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Wu X, Xu H, Xia E, Gao L, Hou Y, Sun L, Zhang H, Cheng Y. Histone modifications in the regulation of erythropoiesis. Ann Med 2025; 57:2490824. [PMID: 40214280 PMCID: PMC11995772 DOI: 10.1080/07853890.2025.2490824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2024] [Revised: 03/13/2025] [Accepted: 04/01/2025] [Indexed: 04/16/2025] Open
Abstract
INTRODUCTION The pathogenesis of anemia and other erythroid dysphasia are mains poorly understood, primarily due to limited knowledge about the differentiation processes and regulatory mechanisms governing erythropoiesis. Erythropoiesis is a highly complex and precise biological process, that can be categorized into three distinct stages: early erythropoiesis, terminal erythroid differentiation, and reticulocyte maturation, and this complex process is tightly controlled by multiple regulatory factors. Emerging evidence highlights the crucial role of epigenetic modifications, particularly histone modifications, in regulating erythropoiesis. Methylation and acetylation are two common modification forms that affect genome accessibility by altering the state of chromatin, thereby regulating gene expression during erythropoiesis. DISCUSSION This review systematically examines the roles of histone methylation and acetylation, along with their respective regulatory enzymes, in regulating the development and differentiation of hematopoietic stem/progenitor cells (HSPCs) and erythroid progenitors. Furthermore, we discuss the involvement of these histone modifications in erythroid-specific developmental processes, including hemoglobin switching, chromatin condensation, and enucleation.Conclusions This review summarizes the current understanding of the role of histone modifications in erythropoiesis based on existing research, as a foundation for further research the mechanisms of epigenetic regulatory in erythropoiesis.
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Affiliation(s)
- Xiuyun Wu
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Hongdi Xu
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Erxi Xia
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Linru Gao
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Yan Hou
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Lei Sun
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Hengchao Zhang
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Ying Cheng
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
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2
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Dreyer J, Ricci G, van den Berg J, Bhardwaj V, Funk J, Armstrong C, van Batenburg V, Sine C, VanInsberghe MA, Tjeerdsma RB, Marsman R, Mandemaker IK, di Sanzo S, Costantini J, Manzo SG, Biran A, Burny C, van Vugt MATM, Völker-Albert M, Groth A, Spencer SL, van Oudenaarden A, Mattiroli F. Acute multi-level response to defective de novo chromatin assembly in S-phase. Mol Cell 2024; 84:4711-4728.e10. [PMID: 39536749 DOI: 10.1016/j.molcel.2024.10.023] [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: 04/09/2024] [Revised: 08/14/2024] [Accepted: 10/16/2024] [Indexed: 11/16/2024]
Abstract
Long-term perturbation of de novo chromatin assembly during DNA replication has profound effects on epigenome maintenance and cell fate. The early mechanistic origin of these defects is unknown. Here, we combine acute degradation of chromatin assembly factor 1 (CAF-1), a key player in de novo chromatin assembly, with single-cell genomics, quantitative proteomics, and live microscopy to uncover these initiating mechanisms in human cells. CAF-1 loss immediately slows down DNA replication speed and renders nascent DNA hyper-accessible. A rapid cellular response, distinct from canonical DNA damage signaling, is triggered and lowers histone mRNAs. In turn, histone variants' usage and their modifications are altered, limiting transcriptional fidelity and delaying chromatin maturation within a single S-phase. This multi-level response induces a p53-dependent cell-cycle arrest after mitosis. Our work reveals the immediate consequences of defective de novo chromatin assembly during DNA replication, indicating how at later times the epigenome and cell fate can be altered.
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Affiliation(s)
- Jan Dreyer
- Hubrecht Institute, KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Giulia Ricci
- Hubrecht Institute, KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Jeroen van den Berg
- Hubrecht Institute, KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Vivek Bhardwaj
- Hubrecht Institute, KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Janina Funk
- Hubrecht Institute, KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Claire Armstrong
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA; BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Vincent van Batenburg
- Hubrecht Institute, KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Chance Sine
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA; BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Michael A VanInsberghe
- Hubrecht Institute, KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Rinskje B Tjeerdsma
- Department of Medical Oncology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Richard Marsman
- Hubrecht Institute, KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Imke K Mandemaker
- Hubrecht Institute, KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Simone di Sanzo
- MOLEQLAR Analytics GmbH, Rosenheimer Street 141 h, 81671 Munich, Germany
| | - Juliette Costantini
- Hubrecht Institute, KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Stefano G Manzo
- Oncode Institute, Utrecht, the Netherlands; Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - Alva Biran
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen 2200, Denmark
| | - Claire Burny
- MOLEQLAR Analytics GmbH, Rosenheimer Street 141 h, 81671 Munich, Germany
| | - Marcel A T M van Vugt
- Department of Medical Oncology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | | | - Anja Groth
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen 2200, Denmark; Biotech Research & Innovation Centre, University of Copenhagen, Copenhagen 2200, Denmark; Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen 2200, Denmark
| | - Sabrina L Spencer
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA; BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Alexander van Oudenaarden
- Hubrecht Institute, KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Francesca Mattiroli
- Hubrecht Institute, KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.
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3
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Conneely LJ, Hurgobin B, Ng S, Tamiru-Oli M, Lewsey MG. Characterization of the Cannabis sativa glandular trichome epigenome. BMC PLANT BIOLOGY 2024; 24:1075. [PMID: 39538149 PMCID: PMC11562870 DOI: 10.1186/s12870-024-05787-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Accepted: 11/05/2024] [Indexed: 11/16/2024]
Abstract
BACKGROUND The relationship between epigenomics and plant specialised metabolism remains largely unexplored despite the fundamental importance of epigenomics in gene regulation and, potentially, yield of products of plant specialised metabolic pathways. The glandular trichomes of Cannabis sativa are an emerging model system that produce large quantities of cannabinoid and terpenoid specialised metabolites with known medicinal and commercial value. To address this lack of epigenomic data, we mapped H3K4 trimethylation, H3K56 acetylation, H3K27 trimethylation post-translational modifications and the histone variant H2A.Z, using chromatin immunoprecipitation, in C. sativa glandular trichomes, leaf, and stem tissues. Corresponding transcriptomic (RNA-seq) datasets were integrated, and tissue-specific analyses conducted to relate chromatin states to glandular trichome specific gene expression. RESULTS The promoters of cannabinoid and terpenoid biosynthetic genes, specialised metabolite transporter genes, defence related genes, and starch and sucrose metabolism were enriched specifically in trichomes for histone marks H3K4me3 and H3K56ac, consistent with active transcription. We identified putative trichome-specific enhancer elements by identifying intergenic regions of H3K56ac enrichment, a histone mark that maintains enhancer accessibility, then associated these to putative target genes using the tissue specific gene transcriptomic data. Bi-valent chromatin loci specific to glandular trichomes, marked with H3K4 trimethylation and H3K27 trimethylation, were associated with genes of MAPK signalling pathways and plant specialised metabolism pathways, supporting recent hypotheses that implicate bi-valent chromatin in plant defence. The histone variant H2A.Z was largely found in intergenic regions and enriched in chromatin that contained genes involved in DNA homeostasis. CONCLUSION We report the first genome-wide histone post-translational modification maps for C. sativa glandular trichomes, and more broadly for glandular trichomes in plants. Our findings have implications in plant adaptation and stress responses and provide a basis for enhancer-mediated, targeted, gene transformation studies in plant glandular trichomes.
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Affiliation(s)
- Lee J Conneely
- La Trobe Institute for Sustainable Agriculture and Food, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia
- Australian Research Council Centre of Excellence in Plants for Space, La Trobe University, Bundoora, VIC, Australia
| | - Bhavna Hurgobin
- La Trobe Institute for Sustainable Agriculture and Food, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia
| | - Sophia Ng
- La Trobe Institute for Sustainable Agriculture and Food, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia
| | - Muluneh Tamiru-Oli
- La Trobe Institute for Sustainable Agriculture and Food, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia
| | - Mathew G Lewsey
- La Trobe Institute for Sustainable Agriculture and Food, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia.
- Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia.
- Australian Research Council Centre of Excellence in Plants for Space, La Trobe University, Bundoora, VIC, Australia.
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4
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Martinez M, Kiselar J, Wang B, Sadalge D, Zawadzke L, Taherbhoy A, Musser D, Davenport Y, Setser J, Chance MR, Bellon S. Mass Spectrometry-Based Protein Footprinting Defines the Binding Pocket of Crotonylated H3K14 in the PHD1 Domain of BAF45D within the BAF Chromatin Remodeling Complex. ACS BIO & MED CHEM AU 2024; 4:204-213. [PMID: 39184054 PMCID: PMC11342342 DOI: 10.1021/acsbiomedchemau.4c00009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 05/14/2024] [Accepted: 05/21/2024] [Indexed: 08/27/2024]
Abstract
The BRG-/BRM-associated factor (BAF) chromatin remodeling complex is a central actor in transcription. One mechanism by which BAF affects gene expression is via its various histone mark readers, including double plant homeodomains (DPF), located in the BAF45D subunit. DPF domains recognize lysine acetyl and acylations, including crotonylation, localized at promoters and enhancers. Despite a significant degree of conservation between DPF domains, attempts to crystallize BAF45D with a crotonylated histone 3 peptide (H3K14Cr) were unsuccessful. In addition, recent cryoEM and modeled structures failed to define the Req domain of BAF45D, which is responsible for reading lysine modifications. Thus, the precise mechanism of crotonyl group recognition and binding by BAF45D within the BAF complex remains unclear. We turned to protein footprinting mass spectrometry to map the binding interface between H3K14Cr and BAF45D. This technique is able to demarcate protein-binding interfaces by modifying surface-accessible residues and is not limited by protein size or composition. Experiments performed in the isolated DPF domain of BAF45D (BAF45DDPF)-delineated H3K14Cr peptide binding across the PHD1 and PHD2 pockets. We observed markedly similar effects on the BAF45D subunit when assessing H3K14Cr binding in the purified full BAF complex. The ATPase motor, BRM, also displayed H3K14Cr-protected peptides in two separate domains that were subsequently evaluated in direct binding assays. These data confirm the BAF45D-crotonylamide interaction within its obligate complex and are the first to demonstrate H3K14Cr direct binding to BRM.
