1
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Barrett AK, Shingare MR, Rechtsteiner A, Rodriguez KM, Le QN, Wijeratne TU, Mitchell CE, Membreno MW, Rubin SM, Müller GA. HDAC activity is dispensable for repression of cell-cycle genes by DREAM and E2F:RB complexes. Nat Commun 2024; 15:4450. [PMID: 38789411 PMCID: PMC11126580 DOI: 10.1038/s41467-024-48724-0] [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: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
Histone deacetylases (HDACs) play a crucial role in transcriptional regulation and are implicated in various diseases, including cancer. They are involved in histone tail deacetylation and canonically linked to transcriptional repression. Previous studies suggested that HDAC recruitment to cell-cycle gene promoters via the retinoblastoma (RB) protein or the DREAM complex through SIN3B is essential for G1/S and G2/M gene repression during cell-cycle arrest and exit. Here we investigate the interplay among DREAM, RB, SIN3 proteins, and HDACs in the context of cell-cycle gene repression. Knockout of SIN3B does not globally derepress cell-cycle genes in non-proliferating HCT116 and C2C12 cells. Loss of SIN3A/B moderately upregulates several cell-cycle genes in HCT116 cells but does so independently of DREAM/RB. HDAC inhibition does not induce general upregulation of RB/DREAM target genes in arrested transformed or non-transformed cells. Our findings suggest that E2F:RB and DREAM complexes can repress cell-cycle genes without relying on HDAC activity.
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Affiliation(s)
- Alison K Barrett
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, USA
| | - Manisha R Shingare
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, USA
| | - Andreas Rechtsteiner
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Kelsie M Rodriguez
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, USA
| | - Quynh N Le
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, USA
| | - Tilini U Wijeratne
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, USA
| | - Corbin E Mitchell
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, USA
| | - Miles W Membreno
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, USA
| | - Seth M Rubin
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, USA.
| | - Gerd A Müller
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, USA.
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2
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Hoareau M, Rincheval-Arnold A, Gaumer S, Guénal I. DREAM a little dREAM of DRM: Model organisms and conservation of DREAM-like complexes: Model organisms uncover the mechanisms of DREAM-mediated transcription regulation. Bioessays 2024; 46:e2300125. [PMID: 38059789 DOI: 10.1002/bies.202300125] [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: 07/07/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 12/08/2023]
Abstract
DREAM complexes are transcriptional regulators that control the expression of hundreds to thousands of target genes involved in the cell cycle, quiescence, differentiation, and apoptosis. These complexes contain many subunits that can vary according to the considered target genes. Depending on their composition and the nature of the partners they recruit, DREAM complexes control gene expression through diverse mechanisms, including chromatin remodeling, transcription cofactor and factor recruitment at various genomic binding sites. This complexity is particularly high in mammals. Since the discovery of the first dREAM complex (drosophila Rb, E2F, and Myb) in Drosophila melanogaster, model organisms such as Caenorhabditis elegans, and plants allowed a deeper understanding of the processes regulated by DREAM-like complexes. Here, we review the conservation of these complexes. We discuss the contribution of model organisms to the study of DREAM-mediated transcriptional regulatory mechanisms and their relevance in characterizing novel activities of DREAM complexes.
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Affiliation(s)
- Marion Hoareau
- Université Paris-Saclay, UVSQ, LGBC, Versailles, France
- Université PSL, EPHE, Paris, France
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3
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Calderon A, Mestvirishvili T, Boccalatte F, Ruggles KV, David G. Chromatin accessibility and cell cycle progression are controlled by the HDAC-associated Sin3B protein in murine hematopoietic stem cells. Epigenetics Chromatin 2024; 17:2. [PMID: 38254205 PMCID: PMC10804615 DOI: 10.1186/s13072-024-00526-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] [Received: 11/07/2023] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND Blood homeostasis requires the daily production of millions of terminally differentiated effector cells that all originate from hematopoietic stem cells (HSCs). HSCs are rare and exhibit unique self-renewal and multipotent properties, which depend on their ability to maintain quiescence through ill-defined processes. Defective control of cell cycle progression can eventually lead to bone marrow failure or malignancy. In particular, the molecular mechanisms tying cell cycle re-entry to cell fate commitment in HSCs remain elusive. Previous studies have identified chromatin coordination as a key regulator of differentiation in embryonic stem cells. RESULTS Here, we utilized genetic inactivation of the chromatin-associated Sin3B protein to manipulate cell cycle control and found dysregulated chromatin accessibility and cell cycle progression in HSCs. Single cell transcriptional profiling of hematopoietic stem and progenitor cells (HSPCs) inactivated for Sin3B reveals aberrant progression through the G1 phase of the cell cycle, which correlates with the engagement of specific signaling pathways, including aberrant expression of cell adhesion molecules and the interferon signaling program in LT-HSCs. In addition, we uncover the Sin3B-dependent accessibility of genomic elements controlling HSC differentiation, which points to cell cycle progression possibly dictating the priming of HSCs for differentiation. CONCLUSIONS Our findings provide new insights into controlled cell cycle progression as a potential regulator of HSC lineage commitment through the modulation of chromatin features.
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Affiliation(s)
- Alexander Calderon
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, 10016, USA
- Perlmutter Cancer Center, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, 10016, USA
| | - Tamara Mestvirishvili
- Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, 10016, USA
| | - Francesco Boccalatte
- Department of Pathology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, 10016, USA
| | - Kelly V Ruggles
- Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, 10016, USA
| | - Gregory David
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, 10016, USA.
- Perlmutter Cancer Center, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, 10016, USA.
- Department of Urology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, 10016, USA.
