1
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Sahrhage M, Paul NB, Beißbarth T, Haubrock M. The importance of DNA sequence for nucleosome positioning in transcriptional regulation. Life Sci Alliance 2024; 7:e202302380. [PMID: 38830772 PMCID: PMC11147951 DOI: 10.26508/lsa.202302380] [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: 09/18/2023] [Revised: 05/15/2024] [Accepted: 05/16/2024] [Indexed: 06/05/2024] Open
Abstract
Nucleosome positioning is a key factor for transcriptional regulation. Nucleosomes regulate the dynamic accessibility of chromatin and interact with the transcription machinery at every stage. Influences to steer nucleosome positioning are diverse, and the according importance of the DNA sequence in contrast to active chromatin remodeling has been the subject of long discussion. In this study, we evaluate the functional role of DNA sequence for all major elements along the process of transcription. We developed a random forest classifier based on local DNA structure that assesses the sequence-intrinsic support for nucleosome positioning. On this basis, we created a simple data resource that we applied genome-wide to the human genome. In our comprehensive analysis, we found a special role of DNA in mediating the competition of nucleosomes with cis-regulatory elements, in enabling steady transcription, for positioning of stable nucleosomes in exons, and for repelling nucleosomes during transcription termination. In contrast, we relate these findings to concurrent processes that generate strongly positioned nucleosomes in vivo that are not mediated by sequence, such as energy-dependent remodeling of chromatin.
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Affiliation(s)
- Malte Sahrhage
- Department of Medical Bioinformatics, University Medical Center, Göttingen, Germany
| | - Niels Benjamin Paul
- Department of Medical Bioinformatics, University Medical Center, Göttingen, Germany
- Department of Cardiology and Pneumology, University Medical Center, Göttingen, Germany
| | - Tim Beißbarth
- Department of Medical Bioinformatics, University Medical Center, Göttingen, Germany
| | - Martin Haubrock
- Department of Medical Bioinformatics, University Medical Center, Göttingen, Germany
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2
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Wakim JG, Spakowitz AJ. Physical modeling of nucleosome clustering in euchromatin resulting from interactions between epigenetic reader proteins. Proc Natl Acad Sci U S A 2024; 121:e2317911121. [PMID: 38900792 PMCID: PMC11214050 DOI: 10.1073/pnas.2317911121] [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: 10/14/2023] [Accepted: 04/15/2024] [Indexed: 06/22/2024] Open
Abstract
Euchromatin is an accessible phase of genetic material containing genes that encode proteins with increased expression levels. The structure of euchromatin in vitro has been described as a 30-nm fiber formed from ordered nucleosome arrays. However, recent advances in microscopy have revealed an in vivo euchromatin architecture that is much more disordered, characterized by variable-length linker DNA and sporadic nucleosome clusters. In this work, we develop a theoretical model to elucidate factors contributing to the disordered in vivo architecture of euchromatin. We begin by developing a 1D model of nucleosome positioning that captures the interactions between bound epigenetic reader proteins to predict the distribution of DNA linker lengths between adjacent nucleosomes. We then use the predicted linker lengths to construct 3D chromatin configurations consistent with the physical properties of DNA within the nucleosome array, and we evaluate the distribution of nucleosome cluster sizes in those configurations. Our model reproduces experimental cluster-size distributions, which are dramatically influenced by the local pattern of epigenetic marks and the concentration of reader proteins. Based on our model, we attribute the disordered arrangement of euchromatin to the heterogeneous binding of reader proteins and subsequent short-range interactions between bound reader proteins on adjacent nucleosomes. By replicating experimental results with our physics-based model, we propose a mechanism for euchromatin organization in the nucleus that impacts gene regulation and the maintenance of epigenetic marks.
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Affiliation(s)
- Joseph G. Wakim
- Department of Chemical Engineering, Stanford University, Stanford, CA94305
| | - Andrew J. Spakowitz
- Department of Chemical Engineering, Stanford University, Stanford, CA94305
- Department of Materials Science and Engineering, Stanford University, Stanford, CA94305
- Biophysics Program, Stanford University, Stanford, CA94305
- Department of Applied Physics, Stanford University, Stanford, CA94305
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3
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Nemsick S, Hansen AS. Molecular models of bidirectional promoter regulation. Curr Opin Struct Biol 2024; 87:102865. [PMID: 38905929 DOI: 10.1016/j.sbi.2024.102865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/30/2024] [Accepted: 05/27/2024] [Indexed: 06/23/2024]
Abstract
Approximately 11% of human genes are transcribed by a bidirectional promoter (BDP), defined as two genes with <1 kb between their transcription start sites. Despite their evolutionary conservation and enrichment for housekeeping genes and oncogenes, the regulatory role of BDPs remains unclear. BDPs have been suggested to facilitate gene coregulation and/or decrease expression noise. This review discusses these potential regulatory functions through the context of six prospective underlying mechanistic models: a single nucleosome free region, shared transcription factor/regulator binding, cooperative negative supercoiling, bimodal histone marks, joint activation by enhancer(s), and RNA-mediated recruitment of regulators. These molecular mechanisms may act independently and/or cooperatively to facilitate the coregulation and/or decreased expression noise predicted of BDPs.
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Affiliation(s)
- Sarah Nemsick
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; The Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
| | - Anders S Hansen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; The Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA.
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4
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Nie Z, Zhao Y, Yu S, Mai J, Gao H, Fan Z, Bao Y, Li R, Xiao J. NucMap 2.0: An Updated Database of Genome-wide Nucleosome Positioning Maps Across Species. J Mol Biol 2024:168655. [PMID: 38878855 DOI: 10.1016/j.jmb.2024.168655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/24/2024] [Accepted: 06/07/2024] [Indexed: 06/24/2024]
Abstract
Nucleosome dynamics plays important roles in many biological processes, such as DNA replication and gene expression. NucMap (https://ngdc.cncb.ac.cn/nucmap) is the first database of genome-wide nucleosome positioning maps across species. Here, we present an updated version, NucMap 2.0, by incorporating more species and MNase-seq samples. In addition, we integrate other related omics data for each MNase-seq sample to provide a comprehensive view of nucleosome positioning, such as gene expression, transcription factor binding sites, histone modifications and DNA methylation. In particular, NucMap 2.0 integrates and pre-analyzes RNA-seq data and ChIP-seq data of human-related samples, which facilitates the interpretation of nucleosome positioning in humans. All processed data are integrated into an in-built genome browser, and users can make comprehensive side-by-side analyses. In addition, more online analytical functions are developed, which allows researchers to identify differential nucleosome regions and explore potential gene regulatory regions. All resources are open access with a user-friendly web interface.