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Affiliation(s)
- Marissa
R. Martinez
- Foghorn
Therapeutics, 500 Technology Square, Suite 700, Cambridge, Massachusetts 02139, United States
| | - Janna Kiselar
- NeoProteomics, Moreland Hills, Ohio 44022, United States
- Center
for Proteomics and Bioinformatics, Department of Nutrition, Case Western Reserve University, 10009 Euclid Ave, Cleveland, Ohio 44106, United States
| | - Benlian Wang
- Center
for Proteomics and Bioinformatics, Department of Nutrition, Case Western Reserve University, 10009 Euclid Ave, Cleveland, Ohio 44106, United States
| | - Dipti Sadalge
- Foghorn
Therapeutics, 500 Technology Square, Suite 700, Cambridge, Massachusetts 02139, United States
| | - Laura Zawadzke
- Foghorn
Therapeutics, 500 Technology Square, Suite 700, Cambridge, Massachusetts 02139, United States
| | - Asad Taherbhoy
- Foghorn
Therapeutics, 500 Technology Square, Suite 700, Cambridge, Massachusetts 02139, United States
| | - Derek Musser
- Foghorn
Therapeutics, 500 Technology Square, Suite 700, Cambridge, Massachusetts 02139, United States
| | - Yunji Davenport
- Foghorn
Therapeutics, 500 Technology Square, Suite 700, Cambridge, Massachusetts 02139, United States
| | - Jeremy Setser
- Foghorn
Therapeutics, 500 Technology Square, Suite 700, Cambridge, Massachusetts 02139, United States
| | - Mark R. Chance
- NeoProteomics, Moreland Hills, Ohio 44022, United States
- Center
for Proteomics and Bioinformatics, Department of Nutrition, Case Western Reserve University, 10009 Euclid Ave, Cleveland, Ohio 44106, United States
| | - Steve Bellon
- Foghorn
Therapeutics, 500 Technology Square, Suite 700, Cambridge, Massachusetts 02139, United States
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5
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Laosuntisuk K, Vennapusa A, Somayanda IM, Leman AR, Jagadish SK, Doherty CJ. A normalization method that controls for total RNA abundance affects the identification of differentially expressed genes, revealing bias toward morning-expressed responses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1241-1257. [PMID: 38289828 DOI: 10.1111/tpj.16654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 02/01/2024]
Abstract
RNA-Sequencing is widely used to investigate changes in gene expression at the transcription level in plants. Most plant RNA-Seq analysis pipelines base the normalization approaches on the assumption that total transcript levels do not vary between samples. However, this assumption has not been demonstrated. In fact, many common experimental treatments and genetic alterations affect transcription efficiency or RNA stability, resulting in unequal transcript abundance. The addition of synthetic RNA controls is a simple correction that controls for variation in total mRNA levels. However, adding spike-ins appropriately is challenging with complex plant tissue, and carefully considering how they are added is essential to their successful use. We demonstrate that adding external RNA spike-ins as a normalization control produces differences in RNA-Seq analysis compared to traditional normalization methods, even between two times of day in untreated plants. We illustrate the use of RNA spike-ins with 3' RNA-Seq and present a normalization pipeline that accounts for differences in total transcriptional levels. We evaluate the effect of normalization methods on identifying differentially expressed genes in the context of identifying the effect of the time of day on gene expression and response to chilling stress in sorghum.
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Affiliation(s)
- Kanjana Laosuntisuk
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, USA
| | - Amaranatha Vennapusa
- Department of Agriculture and Natural Resources, Delaware State University, Dover, Delaware, USA
| | - Impa M Somayanda
- Department of Plant and Soil Science, Texas Tech University, Lubbock, Texas, 79410, USA
| | - Adam R Leman
- Department of Science and Technology, The Good Food Institute, Washington, District of Columbia, 20090, USA
| | - Sv Krishna Jagadish
- Department of Plant and Soil Science, Texas Tech University, Lubbock, Texas, 79410, USA
- Department of Agronomy, Kansas State University, Manhattan, Kansas, 66506, USA
| | - Colleen J Doherty
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, USA
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6
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Zhao Z, Cai Z, Zhang S, Yin X, Jiang T, Shen C, Yin Y, Sun H, Chen Z, Han J, Zhang B. Activation of the FOXM1/ASF1B/PRDX3 axis confers hyperproliferative and antioxidative stress reactivity to gastric cancer. Cancer Lett 2024; 589:216796. [PMID: 38537775 DOI: 10.1016/j.canlet.2024.216796] [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: 10/03/2023] [Revised: 02/02/2024] [Accepted: 03/04/2024] [Indexed: 04/07/2024]
Abstract
Nucleosome assembly during DNA replication is dependent on histone chaperones. Recent studies suggest that dysregulated histone chaperones contribute to cancer progression, including gastric cancer (GC). Further studies are required to explore the prognostic and therapeutic implications of histone chaperones and their mechanisms of action in GC progression. Here we identified histone chaperone ASF1B as a potential biomarker for GC proliferation and prognosis. ASF1B was significantly upregulated in GC, which was associated with poor prognosis. In vitro and in vivo experiments demonstrated that the inhibition of ASF1B suppressed the malignant characteristics of GC, while overexpression of ASF1B had the opposite effect. Mechanistically, transcription factor FOXM1 directly bound to the ASF1B-promoter region, thereby regulating its transcription. Treatment with thiostrepton, a FOXM1 inhibitor, not only suppressed ASF1B expression, but also inhibited GC progression. Furthermore, ASF1B regulated the mitochondrial protein peroxiredoxin 3 (PRDX3) transcription in a FOXM1-dependent manner. The crucial role of ASF1B-regulated PRDX3 in GC cell proliferation and oxidative stress balance was also elucidated. In summary, our study suggests that the FOXM1-ASF1B-PRDX3 axis is a potential therapeutic target for treating GC.
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Affiliation(s)
- Zhou Zhao
- Gastric Cancer Center, Department of General Surgery, Research Laboratory of Tumor Epigenetics and Genomics, West China Hospital, Sichuan University, Chengdu, China; Gastrointestinal Cancer Center, Chongqing University Cancer Hospital, Chongqing, China
| | - Zhaolun Cai
- Gastric Cancer Center, Department of General Surgery, Research Laboratory of Tumor Epigenetics and Genomics, West China Hospital, Sichuan University, Chengdu, China
| | - Su Zhang
- State Key Laboratory of Biotherapy and Cancer Center, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaonan Yin
- Gastric Cancer Center, Department of General Surgery, Research Laboratory of Tumor Epigenetics and Genomics, West China Hospital, Sichuan University, Chengdu, China
| | - Tianxiang Jiang
- Gastric Cancer Center, Department of General Surgery, Research Laboratory of Tumor Epigenetics and Genomics, West China Hospital, Sichuan University, Chengdu, China
| | - Chaoyong Shen
- Gastric Cancer Center, Department of General Surgery, Research Laboratory of Tumor Epigenetics and Genomics, West China Hospital, Sichuan University, Chengdu, China
| | - Yuan Yin
- Gastric Cancer Center, Department of General Surgery, Research Laboratory of Tumor Epigenetics and Genomics, West China Hospital, Sichuan University, Chengdu, China
| | - Hao Sun
- Gastrointestinal Cancer Center, Chongqing University Cancer Hospital, Chongqing, China
| | - Zhixin Chen
- Gastric Cancer Center, Department of General Surgery, Research Laboratory of Tumor Epigenetics and Genomics, West China Hospital, Sichuan University, Chengdu, China
| | - Junhong Han
- State Key Laboratory of Biotherapy and Cancer Center, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China.
| | - Bo Zhang
- Gastric Cancer Center, Department of General Surgery, Research Laboratory of Tumor Epigenetics and Genomics, West China Hospital, Sichuan University, Chengdu, China.
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7
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Chen B, MacAlpine HK, Hartemink AJ, MacAlpine DM. Spatiotemporal kinetics of CAF-1-dependent chromatin maturation ensures transcription fidelity during S-phase. Genome Res 2023; 33:2108-2118. [PMID: 38081658 PMCID: PMC10760526 DOI: 10.1101/gr.278273.123] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 11/13/2023] [Indexed: 12/26/2023]
Abstract
Proper maintenance of epigenetic information after replication is dependent on the rapid assembly and maturation of chromatin. Chromatin Assembly Complex 1 (CAF-1) is a conserved histone chaperone that deposits (H3-H4)2 tetramers as part of the replication-dependent chromatin assembly process. Loss of CAF-1 leads to a delay in chromatin maturation, albeit with minimal impact on steady-state chromatin structure. However, the mechanisms by which CAF-1 mediates the deposition of (H3-H4)2 tetramers and the phenotypic consequences of CAF-1-associated assembly defects are not well understood. We used nascent chromatin occupancy profiling to track the spatiotemporal kinetics of chromatin maturation in both wild-type (WT) and CAF-1 mutant yeast cells. Our results show that loss of CAF-1 leads to a heterogeneous rate of nucleosome assembly, with some nucleosomes maturing at near WT kinetics and others showing significantly slower maturation kinetics. The slow-to-mature nucleosomes are enriched in intergenic and poorly transcribed regions, suggesting that transcription-dependent assembly mechanisms can reset the slow-to-mature nucleosomes following replication. Nucleosomes with slow maturation kinetics are also associated with poly(dA:dT) sequences, which implies that CAF-1 deposits histones in a manner that counteracts resistance from the inflexible DNA sequence, promoting the formation of histone octamers as well as ordered nucleosome arrays. In addition, we show that the delay in chromatin maturation is accompanied by a transient and S-phase-specific loss of gene silencing and transcriptional regulation, revealing that the DNA replication program can directly shape the chromatin landscape and modulate gene expression through the process of chromatin maturation.
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Affiliation(s)
- Boning Chen
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Heather K MacAlpine
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | | | - David M MacAlpine
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA;
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8
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Singh M, Spendlove SJ, Wei A, Bondhus LM, Nava AA, de L Vitorino FN, Amano S, Lee J, Echeverria G, Gomez D, Garcia BA, Arboleda VA. KAT6A mutations in Arboleda-Tham syndrome drive epigenetic regulation of posterior HOXC cluster. Hum Genet 2023; 142:1705-1720. [PMID: 37861717 PMCID: PMC10676314 DOI: 10.1007/s00439-023-02608-3] [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: 08/04/2023] [Accepted: 09/28/2023] [Indexed: 10/21/2023]
Abstract
Arboleda-Tham Syndrome (ARTHS) is a rare genetic disorder caused by heterozygous, de novo mutations in Lysine(K) acetyltransferase 6A (KAT6A). ARTHS is clinically heterogeneous and characterized by several common features, including intellectual disability, developmental and speech delay, and hypotonia, and affects multiple organ systems. KAT6A is the enzymatic core of a histone-acetylation protein complex; however, the direct histone targets and gene regulatory effects remain unknown. In this study, we use ARTHS patient (n = 8) and control (n = 14) dermal fibroblasts and perform comprehensive profiling of the epigenome and transcriptome caused by KAT6A mutations. We identified differential chromatin accessibility within the promoter or gene body of 23% (14/60) of genes that were differentially expressed between ARTHS and controls. Within fibroblasts, we show a distinct set of genes from the posterior HOXC gene cluster (HOXC10, HOXC11, HOXC-AS3, HOXC-AS2, and HOTAIR) that are overexpressed in ARTHS and are transcription factors critical for early development body segment patterning. The genomic loci harboring HOXC genes are epigenetically regulated with increased chromatin accessibility, high levels of H3K23ac, and increased gene-body DNA methylation compared to controls, all of which are consistent with transcriptomic overexpression. Finally, we used unbiased proteomic mass spectrometry and identified two new histone post-translational modifications (PTMs) that are disrupted in ARTHS: H2A and H3K56 acetylation. Our multi-omics assays have identified novel histone and gene regulatory roles of KAT6A in a large group of ARTHS patients harboring diverse pathogenic mutations. This work provides insight into the role of KAT6A on the epigenomic regulation in somatic cell types.