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4
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Mouery BL, Baker EM, Mills CA, Herring LE, Fleifel D, Cook JG. APC/C prevents non-canonical order of cyclin/CDK activity to maintain CDK4/6 inhibitor-induced arrest. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.09.566394. [PMID: 37986787 PMCID: PMC10659421 DOI: 10.1101/2023.11.09.566394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Regulated cell cycle progression ensures homeostasis and prevents cancer. In proliferating cells, premature S phase entry is avoided by the E3 ubiquitin ligase APC/C (anaphase promoting complex/cyclosome), although the APC/C substrates whose degradation restrains G1-S progression are not fully known. The APC/C is also active in arrested cells that exited the cell cycle, but it is not clear if APC/C maintains all types of arrest. Here by expressing the APC/C inhibitor, EMI1, we show that APC/C activity is essential to prevent S phase entry in cells arrested by pharmacological CDK4/6 inhibition (Palbociclib). Thus, active protein degradation is required for arrest alongside repressed cell cycle gene expression. The mechanism of rapid and robust arrest bypass from inhibiting APC/C involves cyclin-dependent kinases acting in an atypical order to inactivate RB-mediated E2F repression. Inactivating APC/C first causes mitotic cyclin B accumulation which then promotes cyclin A expression. We propose that cyclin A is the key substrate for maintaining arrest because APC/C-resistant cyclin A, but not cyclin B, is sufficient to induce S phase entry. Cells bypassing arrest from CDK4/6 inhibition initiate DNA replication with severely reduced origin licensing. The simultaneous accumulation of S phase licensing inhibitors, such as cyclin A and geminin, with G1 licensing activators disrupts the normal order of G1-S progression. As a result, DNA synthesis and cell proliferation are profoundly impaired. Our findings predict that cancers with elevated EMI1 expression will tend to escape CDK4/6 inhibition into a premature, underlicensed S phase and suffer enhanced genome instability.
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Affiliation(s)
- Brandon L Mouery
- Curriculum in Genetics and Molecular Biology. The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599, USA
| | - Eliyambuya M Baker
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599
- Immuno-Oncology, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Christine A Mills
- UNC Proteomics Core Facility, Department of Pharmacology. 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
- UNC Proteomics Core Facility, Department of Pharmacology. 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
- Department of Pharmacology. The University of North Carolina at Chapel Hill. Chapel Hill NC, 27599, USA
| | - Dalia Fleifel
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599
| | - Jeanette Gowen Cook
- Curriculum in Genetics and Molecular Biology. The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599, USA
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599
- 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
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5
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Barrett A, Shingare MR, Rechtsteiner A, Wijeratne TU, Rodriguez KM, Rubin SM, Müller GA. HDAC activity is dispensable for repression of cell-cycle genes by DREAM and E2F:RB complexes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.28.564489. [PMID: 37961464 PMCID: PMC10634886 DOI: 10.1101/2023.10.28.564489] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Histone deacetylases (HDACs) are pivotal in transcriptional regulation, and their dysregulation has been associated with various diseases including cancer. One of the critical roles of HDAC-containing complexes is the deacetylation of histone tails, which is canonically linked to transcriptional repression. Previous research has indicated that HDACs are recruited to cell-cycle gene promoters through the RB protein or the DREAM complex via SIN3B and that HDAC activity is essential for repressing G1/S and G2/M cell-cycle genes during cell-cycle arrest and exit. In this study, we sought to explore the interdependence of DREAM, RB, SIN3 proteins, and HDACs in the context of cell-cycle gene repression. We found that genetic knockout of SIN3B did not lead to derepression of cell-cycle genes in non-proliferating HCT116 and C2C12 cells. A combined loss of SIN3A and SIN3B resulted in a moderate upregulation in mRNA expression of several cell-cycle genes in arrested HCT116 cells, however, these effects appeared to be independent of DREAM or RB. Furthermore, HDAC inhibition did not induce a general upregulation of RB and DREAM target gene expression in arrested transformed or non-transformed cells. Our findings provide evidence that E2F:RB and DREAM complexes can repress cell-cycle genes without reliance on HDAC activity.
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Affiliation(s)
- Alison Barrett
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
- Current Affiliation: Department of Medicine, Division of Immunology and Rheumatology, Stanford University, Stanford, CA 94305, USA
| | - Manisha R. Shingare
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Andreas Rechtsteiner
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, CA 95064, USA
| | - Tilini U. Wijeratne
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
- Current Affiliation: Department of Medicine, Division of Immunology and Rheumatology, Stanford University, Stanford, CA 94305, USA
| | - Kelsie M. Rodriguez
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Seth M. Rubin
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Gerd A. Müller
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
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6
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Morales-Valencia J, Petit C, Calderon A, Saini S, David G. Chromatin-Associated SIN3B Protects Cancer Cells from Genotoxic Stress-Induced Apoptosis and Dictates DNA Damage Repair Pathway Choice. Mol Cancer Res 2023; 21:947-957. [PMID: 37314748 PMCID: PMC10527583 DOI: 10.1158/1541-7786.mcr-22-0466] [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: 06/12/2022] [Revised: 09/11/2022] [Accepted: 06/09/2023] [Indexed: 06/15/2023]
Abstract
Transcription and DNA damage repair act in a coordinated manner. The scaffolding protein SIN3B serves as a transcriptional co-repressor of hundreds of cell cycle-related genes. However, the contribution of SIN3B during the DNA damage response remains unknown. Here, we show that SIN3B inactivation delays the resolution of DNA double-strand breaks and sensitizes cancer cells to DNA-damaging agents, including the chemotherapeutic drugs cisplatin and doxorubicin. Mechanistically, SIN3B is rapidly recruited to DNA damage sites where it directs the accumulation of Mediator of DNA Damage Checkpoint 1 (MDC1). In addition, we show that SIN3B inactivation favors the engagement of the alternative nonhomologous end joining (NHEJ) repair pathway over the canonical NHEJ. Altogether, our findings impute an unexpected function for the transcriptional co-repressor SIN3B as a gatekeeper of genomic integrity and a determining factor in the DNA repair choice pathway, and point to the inhibition of the SIN3B chromatin-modifying complex as a novel therapeutic vulnerability in cancer cells. IMPLICATIONS Identifying SIN3B as a modulator of DNA damage repair choice provides novel potential therapeutic avenues to sensitize cancer cells to cytotoxic therapies.