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Affiliation(s)
- Zhi Nie
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yongbing Zhao
- University of Chinese Academy of Sciences, Beijing 100049, China; Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
| | - Shuhuan Yu
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Jialin Mai
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Hao Gao
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Zhuojing Fan
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.
| | - Yiming Bao
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Rujiao Li
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.
| | - Jingfa Xiao
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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5
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Prescott NA, Mansisidor A, Bram Y, Biaco T, Rendleman J, Faulkner SC, Lemmon AA, Lim C, Hamard PJ, Koche RP, Risca VI, Schwartz RE, David Y. A nucleosome switch primes Hepatitis B Virus infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.03.03.531011. [PMID: 38915612 PMCID: PMC11195122 DOI: 10.1101/2023.03.03.531011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Chronic hepatitis B virus (HBV) infection is an incurable global health threat responsible for causing liver disease and hepatocellular carcinoma. During the genesis of infection, HBV establishes an independent minichromosome consisting of the viral covalently closed circular DNA (cccDNA) genome and host histones. The viral X gene must be expressed immediately upon infection to induce degradation of the host silencing factor, Smc5/6. However, the relationship between cccDNA chromatinization and X gene transcription remains poorly understood. Establishing a reconstituted viral minichromosome platform, we found that nucleosome occupancy in cccDNA drives X transcription. We corroborated these findings in cells and further showed that the chromatin destabilizing molecule CBL137 inhibits X transcription and HBV infection in hepatocytes. Our results shed light on a long-standing paradox and represent a potential new therapeutic avenue for the treatment of chronic HBV infection.
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Hoggard T, Chacin E, Hollatz AJ, Kurat CF, Fox CA. The budding yeast Fkh1 Forkhead associated (FHA) domain promoted a G1-chromatin state and the activity of chromosomal DNA replication origins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.16.580712. [PMID: 38405780 PMCID: PMC10889021 DOI: 10.1101/2024.02.16.580712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
In Saccharomyces cerevisiae, the forkhead (Fkh) transcription factor Fkh1 (forkhead homolog) enhances the activity of many DNA replication origins that act in early S-phase (early origins). Current models posit that Fkh1 acts directly to promote these origins' activity by binding to origin-adjacent Fkh1 binding sites (FKH sites). However, the post-DNA binding functions that Fkh1 uses to promote early origin activity are poorly understood. Fkh1 contains a conserved FHA (forkhead associated) domain, a protein-binding module with specificity for phosphothreonine (pT)-containing partner proteins. At a small subset of yeast origins, the Fkh1-FHA domain enhances the ORC (origin recognition complex)-origin binding step, the G1-phase event that initiates the origin cycle. However, the importance of the Fkh1-FHA domain to either chromosomal replication or ORC-origin interactions at genome scale is unclear. Here, S-phase SortSeq experiments were used to compare genome replication in proliferating FKH1 and fkh1-R80A mutant cells. The Fkh1-FHA domain promoted the activity of 100 origins that act in early to mid- S-phase, including the majority of centromere-associated origins, while simultaneously inhibiting 100 late origins. Thus, in the absence of a functional Fkh1-FHA domain, the temporal landscape of the yeast genome was flattened. Origins are associated with a positioned nucleosome array that frames a nucleosome depleted region (NDR) over the origin, and ORC-origin binding is necessary but not sufficient for this chromatin organization. To ask whether the Fkh1-FHA domain had an impact on this chromatin architecture at origins, ORC ChIPSeq data generated from proliferating cells and MNaseSeq data generated from G1-arrested and proliferating cell populations were assessed. Origin groups that were differentially regulated by the Fkh1-FHA domain were characterized by distinct effects of this domain on ORC-origin binding and G1-phase chromatin. Thus, the Fkh1-FHA domain controlled the distinct chromatin architecture at early origins in G1-phase and regulated origin activity in S-phase.
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Affiliation(s)
- Timothy Hoggard
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison
| | - Erika Chacin
- Biomedical Center Munich (BMC), Division of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Martinsried, Germany
| | - Allison J. Hollatz
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison
- Integrated Program in Biochemistry, University of Wisconsin, Madison
| | - Christoph F. Kurat
- Biomedical Center Munich (BMC), Division of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Martinsried, Germany
| | - Catherine A. Fox
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison
- Integrated Program in Biochemistry, University of Wisconsin, Madison
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7
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Zhao Y, Zhang N, Perez Novo C, Wang Y, Zhang L. Decreased histone expression in chronic rhinosinusitis with nasal polyps. Asia Pac Allergy 2024; 14:70-76. [PMID: 38827263 PMCID: PMC11142755 DOI: 10.5415/apallergy.0000000000000140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 01/23/2024] [Indexed: 06/04/2024] Open
Abstract
Background Histones have been associated with human diseases. However, the implication of extranuclear histone proteins and their potential mechanism in the pathophysiology of chronic rhinosinusitis (CRS) have not been thoroughly investigated. This study was designed to evaluate the role of histones in patients with CRS by comparing histone expression between patients and controls. Methods Nasal polyp (NP) tissues were obtained, and their comprehensive gene expression profiles were investigated by microarray analysis. Differences in expression were verified by reverse transcriptase polymerase chain reaction and immunohistochemical staining. Cell culture and flow cytometry were used to evaluate the role of histones in the pathogenesis of polyps. Results Significant differences in the microarray analysis were observed between the patient and control groups (P < 0.01). It was found by flow cytometry that the histone (H2BK) can promote cell apoptosis in NPs. Conclusion Our results indicate that reduced expression of H2BK may contribute to the imbalance process of cell proliferation and apoptosis in CRS with NP.
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Affiliation(s)
- Yanming Zhao
- Department of Otolaryngology Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, China
| | - Nan Zhang
- Upper Airways Research Laboratory (URL), Department of Oto-Rhino-Laryngology, Ghent University Hospital, Ghent, Belgium
| | - Claudina Perez Novo
- Upper Airways Research Laboratory (URL), Department of Oto-Rhino-Laryngology, Ghent University Hospital, Ghent, Belgium
| | - Yang Wang
- Beijing key laboratory of nasal diseases, Beijing Institute of Otolaryngology, Beijing, China
| | - Luo Zhang
- Department of Otolaryngology Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, China
- Beijing key laboratory of nasal diseases, Beijing Institute of Otolaryngology, Beijing, China
- Department of Allergy, Beijing TongRen Hospital, Capital Medical University, Beijing, China
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8
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Hövel I, Bader R, Louwers M, Haring M, Peek K, Gent JI, Stam M. RNA-directed DNA methylation mutants reduce histone methylation at the paramutated maize booster1 enhancer. PLANT PHYSIOLOGY 2024; 195:1161-1179. [PMID: 38366582 PMCID: PMC11142347 DOI: 10.1093/plphys/kiae072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 12/19/2023] [Accepted: 12/25/2023] [Indexed: 02/18/2024]
Abstract
Paramutation is the transfer of mitotically and meiotically heritable silencing information between two alleles. With paramutation at the maize (Zea mays) booster1 (b1) locus, the low-expressed B' epiallele heritably changes the high-expressed B-I epiallele into B' with 100% frequency. This requires specific tandem repeats and multiple components of the RNA-directed DNA methylation pathway, including the RNA-dependent RNA polymerase (encoded by mediator of paramutation1, mop1), the second-largest subunit of RNA polymerase IV and V (NRP(D/E)2a, encoded by mop2), and the largest subunit of RNA Polymerase IV (NRPD1, encoded by mop3). Mutations in mop genes prevent paramutation and release silencing at the B' epiallele. In this study, we investigated the effect of mutations in mop1, mop2, and mop3 on chromatin structure and DNA methylation at the B' epiallele, and especially the regulatory hepta-repeat 100 kb upstream of the b1 gene. Mutations in mop1 and mop3 resulted in decreased repressive histone modifications H3K9me2 and H3K27me2 at the hepta-repeat. Associated with this decrease were partial activation of the hepta-repeat enhancer function, formation of a multi-loop structure, and elevated b1 expression. In mop2 mutants, which do not show elevated b1 expression, H3K9me2, H3K27me2 and a single-loop structure like in wild-type B' were retained. Surprisingly, high CG and CHG methylation levels at the B' hepta-repeat remained in all three mutants, and CHH methylation was low in both wild type and mutants. Our results raise the possibility of MOP factors mediating RNA-directed histone methylation rather than RNA-directed DNA methylation at the b1 locus.