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Affiliation(s)
- Meghna Singh
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Sarah J Spendlove
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Interdepartmental BioInformatics Program, UCLA, Los Angeles, CA, USA
| | - Angela Wei
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Interdepartmental BioInformatics Program, UCLA, Los Angeles, CA, USA
| | - Leroy M Bondhus
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Aileen A Nava
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Francisca N de L Vitorino
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO, USA
| | - Seth Amano
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Jacob Lee
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Gesenia Echeverria
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Dianne Gomez
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO, USA
| | - Valerie A Arboleda
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA, 90095, USA.
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
- Interdepartmental BioInformatics Program, UCLA, Los Angeles, CA, USA.
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9
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Khan P, Singha P, Nag Chaudhuri R. RNA Polymerase II Dependent Crosstalk between H4K16 Deacetylation and H3K56 Acetylation Promotes Transcription of Constitutively Expressed Genes. Mol Cell Biol 2023; 43:596-610. [PMID: 37937370 PMCID: PMC10761024 DOI: 10.1080/10985549.2023.2270912] [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: 05/25/2023] [Accepted: 10/05/2023] [Indexed: 11/09/2023] Open
Abstract
Nucleosome dynamics in the coding region of a transcriptionally active locus is critical for understanding how RNA polymerase II progresses through the gene body. Histone acetylation and deacetylation critically influence nucleosome accessibility during DNA metabolic processes like transcription. Effect of such histone modifications is context and residue dependent. Rather than effect of individual histone residues, the network of modifications of several histone residues in combination generates a chromatin landscape that is conducive for transcription. Here we show that in Saccharomyces cerevisiae, crosstalk between deacetylation of the H4 N-terminal tail residue H4K16 and acetylation of the H3 core domain residue H3K56, promotes RNA polymerase II progression through the gene body. Results indicate that deacetylation of H4K16 precedes and in turn induces H3K56 acetylation. Effectively, recruitment of Rtt109, the HAT responsible for H3K56 acetylation is essentially dependent on H4K16 deacetylation. In Hos2 deletion strains, where H4K16 deacetylation is abolished, both H3K56 acetylation and RNA polymerase II recruitment gets significantly impaired. Notably, H4K16 deacetylation and H3K56 acetylation are found to be essentially dependent on active transcription. In summary, H4K16 deacetylation promotes H3K56 acetylation and the two modifications together work towards successful functioning of RNA polymerase II during active transcription.
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Affiliation(s)
- Preeti Khan
- Department of Biotechnology, St Xavier’s College, Kolkata, India
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10
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Bryll AR, Peterson CL. The circular logic of mRNA homeostasis. Transcription 2023; 14:18-26. [PMID: 36843061 PMCID: PMC10353332 DOI: 10.1080/21541264.2023.2183684] [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: 12/21/2022] [Revised: 02/13/2023] [Accepted: 02/17/2023] [Indexed: 02/28/2023] Open
Abstract
Eukaryotic cells rely upon dynamic, multifaceted regulation at each step of RNA biogenesis to maintain mRNA pools and ensure normal protein synthesis. Studies in budding yeast indicate a buffering phenomenon that preserves global mRNA levels through the reciprocal balancing of RNA synthesis rates and mRNA decay. In short, changes in transcription impact the efficiency of mRNA degradation and defects in either nuclear or cytoplasmic mRNA degradation are somehow sensed and relayed to control a compensatory change in mRNA transcription rates. Here, we review current views on molecular mechanisms that might explain this apparent bidirectional sensing process that ensures homeostasis of the stable mRNA pool.
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Affiliation(s)
- Alysia R. Bryll
- Program of Molecular Medicine, University of Massachusetts Chan Medical School, Worcester
- Medical Scientist Training Program, University of Massachusetts Chan Medical School, Worcester
| | - Craig L. Peterson
- Program of Molecular Medicine, University of Massachusetts Chan Medical School, Worcester
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11
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Bennett SA, Cobos SN, Son E, Segal R, Mathew S, Yousuf H, Torrente MP. Impaired RNA Binding Does Not Prevent Histone Modification Changes in a FUS ALS/FTD Yeast Model. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000895. [PMID: 37746061 PMCID: PMC10517347 DOI: 10.17912/micropub.biology.000895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/04/2023] [Accepted: 08/31/2023] [Indexed: 09/26/2023]
Abstract
Mutations in the RNA-binding protein FUS are linked to amyotrophic lateral sclerosis and frontotemporal dementia (ALS/FTD). FUS mutants mislocalize and aggregate in dying neurons. We previously established that FUS proteinopathy is linked to changes in the histone modification landscape in a yeast ALS/FTD model. Here, we examine whether FUS' RNA binding is necessary for this connection. We find that overexpression of a FUS mutant unable to bind RNA is still associated with reduced levels of H3S10ph, H3K14ac and H3K56ac. Hence, FUS' ability to bind RNA is not required in the mechanism connecting FUS proteinopathy to altered histone post-translational modifications.
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Affiliation(s)
- Seth A. Bennett
- PhD. Program in Biochemistry, City University of New York - The Graduate Center, New York, NY, USA 10016
| | - Samantha N. Cobos
- PhD. Program in Chemistry, City University of New York - The Graduate Center, New York, NY, USA 10016
| | - Elizaveta Son
- Department of Chemistry and Biochemistry, Brooklyn College, Brooklyn, NY, USA 11210
| | - Rianna Segal
- Department of Chemistry and Biochemistry, Brooklyn College, Brooklyn, NY, USA 11210
| | - Shana Mathew
- Department of Chemistry and Biochemistry, Brooklyn College, Brooklyn, NY, USA 11210
| | - Huda Yousuf
- Department of Chemistry and Biochemistry, Brooklyn College, Brooklyn, NY, USA 11210
| | - Mariana P. Torrente
- Department of Chemistry and Biochemistry, Brooklyn College, Brooklyn, NY, USA 11210
- PhD. Programs in Chemistry, Biochemistry, and Biology, City University of New York - The Graduate Center, New York, NY, USA 10016
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12
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Singh M, Spendlove S, Wei A, Bondhus L, Nava A, de L. Vitorino FN, Amano S, Lee J, Echeverria G, Gomez D, Garcia BA, Arboleda VA. KAT6A mutations in Arboleda-Tham syndrome drive epigenetic regulation of posterior HOXC cluster. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.03.550595. [PMID: 37577627 PMCID: PMC10418288 DOI: 10.1101/2023.08.03.550595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Arboleda-Tham Syndrome (ARTHS) is a rare genetic disorder caused by heterozygous, de novo truncating mutations in Lysine(K) acetyltransferase 6A (KAT6A). ARTHS is clinically heterogeneous and characterized by several common features including intellectual disability, developmental and speech delay, hypotonia and affects multiple organ systems. KAT6A is highly expressed in early development and plays a key role in cell-type specific differentiation. KAT6A is the enzymatic core of a histone-acetylation protein complex, however the direct histone targets and gene regulatory effects remain unknown. In this study, we use ARTHS patient (n=8) and control (n=14) dermal fibroblasts and perform comprehensive profiling of the epigenome and transcriptome caused by KAT6A mutations. We identified differential chromatin accessibility within the promoter or gene body of 23%(14/60) of genes that were differentially expressed between ARTHS and controls. Within fibroblasts, we show a distinct set of genes from the posterior HOXC gene cluster (HOXC10, HOXC11, HOXC-AS3, HOXC-AS2, HOTAIR) that are overexpressed in ARTHS and are transcription factors critical for early development body segment patterning. The genomic loci harboring HOXC genes are epigenetically regulated with increased chromatin accessibility, high levels of H3K23ac, and increased gene-body DNA methylation compared to controls, all of which are consistent with transcriptomic overexpression. Finally, we used unbiased proteomic mass spectrometry and identified two new histone post-translational modifications (PTMs) that are disrupted in ARTHS: H2A and H3K56 acetylation. Our multi-omics assays have identified novel histone and gene regulatory roles of KAT6A in a large group of ARTHS patients harboring diverse pathogenic mutations. This work provides insight into the role of KAT6A on the epigenomic regulation in somatic cell types.
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Affiliation(s)
- Meghna Singh
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Sarah Spendlove
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Interdepartmental BioInformatics Program, UCLA
| | - Angela Wei
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Interdepartmental BioInformatics Program, UCLA
| | - Leroy Bondhus
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Aileen Nava
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | | | - Seth Amano
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Jacob Lee
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Gesenia Echeverria
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Dianne Gomez
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Benjamin A. Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis
| | - Valerie A. Arboleda
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Interdepartmental BioInformatics Program, UCLA
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13
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Barrientos-Moreno M, Maya-Miles D, Murillo-Pineda M, Fontalva S, Pérez-Alegre M, Andujar E, Prado F. Transcription and FACT facilitate the restoration of replication-coupled chromatin assembly defects. Sci Rep 2023; 13:11397. [PMID: 37452085 PMCID: PMC10349138 DOI: 10.1038/s41598-023-38280-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 07/06/2023] [Indexed: 07/18/2023] Open
Abstract
Genome duplication occurs through the coordinated action of DNA replication and nucleosome assembly at replication forks. Defective nucleosome assembly causes DNA lesions by fork breakage that need to be repaired. In addition, it causes a loss of chromatin integrity. These chromatin alterations can be restored, even though the mechanisms are unknown. Here, we show that the process of chromatin restoration can deal with highly severe chromatin defects induced by the absence of the chaperones CAF1 and Rtt106 or a strong reduction in the pool of available histones, and that this process can be followed by analyzing the topoisomer distribution of the 2µ plasmid. Using this assay, we demonstrate that chromatin restoration is slow and independent of checkpoint activation, whereas it requires the action of transcription and the FACT complex. Therefore, cells are able to "repair" not only DNA lesions but also chromatin alterations associated with defective nucleosome assembly.