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Affiliation(s)
- Jorge Morales-Valencia
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Medical Center, New York, NY 10016, USA
- NYU Langone Perlmutter Cancer Center, NYU Langone Medical Center, New York, NY 10016, USA
| | - Coralie Petit
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Medical Center, New York, NY 10016, USA
| | - Alexander Calderon
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Medical Center, New York, NY 10016, USA
| | - Siddharth Saini
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Medical Center, New York, NY 10016, USA
| | - Gregory David
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Medical Center, New York, NY 10016, USA
- NYU Langone Perlmutter Cancer Center, NYU Langone Medical Center, New York, NY 10016, USA
- Department of Urology, NYU Langone Medical Center, New York, NY 10016, USA
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7
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Wan MSM, Muhammad R, Koliopoulos MG, Roumeliotis TI, Choudhary JS, Alfieri C. Mechanism of assembly, activation and lysine selection by the SIN3B histone deacetylase complex. Nat Commun 2023; 14:2556. [PMID: 37137925 PMCID: PMC10156912 DOI: 10.1038/s41467-023-38276-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 04/22/2023] [Indexed: 05/05/2023] Open
Abstract
Lysine acetylation in histone tails is a key post-translational modification that controls transcription activation. Histone deacetylase complexes remove histone acetylation, thereby repressing transcription and regulating the transcriptional output of each gene. Although these complexes are drug targets and crucial regulators of organismal physiology, their structure and mechanisms of action are largely unclear. Here, we present the structure of a complete human SIN3B histone deacetylase holo-complex with and without a substrate mimic. Remarkably, SIN3B encircles the deacetylase and contacts its allosteric basic patch thereby stimulating catalysis. A SIN3B loop inserts into the catalytic tunnel, rearranges to accommodate the acetyl-lysine moiety, and stabilises the substrate for specific deacetylation, which is guided by a substrate receptor subunit. Our findings provide a model of specificity for a main transcriptional regulator conserved from yeast to human and a resource of protein-protein interactions for future drug designs.
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Affiliation(s)
- Mandy S M Wan
- Division of Structural Biology, Chester Beatty Laboratories, The Institute of Cancer Research, London, UK
| | - Reyhan Muhammad
- Division of Structural Biology, Chester Beatty Laboratories, The Institute of Cancer Research, London, UK
| | - Marios G Koliopoulos
- Division of Structural Biology, Chester Beatty Laboratories, The Institute of Cancer Research, London, UK
| | - Theodoros I Roumeliotis
- Functional Proteomics, Chester Beatty Laboratories, Cancer Biology Division, The Institute of Cancer Research, London, UK
| | - Jyoti S Choudhary
- Functional Proteomics, Chester Beatty Laboratories, Cancer Biology Division, The Institute of Cancer Research, London, UK
| | - Claudio Alfieri
- Division of Structural Biology, Chester Beatty Laboratories, The Institute of Cancer Research, London, UK.
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8
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Chen J, Fuhler NA, Noguchi KK, Dougherty JD. MYT1L is required for suppressing earlier neuronal development programs in the adult mouse brain. Genome Res 2023; 33:541-556. [PMID: 37100461 PMCID: PMC10234307 DOI: 10.1101/gr.277413.122] [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: 10/18/2022] [Accepted: 03/09/2023] [Indexed: 04/28/2023]
Abstract
In vitro studies indicate the neurodevelopmental disorder gene myelin transcription factor 1-like (MYT1L) suppresses non-neuronal lineage genes during fibroblast-to-neuron direct differentiation. However, MYT1L's molecular and cellular functions in the adult mammalian brain have not been fully characterized. Here, we found that MYT1L loss leads to up-regulated deep layer (DL) gene expression, corresponding to an increased ratio of DL/UL neurons in the adult mouse cortex. To define potential mechanisms, we conducted Cleavage Under Targets & Release Using Nuclease (CUT&RUN) to map MYT1L binding targets and epigenetic changes following MYT1L loss in mouse developing cortex and adult prefrontal cortex (PFC). We found MYT1L mainly binds to open chromatin, but with different transcription factor co-occupancies between promoters and enhancers. Likewise, multiomic data set integration revealed that, at promoters, MYT1L loss does not change chromatin accessibility but increases H3K4me3 and H3K27ac, activating both a subset of earlier neuronal development genes as well as Bcl11b, a key regulator for DL neuron development. Meanwhile, we discovered that MYT1L normally represses the activity of neurogenic enhancers associated with neuronal migration and neuronal projection development by closing chromatin structures and promoting removal of active histone marks. Further, we showed that MYT1L interacts with HDAC2 and transcriptional repressor SIN3B in vivo, providing potential mechanisms underlying repressive effects on histone acetylation and gene expression. Overall, our findings provide a comprehensive map of MYT1L binding in vivo and mechanistic insights into how MYT1L loss leads to aberrant activation of earlier neuronal development programs in the adult mouse brain.
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Affiliation(s)
- Jiayang Chen
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Nicole A Fuhler
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Kevin K Noguchi
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Joseph D Dougherty
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA;
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, Missouri 63108, USA
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9
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Calderon A, Mestvirishvili T, Boccalatte F, Ruggles K, David G. The Sin3B chromatin modifier restricts cell cycle progression to dictate hematopoietic stem cell differentiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.23.525185. [PMID: 36747851 PMCID: PMC9900761 DOI: 10.1101/2023.01.23.525185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
To maintain blood homeostasis, millions of terminally differentiated effector cells are produced every day. At the apex of this massive and constant blood production lie hematopoietic stem cells (HSCs), a rare cell type harboring unique self-renewal and multipotent properties. A key feature of HSCs is their ability to temporarily exit the cell cycle in a state termed quiescence. Defective control of cell cycle progression can eventually lead to bone marrow failure or malignant transformation. Recent work in embryonic stem cells has suggested that cells can more robustly respond to differentiation cues in the early phases of the cell cycle, owing to a discrete chromatin state permissive to cell fate commitment. However, the molecular mechanisms tying cell cycle re-entry to cell fate commitment in adult stem cells such as HSCs remain elusive. Here, we report that the chromatin-associated Sin3B protein is necessary for HSCs' commitment to differentiation, but dispensable for their self-renewal or survival. Transcriptional profiling of hematopoietic stem and progenitor cells (HSPCs) genetically inactivated for Sin3B at the single cell level reveals aberrant cell cycle gene expression, correlating with the defective engagement of discrete signaling programs. In particular, the loss of Sin3B in the hematopoietic compartment results in aberrant expression of cell adhesion molecules and essential components of the interferon signaling cascade in LT-HSCs. Finally, chromatin accessibility profiling in LT-HSCs suggests a link between Sin3B-dependent cell cycle progression and priming of hematopoietic stem cells for differentiation. Together, these results point to controlled progression through the G1 phase of the cell cycle as a likely regulator of HSC lineage commitment through the modulation of chromatin features.