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Affiliation(s)
- Iris Hövel
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, P.O. Box 1210, 1090 GE Amsterdam, The Netherlands
| | - Rechien Bader
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, P.O. Box 1210, 1090 GE Amsterdam, The Netherlands
| | - Marieke Louwers
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, P.O. Box 1210, 1090 GE Amsterdam, The Netherlands
- argenx BV, Industriepark Zwijnaarde 7, 9052 Zwijnaarde (Ghent), Belgium
| | - Max Haring
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, P.O. Box 1210, 1090 GE Amsterdam, The Netherlands
- University Library, Universiteit van Amsterdam, P.O. Box 19185, 1000 GD Amsterdam, The Netherlands
| | - Kevin Peek
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, P.O. Box 1210, 1090 GE Amsterdam, The Netherlands
| | - Jonathan I Gent
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Maike Stam
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, P.O. Box 1210, 1090 GE Amsterdam, The Netherlands
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9
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Bujosa P, Reina O, Caballé A, Casas-Lamesa A, Torras-Llort M, Pérez-Roldán J, Nacht AS, Vicent GP, Bernués J, Azorín F. Linker histone H1 regulates homeostasis of heterochromatin-associated cRNAs. Cell Rep 2024; 43:114137. [PMID: 38662543 DOI: 10.1016/j.celrep.2024.114137] [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: 04/14/2023] [Revised: 12/23/2023] [Accepted: 04/08/2024] [Indexed: 06/01/2024] Open
Abstract
Chromatin-associated RNAs (cRNAs) are a poorly characterized fraction of cellular RNAs that co-purify with chromatin. Their full complexity and the mechanisms regulating their packaging and chromatin association remain poorly understood. Here, we address these questions in Drosophila. We find that cRNAs constitute a heterogeneous group of RNA species that is abundant in heterochromatic transcripts. We show that heterochromatic cRNAs interact with the heterogeneous nuclear ribonucleoproteins (hnRNP) hrp36/hrp48 and that depletion of linker histone dH1 impairs this interaction. dH1 depletion induces the accumulation of RNA::DNA hybrids (R-loops) in heterochromatin and, as a consequence, increases retention of heterochromatic cRNAs. These effects correlate with increased RNA polymerase II (RNAPII) occupancy at heterochromatin. Notably, impairing cRNA assembly by depletion of hrp36/hrp48 mimics heterochromatic R-loop accumulation induced by dH1 depletion. We also show that dH1 depletion alters nucleosome organization, increasing accessibility of heterochromatin. Altogether, these perturbations facilitate annealing of cRNAs to the DNA template, enhancing R-loop formation and cRNA retention at heterochromatin.
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Affiliation(s)
- Paula Bujosa
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 4, 08028 Barcelona, Spain; Institute for Research in Biomedicine, IRB Barcelona. The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Oscar Reina
- Institute for Research in Biomedicine, IRB Barcelona. The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Adrià Caballé
- Institute for Research in Biomedicine, IRB Barcelona. The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Anna Casas-Lamesa
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 4, 08028 Barcelona, Spain; Institute for Research in Biomedicine, IRB Barcelona. The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Mònica Torras-Llort
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 4, 08028 Barcelona, Spain; Institute for Research in Biomedicine, IRB Barcelona. The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Juan Pérez-Roldán
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 4, 08028 Barcelona, Spain; Institute for Research in Biomedicine, IRB Barcelona. The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Ana Silvina Nacht
- Centre de Regulació Genòmica (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Guillermo P Vicent
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 4, 08028 Barcelona, Spain; Centre de Regulació Genòmica (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jordi Bernués
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 4, 08028 Barcelona, Spain; Institute for Research in Biomedicine, IRB Barcelona. The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain.
| | - Fernando Azorín
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 4, 08028 Barcelona, Spain; Institute for Research in Biomedicine, IRB Barcelona. The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain.
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10
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Moyung K, Li Y, Hartemink AJ, MacAlpine DM. Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.24.595391. [PMID: 38826400 PMCID: PMC11142231 DOI: 10.1101/2024.05.24.595391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Epigenetic mechanisms contribute to gene regulation by altering chromatin accessibility through changes in transcription factor (TF) and nucleosome occupancy throughout the genome. Despite numerous studies focusing on changes in gene expression, the intricate chromatin-mediated regulatory code remains largely unexplored on a comprehensive scale. We address this by employing a factor-agnostic, reverse-genetics approach that uses MNase-seq to capture genome-wide TF and nucleosome occupancies in response to the individual deletion of 201 transcriptional regulators in Saccharomyces cerevisiae, thereby assaying nearly one million mutant-gene interactions. We develop a principled approach to identify and quantify chromatin changes genome-wide, observing differences in TF and nucleosome occupancy that recapitulate well-established pathways identified by gene expression data. We also discover distinct chromatin signatures associated with the up- and downregulation of genes, and use these signatures to reveal regulatory mechanisms previously unexplored in expression-based studies. Finally, we demonstrate that chromatin features are predictive of transcriptional activity and leverage these features to reconstruct chromatin-based transcriptional regulatory networks. Overall, these results illustrate the power of an approach combining genetic perturbation with high-resolution epigenomic profiling; the latter enables a close examination of the interplay between TFs and nucleosomes genome-wide, providing a deeper, more mechanistic understanding of the complex relationship between chromatin organization and transcription.
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Affiliation(s)
- Kevin Moyung
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710
| | - Yulong Li
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710
- Department of Computer Science, Duke University, Durham, NC 27708
| | - Alexander J. Hartemink
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708
- Department of Computer Science, Duke University, Durham, NC 27708
| | - David M. MacAlpine
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710
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11
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Khan MA, Herring G, Zhu JY, Oliva M, Fourie E, Johnston B, Zhang Z, Potter J, Pineda L, Pflueger J, Swain T, Pflueger C, Lloyd JPB, Secco D, Small I, Kidd BN, Lister R. CRISPRi-based circuits to control gene expression in plants. Nat Biotechnol 2024:10.1038/s41587-024-02236-w. [PMID: 38769424 DOI: 10.1038/s41587-024-02236-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 04/10/2024] [Indexed: 05/22/2024]
Abstract
The construction of synthetic gene circuits in plants has been limited by a lack of orthogonal and modular parts. Here, we implement a CRISPR (clustered regularly interspaced short palindromic repeats) interference (CRISPRi)-based reversible gene circuit platform in plants. We create a toolkit of engineered repressible promoters of different strengths and construct NOT and NOR gates in Arabidopsis thaliana protoplasts. We determine the optimal processing system to express single guide RNAs from RNA Pol II promoters to introduce NOR gate programmability for interfacing with host regulatory sequences. The performance of a NOR gate in stably transformed Arabidopsis plants demonstrates the system's programmability and reversibility in a complex multicellular organism. Furthermore, cross-species activity of CRISPRi-based logic gates is shown in Physcomitrium patens, Triticum aestivum and Brassica napus protoplasts. Layering multiple NOR gates together creates OR, NIMPLY and AND logic functions, highlighting the modularity of our system. Our CRISPRi circuits are orthogonal, compact, reversible, programmable and modular and provide a platform for sophisticated spatiotemporal control of gene expression in plants.