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Affiliation(s)
- Marta Barrientos-Moreno
- Department of Genome Biology, Andalusian Molecular Biology and Regenerative Medicine (CABIMER), CSIC‑University of Seville‑University Pablo de Olavide, Seville, Spain
| | - Douglas Maya-Miles
- Department of Genome Biology, Andalusian Molecular Biology and Regenerative Medicine (CABIMER), CSIC‑University of Seville‑University Pablo de Olavide, Seville, Spain
| | - Marina Murillo-Pineda
- Department of Genome Biology, Andalusian Molecular Biology and Regenerative Medicine (CABIMER), CSIC‑University of Seville‑University Pablo de Olavide, Seville, Spain
| | - Sara Fontalva
- Department of Genome Biology, Andalusian Molecular Biology and Regenerative Medicine (CABIMER), CSIC‑University of Seville‑University Pablo de Olavide, Seville, Spain
| | - Mónica Pérez-Alegre
- Genomic Unit, Andalusian Molecular Biology and Regenerative Medicine Center (CABIMER), CSIC‑University of Seville‑University Pablo de Olavide, Seville, Spain
| | - Eloísa Andujar
- Genomic Unit, Andalusian Molecular Biology and Regenerative Medicine Center (CABIMER), CSIC‑University of Seville‑University Pablo de Olavide, Seville, Spain
| | - Félix Prado
- Department of Genome Biology, Andalusian Molecular Biology and Regenerative Medicine (CABIMER), CSIC‑University of Seville‑University Pablo de Olavide, Seville, Spain.
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14
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Kujirai T, Ehara H, Sekine SI, Kurumizaka H. Structural Transition of the Nucleosome during Transcription Elongation. Cells 2023; 12:1388. [PMID: 37408222 DOI: 10.3390/cells12101388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 07/07/2023] Open
Abstract
In eukaryotes, genomic DNA is tightly wrapped in chromatin. The nucleosome is a basic unit of chromatin, but acts as a barrier to transcription. To overcome this impediment, the RNA polymerase II elongation complex disassembles the nucleosome during transcription elongation. After the RNA polymerase II passage, the nucleosome is rebuilt by transcription-coupled nucleosome reassembly. Nucleosome disassembly-reassembly processes play a central role in preserving epigenetic information, thus ensuring transcriptional fidelity. The histone chaperone FACT performs key functions in nucleosome disassembly, maintenance, and reassembly during transcription in chromatin. Recent structural studies of transcribing RNA polymerase II complexed with nucleosomes have provided structural insights into transcription elongation on chromatin. Here, we review the structural transitions of the nucleosome during transcription.
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Affiliation(s)
- Tomoya Kujirai
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
- Laboratory for Transcription Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Haruhiko Ehara
- Laboratory for Transcription Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Shun-Ichi Sekine
- Laboratory for Transcription Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
- Laboratory for Transcription Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
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15
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González L, Kolbin D, Trahan C, Jeronimo C, Robert F, Oeffinger M, Bloom K, Michnick SW. Adaptive partitioning of a gene locus to the nuclear envelope in Saccharomyces cerevisiae is driven by polymer-polymer phase separation. Nat Commun 2023; 14:1135. [PMID: 36854718 PMCID: PMC9975218 DOI: 10.1038/s41467-023-36391-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 01/30/2023] [Indexed: 03/03/2023] Open
Abstract
Partitioning of active gene loci to the nuclear envelope (NE) is a mechanism by which organisms increase the speed of adaptation and metabolic robustness to fluctuating resources in the environment. In the yeast Saccharomyces cerevisiae, adaptation to nutrient depletion or other stresses, manifests as relocalization of active gene loci from nucleoplasm to the NE, resulting in more efficient transport and translation of mRNA. The mechanism by which this partitioning occurs remains a mystery. Here, we demonstrate that the yeast inositol depletion-responsive gene locus INO1 partitions to the nuclear envelope, driven by local histone acetylation-induced polymer-polymer phase separation from the nucleoplasmic phase. This demixing is consistent with recent evidence for chromatin phase separation by acetylation-mediated dissolution of multivalent histone association and fits a physical model where increased bending stiffness of acetylated chromatin polymer causes its phase separation from de-acetylated chromatin. Increased chromatin spring stiffness could explain nucleation of transcriptional machinery at active gene loci.
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Affiliation(s)
- Lidice González
- Département de Biochimie, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, QC, H3C 3J7, Canada
| | - Daniel Kolbin
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Christian Trahan
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
| | - Célia Jeronimo
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
| | - François Robert
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
- Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC, H3A 1A3, Canada
- Département de Médecine, Faculté de Médecine, Université de Montréal, 2900 Boul. Édouard-Montpetit, Montréal, QC, H3T 1J4, Canada
| | - Marlene Oeffinger
- Département de Biochimie, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, QC, H3C 3J7, Canada
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
- Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC, H3A 1A3, Canada
| | - Kerry Bloom
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Stephen W Michnick
- Département de Biochimie, Université de Montréal, C.P. 6128, Succursale centre-ville, Montréal, QC, H3C 3J7, Canada.
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16
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Gospodinov A, Dzhokova S, Petrova M, Ugrinova I. Chromatin regulators in DNA replication and genome stability maintenance during S-phase. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 135:243-280. [PMID: 37061334 DOI: 10.1016/bs.apcsb.2023.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
The duplication of genetic information is central to life. The replication of genetic information is strictly controlled to ensure that each piece of genomic DNA is copied only once during a cell cycle. Factors that slow or stop replication forks cause replication stress. Replication stress is a major source of genome instability in cancer cells. Multiple control mechanisms facilitate the unimpeded fork progression, prevent fork collapse and coordinate fork repair. Chromatin alterations, caused by histone post-translational modifications and chromatin remodeling, have critical roles in normal replication and in avoiding replication stress and its consequences. This text reviews the chromatin regulators that ensure DNA replication and the proper response to replication stress. We also briefly touch on exploiting replication stress in therapeutic strategies. As chromatin regulators are frequently mutated in cancer, manipulating their activity could provide many possibilities for personalized treatment.
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Affiliation(s)
- Anastas Gospodinov
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria.
| | - Stefka Dzhokova
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Maria Petrova
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Iva Ugrinova
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria
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17
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Cobos SN, Janani C, Cruz G, Rana N, Son E, Frederic R, Paredes Casado J, Khan M, Bennett SA, Torrente MP. [PRION +] States Are Associated with Specific Histone H3 Post-Translational Modification Changes. Pathogens 2022; 11:pathogens11121436. [PMID: 36558770 PMCID: PMC9786042 DOI: 10.3390/pathogens11121436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 11/30/2022] Open
Abstract
Prions are proteins able to take on alternative conformations and propagate them in a self-templating process. In Saccharomyces cerevisiae, prions enable heritable responses to environmental conditions through bet-hedging mechanisms. Hence, [PRION+] states may serve as an atypical form of epigenetic control, producing heritable phenotypic change via protein folding. However, the connections between prion states and the epigenome remain unknown. Do [PRION+] states link to canonical epigenetic channels, such as histone post-translational modifications? Here, we map out the histone H3 modification landscape in the context of the [SWI+] and [PIN+] prion states. [SWI+] is propagated by Swi1, a subunit of the SWI/SNF chromatin remodeling complex, while [PIN+] is propagated by Rnq1, a protein of unknown function. We find [SWI+] yeast display decreases in the levels of H3K36me2 and H3K56ac compared to [swi-] yeast. In contrast, decreases in H3K4me3, H3K36me2, H3K36me3 and H3K79me3 are connected to the [PIN+] state. Curing of the prion state by treatment with guanidine hydrochloride restored histone PTM to [prion-] state levels. We find histone PTMs in the [PRION+] state do not match those in loss-of-function models. Our findings shed light into the link between prion states and histone modifications, revealing novel insight into prion function in yeast.
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Affiliation(s)
- Samantha N. Cobos
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
- Chemistry Department, Brooklyn College, Brooklyn, NY 11210, USA
| | - Chaim Janani
- Chemistry Department, Brooklyn College, Brooklyn, NY 11210, USA
| | - Gabriel Cruz
- Chemistry Department, Brooklyn College, Brooklyn, NY 11210, USA
| | - Navin Rana
- Chemistry Department, Brooklyn College, Brooklyn, NY 11210, USA
| | - Elizaveta Son
- Chemistry Department, Brooklyn College, Brooklyn, NY 11210, USA
| | - Rania Frederic
- Chemistry Department, Brooklyn College, Brooklyn, NY 11210, USA
| | | | - Maliha Khan
- Biology Department, Brooklyn College, Brooklyn, NY 11210, USA
| | - Seth A. Bennett
- Chemistry Department, Brooklyn College, Brooklyn, NY 11210, USA
- Graduate Program in Biochemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
| | - Mariana P. Torrente
- Chemistry Department, Brooklyn College, Brooklyn, NY 11210, USA
- Ph.D. Programs in Chemistry, Biochemistry, and Biology, The Graduate Center of the City University of New York, New York, NY 10016, USA
- Correspondence:
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18
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Afonso CF, Marques MC, António JPM, Cordeiro C, Gois PMP, Cal PMSD, Bernardes GJL. Cysteine-Assisted Click-Chemistry for Proximity-Driven, Site-Specific Acetylation of Histones. Angew Chem Int Ed Engl 2022; 61:e202208543. [PMID: 36124857 PMCID: PMC9828500 DOI: 10.1002/anie.202208543] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Indexed: 01/12/2023]
Abstract
Post-translational modifications of histones are essential in the regulation of chromatin structure and function. Among these modifications, lysine acetylation is one of the most established. Earlier studies relied on the use of chromatin containing heterogeneous mixtures of histones acetylated at multiple sites. Differentiating the individual contribution of single acetylation events towards chromatin regulation is thus of great relevance. However, it is difficult to access homogeneous samples of histones, with a single acetylation, in sufficient quantities for such studies. By engineering histone H3 with a cysteine in proximity of the lysine of interest, we demonstrate that conjugation with maleimide-DBCO followed by a strain-promoted alkyne-azide cycloaddition reaction results in the acetylation of a single lysine in a controlled, site-specific manner. The chemical precision offered by our click-to-acetylate approach will facilitate access to and the study of acetylated histones.
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Affiliation(s)
- Cláudia F. Afonso
- Instituto de Medicina Molecular João Lobo AntunesFaculdade de MedicinaUniversidade de LisboaAvenida Professor Egas Moniz1649-028LisboaPortugal
| | - Marta C. Marques
- Instituto de Medicina Molecular João Lobo AntunesFaculdade de MedicinaUniversidade de LisboaAvenida Professor Egas Moniz1649-028LisboaPortugal
| | - João P. M. António
- Research Institute for Medicines (iMed.ULisboa)Faculdade de FarmáciaUniversidade de LisboaAv. Prof. Gama Pinto1649-003LisboaPortugal
| | - Carlos Cordeiro
- Laboratório de FT-ICR e Espectrometria de Massa EstruturalFaculdade de CiênciasUniversidade de LisboaCampo Grande1749-016LisboaPortugal
| | - Pedro M. P. Gois
- Research Institute for Medicines (iMed.ULisboa)Faculdade de FarmáciaUniversidade de LisboaAv. Prof. Gama Pinto1649-003LisboaPortugal
| | - Pedro M. S. D. Cal
- Instituto de Medicina Molecular João Lobo AntunesFaculdade de MedicinaUniversidade de LisboaAvenida Professor Egas Moniz1649-028LisboaPortugal
| | - Gonçalo J. L. Bernardes
- Instituto de Medicina Molecular João Lobo AntunesFaculdade de MedicinaUniversidade de LisboaAvenida Professor Egas Moniz1649-028LisboaPortugal,Yusuf Hamied Department of ChemistryUniversity of CambridgeLensfield RoadCB2 1EWCambridgeUK
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19
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Conte M, Eletto D, Pannetta M, Petrone AM, Monti MC, Cassiano C, Giurato G, Rizzo F, Tessarz P, Petrella A, Tosco A, Porta A. Effects of Hst3p inhibition in Candida albicans: a genome-wide H3K56 acetylation analysis. Front Cell Infect Microbiol 2022; 12:1031814. [PMID: 36389164 PMCID: PMC9647175 DOI: 10.3389/fcimb.2022.1031814] [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: 08/30/2022] [Accepted: 10/10/2022] [Indexed: 11/30/2022] Open
Abstract
Candida spp. represent the third most frequent worldwide cause of infection in Intensive Care Units with a mortality rate of almost 40%. The classes of antifungals currently available include azoles, polyenes, echinocandins, pyrimidine derivatives, and allylamines. However, the therapeutical options for the treatment of candidiasis are drastically reduced by the increasing antifungal resistance. The growing need for a more targeted antifungal therapy is limited by the concern of finding molecules that specifically recognize the microbial cell without damaging the host. Epigenetic writers and erasers have emerged as promising targets in different contexts, including the treatment of fungal infections. In C. albicans, Hst3p, a sirtuin that deacetylates H3K56ac, represents an attractive antifungal target as it is essential for the fungus viability and virulence. Although the relevance of such epigenetic regulator is documented for the development of new antifungal therapies, the molecular mechanism behind Hst3p-mediated epigenetic regulation remains unrevealed. Here, we provide the first genome-wide profiling of H3K56ac in C. albicans resulting in H3K56ac enriched regions associated with Candida sp. pathogenicity. Upon Hst3p inhibition, 447 regions gain H3K56ac. Importantly, these genomic areas contain genes encoding for adhesin proteins, degradative enzymes, and white-opaque switching. Moreover, our RNA-seq analysis revealed 1330 upregulated and 1081 downregulated transcripts upon Hst3p inhibition, and among them, we identified 87 genes whose transcriptional increase well correlates with the enrichment of H3K56 acetylation on their promoters, including some well-known regulators of phenotypic switching and virulence. Based on our evidence, Hst3p is an appealing target for the development of new potential antifungal drugs.
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Affiliation(s)
- Marisa Conte
- Department of Pharmacy, University of Salerno, Fisciano, Salerno, Italy
- Ph.D. Program in Drug Discovery and Development, University of Salerno, Fisciano, Salerno, Italy
| | - Daniela Eletto
- Department of Pharmacy, University of Salerno, Fisciano, Salerno, Italy
| | - Martina Pannetta
- Department of Pharmacy, University of Salerno, Fisciano, Salerno, Italy
- Ph.D. Program in Drug Discovery and Development, University of Salerno, Fisciano, Salerno, Italy
| | - Anna M. Petrone
- Ph.D. Program in Drug Discovery and Development, University of Salerno, Fisciano, Salerno, Italy
| | - Maria C. Monti
- Department of Pharmacy, University of Salerno, Fisciano, Salerno, Italy
| | - Chiara Cassiano
- Department of Pharmacy, University of Salerno, Fisciano, Salerno, Italy
- Department of Pharmacy, University of Naples ‘Federico II’, Naples, Italy
| | - Giorgio Giurato
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, Baronissi, Salerno, Italy
| | - Francesca Rizzo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, Baronissi, Salerno, Italy
| | - Peter Tessarz
- Max Planck Research Group “Chromatin and Ageing”, Max Planck Institute for Biology of Ageing, Cologne, Germany
- Cologne Excellence Cluster on Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | | | - Alessandra Tosco
- Department of Pharmacy, University of Salerno, Fisciano, Salerno, Italy
| | - Amalia Porta
- Department of Pharmacy, University of Salerno, Fisciano, Salerno, Italy
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20
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Yin X, Zhou M, Zhang L, Fu Y, Xu M, Wang X, Cui Z, Gao Z, Li M, Dong Y, Feng H, Ma S, Chen C. Histone chaperone ASF1A accelerates chronic myeloid leukemia blast crisis by activating Notch signaling. Cell Death Dis 2022; 13:842. [PMID: 36184659 PMCID: PMC9527247 DOI: 10.1038/s41419-022-05234-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 08/29/2022] [Accepted: 09/05/2022] [Indexed: 11/30/2022]
Abstract
The blast crisis (BC) is the final deadly phase of chronic myeloid leukemia (CML), which remains a major challenge in clinical management. However, the underlying molecular mechanism driving blastic transformation remains unclear. Here, we show that ASF1A, an essential activator, enhanced the transformation to CML-BC by mediating cell differentiation arrest. ASF1A expression was aberrantly increased in bone marrow samples from CML-BC patients compared with newly diagnosed CML-chronic phase (CP) patients. ASF1A inhibited cell differentiation and promoted CML development in vivo. Mechanistically, we identified ASF1A as a coactivator of the Notch transcriptional complex that induces H3K56ac modification in the promoter regions of Notch target genes, and subsequently enhanced RBPJ binding to these promoter regions, thereby enhancing Notch signaling activation to mediate differentiation arrest in CML cells. Thus, our work suggests that targeting ASF1A might represent a promising therapeutic approach and a biomarker to detect disease progression in CML patients.
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Affiliation(s)
- Xiaolin Yin
- grid.27255.370000 0004 1761 1174Department of Hematology, Qilu Hospital, Shandong University, Jinan, Shandong China
| | - Minran Zhou
- grid.27255.370000 0004 1761 1174Department of Hematology, Qilu Hospital, Shandong University, Jinan, Shandong China
| | - Lu Zhang
- grid.27255.370000 0004 1761 1174Department of Hematology, Qilu Hospital, Shandong University, Jinan, Shandong China
| | - Yue Fu
- grid.27255.370000 0004 1761 1174Department of Hematology, Qilu Hospital, Shandong University, Jinan, Shandong China ,grid.27255.370000 0004 1761 1174Department of Physiology & Pathophysiology, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, Shandong China
| | - Man Xu
- grid.27255.370000 0004 1761 1174Department of Hematology, Qilu Hospital, Shandong University, Jinan, Shandong China
| | - Xiaoming Wang
- grid.27255.370000 0004 1761 1174Department of Hematology, Qilu Hospital, Shandong University, Jinan, Shandong China
| | - Zelong Cui
- grid.27255.370000 0004 1761 1174Department of Hematology, Qilu Hospital, Shandong University, Jinan, Shandong China
| | - Zhenxing Gao
- grid.27255.370000 0004 1761 1174Department of Hematology, Qilu Hospital, Shandong University, Jinan, Shandong China
| | - Miao Li
- grid.27255.370000 0004 1761 1174Department of Hematology, Qilu Hospital, Shandong University, Jinan, Shandong China
| | - Yuting Dong
- grid.27255.370000 0004 1761 1174Department of Hematology, Qilu Hospital, Shandong University, Jinan, Shandong China
| | - Huimin Feng
- grid.27255.370000 0004 1761 1174Department of Hematology, Qilu Hospital, Shandong University, Jinan, Shandong China
| | - Sai Ma
- grid.27255.370000 0004 1761 1174Department of Hematology, Qilu Hospital, Shandong University, Jinan, Shandong China
| | - Chunyan Chen
- grid.27255.370000 0004 1761 1174Department of Hematology, Qilu Hospital, Shandong University, Jinan, Shandong China
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21
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López-Jiménez E, González-Aguilera C. Role of Chromatin Replication in Transcriptional Plasticity, Cell Differentiation and Disease. Genes (Basel) 2022; 13:genes13061002. [PMID: 35741764 PMCID: PMC9222293 DOI: 10.3390/genes13061002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 05/27/2022] [Accepted: 05/30/2022] [Indexed: 11/16/2022] Open
Abstract
Chromatin organization is essential to maintain a correct regulation of gene expression and establish cell identity. However, during cell division, the replication of the genetic material produces a global disorganization of chromatin structure. In this paper, we describe the new scientific breakthroughs that have revealed the nature of the post-replicative chromatin and the mechanisms that facilitate its restoration. Moreover, we highlight the implications of these chromatin alterations in gene expression control and their impact on key biological processes, such as cell differentiation, cell reprogramming or human diseases linked to cell proliferation, such as cancer.
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Affiliation(s)
- Elena López-Jiménez
- Faculty of Medicine, National Heart and Lung Institute, Margaret Turner Warwick Centre for Fibrosing Lung Disease, Royal Brompton Campus, Imperial College London, London SW3 6LY, UK;
| | - Cristina González-Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain
- Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, 41013 Seville, Spain
- Correspondence:
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22
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Jonas F, Yaakov G, Barkai N. Rtt109 promotes nucleosome replacement ahead of the replication fork. Genome Res 2022; 32:1089-1098. [PMID: 35609993 PMCID: PMC9248883 DOI: 10.1101/gr.276674.122] [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: 02/09/2022] [Accepted: 05/05/2022] [Indexed: 11/25/2022]
Abstract
DNA replication perturbs chromatin by triggering the eviction, replacement, and incorporation of nucleosomes. How this dynamic is orchestrated in time and space is poorly understood. Here, we apply a genetically encoded sensor for histone exchange to follow the time-resolved histone H3 exchange profile in budding yeast cells undergoing slow synchronous replication in nucleotide-limiting conditions. We find that new histones are incorporated not only behind, but also ahead of the replication fork. We provide evidence that Rtt109, the S-phase-induced acetyltransferase, stabilizes nucleosomes behind the fork but promotes H3 replacement ahead of the fork. Increased replacement ahead of the fork is independent of the primary Rtt109 acetylation target H3K56 and rather results from Vps75-dependent Rtt109 activity toward the H3 N terminus. Our results suggest that, at least under nucleotide-limiting conditions, selective incorporation of differentially modified H3s behind and ahead of the replication fork results in opposing effects on histone exchange, likely reflecting the distinct challenges for genome stability at these different regions.
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Affiliation(s)
- Felix Jonas
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Gilad Yaakov
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Naama Barkai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
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23
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Li S, Edwards G, Radebaugh CA, Luger K, A Stargell L. Spn1 and its dynamic interactions with Spt6, histones and nucleosomes. J Mol Biol 2022; 434:167630. [PMID: 35595162 DOI: 10.1016/j.jmb.2022.167630] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/06/2022] [Accepted: 05/10/2022] [Indexed: 11/25/2022]
Abstract
Histone chaperones facilitate the assembly and disassembly of nucleosomes and regulate DNA accessibility for critical cellular processes. Spn1 is an essential, highly conserved histone chaperone that functions in transcription initiation and elongation in a chromatin context. Here we demonstrate that Spn1 binds H3-H4 with low nanomolar affinity, residues 85-99 within the acidic N-terminal region of Spn1 are required for H3-H4 binding, and Spn1 binding to H3-H4 dimers does not impede (H3-H4)2 tetramer formation. Previous work has shown the central region of Spn1 (residues 141-305) is important for interaction with Spt6, another conserved and essential histone chaperone. We show that the C-terminal region of Spn1 also contributes to Spt6 binding and is critical for Spn1 binding to nucleosomes. We also show Spt6 preferentially binds H3-H4 tetramers and Spt6 competes with nucleosomes for Spn1 binding. Combined with previous results, this indicates the Spn1-Spt6 complex does not bind nucleosomes. In contrast to nucleosome binding, we found that the Spn1-Spt6 complex can bind H3-H4 dimers and tetramers and H2A-H2B to form ternary complexes. These important results provide new information about the functions of Spn1, Spt6, and the Spn1-Spt6 complex, two essential and highly conserved histone chaperones.
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Affiliation(s)
- Sha Li
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523-1870, USA; Department of Biochemistry, University of Colorado, Boulder, CO, 80309, USA
| | - Garrett Edwards
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309, USA
| | - Catherine A Radebaugh
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523-1870, USA
| | - Karolin Luger
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309, USA; Howard Hughes Medical Institute, University of Colorado, Boulder, CO, 80309, USA
| | - Laurie A Stargell
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523-1870, USA
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24
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Khan P, Chaudhuri RN. Acetylation of H3K56 orchestrates UV-responsive chromatin events that generate DNA accessibility during Nucleotide Excision Repair. DNA Repair (Amst) 2022; 113:103317. [PMID: 35290816 DOI: 10.1016/j.dnarep.2022.103317] [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: 11/14/2021] [Revised: 02/25/2022] [Accepted: 03/07/2022] [Indexed: 11/22/2022]
Abstract
Histone modifications have long been related to DNA damage response. Nucleotide excision repair pathway that removes helix-distorting lesions necessitates DNA accessibility through chromatin modifications. Previous studies have linked H3 tail residue acetylation to UV-induced NER. Here we present evidences that acetylation of H3K56 is crucial for early phases of NER. Using H3K56 mutants K56Q and K56R, which mimic acetylated and unacetylated lysines respectively, we show that recruitment of the repair factor Rad16, a Swi/Snf family member is dependent on H3K56 acetylation. With constitutive H3K56 acetylation, Rad16 recruitment became UV-independent. Furthermore, H3K56 acetylation promoted UV-induced hyperacetylation of H3K9 and H3K14. Importantly, constitutive H3K56 acetylation prominently increased chromatin accessibility. During NER, lack of H3K56 acetylation that effectively aborted H3 tail residue acetylation and Rad16 recruitment, thus failed to impart essential chromatin modulations. The NER-responsive oscillation of chromatin structure observed in wild type, was distinctly eliminated in absence of H3K56 acetylation. In vitro assay with wild type and H3K56 mutant cell extracts further indicated that absence of H3K56 acetylation negatively affected DNA relaxation during NER. Overall, H3K56 acetylation regulates Rad16 redistribution and UV-induced H3 tail residue hyperacetylation, and the resultant modification code promotes chromatin accessibility and recruitment of subsequent repair factors during NER.
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Affiliation(s)
- Preeti Khan
- Department of Biotechnology, St. Xavier's College, 30, Mother Teresa Sarani, Kolkata 700016, India
| | - Ronita Nag Chaudhuri
- Department of Biotechnology, St. Xavier's College, 30, Mother Teresa Sarani, Kolkata 700016, India.
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25
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Histone Chaperone Nrp1 Mutation Affects the Acetylation of H3K56 in Tetrahymena thermophila. Cells 2022; 11:cells11030408. [PMID: 35159218 PMCID: PMC8833950 DOI: 10.3390/cells11030408] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/12/2022] [Accepted: 01/20/2022] [Indexed: 02/04/2023] Open
Abstract
Histone modification and nucleosome assembly are mainly regulated by various histone-modifying enzymes and chaperones. The roles of histone-modification enzymes have been well analyzed, but the molecular mechanism of histone chaperones in histone modification and nucleosome assembly is incompletely understood. We previously found that the histone chaperone Nrp1 is localized in the micronucleus (MIC) and the macronucleus (MAC) and involved in the chromatin stability and nuclear division of Tetrahymena thermophila. In the present work, we found that truncated C-terminal mutant HA-Nrp1TrC abnormally localizes in the cytoplasm. The truncated-signal-peptide mutants HA-Nrp1TrNLS1 and HA-Nrp1TrNLS2 are localized in the MIC and MAC. Overexpression of Nrp1TrNLS1 inhibited cellular proliferation and disrupted micronuclear mitosis during the vegetative growth stage. During sexual development, Nrp1TrNLS1 overexpression led to abnormal bouquet structures and meiosis arrest. Furthermore, Histone H3 was not transported into the nucleus; instead, it formed an abnormal speckled cytoplastic distribution in the Nrp1TrNLS1 mutants. The acetylation level of H3K56 in the mutants also decreased, leading to significant changes in the transcription of the genome of the Nrp1TrNLS1 mutants. The histone chaperone Nrp1 regulates the H3 nuclear import and acetylation modification of H3K56 and affects chromatin stability and genome transcription in Tetrahymena.
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26
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Ziane R, Camasses A, Radman-Livaja M. The asymmetric distribution of RNA polymerase II and nucleosomes on replicated daughter genomes is caused by differences in replication timing between the lagging and the leading strand. Genome Res 2022; 32:337-356. [PMID: 35042724 PMCID: PMC8805712 DOI: 10.1101/gr.275387.121] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 12/19/2021] [Indexed: 11/24/2022]
Abstract
Chromatin features are thought to have a role in the epigenetic transmission of transcription states from one cell generation to the next. It is unclear how chromatin structure survives disruptions caused by genomic replication or whether chromatin features are instructive of the transcription state of the underlying gene. We developed a method to monitor budding yeast replication, transcription, and chromatin maturation dynamics on each daughter genome in parallel, with which we identified clusters of secondary origins surrounding known origins. We found a difference in the timing of lagging and leading strand replication on the order of minutes at most yeast genes. We propose a model in which the majority of old histones and RNA polymerase II (RNAPII) bind to the gene copy that replicated first, while newly synthesized nucleosomes are assembled on the copy that replicated second. RNAPII enrichment then shifts to the sister copy that replicated second. The order of replication is largely determined by genic orientation: If transcription and replication are codirectional, the leading strand replicates first; if they are counterdirectional, the lagging strand replicates first. A mutation in the Mcm2 subunit of the replicative helicase Mcm2-7 that impairs Mcm2 interactions with histone H3 slows down replication forks but does not qualitatively change the asymmetry in nucleosome distribution observed in the WT. We propose that active transcription states are inherited simultaneously and independently of their underlying chromatin states through the recycling of the transcription machinery and old histones, respectively. Transcription thus actively contributes to the reestablishment of the active chromatin state.
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Affiliation(s)
- Rahima Ziane
- Institut de Génétique Moléculaire de Montpellier, UMR 5535, CNRS, 34293 Montpellier Cedex 5, France.,Université de Montpellier, 34090 Montpellier, France
| | - Alain Camasses
- Institut de Génétique Moléculaire de Montpellier, UMR 5535, CNRS, 34293 Montpellier Cedex 5, France.,Université de Montpellier, 34090 Montpellier, France
| | - Marta Radman-Livaja
- Institut de Génétique Moléculaire de Montpellier, UMR 5535, CNRS, 34293 Montpellier Cedex 5, France.,Université de Montpellier, 34090 Montpellier, France
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27
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Therapeutical interference with the epigenetic landscape of germ cell tumors: a comparative drug study and new mechanistical insights. Clin Epigenetics 2022; 14:5. [PMID: 34996497 PMCID: PMC8742467 DOI: 10.1186/s13148-021-01223-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/18/2021] [Indexed: 12/18/2022] Open
Abstract
Background Type II germ cell tumors (GCT) are the most common solid cancers in males of age 15 to 35 years. Treatment of these tumors includes cisplatin-based therapy achieving high cure rates, but also leading to late toxicities. As mainly young men are suffering from GCTs, late toxicities play a major role regarding life expectancy, and the development of therapy resistance emphasizes the need for alternative therapeutic options. GCTs are highly susceptible to interference with the epigenetic landscape; therefore, this study focuses on screening of drugs against epigenetic factors as a treatment option for GCTs.
Results We present seven different epigenetic inhibitors efficiently decreasing cell viability in GCT cell lines including cisplatin-resistant subclones at low concentrations by targeting epigenetic modifiers and interactors, like histone deacetylases (Quisinostat), histone demethylases (JIB-04), histone methyltransferases (Chaetocin), epigenetic readers (MZ-1, LP99) and polycomb-repressive complexes (PRT4165, GSK343). Mass spectrometry-based analyses of the histone modification landscape revealed effects beyond the expected mode-of-action of each drug, suggesting a wider spectrum of activity than initially assumed. Moreover, we characterized the effects of each drug on the transcriptome of GCT cells by RNA sequencing and found common deregulations in gene expression of ion transporters and DNA-binding factors. A kinase array revealed deregulations of signaling pathways, like cAMP, JAK-STAT and WNT. Conclusion Our study identified seven drugs against epigenetic modifiers to treat cisplatin-resistant GCTs. Further, we extensively analyzed off-target effects and modes-of-action, which are important for risk assessment of the individual drugs. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01223-1.
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28
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Bryll AR, Peterson CL. Functional interaction between the RNA exosome and the sirtuin deacetylase Hst3 maintains transcriptional homeostasis. Genes Dev 2021; 36:17-22. [PMID: 34916303 PMCID: PMC8763048 DOI: 10.1101/gad.348923.121] [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: 08/10/2021] [Accepted: 11/22/2021] [Indexed: 11/24/2022]
Abstract
In this study, Bryll et al. found that inactivation of the RNA exosome leads to global reduction of nascent mRNA transcripts, and that this defect is accentuated by loss of deposition of histone variant H2A.Z. They identify the mRNA for the sirtuin deacetylase Hst3 as a key target for the RNA exosome that mediates communication between RNA degradation and transcription machineries. Eukaryotic cells maintain an optimal level of mRNAs through unknown mechanisms that balance RNA synthesis and degradation. We found that inactivation of the RNA exosome leads to global reduction of nascent mRNA transcripts, and that this defect is accentuated by loss of deposition of histone variant H2A.Z. We identify the mRNA for the sirtuin deacetylase Hst3 as a key target for the RNA exosome that mediates communication between RNA degradation and transcription machineries. These findings reveal how the RNA exosome and H2A.Z function together to control a deacetylase, ensuring proper levels of transcription in response to changes in RNA degradation.
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Affiliation(s)
- Alysia R Bryll
- Program of Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.,Medical Scientist Training Program, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Craig L Peterson
- Program of Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
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29
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PCNA Loaders and Unloaders-One Ring That Rules Them All. Genes (Basel) 2021; 12:genes12111812. [PMID: 34828416 PMCID: PMC8618651 DOI: 10.3390/genes12111812] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/15/2021] [Accepted: 11/17/2021] [Indexed: 12/23/2022] Open
Abstract
During each cell duplication, the entirety of the genomic DNA in every cell must be accurately and quickly copied. Given the short time available for the chore, the requirement of many proteins, and the daunting amount of DNA present, DNA replication poses a serious challenge to the cell. A high level of coordination between polymerases and other DNA and chromatin-interacting proteins is vital to complete this task. One of the most important proteins for maintaining such coordination is PCNA. PCNA is a multitasking protein that forms a homotrimeric ring that encircles the DNA. It serves as a processivity factor for DNA polymerases and acts as a landing platform for different proteins interacting with DNA and chromatin. Therefore, PCNA is a signaling hub that influences the rate and accuracy of DNA replication, regulates DNA damage repair, controls chromatin formation during the replication, and the proper segregation of the sister chromatids. With so many essential roles, PCNA recruitment and turnover on the chromatin is of utmost importance. Three different, conserved protein complexes are in charge of loading/unloading PCNA onto DNA. Replication factor C (RFC) is the canonical complex in charge of loading PCNA during the S-phase. The Ctf18 and Elg1 (ATAD5 in mammalian) proteins form complexes similar to RFC, with particular functions in the cell’s nucleus. Here we summarize our current knowledge about the roles of these important factors in yeast and mammals.
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30
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Aricthota S, Haldar D. DDK/Hsk1 phosphorylates and targets fission yeast histone deacetylase Hst4 for degradation to stabilize stalled DNA replication forks. eLife 2021; 10:70787. [PMID: 34608864 PMCID: PMC8565929 DOI: 10.7554/elife.70787] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 10/01/2021] [Indexed: 01/01/2023] Open
Abstract
In eukaryotes, paused replication forks are prone to collapse, which leads to genomic instability, a hallmark of cancer. Dbf4-dependent kinase (DDK)/Hsk1Cdc7 is a conserved replication initiator kinase with conflicting roles in replication stress response. Here, we show that fission yeast DDK/Hsk1 phosphorylates sirtuin, Hst4 upon replication stress at C-terminal serine residues. Phosphorylation of Hst4 by DDK marks it for degradation via the ubiquitin ligase SCFpof3. Phosphorylation-defective hst4 mutant (4SA-hst4) displays defective recovery from replication stress, faulty fork restart, slow S-phase progression and decreased viability. The highly conserved fork protection complex (FPC) stabilizes stalled replication forks. We found that the recruitment of FPC components, Swi1 and Mcl1 to the chromatin is compromised in the 4SA-hst4 mutant, although whole cell levels increased. These defects are dependent upon H3K56ac and independent of intra S-phase checkpoint activation. Finally, we show conservation of H3K56ac-dependent regulation of Timeless, Tipin, and And-1 in human cells. We propose that degradation of Hst4 via DDK increases H3K56ac, changing the chromatin state in the vicinity of stalled forks facilitating recruitment and function of FPC. Overall, this study identified a crucial role of DDK and FPC in the regulation of replication stress response with implications in cancer therapeutics.
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Affiliation(s)
- Shalini Aricthota
- Laboratory of Chromatin Biology and Epigenetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India.,Graduate Studies, Manipal Academy of Higher Education, Manipal, India
| | - Devyani Haldar
- Laboratory of Chromatin Biology and Epigenetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
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Kochan DZ, Mawer JSP, Massen J, Tishinov K, Parekh S, Graef M, Spang A, Tessarz P. The RNA-binding protein Puf5 contributes to buffering of mRNA upon chromatin-mediated changes in nascent transcription. J Cell Sci 2021; 134:jcs259051. [PMID: 34350963 PMCID: PMC8353526 DOI: 10.1242/jcs.259051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 07/03/2021] [Indexed: 11/23/2022] Open
Abstract
Gene expression involves regulation of chromatin structure and transcription, as well as processing of the transcribed mRNA. While there are feedback mechanisms, it is not clear whether these include crosstalk between chromatin architecture and mRNA decay. To address this, we performed a genome-wide genetic screen using a Saccharomyces cerevisiae strain harbouring the H3K56A mutation, which is known to perturb chromatin structure and nascent transcription. We identified Puf5 (also known as Mpt5) as essential in an H3K56A background. Depletion of Puf5 in this background leads to downregulation of Puf5 targets. We suggest that Puf5 plays a role in post-transcriptional buffering of mRNAs, and support this by transcriptional shutoff experiments in which Puf5 mRNA targets are degraded slower in H3K56A cells compared to wild-type cells. Finally, we show that post-transcriptional buffering of Puf5 targets is widespread and does not occur only in an H3K56A mutant, but also in an H3K4R background, which leads to a global increase in nascent transcription. Our data suggest that Puf5 determines the fate of its mRNA targets in a context-dependent manner acting as an mRNA surveillance hub balancing deregulated nascent transcription to maintain physiological mRNA levels.
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Affiliation(s)
- David Z. Kochan
- Max Planck Research Group ‘Chromatin and Ageing’, Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Julia S. P. Mawer
- Max Planck Research Group ‘Chromatin and Ageing’, Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Jennifer Massen
- Max Planck Research Group ‘Chromatin and Ageing’, Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Kiril Tishinov
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Swati Parekh
- Max Planck Research Group ‘Chromatin and Ageing’, Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Martin Graef
- Max Planck Research Group ‘Autophagy and Cellular Ageing’, Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
- Cologne Excellence Cluster on Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Anne Spang
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Peter Tessarz
- Max Planck Research Group ‘Chromatin and Ageing’, Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
- Cologne Excellence Cluster on Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
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Ivanov M, Sandelin A, Marquardt S. TrancriptomeReconstructoR: data-driven annotation of complex transcriptomes. BMC Bioinformatics 2021; 22:290. [PMID: 34058980 PMCID: PMC8166035 DOI: 10.1186/s12859-021-04208-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 05/18/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The quality of gene annotation determines the interpretation of results obtained in transcriptomic studies. The growing number of genome sequence information calls for experimental and computational pipelines for de novo transcriptome annotation. Ideally, gene and transcript models should be called from a limited set of key experimental data. RESULTS We developed TranscriptomeReconstructoR, an R package which implements a pipeline for automated transcriptome annotation. It relies on integrating features from independent and complementary datasets: (i) full-length RNA-seq for detection of splicing patterns and (ii) high-throughput 5' and 3' tag sequencing data for accurate definition of gene borders. The pipeline can also take a nascent RNA-seq dataset to supplement the called gene model with transient transcripts. We reconstructed de novo the transcriptional landscape of wild type Arabidopsis thaliana seedlings and Saccharomyces cerevisiae cells as a proof-of-principle. A comparison to the existing transcriptome annotations revealed that our gene model is more accurate and comprehensive than the most commonly used community gene models, TAIR10 and Araport11 for A.thaliana and SacCer3 for S.cerevisiae. In particular, we identify multiple transient transcripts missing from the existing annotations. Our new annotations promise to improve the quality of A.thaliana and S.cerevisiae genome research. CONCLUSIONS Our proof-of-concept data suggest a cost-efficient strategy for rapid and accurate annotation of complex eukaryotic transcriptomes. We combine the choice of library preparation methods and sequencing platforms with the dedicated computational pipeline implemented in the TranscriptomeReconstructoR package. The pipeline only requires prior knowledge on the reference genomic DNA sequence, but not the transcriptome. The package seamlessly integrates with Bioconductor packages for downstream analysis.
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Affiliation(s)
- Maxim Ivanov
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiskberg C, Denmark.
| | - Albin Sandelin
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.,Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Sebastian Marquardt
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiskberg C, Denmark.
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INO80C Remodeler Maintains Genomic Stability by Preventing Promiscuous Transcription at Replication Origins. Cell Rep 2021; 32:108106. [PMID: 32905765 PMCID: PMC7540730 DOI: 10.1016/j.celrep.2020.108106] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 06/26/2020] [Accepted: 08/12/2020] [Indexed: 02/07/2023] Open
Abstract
The proper coordination of transcription with DNA replication and repair is central for genomic stability. We investigate how the INO80C chromatin remodeling enzyme might coordinate these genomic processes. We find that INO80C co-localizes with the origin recognition complex (ORC) at yeast replication origins and is bound to replication initiation sites in mouse embryonic stem cells (mESCs). In yeast· INO80C recruitment requires origin sequences but does not require ORC· suggesting that recruitment is independent of pre-replication complex assembly. In both yeast and ESCs· INO80C co-localizes at origins with Mot1 and NC2 transcription factors· and genetic studies suggest that they function together to promote genome stability. Interestingly· nascent transcript sequencing demonstrates that INO80C and Mot1 prevent pervasive transcription through origin sequences· and absence of these factors leads to formation of new DNA double-strand breaks. We propose that INO80C and Mot1/NC2 function through distinct pathways to limit origin transcription· maintaining genomic stability. The INO80C chromatin remodeler is known to regulate transcription and genomic stability. Topal et al. find that INO80C functions with Mot1 repressor to prevent pervasive transcription at replication origins in yeast and mESCs. Increased ncRNAs lead to new DNA double-strand breaks at origins, linking transcriptional regulation to genomic stability.
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Hammond-Martel I, Verreault A, Wurtele H. Chromatin dynamics and DNA replication roadblocks. DNA Repair (Amst) 2021; 104:103140. [PMID: 34087728 DOI: 10.1016/j.dnarep.2021.103140] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/18/2021] [Accepted: 05/20/2021] [Indexed: 11/27/2022]
Abstract
A broad spectrum of spontaneous and genotoxin-induced DNA lesions impede replication fork progression. The DNA damage response that acts to promote completion of DNA replication is associated with dynamic changes in chromatin structure that include two distinct processes which operate genome-wide during S-phase. The first, often referred to as histone recycling or parental histone segregation, is characterized by the transfer of parental histones located ahead of replication forks onto nascent DNA. The second, known as de novo chromatin assembly, consists of the deposition of new histone molecules onto nascent DNA. Because these two processes occur at all replication forks, their potential to influence a multitude of DNA repair and DNA damage tolerance mechanisms is considerable. The purpose of this review is to provide a description of parental histone segregation and de novo chromatin assembly, and to illustrate how these processes influence cellular responses to DNA replication roadblocks.
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Affiliation(s)
- Ian Hammond-Martel
- Centre de recherche de l'Hôpital Maisonneuve-Rosemont, 5415 boulevard de l'Assomption, Montreal, H1T 2M4, Canada
| | - Alain Verreault
- Institute for Research in Immunology and Cancer, Université de Montréal, P.O. Box 6128, Succursale Centre-Ville, Montreal, H3C 3J7, Canada; Département de Pathologie et Biologie Cellulaire, Université de Montréal, 2900 Edouard Montpetit Blvd, Montreal, H3T 1J4, Canada
| | - Hugo Wurtele
- Centre de recherche de l'Hôpital Maisonneuve-Rosemont, 5415 boulevard de l'Assomption, Montreal, H1T 2M4, Canada; Département de Médecine, Université de Montréal, Université de Montréal, 2900 Edouard Montpetit Blvd, Montreal, H3T 1J4, Canada.
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Moretto F, Wood NE, Chia M, Li C, Luscombe NM, van Werven FJ. Transcription levels of a noncoding RNA orchestrate opposing regulatory and cell fate outcomes in yeast. Cell Rep 2021; 34:108643. [PMID: 33472063 PMCID: PMC7816125 DOI: 10.1016/j.celrep.2020.108643] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 10/28/2020] [Accepted: 12/22/2020] [Indexed: 12/21/2022] Open
Abstract
Transcription through noncoding regions of the genome is pervasive. How these transcription events regulate gene expression remains poorly understood. Here, we report that, in S. cerevisiae, the levels of transcription through a noncoding region, IRT2, located upstream in the promoter of the inducer of meiosis, IME1, regulate opposing chromatin and transcription states. At low levels, the act of IRT2 transcription promotes histone exchange, delivering acetylated histone H3 lysine 56 to chromatin locally. The subsequent open chromatin state directs transcription factor recruitment and induces downstream transcription to repress the IME1 promoter and meiotic entry. Conversely, increasing transcription turns IRT2 into a repressor by promoting transcription-coupled chromatin assembly. The two opposing functions of IRT2 transcription shape a regulatory circuit, which ensures a robust cell-type-specific control of IME1 expression and yeast meiosis. Our data illustrate how intergenic transcription levels are key to controlling local chromatin state, gene expression, and cell fate outcomes.
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Affiliation(s)
- Fabien Moretto
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Heraklion, Crete 70013, Greece
| | - N Ezgi Wood
- Department of Cell Biology, UT Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Minghao Chia
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01, Singapore 138672, Singapore
| | - Cai Li
- Bioinformatics and Computational Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Nicholas M Luscombe
- Bioinformatics and Computational Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan; UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Folkert J van Werven
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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36
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Cooke SL, Soares BL, Müller CA, Nieduszynski CA, Bastos de Oliveira FM, de Bruin RAM. Tos4 mediates gene expression homeostasis through interaction with HDAC complexes independently of H3K56 acetylation. J Biol Chem 2021; 296:100533. [PMID: 33713703 PMCID: PMC8054192 DOI: 10.1016/j.jbc.2021.100533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 03/03/2021] [Accepted: 03/09/2021] [Indexed: 11/25/2022] Open
Abstract
Saccharomyces cerevisiae exhibits gene expression homeostasis, which is defined as the buffering of transcription levels against changes in DNA copy number during the S phase of the cell cycle. It has been suggested that S. cerevisiae employs an active mechanism to maintain gene expression homeostasis through Rtt109-Asf1-dependent acetylation of histone H3 on lysine 56 (H3K56). Here, we show that gene expression homeostasis can be achieved independently of H3K56 acetylation by Tos4 (Target of Swi6-4). Using Nanostring technology, we establish that Tos4-dependent gene expression homeostasis depends on its forkhead-associated (FHA) domain, which is a phosphopeptide recognition domain required to bind histone deacetylases (HDACs). We demonstrate that the mechanism of Tos4-dependent gene expression homeostasis requires its interaction with the Rpd3L HDAC complex. However, this is independent of Rpd3's well-established roles in both histone deacetylation and controlling the DNA replication timing program, as established by deep sequencing of Fluorescence-Activated Cell Sorted (FACS) S and G2 phase populations. Overall, our data reveals that Tos4 mediates gene expression homeostasis through its FHA domain-dependent interaction with the Rpd3L complex, which is independent of H3K56ac.
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Affiliation(s)
- Sophie L Cooke
- MRC Laboratory Molecular Cell Biology, University College London, London, UK
| | - Barbara L Soares
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Carolin A Müller
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Conrad A Nieduszynski
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK; Genome Damage and Stability Centre, University of Sussex, Brighton, UK
| | | | - Robertus A M de Bruin
- MRC Laboratory Molecular Cell Biology, University College London, London, UK; UCL Cancer Institute, University College London, London, UK.
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Ray A, Khan P, Nag Chaudhuri R. Deacetylation of H4 lysine16 affects acetylation of lysine residues in histone H3 and H4 and promotes transcription of constitutive genes. Epigenetics 2020; 16:597-617. [PMID: 32795161 DOI: 10.1080/15592294.2020.1809896] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Histone modification map of H4 N-terminal tail residues in Saccharomyces cerevisiae reveals the prominence of lysine acetylation. Previous reports have indicated the importance of lysine acetylation in maintaining chromatin structure and function. H4K16, a residue with highly regulated acetylation dynamics has unique functions not overlapping with the other H4 N- terminal acetylable residues. The present work unravels the role of H4K16 acetylation in regulating expression of constitutive genes. H4K16 gets distinctly deacetylated over the coding region of constitutively expressed genes. Deacetylation of H4K16 reduces H3K9 acetylation at the cellular and gene level. Reduced H3K9 acetylation however did not negatively correlate with active gene transcription. Significantly, H4K16 deacetylation was found to be associated with hypoacetylated H4K12 throughout the locus of constitutive genes. H4K16 and K12 deacetylation is known to favour active transcription. Sas2, the HAT mutant showed similar patterns of hypoacetylated H3K9 and H4K12 at the active loci, clearly implying that the modifications were associated with deacetylation state of H4K16. Deacetylation of H4K16 was also concurrent with increased H3K56 acetylation in the promoter region and ORF of the constitutive genes. Combination of all these histone modifications significantly reduced H3 occupancy, increased promoter accessibility and enhanced RNAPII recruitment at the constitutively active loci. Consequently, we found that expression of active genes was higher in H4K16R mutant which mimic deacetylated state, but not in H4K16Q mimicking constitutive acetylation. To summarize, H4K16 deacetylation linked with H4K12 and H3K9 hypoacetylation along with H3K56 hyperacetylation generate a chromatin landscape that is conducive for transcription of constitutive genes.
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Affiliation(s)
- Anagh Ray
- Department of Biotechnology, St. Xavier's College, Kolkata, India
| | - Preeti Khan
- Department of Biotechnology, St. Xavier's College, Kolkata, India
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38
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Karányi Z, Hornyák L, Székvölgyi L. Histone H3 Lysine 56 Acetylation Is Required for Formation of Normal Levels of Meiotic DNA Breaks in S. cerevisiae. Front Cell Dev Biol 2020; 7:364. [PMID: 31998719 PMCID: PMC6970188 DOI: 10.3389/fcell.2019.00364] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 12/12/2019] [Indexed: 01/27/2023] Open
Abstract
Meiotic recombination is initiated by Spo11-catalyzed DNA double-strand breaks (DSBs) that are promoted by histone modifications and histone modifying enzymes. Herein we investigated the role of histone H3 lysine 56 acetylation (H3K56ac) located near the entry/exit points of the DNA in the globular H3 domain. We generated a series of mutant cells (asf1Δ, rtt109Δ, hst3/4Δ, and H3K56A) in which the endogenous level of H3K56ac was manipulated and tracked during meiotic growth. We show that complete loss or increased abundance of H3K56ac in these mutants allows timely entry into meiosis and sporulation and does not impair S phase progression, first and second meiotic cell divisions, and spore viability. In the asf1Δ, rtt109Δ, hst3/4Δ mutants, DSBs and crossovers form normal levels with a short (60-min) delay at the HIS4-LEU2 artificial recombination hotspot, however, DSB formation shows a ∼threefold decrease in the H3K56A mutant at the natural BUD23-ARE1 hotspot. The latter DSB phenotype, showing significant DSB reduction in the H3K56A mutant, was also observed at DSB sites using genome-wide mapping of Rfa1-coated single-stranded DNA flanking DSBs (RPA ChIP). Parallel mapping of H3K56-acetylated histones in wild type cells revealed strong depletion of the H3K56ac ChIP signal over Spo11-oligo DSBs, albeit most H3K56-acetylated histones were enriched adjacent to the identified RPA ChIP binding sites. Taken together, these associations demonstrate a prominent role of H3 lysine 56 acetylation in the formation of DNA breaks within recombination hotspot regions.
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Affiliation(s)
- Zsolt Karányi
- MTA-DE Momentum Genome Architecture and Recombination Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.,Department of Internal Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Lilla Hornyák
- MTA-DE Momentum Genome Architecture and Recombination Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Lóránt Székvölgyi
- MTA-DE Momentum Genome Architecture and Recombination Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
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