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10
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Fischer M, Schade AE, Branigan TB, Müller GA, DeCaprio JA. Coordinating gene expression during the cell cycle. Trends Biochem Sci 2022; 47:1009-1022. [PMID: 35835684 DOI: 10.1016/j.tibs.2022.06.007] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 06/08/2022] [Accepted: 06/14/2022] [Indexed: 02/08/2023]
Abstract
Cell cycle-dependent gene transcription is tightly controlled by the retinoblastoma (RB):E2F and DREAM complexes, which repress all cell cycle genes during quiescence. Cyclin-dependent kinase (CDK) phosphorylation of RB and DREAM allows for the expression of two gene sets. The first set of genes, with peak expression in G1/S, is activated by E2F transcription factors (TFs) and is required for DNA synthesis. The second set, with maximum expression during G2/M, is required for mitosis and is coordinated by the MuvB complex, together with B-MYB and Forkhead box M1 (FOXM1). In this review, we summarize the key findings that established the distinct control mechanisms regulating G1/S and G2/M gene expression in mammals and discuss recent advances in the understanding of the temporal control of these genes.
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Affiliation(s)
- Martin Fischer
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), 07745, Jena, Germany.
| | - Amy E Schade
- Genetics Division, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Timothy B Branigan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Gerd A Müller
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - James A DeCaprio
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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11
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Structure and function of MuvB complexes. Oncogene 2022; 41:2909-2919. [PMID: 35468940 DOI: 10.1038/s41388-022-02321-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/06/2022] [Accepted: 04/08/2022] [Indexed: 11/08/2022]
Abstract
Proper progression through the cell-division cycle is critical to normal development and homeostasis and is necessarily misregulated in cancer. The key to cell-cycle regulation is the control of two waves of transcription that occur at the onset of DNA replication (S phase) and mitosis (M phase). MuvB complexes play a central role in the regulation of these genes. When cells are not actively dividing, the MuvB complex DREAM represses G1/S and G2/M genes. Remarkably, MuvB also forms activator complexes together with the oncogenic transcription factors B-MYB and FOXM1 that are required for the expression of the mitotic genes in G2/M. Despite this essential role in the control of cell division and the relationship to cancer, it has been unclear how MuvB complexes inhibit and stimulate gene expression. Here we review recent discoveries of MuvB structure and molecular interactions, including with nucleosomes and other chromatin-binding proteins, which have led to the first mechanistic models for the biochemical function of MuvB complexes.
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12
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Fischer M, Schwarz R, Riege K, DeCaprio JA, Hoffmann S. TargetGeneReg 2.0: a comprehensive web-atlas for p53, p63, and cell cycle-dependent gene regulation. NAR Cancer 2022; 4:zcac009. [PMID: 35350773 PMCID: PMC8946727 DOI: 10.1093/narcan/zcac009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 02/03/2022] [Accepted: 03/07/2022] [Indexed: 02/03/2023] Open
Abstract
In recent years, our web-atlas at www.TargetGeneReg.org has enabled many researchers to uncover new biological insights and to identify novel regulatory mechanisms that affect p53 and the cell cycle – signaling pathways that are frequently dysregulated in diseases like cancer. Here, we provide a substantial upgrade of the database that comprises an extension to include non-coding genes and the transcription factors ΔNp63 and RFX7. TargetGeneReg 2.0 combines gene expression profiling and transcription factor DNA binding data to determine, for each gene, the response to p53, ΔNp63, and cell cycle signaling. It can be used to dissect common, cell type and treatment-specific effects, identify the most promising candidates, and validate findings. We demonstrate the increased power and more intuitive layout of the resource using realistic examples.
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Affiliation(s)
- Martin Fischer
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Robert Schwarz
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Konstantin Riege
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - James A DeCaprio
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Steve Hoffmann
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
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13
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Asthana A, Ramanan P, Hirschi A, Guiley KZ, Wijeratne TU, Shelansky R, Doody MJ, Narasimhan H, Boeger H, Tripathi S, Müller GA, Rubin SM. The MuvB complex binds and stabilizes nucleosomes downstream of the transcription start site of cell-cycle dependent genes. Nat Commun 2022; 13:526. [PMID: 35082292 PMCID: PMC8792015 DOI: 10.1038/s41467-022-28094-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 01/10/2022] [Indexed: 11/25/2022] Open
Abstract
The chromatin architecture in promoters is thought to regulate gene expression, but it remains uncertain how most transcription factors (TFs) impact nucleosome position. The MuvB TF complex regulates cell-cycle dependent gene-expression and is critical for differentiation and proliferation during development and cancer. MuvB can both positively and negatively regulate expression, but the structure of MuvB and its biochemical function are poorly understood. Here we determine the overall architecture of MuvB assembly and the crystal structure of a subcomplex critical for MuvB function in gene repression. We find that the MuvB subunits LIN9 and LIN37 function as scaffolding proteins that arrange the other subunits LIN52, LIN54 and RBAP48 for TF, DNA, and histone binding, respectively. Biochemical and structural data demonstrate that MuvB binds nucleosomes through an interface that is distinct from LIN54-DNA consensus site recognition and that MuvB increases nucleosome occupancy in a reconstituted promoter. We find in arrested cells that MuvB primarily associates with a tightly positioned +1 nucleosome near the transcription start site (TSS) of MuvB-regulated genes. These results support a model that MuvB binds and stabilizes nucleosomes just downstream of the TSS on its target promoters to repress gene expression. The MuvB protein complex regulates genes that are differentially expressed through the cell cycle, yet its precise molecular function has remained unclear. Here the authors reveal MuvB associates with the nucleosome adjacent to the transcription start site of cell-cycle genes and that the tight positioning of this nucleosome correlates with MuvB-dependent gene repression.
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Affiliation(s)
- Anushweta Asthana
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, 95064, USA
| | - Parameshwaran Ramanan
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, 95064, USA
| | - Alexander Hirschi
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, 95064, USA
| | - Keelan Z Guiley
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, 95064, USA
| | - Tilini U Wijeratne
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, 95064, USA
| | - Robert Shelansky
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, CA, 95064, USA
| | - Michael J Doody
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, CA, 95064, USA
| | - Haritha Narasimhan
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, 95064, USA
| | - Hinrich Boeger
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, CA, 95064, USA
| | - Sarvind Tripathi
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, 95064, USA
| | - Gerd A Müller
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, 95064, USA.
| | - Seth M Rubin
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, 95064, USA.
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14
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Argüello-Miranda O, Marchand AJ, Kennedy T, Russo MAX, Noh J. Cell cycle-independent integration of stress signals by Xbp1 promotes Non-G1/G0 quiescence entry. J Cell Biol 2022; 221:212720. [PMID: 34694336 PMCID: PMC8548912 DOI: 10.1083/jcb.202103171] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 08/27/2021] [Accepted: 10/05/2021] [Indexed: 12/15/2022] Open
Abstract
Cellular quiescence is a nonproliferative state required for cell survival under stress and during development. In most quiescent cells, proliferation is stopped in a reversible state of low Cdk1 kinase activity; in many organisms, however, quiescent states with high-Cdk1 activity can also be established through still uncharacterized stress or developmental mechanisms. Here, we used a microfluidics approach coupled to phenotypic classification by machine learning to identify stress pathways associated with starvation-triggered high-Cdk1 quiescent states in Saccharomyces cerevisiae. We found that low- and high-Cdk1 quiescent states shared a core of stress-associated processes, such as autophagy, protein aggregation, and mitochondrial up-regulation, but differed in the nuclear accumulation of the stress transcription factors Xbp1, Gln3, and Sfp1. The decision between low- or high-Cdk1 quiescence was controlled by cell cycle-independent accumulation of Xbp1, which acted as a time-delayed integrator of the duration of stress stimuli. Our results show how cell cycle-independent stress-activated factors promote cellular quiescence outside G1/G0.
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Affiliation(s)
- Orlando Argüello-Miranda
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX.,Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX
| | - Ashley J Marchand
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Taylor Kennedy
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX.,School of Natural Sciences and Mathematics, University of Texas at Dallas, Richardson, TX
| | - Marielle A X Russo
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Jungsik Noh
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX
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15
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Gal C, Carelli FN, Appert A, Cerrato C, Huang N, Dong Y, Murphy J, Frapporti A, Ahringer J. DREAM represses distinct targets by cooperating with different THAP domain proteins. Cell Rep 2021; 37:109835. [PMID: 34686342 PMCID: PMC8552245 DOI: 10.1016/j.celrep.2021.109835] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 06/03/2021] [Accepted: 09/24/2021] [Indexed: 01/09/2023] Open
Abstract
The DREAM (dimerization partner [DP], retinoblastoma [Rb]-like, E2F, and MuvB) complex controls cellular quiescence by repressing cell-cycle and other genes, but its mechanism of action is unclear. Here, we demonstrate that two C. elegans THAP domain proteins, LIN-15B and LIN-36, co-localize with DREAM and function by different mechanisms for repression of distinct sets of targets. LIN-36 represses classical cell-cycle targets by promoting DREAM binding and gene body enrichment of H2A.Z, and we find that DREAM subunit EFL-1/E2F is specific for LIN-36 targets. In contrast, LIN-15B represses germline-specific targets in the soma by facilitating H3K9me2 promoter marking. We further find that LIN-36 and LIN-15B differently regulate DREAM binding. In humans, THAP proteins have been implicated in cell-cycle regulation by poorly understood mechanisms. We propose that THAP domain proteins are key mediators of Rb/DREAM function.
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Affiliation(s)
- Csenge Gal
- Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Francesco Nicola Carelli
- Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Alex Appert
- Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Chiara Cerrato
- Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Ni Huang
- Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Yan Dong
- Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Jane Murphy
- Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Andrea Frapporti
- Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Julie Ahringer
- Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK.
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16
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Abstract
Perfectly orchestrated periodic gene expression during cell cycle progression is essential for maintaining genome integrity and ensuring that cell proliferation can be stopped by environmental signals. Genetic and proteomic studies during the past two decades revealed remarkable evolutionary conservation of the key mechanisms that control cell cycle-regulated gene expression, including multisubunit DNA-binding DREAM complexes. DREAM complexes containing a retinoblastoma family member, an E2F transcription factor and its dimerization partner, and five proteins related to products of Caenorhabditis elegans multivulva (Muv) class B genes lin-9, lin-37, lin-52, lin-53, and lin-54 (comprising the MuvB core) have been described in diverse organisms, from worms to humans. This review summarizes the current knowledge of the structure, function, and regulation of DREAM complexes in different organisms, as well as the role of DREAM in human disease. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Hayley Walston
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia 23298, USA;
| | - Audra N Iness
- School of Medicine, Virginia Commonwealth University, Richmond, Virginia 23298, USA
| | - Larisa Litovchick
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia 23298, USA; .,Division of Hematology, Oncology and Palliative Care, Department of Internal Medicine, Virginia Commonwealth University, Richmond, Virginia 23298, USA.,Massey Cancer Center, Richmond, Virginia 23298, USA
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17
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Koliopoulos MG, Alfieri C. Cell cycle regulation by complex nanomachines. FEBS J 2021; 289:5100-5120. [PMID: 34143558 DOI: 10.1111/febs.16082] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 05/05/2021] [Accepted: 05/17/2021] [Indexed: 12/13/2022]
Abstract
The cell cycle is the essential biological process where one cell replicates its genome and segregates the resulting two copies into the daughter cells during mitosis. Several aspects of this process have fascinated humans since the nineteenth century. Today, the cell cycle is exhaustively investigated because of its profound connections with human diseases and cancer. At the heart of the molecular network controlling the cell cycle, we find the cyclin-dependent kinases (CDKs) acting as an oscillator to impose an orderly and highly regulated progression through the different cell cycle phases. This oscillator integrates both internal and external signals via a multitude of signalling pathways involving posttranslational modifications including phosphorylation, protein ubiquitination and mechanisms of transcriptional regulation. These tasks are specifically performed by multi-subunit complexes, which are intensively studied both biochemically and structurally with the aim to unveil mechanistic insights into their molecular function. The scope of this review is to summarise the structural biology of the cell cycle machinery, with specific focus on the core cell cycle machinery involving the CDK-cyclin oscillator. We highlight the contribution of cryo-electron microscopy, which has started to revolutionise our understanding of the molecular function and dynamics of the key players of the cell cycle.
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Affiliation(s)
- Marios G Koliopoulos
- Chester Beatty Laboratories, Structural Biology Division, Institute of Cancer Research, London, UK
| | - Claudio Alfieri
- Chester Beatty Laboratories, Structural Biology Division, Institute of Cancer Research, London, UK
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18
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Latypova X, Vincent M, Mollé A, Adebambo OA, Fourgeux C, Khan TN, Caro A, Rosello M, Orellana C, Niyazov D, Lederer D, Deprez M, Capri Y, Kannu P, Tabet AC, Levy J, Aten E, den Hollander N, Splitt M, Walia J, Immken LL, Stankiewicz P, McWalter K, Suchy S, Louie RJ, Bell S, Stevenson RE, Rousseau J, Willem C, Retiere C, Yang XJ, Campeau PM, Martinez F, Rosenfeld JA, Le Caignec C, Küry S, Mercier S, Moradkhani K, Conrad S, Besnard T, Cogné B, Katsanis N, Bézieau S, Poschmann J, Davis EE, Isidor B. Haploinsufficiency of the Sin3/HDAC corepressor complex member SIN3B causes a syndromic intellectual disability/autism spectrum disorder. Am J Hum Genet 2021; 108:929-941. [PMID: 33811806 DOI: 10.1016/j.ajhg.2021.03.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 03/18/2021] [Indexed: 11/28/2022] Open
Abstract
Proteins involved in transcriptional regulation harbor a demonstrated enrichment of mutations in neurodevelopmental disorders. The Sin3 (Swi-independent 3)/histone deacetylase (HDAC) complex plays a central role in histone deacetylation and transcriptional repression. Among the two vertebrate paralogs encoding the Sin3 complex, SIN3A variants cause syndromic intellectual disability, but the clinical consequences of SIN3B haploinsufficiency in humans are uncharacterized. Here, we describe a syndrome hallmarked by intellectual disability, developmental delay, and dysmorphic facial features with variably penetrant autism spectrum disorder, congenital malformations, corpus callosum defects, and impaired growth caused by disruptive SIN3B variants. Using chromosomal microarray or exome sequencing, and through international data sharing efforts, we identified nine individuals with heterozygous SIN3B deletion or single-nucleotide variants. Five individuals harbor heterozygous deletions encompassing SIN3B that reside within a ∼230 kb minimal region of overlap on 19p13.11, two individuals have a rare nonsynonymous substitution, and two individuals have a single-nucleotide deletion that results in a frameshift and predicted premature termination codon. To test the relevance of SIN3B impairment to measurable aspects of the human phenotype, we disrupted the orthologous zebrafish locus by genome editing and transient suppression. The mutant and morphant larvae display altered craniofacial patterning, commissural axon defects, and reduced body length supportive of an essential role for Sin3 function in growth and patterning of anterior structures. To investigate further the molecular consequences of SIN3B variants, we quantified genome-wide enhancer and promoter activity states by using H3K27ac ChIP-seq. We show that, similar to SIN3A mutations, SIN3B disruption causes hyperacetylation of a subset of enhancers and promoters in peripheral blood mononuclear cells. Together, these data demonstrate that SIN3B haploinsufficiency leads to a hitherto unknown intellectual disability/autism syndrome, uncover a crucial role of SIN3B in the central nervous system, and define the epigenetic landscape associated with Sin3 complex impairment.
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Affiliation(s)
- Xenia Latypova
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France; Center for Human Disease Modeling, Duke University Medical Center, Durham, NC 27701, USA; L'Institut du Thorax, INSERM, CNRS, Université de Nantes, 44007 Nantes, France
| | - Marie Vincent
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France; L'Institut du Thorax, INSERM, CNRS, Université de Nantes, 44007 Nantes, France
| | - Alice Mollé
- Université de Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, 44000 Nantes, France
| | | | - Cynthia Fourgeux
- Université de Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, 44000 Nantes, France
| | - Tahir N Khan
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC 27701, USA; Department of Biological Sciences, National University of Medical Sciences, 46000 Rawalpindi, Pakistan
| | - Alfonso Caro
- Unidad de Genética, Grupo de Investigación Traslacional en Genética, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain
| | - Monica Rosello
- Unidad de Genética, Grupo de Investigación Traslacional en Genética, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain
| | - Carmen Orellana
- Unidad de Genética, Grupo de Investigación Traslacional en Genética, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain
| | - Dmitriy Niyazov
- Department of Pediatrics, Ochsner Clinic, New Orleans, LA 70128, USA
| | - Damien Lederer
- Centre de Génétique Humaine, IPG, 6041 Gosselies, Belgium
| | - Marie Deprez
- Service de Neuropédiatrie, Clinique Saint Elizabeth, 5000 Namur, Belgium
| | - Yline Capri
- Service de Génétique Médicale, Hôpital Robert Debré, 75019 Paris, France
| | - Peter Kannu
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | | | - Jonathan Levy
- Service de Cytogénétique, Hôpital Robert Debré, 75019 Paris, France
| | - Emmelien Aten
- Department of Clinical Genetics, Leiden University Medical Center, 2333 Leiden, the Netherlands
| | - Nicolette den Hollander
- Department of Clinical Genetics, Leiden University Medical Center, 2333 Leiden, the Netherlands
| | - Miranda Splitt
- Northern Genetics Service, Institute of Genetic Medicine, Newcastle Upon Tyne NE1 3BZ, UK
| | - Jagdeep Walia
- Kingston General Hospital Research Institute, 76 Stuart Street, Kingston, ON K7L 2V7, Canada
| | - Ladonna L Immken
- Clinical Genetics, Dell Children's Medical Group, Austin, TX 78731, USA
| | - Pawel Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Sharon Suchy
- GeneDx, 207 Perry Parkway, Gaithersburg, MD 20877, USA
| | - Raymond J Louie
- Greenwood Genetic Center, 106 Gregor Mendel Cir, Greenwood, SC 29646, USA
| | - Shannon Bell
- Greenwood Genetic Center, 106 Gregor Mendel Cir, Greenwood, SC 29646, USA
| | - Roger E Stevenson
- Greenwood Genetic Center, 106 Gregor Mendel Cir, Greenwood, SC 29646, USA
| | - Justine Rousseau
- Sainte-Justine Hospital, 3175, Cote-Sainte-Catherine, Montreal, QC, Canada
| | | | - Christelle Retiere
- Etablissement Français du Sang, 44000 Nantes, France; CRCINA, INSERM, CNRS, Université d'Angers, Université de Nantes, 44000 Nantes, France; LabEx IGO, Nantes 44000, France
| | - Xiang-Jiao Yang
- Rosalind & Morris Goodman Cancer Research Center and Department of Medicine, McGill University, Montreal, QC H3A 1A3, Canada
| | - Philippe M Campeau
- Sainte-Justine Hospital, 3175, Cote-Sainte-Catherine, Montreal, QC, Canada
| | - Francisco Martinez
- Unidad de Genética, Grupo de Investigación Traslacional en Genética, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Cédric Le Caignec
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France; L'Institut du Thorax, INSERM, CNRS, Université de Nantes, 44007 Nantes, France
| | - Sébastien Küry
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France; L'Institut du Thorax, INSERM, CNRS, Université de Nantes, 44007 Nantes, France
| | - Sandra Mercier
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France; L'Institut du Thorax, INSERM, CNRS, Université de Nantes, 44007 Nantes, France
| | - Kamran Moradkhani
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France
| | - Solène Conrad
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France
| | - Thomas Besnard
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France; L'Institut du Thorax, INSERM, CNRS, Université de Nantes, 44007 Nantes, France
| | - Benjamin Cogné
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France; L'Institut du Thorax, INSERM, CNRS, Université de Nantes, 44007 Nantes, France
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC 27701, USA; Advanced Center for Translational and Genetic Medicine, Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA; Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Stéphane Bézieau
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France; L'Institut du Thorax, INSERM, CNRS, Université de Nantes, 44007 Nantes, France
| | - Jeremie Poschmann
- Université de Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, 44000 Nantes, France.
| | - Erica E Davis
- Advanced Center for Translational and Genetic Medicine, Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA; Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
| | - Bertrand Isidor
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France; L'Institut du Thorax, INSERM, CNRS, Université de Nantes, 44007 Nantes, France.
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19
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Jones MJK, Gelot C, Munk S, Koren A, Kawasoe Y, George KA, Santos RE, Olsen JV, McCarroll SA, Frattini MG, Takahashi TS, Jallepalli PV. Human DDK rescues stalled forks and counteracts checkpoint inhibition at unfired origins to complete DNA replication. Mol Cell 2021; 81:426-441.e8. [PMID: 33545059 DOI: 10.1016/j.molcel.2021.01.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 09/25/2020] [Accepted: 01/05/2021] [Indexed: 12/14/2022]
Abstract
Eukaryotic genomes replicate via spatially and temporally regulated origin firing. Cyclin-dependent kinase (CDK) and Dbf4-dependent kinase (DDK) promote origin firing, whereas the S phase checkpoint limits firing to prevent nucleotide and RPA exhaustion. We used chemical genetics to interrogate human DDK with maximum precision, dissect its relationship with the S phase checkpoint, and identify DDK substrates. We show that DDK inhibition (DDKi) leads to graded suppression of origin firing and fork arrest. S phase checkpoint inhibition rescued origin firing in DDKi cells and DDK-depleted Xenopus egg extracts. DDKi also impairs RPA loading, nascent-strand protection, and fork restart. Via quantitative phosphoproteomics, we identify the BRCA1-associated (BRCA1-A) complex subunit MERIT40 and the cohesin accessory subunit PDS5B as DDK effectors in fork protection and restart. Phosphorylation neutralizes autoinhibition mediated by intrinsically disordered regions in both substrates. Our results reveal mechanisms through which DDK controls the duplication of large vertebrate genomes.
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Affiliation(s)
- Mathew J K Jones
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD 4102, Australia.
| | - Camille Gelot
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Stephanie Munk
- University of Copenhagen and Novo Nordisk Foundation Center for Protein Research, Copenhagen 2200, Denmark
| | - Amnon Koren
- Cornell University, Department of Molecular Biology and Genetics, Ithaca, NY 14853, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Yoshitaka Kawasoe
- Graduate School of Science, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
| | - Kelly A George
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ruth E Santos
- Division of Hematology/Oncology, Columbia University Medical Center, New York, NY 10032, USA
| | - Jesper V Olsen
- University of Copenhagen and Novo Nordisk Foundation Center for Protein Research, Copenhagen 2200, Denmark
| | | | - Mark G Frattini
- Division of Hematology/Oncology, Columbia University Medical Center, New York, NY 10032, USA
| | - Tatsuro S Takahashi
- Graduate School of Science, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
| | - Prasad V Jallepalli
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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20
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Mitra A, Raicu AM, Hickey SL, Pile LA, Arnosti DN. Soft repression: Subtle transcriptional regulation with global impact. Bioessays 2020; 43:e2000231. [PMID: 33215731 PMCID: PMC9068271 DOI: 10.1002/bies.202000231] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/05/2020] [Accepted: 10/06/2020] [Indexed: 12/29/2022]
Abstract
Pleiotropically acting eukaryotic corepressors such as retinoblastoma and SIN3 have been found to physically interact with many widely expressed “housekeeping” genes. Evidence suggests that their roles at these loci are not to provide binary on/off switches, as is observed at many highly cell-type specific genes, but rather to serve as governors, directly modulating expression within certain bounds, while not shutting down gene expression. This sort of regulation is challenging to study, as the differential expression levels can be small. We hypothesize that depending on context, corepressors mediate “soft repression,” attenuating expression in a less dramatic but physiologically appropriate manner. Emerging data indicate that such regulation is a pervasive characteristic of most eukaryotic systems, and may reflect the mechanistic differences between repressor action at promoter and enhancer locations. Soft repression may represent an essential component of the cybernetic systems underlying metabolic adaptations, enabling modest but critical adjustments on a continual basis.
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Affiliation(s)
- Anindita Mitra
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
| | - Ana-Maria Raicu
- Cell and Molecular Biology Program, Michigan State University, East Lansing, Michigan, USA
| | - Stephanie L Hickey
- Department of Computational Mathematics, Science, and Engineering, Michigan State University, East Lansing, Michigan, USA.,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Lori A Pile
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
| | - David N Arnosti
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
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21
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Wahab S, Saettone A, Nabeel-Shah S, Dannah N, Fillingham J. Exploring the Histone Acetylation Cycle in the Protozoan Model Tetrahymena thermophila. Front Cell Dev Biol 2020; 8:509. [PMID: 32695779 PMCID: PMC7339932 DOI: 10.3389/fcell.2020.00509] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 05/28/2020] [Indexed: 12/22/2022] Open
Abstract
The eukaryotic histone acetylation cycle is composed of three classes of proteins, histone acetyltransferases (HATs) that add acetyl groups to lysine amino acids, bromodomain (BRD) containing proteins that are one of the most characterized of several protein domains that recognize acetyl-lysine (Kac) and effect downstream function, and histone deacetylases (HDACs) that catalyze the reverse reaction. Dysfunction of selected proteins of these three classes is associated with human disease such as cancer. Additionally, the HATs, BRDs, and HDACs of fungi and parasitic protozoa present potential drug targets. Despite their importance, the function and mechanisms of HATs, BRDs, and HDACs and how they relate to chromatin remodeling (CR) remain incompletely understood. Tetrahymena thermophila (Tt) provides a highly tractable single-celled free-living protozoan model for studying histone acetylation, featuring a massively acetylated somatic genome, a property that was exploited in the identification of the first nuclear/type A HAT Gcn5 in the 1990s. Since then, Tetrahymena remains an under-explored model for the molecular analysis of HATs, BRDs, and HDACs. Studies of HATs, BRDs, and HDACs in Tetrahymena have the potential to reveal the function of HATs and BRDs relevant to both fundamental eukaryotic biology and to the study of disease mechanisms in parasitic protozoa.
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Affiliation(s)
| | | | | | | | - Jeffrey Fillingham
- Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada
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Xu Z, Zou C, Guo M, Bian H, Zhao W, Wang J. Metastasis-associated protein 1 (MTA1) regulates the catecholamine production homeostasis via transcriptional repression of aromatic l-amino acid decarboxylase (Aadc) in the interstitial cells of Cajal of mouse prostate. Biochem Biophys Res Commun 2020; 528:732-739. [PMID: 32522342 DOI: 10.1016/j.bbrc.2020.05.125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 05/17/2020] [Indexed: 12/30/2022]
Abstract
Based on the lately identified role for the interstitial cells of Cajal (ICCs) of mouse prostate in catecholamine production, as well as the well-established role for the master coregulator metastasis-associated protein 1 (MTA1) in inflammation, we probed into the functional link between aberrant MTA1 expression and pathogenesis of chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) using both a MTA1-/- mouse model of experimental autoimmune prostatitis (EAP) and an in vitro chronic prostatitis model in cultured murine ICCs. EAP-induced MTA1 expression was enriched in ICCs of mouse prostate. EAP resulted in a higher increase in the pelvic pain response in MTA1-/- mice compared to WT mice. Consistently, the ICCs from MTA1-/- mice produced higher levels of catecholamines upon induction of in vitro chronic prostatitis. Mechanistically, MTA1 could directly suppress the transcription of Aadc, a rate-limiting enzyme during catecholamine synthesis, in a HDAC2-depdendent manner. Importantly, treatment with AADC inhibitor NSD-1015 significantly ameliorated EAP-elicited pain response and catecholamine overactivity in MTA1-/- mice. Taken together, our findings reveal an inherent regulatory role of the MTA1/AADC pathway in the maintenance of catecholamine production homeostasis in prostate ICCs, and also point to a potential use of HDAC inhibitors and/or AADC inhibitors to treat CP/CPPS.
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Affiliation(s)
- Zhibin Xu
- Department of Urology, Taizhou People's Hospital, Taizhou, 225300, Jiangsu Province, PR China
| | - Chunbo Zou
- Department of Urology, Taizhou People's Hospital, Taizhou, 225300, Jiangsu Province, PR China
| | - MaoMao Guo
- Department of Urology, Taizhou People's Hospital, Taizhou, 225300, Jiangsu Province, PR China
| | - Hao Bian
- Department of Urology, Taizhou People's Hospital, Taizhou, 225300, Jiangsu Province, PR China
| | - Wenchao Zhao
- Department of Urology, Taizhou People's Hospital, Taizhou, 225300, Jiangsu Province, PR China
| | - Jiangping Wang
- Department of Urology, Taizhou People's Hospital, Taizhou, 225300, Jiangsu Province, PR China.
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Umeda M, Aki SS, Takahashi N. Gap 2 phase: making the fundamental decision to divide or not. CURRENT OPINION IN PLANT BIOLOGY 2019; 51:1-6. [PMID: 30954849 DOI: 10.1016/j.pbi.2019.03.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 03/05/2019] [Indexed: 06/09/2023]
Abstract
The Gap phases of the cell cycle are essential to perceive internal and external signals and control cell division and differentiation. However, our knowledge of molecular mechanisms underlying G2 progression in plants remains quite limited. In this review, we summarize recent findings about core G2-phase regulators, such as B-type cyclin-dependent kinases (CDKs) and R1R2R3-type MYB transcription factors. We highlight developmental and stress signals that regulate expression and accumulation of the G2-phase regulators, and discuss how they fine-tune mitotic CDK activity and control cell proliferation, endoreplication and cell cycle checkpoints. A particular focus is on DNA damage-induced G2 arrest, which is prerequisite for maintenance of genome stability.
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Affiliation(s)
- Masaaki Umeda
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara 630-0192, Japan.
| | - Shiori S Aki
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara 630-0192, Japan
| | - Naoki Takahashi
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara 630-0192, Japan
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24
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Zwinderman MRH, de Weerd S, Dekker FJ. Targeting HDAC Complexes in Asthma and COPD. EPIGENOMES 2019; 3:19. [PMID: 34968229 PMCID: PMC8594684 DOI: 10.3390/epigenomes3030019] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/02/2019] [Accepted: 09/04/2019] [Indexed: 01/08/2023] Open
Abstract
Around three million patients die due to airway inflammatory diseases each year. The most notable of these diseases are asthma and chronic obstructive pulmonary disease (COPD). Therefore, new therapies are urgently needed. Promising targets are histone deacetylases (HDACs), since they regulate posttranslational protein acetylation. Over a thousand proteins are reversibly acetylated, and acetylation critically influences aberrant intracellular signaling pathways in asthma and COPD. The diverse set of selective and non-selective HDAC inhibitors used in pre-clinical models of airway inflammation show promising results, but several challenges still need to be overcome. One such challenge is the design of HDAC inhibitors with unique selectivity profiles, such as selectivity towards specific HDAC complexes. Novel strategies to disrupt HDAC complexes should be developed to validate HDACs further as targets for new anti-inflammatory pulmonary treatments.
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Affiliation(s)
| | | | - Frank J. Dekker
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, 9713 AV Groningen, The Netherlands (M.R.H.Z.) (S.d.W.)
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