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Affiliation(s)
- Muhammad Adil Khan
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Australian Research Council Centre of Excellence in Plants for Space, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Gabrielle Herring
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Australian Research Council Centre of Excellence in Plants for Space, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Jia Yuan Zhu
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Australian Research Council Centre of Excellence in Plants for Space, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Marina Oliva
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Australian Research Council Centre of Excellence in Plants for Space, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Elliott Fourie
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Australian Research Council Centre of Excellence in Plants for Space, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Benjamin Johnston
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Zhining Zhang
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Jarred Potter
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Luke Pineda
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Jahnvi Pflueger
- Harry Perkins Institute of Medical Research, The University of Western Australia, Perth, Western Australia, Australia
| | - Tessa Swain
- Harry Perkins Institute of Medical Research, The University of Western Australia, Perth, Western Australia, Australia
| | - Christian Pflueger
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Harry Perkins Institute of Medical Research, The University of Western Australia, Perth, Western Australia, Australia
| | - James P B Lloyd
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Australian Research Council Centre of Excellence in Plants for Space, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - David Secco
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Ian Small
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Australian Research Council Centre of Excellence in Plants for Space, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Brendan N Kidd
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia.
- CSIRO Synthetic Biology Future Science Platform, Brisbane, Queensland, Australia.
| | - Ryan Lister
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia.
- Australian Research Council Centre of Excellence in Plants for Space, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia.
- Harry Perkins Institute of Medical Research, The University of Western Australia, Perth, Western Australia, Australia.
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12
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Rudenko V, Korotkov E. Study of Dispersed Repeats in the Cyanidioschyzon merolae Genome. Int J Mol Sci 2024; 25:4441. [PMID: 38674025 PMCID: PMC11050394 DOI: 10.3390/ijms25084441] [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: 02/19/2024] [Revised: 04/08/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
In this study, we applied the iterative procedure (IP) method to search for families of highly diverged dispersed repeats in the genome of Cyanidioschyzon merolae, which contains over 16 million bases. The algorithm included the construction of position weight matrices (PWMs) for repeat families and the identification of more dispersed repeats based on the PWMs using dynamic programming. The results showed that the C. merolae genome contained 20 repeat families comprising a total of 33,938 dispersed repeats, which is significantly more than has been previously found using other methods. The repeats varied in length from 108 to 600 bp (522.54 bp in average) and occupied more than 72% of the C. merolae genome, whereas previously identified repeats, including tandem repeats, have been shown to constitute only about 28%. The high genomic content of dispersed repeats and their location in the coding regions suggest a significant role in the regulation of the functional activity of the genome.
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Affiliation(s)
- Valentina Rudenko
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia;
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13
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Zhang C, Liu D. Transcription Factor Binding Site in Promoter Determines the Pattern of Plasmid-Based Transgene Expression In Vivo. Pharmaceutics 2024; 16:544. [PMID: 38675205 PMCID: PMC11055139 DOI: 10.3390/pharmaceutics16040544] [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: 02/08/2024] [Revised: 04/11/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
Understanding the regulation of transgene expression is critical for the success of plasmid-based gene therapy and vaccine development. In this study, we used two sets of plasmid vectors containing secreted embryonic alkaline phosphatase or the mouse IL-10 gene as a reporter and investigated the role of promoter elements in regulating transgene expression in vivo. We demonstrated in mice that hydrodynamic transfer of plasmids with the CMV promoter resulted in a high level of reporter gene expression that declined rapidly over time. In contrast, when plasmids with albumin promoters were used, a lower but sustained gene expression pattern was observed. We also found that plasmids containing a shorter CMV promoter sequence with fewer transcription factor binding sites showed a decrease in the peak level of gene expression without changing the overall pattern of reporter gene expression. The replacement of regulatory elements in the CMV promoter with a single regulatory element of the albumin promoter changed the pattern of transient gene expression seen in the CMV promoter to a pattern of sustained gene expression identical to that of a full albumin promoter. ChIP analyses demonstrated an elevated binding of acetylated histones and TATA box-binding protein to the promoter carrying regulatory elements of the albumin promoter. These results suggest that the strength of a promoter is determined by the number of appropriate transcription factor binding sites, while gene expression persistence is determined by the presence of regulatory elements capable of recruiting epigenetic modifying complexes that make the promoter accessible for transcription. This study provides important insights into the mechanisms underlying gene expression regulation in vivo, which can be used to improve plasmid-based gene therapy and vaccine development.
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Affiliation(s)
| | - Dexi Liu
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia College of Pharmacy, Athens, GA 30602, USA;
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14
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Xi S, Nguyen T, Murray S, Lorenz P, Mellor J. Size fractionated NET-Seq reveals a conserved architecture of transcription units around yeast genes. Yeast 2024; 41:222-241. [PMID: 38433440 DOI: 10.1002/yea.3931] [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: 10/30/2023] [Revised: 02/06/2024] [Accepted: 02/09/2024] [Indexed: 03/05/2024] Open
Abstract
Genomes from yeast to humans are subject to pervasive transcription. A single round of pervasive transcription is sufficient to alter local chromatin conformation, nucleosome dynamics and gene expression, but is hard to distinguish from background signals. Size fractionated native elongating transcript sequencing (sfNET-Seq) was developed to precisely map nascent transcripts independent of expression levels. RNAPII-associated nascent transcripts are fractionation into different size ranges before library construction. When anchored to the transcription start sites (TSS) of annotated genes, the combined pattern of the output metagenes gives the expected reference pattern. Bioinformatic pattern matching to the reference pattern identified 9542 transcription units in Saccharomyces cerevisiae, of which 47% are coding and 53% are noncoding. In total, 3113 (33%) are unannotated noncoding transcription units. Anchoring all transcription units to the TSS or polyadenylation site (PAS) of annotated genes reveals distinctive architectures of linked pairs of divergent transcripts approximately 200nt apart. The Reb1 transcription factor is enriched 30nt downstream of the PAS only when an upstream (TSS -60nt with respect to PAS) noncoding transcription unit co-occurs with a downstream (TSS +150nt) coding transcription unit and acts to limit levels of upstream antisense transcripts. The potential for extensive transcriptional interference is evident from low abundance unannotated transcription units with variable TSS (median -240nt) initiating within a 500nt window upstream of, and transcribing over, the promoters of protein-coding genes. This study confirms a highly interleaved yeast genome with different types of transcription units altering the chromatin landscape in distinctive ways, with the potential to exert extensive regulatory control.
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Affiliation(s)
- Shidong Xi
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Tania Nguyen
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Struan Murray
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Phil Lorenz
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Jane Mellor
- Department of Biochemistry, University of Oxford, Oxford, UK
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15
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Eustermann S, Patel AB, Hopfner KP, He Y, Korber P. Energy-driven genome regulation by ATP-dependent chromatin remodellers. Nat Rev Mol Cell Biol 2024; 25:309-332. [PMID: 38081975 DOI: 10.1038/s41580-023-00683-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2023] [Indexed: 03/28/2024]
Abstract
The packaging of DNA into chromatin in eukaryotes regulates gene transcription, DNA replication and DNA repair. ATP-dependent chromatin remodelling enzymes (re)arrange nucleosomes at the first level of chromatin organization. Their Snf2-type motor ATPases alter histone-DNA interactions through a common DNA translocation mechanism. Whether remodeller activities mainly catalyse nucleosome dynamics or accurately co-determine nucleosome organization remained unclear. In this Review, we discuss the emerging mechanisms of chromatin remodelling: dynamic remodeller architectures and their interactions, the inner workings of the ATPase cycle, allosteric regulation and pathological dysregulation. Recent mechanistic insights argue for a decisive role of remodellers in the energy-driven self-organization of chromatin, which enables both stability and plasticity of genome regulation - for example, during development and stress. Different remodellers, such as members of the SWI/SNF, ISWI, CHD and INO80 families, process (epi)genetic information through specific mechanisms into distinct functional outputs. Combinatorial assembly of remodellers and their interplay with histone modifications, histone variants, DNA sequence or DNA-bound transcription factors regulate nucleosome mobilization or eviction or histone exchange. Such input-output relationships determine specific nucleosome positions and compositions with distinct DNA accessibilities and mediate differential genome regulation. Finally, remodeller genes are often mutated in diseases characterized by genome dysregulation, notably in cancer, and we discuss their physiological relevance.
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Affiliation(s)
- Sebastian Eustermann
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Avinash B Patel
- Department of Molecular Biosciences, Robert H. Lurie Comprehensive Cancer Center, Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
| | - Karl-Peter Hopfner
- Gene Center and Department of Biochemistry, Faculty of Chemistry and Pharmacy, LMU Munich, Munich, Germany
| | - Yuan He
- Department of Molecular Biosciences, Robert H. Lurie Comprehensive Cancer Center, Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA.
| | - Philipp Korber
- Biomedical Center (BMC), Molecular Biology, Faculty of Medicine, LMU Munich, Martinsried, Germany.
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16
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Georis I, Ronsmans A, Vierendeels F, Dubois E. Differing SAGA module requirements for NCR-sensitive gene transcription in yeast. Yeast 2024; 41:207-221. [PMID: 37357465 DOI: 10.1002/yea.3885] [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: 10/02/2022] [Revised: 04/24/2023] [Accepted: 05/25/2023] [Indexed: 06/27/2023] Open
Abstract
Nitrogen catabolite repression (NCR) is a means for yeast to adapt its transcriptome to changing nitrogen sources in its environment. In conditions of derepression (under poor nitrogen conditions, upon rapamycin treatment, or when glutamine production is inhibited), two transcriptional activators of the GATA family are recruited to NCR-sensitive promoters and activate transcription of NCR-sensitive genes. Earlier observations have involved the Spt-Ada-Gcn5 acetyltransferase (SAGA) chromatin remodeling complex in these transcriptional regulations. In this report, we provide an illustration of the varying NCR-sensitive responses and question whether differing SAGA recruitment could explain this diversity of responses.
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Affiliation(s)
| | | | | | - Evelyne Dubois
- Labiris, Brussels, Belgium
- Université Libre de Bruxelles, Brussels, Belgium
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17
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Atanasoff-Kardjalieff AK, Berger H, Steinert K, Janevska S, Ponts N, Humpf HU, Kalinina S, Studt-Reinhold L. Incorporation of the histone variant H2A.Z counteracts gene silencing mediated by H3K27 trimethylation in Fusarium fujikuroi. Epigenetics Chromatin 2024; 17:7. [PMID: 38509556 PMCID: PMC10953111 DOI: 10.1186/s13072-024-00532-y] [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: 09/23/2023] [Accepted: 02/15/2024] [Indexed: 03/22/2024] Open
Abstract
BACKGROUND Fusarium fujikuroi is a pathogen of rice causing diverse disease symptoms such as 'bakanae' or stunting, most likely due to the production of various natural products (NPs) during infection. Fusaria have the genetic potential to synthesize a plethora of these compounds with often diverse bioactivity. The capability to synthesize NPs exceeds the number of those being produced by far, implying a gene regulatory network decisive to induce production. One such regulatory layer is the chromatin structure and chromatin-based modifications associated with it. One prominent example is the exchange of histones against histone variants such as the H2A variant H2A.Z. Though H2A.Z already is well studied in several model organisms, its regulatory functions are not well understood. Here, we used F. fujikuroi as a model to explore the role of the prominent histone variant FfH2A.Z in gene expression within euchromatin and facultative heterochromatin. RESULTS Through the combination of diverse '-omics' methods, we show the global distribution of FfH2A.Z and analyze putative crosstalks between the histone variant and two prominent histone marks, i.e., H3K4me3 and H3K27me3, important for active gene transcription and silencing, respectively. We demonstrate that, if FfH2A.Z is positioned at the + 1-nucleosome, it poises chromatin for gene transcription, also within facultative heterochromatin. Lastly, functional characterization of FfH2A.Z overexpression and depletion mutants revealed that FfH2A.Z is important for wild type-like fungal development and secondary metabolism. CONCLUSION In this study, we show that the histone variant FfH2A.Z is a mark of positive gene transcription and acts independently of the chromatin state most likely through the stabilization of the + 1-nucleosome. Furthermore, we demonstrate that FfH2A.Z depletion does not influence the establishment of both H3K27me3 and H3K4me3, thus indicating no crosstalk between FfH2A.Z and both histone marks. These results highlight the manifold functions of the histone variant FfH2A.Z in the phytopathogen F. fujikuroi, which are distinct regarding gene transcription and crosstalk with the two prominent histone marks H3K27me3 and H3K4me3, as proposed for other model organisms.
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Affiliation(s)
- Anna K Atanasoff-Kardjalieff
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz Strasse 24, Tulln an der Donau, 3430, Austria
| | - Harald Berger
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz Strasse 24, Tulln an der Donau, 3430, Austria
| | - Katharina Steinert
- Institute of Food Chemistry, University of Münster, Corrensstraße 45, 48149, Münster, Germany
| | - Slavica Janevska
- (Epi-)Genetic Regulation of Fungal Virulence, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, 07745, Jena, Germany
| | - Nadia Ponts
- INRAE, UR1264 Mycology and Food Safety (MycSA), Villenave d'Ornon, 33882, France
| | - Hans-Ulrich Humpf
- Institute of Food Chemistry, University of Münster, Corrensstraße 45, 48149, Münster, Germany
| | - Svetlana Kalinina
- Institute of Food Chemistry, University of Münster, Corrensstraße 45, 48149, Münster, Germany
| | - Lena Studt-Reinhold
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz Strasse 24, Tulln an der Donau, 3430, Austria.
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18
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Sabantsev A, Deindl S. The voyage is as important as the harbor. eLife 2024; 13:e96836. [PMID: 38488335 PMCID: PMC10942777 DOI: 10.7554/elife.96836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2024] Open
Abstract
To find nucleosomes, chromatin remodelers slide and hop along DNA, and their direction of approach affects the direction that nucleosomes slide in.
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Affiliation(s)
- Anton Sabantsev
- Department of Cell and Molecular Biology, Uppsala UniversityUppsalaSweden
| | - Sebastian Deindl
- Department of Cell and Molecular Biology, Uppsala UniversityUppsalaSweden
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19
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Chen X, Xu Y. Interplay between the transcription preinitiation complex and the +1 nucleosome. Trends Biochem Sci 2024; 49:145-155. [PMID: 38218671 DOI: 10.1016/j.tibs.2023.12.001] [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: 08/18/2023] [Revised: 11/27/2023] [Accepted: 12/01/2023] [Indexed: 01/15/2024]
Abstract
Eukaryotic transcription starts with the assembly of a preinitiation complex (PIC) on core promoters. Flanking this region is the +1 nucleosome, the first nucleosome downstream of the core promoter. While this nucleosome is rich in epigenetic marks and plays a key role in transcription regulation, how the +1 nucleosome interacts with the transcription machinery has been a long-standing question. Here, we summarize recent structural and functional studies of the +1 nucleosome in complex with the PIC. We specifically focus on how differently organized promoter-nucleosome templates affect the assembly of the PIC and PIC-Mediator on chromatin and result in distinct transcription initiation.
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Affiliation(s)
- Xizi Chen
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yanhui Xu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China.
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20
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Li L, Chen K, Sia Y, Hu P, Ye Y, Chen Z. Structure of the ISW1a complex bound to the dinucleosome. Nat Struct Mol Biol 2024; 31:266-274. [PMID: 38177688 DOI: 10.1038/s41594-023-01174-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 11/03/2023] [Indexed: 01/06/2024]
Abstract
Nucleosomes are basic repeating units of chromatin and form regularly spaced arrays in cells. Chromatin remodelers alter the positions of nucleosomes and are vital in regulating chromatin organization and gene expression. Here we report the cryo-EM structure of chromatin remodeler ISW1a complex from Saccharomyces cerevisiae bound to the dinucleosome. Each subunit of the complex recognizes a different nucleosome. The motor subunit binds to the mobile nucleosome and recognizes the acidic patch through two arginine residues, while the DNA-binding module interacts with the entry DNA at the nucleosome edge. This nucleosome-binding mode provides the structural basis for linker DNA sensing of the motor. Notably, the Ioc3 subunit recognizes the disk face of the adjacent nucleosome through interacting with the H4 tail, the acidic patch and the nucleosomal DNA, which plays a role in the spacing activity in vitro and in nucleosome organization and cell fitness in vivo. Together, these findings support the nucleosome spacing activity of ISW1a and add a new mode of nucleosome remodeling in the context of a chromatin environment.
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Affiliation(s)
- Lifei Li
- MOE Key Laboratory of Protein Science, Tsinghua University, Beijing, P.R. China
- School of Life Science, Tsinghua University, Beijing, P.R. China
- Tsinghua-Peking Joint Center for Life Sciences, Beijing, P.R. China
- Beijing Frontier Research Center for Biological Structure, Beijing, P.R. China
| | - Kangjing Chen
- MOE Key Laboratory of Protein Science, Tsinghua University, Beijing, P.R. China
- School of Life Science, Tsinghua University, Beijing, P.R. China
- Tsinghua-Peking Joint Center for Life Sciences, Beijing, P.R. China
- Beijing Frontier Research Center for Biological Structure, Beijing, P.R. China
| | - Youyang Sia
- MOE Key Laboratory of Protein Science, Tsinghua University, Beijing, P.R. China
- School of Life Science, Tsinghua University, Beijing, P.R. China
- Tsinghua-Peking Joint Center for Life Sciences, Beijing, P.R. China
- Beijing Frontier Research Center for Biological Structure, Beijing, P.R. China
| | - Pengjing Hu
- MOE Key Laboratory of Protein Science, Tsinghua University, Beijing, P.R. China
- School of Life Science, Tsinghua University, Beijing, P.R. China
- Tsinghua-Peking Joint Center for Life Sciences, Beijing, P.R. China
- Beijing Frontier Research Center for Biological Structure, Beijing, P.R. China
| | - Youpi Ye
- MOE Key Laboratory of Protein Science, Tsinghua University, Beijing, P.R. China
- School of Life Science, Tsinghua University, Beijing, P.R. China
- Tsinghua-Peking Joint Center for Life Sciences, Beijing, P.R. China
- Beijing Frontier Research Center for Biological Structure, Beijing, P.R. China
| | - Zhucheng Chen
- MOE Key Laboratory of Protein Science, Tsinghua University, Beijing, P.R. China.
- School of Life Science, Tsinghua University, Beijing, P.R. China.
- Tsinghua-Peking Joint Center for Life Sciences, Beijing, P.R. China.
- Beijing Frontier Research Center for Biological Structure, Beijing, P.R. China.
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21
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Liu SJ, Casey-Clyde T, Cho NW, Swinderman J, Pekmezci M, Dougherty MC, Foster K, Chen WC, Villanueva-Meyer JE, Swaney DL, Vasudevan HN, Choudhury A, Pak J, Breshears JD, Lang UE, Eaton CD, Hiam-Galvez KJ, Stevenson E, Chen KH, Lien BV, Wu D, Braunstein SE, Sneed PK, Magill ST, Lim D, McDermott MW, Berger MS, Perry A, Krogan NJ, Hansen MR, Spitzer MH, Gilbert L, Theodosopoulos PV, Raleigh DR. Epigenetic reprogramming shapes the cellular landscape of schwannoma. Nat Commun 2024; 15:476. [PMID: 38216587 PMCID: PMC10786948 DOI: 10.1038/s41467-023-40408-5] [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: 02/06/2023] [Accepted: 05/25/2023] [Indexed: 01/14/2024] Open
Abstract
Mechanisms specifying cancer cell states and response to therapy are incompletely understood. Here we show epigenetic reprogramming shapes the cellular landscape of schwannomas, the most common tumors of the peripheral nervous system. We find schwannomas are comprised of 2 molecular groups that are distinguished by activation of neural crest or nerve injury pathways that specify tumor cell states and the architecture of the tumor immune microenvironment. Moreover, we find radiotherapy is sufficient for interconversion of neural crest schwannomas to immune-enriched schwannomas through epigenetic and metabolic reprogramming. To define mechanisms underlying schwannoma groups, we develop a technique for simultaneous interrogation of chromatin accessibility and gene expression coupled with genetic and therapeutic perturbations in single-nuclei. Our results elucidate a framework for understanding epigenetic drivers of tumor evolution and establish a paradigm of epigenetic and metabolic reprograming of cancer cells that shapes the immune microenvironment in response to radiotherapy.
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Affiliation(s)
- S John Liu
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
- Arc Institute, Palo Alto, CA, 94304, USA
| | - Tim Casey-Clyde
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Nam Woo Cho
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94143, USA
- Parker Institute for Cancer Immunotherapy, Chan Zuckerberg Biohub, and Departments of Otolaryngology, and Microbiology and Immunology, University of California San Francisco, San Francisco, CA, 94115, USA
| | - Jason Swinderman
- Arc Institute, Palo Alto, CA, 94304, USA
- Department of Urology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Melike Pekmezci
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Mark C Dougherty
- Departments of Otolaryngology and Neurosurgery, University of Iowa, Iowa City, IA, 52242, USA
| | - Kyla Foster
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - William C Chen
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Javier E Villanueva-Meyer
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, USA
| | - Danielle L Swaney
- J. David Gladstone Institutes, California Institute for Quantitative Biosciences, Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Harish N Vasudevan
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Abrar Choudhury
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Joanna Pak
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
- Arc Institute, Palo Alto, CA, 94304, USA
| | - Jonathan D Breshears
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Ursula E Lang
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Dermatology, University of California San Francisco, San Francisco, CA, 94115, USA
| | - Charlotte D Eaton
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Kamir J Hiam-Galvez
- Parker Institute for Cancer Immunotherapy, Chan Zuckerberg Biohub, and Departments of Otolaryngology, and Microbiology and Immunology, University of California San Francisco, San Francisco, CA, 94115, USA
| | - Erica Stevenson
- J. David Gladstone Institutes, California Institute for Quantitative Biosciences, Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Kuei-Ho Chen
- J. David Gladstone Institutes, California Institute for Quantitative Biosciences, Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Brian V Lien
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, 94143, USA
| | - David Wu
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Steve E Braunstein
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Penny K Sneed
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Stephen T Magill
- Department of Neurological Surgery, Northwestern University, Chicago, IL, 60611, USA
| | - Daniel Lim
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, 94143, USA
| | | | - Mitchel S Berger
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Arie Perry
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Nevan J Krogan
- J. David Gladstone Institutes, California Institute for Quantitative Biosciences, Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Marlan R Hansen
- Departments of Otolaryngology and Neurosurgery, University of Iowa, Iowa City, IA, 52242, USA
| | - Matthew H Spitzer
- Parker Institute for Cancer Immunotherapy, Chan Zuckerberg Biohub, and Departments of Otolaryngology, and Microbiology and Immunology, University of California San Francisco, San Francisco, CA, 94115, USA
| | - Luke Gilbert
- Arc Institute, Palo Alto, CA, 94304, USA
- Department of Urology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Philip V Theodosopoulos
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, 94143, USA
| | - David R Raleigh
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94143, USA.
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, 94143, USA.
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA.
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22
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Boltengagen M, Verhagen D, Wolff MR, Oberbeckmann E, Hanke M, Gerland U, Korber P, Mueller-Planitz F. A single fiber view of the nucleosome organization in eukaryotic chromatin. Nucleic Acids Res 2024; 52:166-185. [PMID: 37994698 PMCID: PMC10783498 DOI: 10.1093/nar/gkad1098] [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: 02/07/2023] [Revised: 10/13/2023] [Accepted: 10/31/2023] [Indexed: 11/24/2023] Open
Abstract
Eukaryotic cells are thought to arrange nucleosomes into extended arrays with evenly spaced nucleosomes phased at genomic landmarks. Here we tested to what extent this stereotypic organization describes the nucleosome organization in Saccharomyces cerevisiae using Fiber-Seq, a long-read sequencing technique that maps entire nucleosome arrays on individual chromatin fibers in a high throughput manner. With each fiber coming from a different cell, Fiber-Seq uncovers cell-to-cell heterogeneity. The long reads reveal the nucleosome architecture even over repetitive DNA such as the ribosomal DNA repeats. The absolute nucleosome occupancy, a parameter that is difficult to obtain with conventional sequencing approaches, is a direct readout of Fiber-Seq. We document substantial deviations from the stereotypical nucleosome organization with unexpectedly long linker DNAs between nucleosomes, gene bodies missing entire nucleosomes, cell-to-cell heterogeneity in nucleosome occupancy, heterogeneous phasing of arrays and irregular nucleosome spacing. Nucleosome array structures are indistinguishable throughout the gene body and with respect to the direction of transcription arguing against transcription promoting array formation. Acute nucleosome depletion destroyed most of the array organization indicating that nucleosome remodelers cannot efficiently pack nucleosomes under those conditions. Given that nucleosomes are cis-regulatory elements, the cell-to-cell heterogeneity uncovered by Fiber-Seq provides much needed information to understand chromatin structure and function.
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Affiliation(s)
- Mark Boltengagen
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307 Dresden, Germany
| | - Daan Verhagen
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307 Dresden, Germany
- Molecular Biology, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Michael Roland Wolff
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307 Dresden, Germany
- Physics of Complex Biosystems, Physics Department, Technical University of Munich, Garching, Germany
| | - Elisa Oberbeckmann
- Molecular Biology, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Matthias Hanke
- Physics of Complex Biosystems, Physics Department, Technical University of Munich, Garching, Germany
| | - Ulrich Gerland
- Physics of Complex Biosystems, Physics Department, Technical University of Munich, Garching, Germany
| | - Philipp Korber
- Molecular Biology, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Felix Mueller-Planitz
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307 Dresden, Germany
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23
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Zeitler L, André K, Alberti A, Denby Wilkes C, Soutourina J, Goldar A. A genome-wide comprehensive analysis of nucleosome positioning in yeast. PLoS Comput Biol 2024; 20:e1011799. [PMID: 38266035 PMCID: PMC10843174 DOI: 10.1371/journal.pcbi.1011799] [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: 06/27/2023] [Revised: 02/05/2024] [Accepted: 01/03/2024] [Indexed: 01/26/2024] Open
Abstract
In eukaryotic cells, the one-dimensional DNA molecules need to be tightly packaged into the spatially constraining nucleus. Folding is achieved on its lowest level by wrapping the DNA around nucleosomes. Their arrangement regulates other nuclear processes, such as transcription and DNA repair. Despite strong efforts to study nucleosome positioning using Next Generation Sequencing (NGS) data, the mechanism of their collective arrangement along the gene body remains poorly understood. Here, we classify nucleosome distributions of protein-coding genes in Saccharomyces cerevisiae according to their profile similarity and analyse their differences using functional Principal Component Analysis. By decomposing the NGS signals into their main descriptive functions, we compared wild type and chromatin remodeler-deficient strains, keeping position-specific details preserved whilst considering the nucleosome arrangement as a whole. A correlation analysis with other genomic properties, such as gene size and length of the upstream Nucleosome Depleted Region (NDR), identified key factors that influence the nucleosome distribution. We reveal that the RSC chromatin remodeler-which is responsible for NDR maintenance-is indispensable for decoupling nucleosome arrangement within the gene from positioning outside, which interfere in rsc8-depleted conditions. Moreover, nucleosome profiles in chd1Δ strains displayed a clear correlation with RNA polymerase II presence, whereas wild type cells did not indicate a noticeable interdependence. We propose that RSC is pivotal for global nucleosome organisation, whilst Chd1 plays a key role for maintaining local arrangement.
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Affiliation(s)
- Leo Zeitler
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC),Gif-sur-Yvette, France
| | - Kévin André
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC),Gif-sur-Yvette, France
| | - Adriana Alberti
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC),Gif-sur-Yvette, France
| | - Cyril Denby Wilkes
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC),Gif-sur-Yvette, France
| | - Julie Soutourina
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC),Gif-sur-Yvette, France
| | - Arach Goldar
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC),Gif-sur-Yvette, France
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24
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Haresh Liya D, Elanchezhian M, Pahari M, Mouroug Anand N, Suresh S, Balaji N, Kumar Jainarayanan A. QPromoters: sequence based prediction of promoter strength in Saccharomyces cesrevisiae. ALL LIFE 2023. [DOI: 10.1080/26895293.2023.2168304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Devang Haresh Liya
- Department of Physical Sciences, Indian Institute of Science Education and Research, Mohali, India
| | - Mirudula Elanchezhian
- Department of Biological Sciences, Indian Institute of Science Education and Research, Mohali, India
| | - Mukulika Pahari
- Department of Computer Engineering, Ramrao Adik Institute of Technology, DY Patil Deemed to be University, Navi Mumbai, India
| | - Nithishwer Mouroug Anand
- Department of Physical Sciences, Indian Institute of Science Education and Research, Mohali, India
| | - Shivani Suresh
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Nivedha Balaji
- School of Biology and Environmental Sciences (SBES), University College Dublin, Dublin, Ireland
| | - Ashwin Kumar Jainarayanan
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
- Interdisciplinary Bioscience Doctoral Training Program and Exeter College, University of Oxford, Oxford, UK
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25
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Khamwachirapithak P, Guillaume-Schoepfer D, Chansongkrow P, Teichmann SA, Wigge PA, Charoensawan V. Characterizing Different Modes of Interplay Between Rap1 and H3 Using Inducible H3-depletion Yeast. J Mol Biol 2023; 435:168355. [PMID: 37935256 DOI: 10.1016/j.jmb.2023.168355] [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: 08/02/2023] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 11/09/2023]
Abstract
Histones and transcription factors (TFs) are two important DNA-binding proteins that interact, compete, and together regulate transcriptional processes in response to diverse internal and external stimuli. Condition-specific depletion of histones in Saccharomyces cerevisiae using a galactose-inducible H3 promoter provides a suitable framework for examining transcriptional alteration resulting from reduced nucleosome content. However, the effect on DNA binding activities of TFs is yet to be fully explored. In this work, we combine ChIP-seq of H3 with RNA-seq to elucidate the genome-scale relationships between H3 occupancy patterns and transcriptional dynamics before and after global H3 depletion. ChIP-seq of Rap1 is also conducted in the H3-depletion and control treatments, to investigate the interplay between this master regulator TF and nucleosomal H3, and to explore the impact on diverse transcriptional responses of different groups of target genes and functions. Ultimately, we propose a working model and testable hypotheses regarding the impact of global and local H3 depletion on transcriptional changes. We also demonstrate different potential modes of interaction between Rap1 and H3, which sheds light on the potential multifunctional regulatory capabilities of Rap1 and potentially other pioneer factors.
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Affiliation(s)
- Peerapat Khamwachirapithak
- Doctor of Philosophy Program in Biochemistry (International Program), Faculty of Science, Mahidol University, Bangkok, Thailand; Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | | | - Pakkanan Chansongkrow
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK; Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, UK.
| | - Philip A Wigge
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom; University Potsdam, Institute for Biochemistry and Biology, Molecular Biology, Karl-Liebknecht-Str, Potsdam-Golm, Germany; Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany.
| | - Varodom Charoensawan
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand; Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom; Systems Biology of Diseases Research Unit, Faculty of Science, Mahidol University, Bangkok, Thailand; Integrative Computational BioScience (ICBS) center, Mahidol University, Nakhon Pathom, Thailand; School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, Thailand.
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26
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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:gr.278273.123. [PMID: 38081658 PMCID: PMC10760526 DOI: 10.1101/gr.278273.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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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27
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Converso C, Pierrakeas L, Chan L, Chowdhury S, Kuznetsov VI, Denu JM, Luk E. Nucleic acid sequence contributes to remodeler-mediated targeting of histone H2A.Z. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.06.570360. [PMID: 38106078 PMCID: PMC10723385 DOI: 10.1101/2023.12.06.570360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
The variant histone H2A.Z is inserted into nucleosomes immediately downstream of promoters and is important for transcription. The site-specific deposition of H2A.Z is catalyzed by SWR, a conserved chromatin remodeler with affinity for promoter-proximal nucleosome depleted regions (NDRs) and histone acetylation. By comparing the genomic distribution of H2A.Z in wild-type and SWR-deficient cells, we found that SWR is also responsible for depositing H2A.Z at thousands of non-canonical sites not directly linked to NDRs or histone acetylation. To understand the targeting mechanism of H2A.Z, we presented SWR with a library of nucleosomes isolated from yeast and characterized those preferred by SWR. We found that SWR prefers nucleosomes associated with intergenic over coding regions, especially when polyadenine tracks are present. Insertion of polyadenine sequences into recombinant nucleosomes near the H2A-H2B binding site stimulated the H2A.Z insertion activity of SWR. Therefore, the genome is encoded with information contributing to remodeler-mediated targeting of H2A.Z.
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28
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Brennan L, Disatham J, Menko AS, Kantorow M. Multiomic analysis implicates FOXO4 in genetic regulation of chick lens fiber cell differentiation. Dev Biol 2023; 504:25-37. [PMID: 37722500 PMCID: PMC10843493 DOI: 10.1016/j.ydbio.2023.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 09/06/2023] [Accepted: 09/14/2023] [Indexed: 09/20/2023]
Abstract
A classic model for identification of novel differentiation mechanisms and pathways is the eye lens that consists of a monolayer of quiescent epithelial cells that are the progenitors of a core of mature fully differentiated fiber cells. The differentiation of lens epithelial cells into fiber cells follows a coordinated program involving cell cycle exit, expression of key structural proteins and the hallmark elimination of organelles to achieve transparency. Although multiple mechanisms and pathways have been identified to play key roles in lens differentiation, the entirety of mechanisms governing lens differentiation remain to be discovered. A previous study established that specific chromatin accessibility changes were directly associated with the expression of essential lens fiber cell genes, suggesting that the activity of transcription factors needed for expression of these genes could be regulated through binding access to the identified chromatin regions. Sequence analysis of the identified chromatin accessible regions revealed enhanced representation of the binding sequence for the transcription factor FOXO4 suggesting a direct role for FOXO4 in expression of these genes. FOXO4 is known to regulate a variety of cellular processes including cellular response to metabolic and oxidative stress, cell cycle withdrawal, and homeostasis, suggesting a previously unidentified role for FOXO4 in the regulation of lens cell differentiation. To further evaluate the role of FOXO4 we employed a multiomics approach to analyze the relationship between genome-wide FOXO4 binding, the differentiation-specific expression of key genes, and chromatin accessibility. To better identify active promoters and enhancers we also examined histone modification through analysis of H3K27ac. Specific methods included CUT&RUN (FOXO4 binding and H3K27ac modification), RNA-seq (differentiation state specific gene expression), and ATAC-seq (chromatin accessibility). CUT&RUN identified 20,966 FOXO4 binding sites and 33,921 H3K27ac marked regions across the lens fiber cell genome. RNA-seq identified 956 genes with significantly greater expression levels in fiber cells compared to epithelial cells (log2FC > 0.7, q < 0.05) and 2548 genes with significantly lower expression levels (log2FC < -0.7, q < 0.05). Integrated analysis identified 1727 differentiation-state specific genes that were nearest neighbors to at least one FOXO4 binding site, including genes encoding lens gap junctions (GJA1, GJA3), lens structural proteins (BFSP1, CRYBB1, ASL1), and genes required for lens transparency (HSF4, NRCAM). Multiomics analysis comparing the identified FOXO4 binding sites in published ATAC-seq data revealed that chromatin accessibility was associated with FOXO4-dependent gene expression during lens differentiation. The results provide evidence for an important requirement for FOXO4 in the regulated expression of key genes required for lens differentiation and link epigenetic regulation of chromatin accessibility and H3K27ac histone modification with the function of FOXO4 in controlling lens gene expression during lens fiber cell differentiation.
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Affiliation(s)
- Lisa Brennan
- Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL, USA
| | - Joshua Disatham
- Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL, USA
| | - A Sue Menko
- Department of Pathology and Genomic Medicine, