA
| | - Carolyn Hsu
- Lineberger Comprehensive Cancer Center. The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599, USA
| | - Thomas Bonacci
- Lineberger Comprehensive Cancer Center. The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599, USA
- Department of Pharmacology. The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599, USA
| | - Derek L Bolhuis
- Department of Biochemistry and Biophysics. The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599, USA
| | - Xianxi Wang
- Lineberger Comprehensive Cancer Center. The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599, USA
- Department of Pharmacology. The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599, USA
| | - Christine A Mills
- UNC Proteomics Core Facility, Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - E Drew Toomer
- Lineberger Comprehensive Cancer Center. The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599, USA
- Department of Pharmacology. The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599, USA
| | - Owen G Canterbury
- Department of Pharmacology. The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599, USA
| | - Kevin C Robertson
- Lineberger Comprehensive Cancer Center. The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599, USA
- Department of Pharmacology. The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599, USA
| | - Timothy B Branigan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Nicholas G Brown
- Lineberger Comprehensive Cancer Center. The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599, USA
- Department of Pharmacology. The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599, USA
| | - Laura E Herring
- Lineberger Comprehensive Cancer Center. The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599, USA
- Department of Pharmacology. The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599, USA
- UNC Proteomics Core Facility, Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Michael J Emanuele
- Lineberger Comprehensive Cancer Center. The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599, USA
- Department of Pharmacology. The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599, USA
| |
Collapse
|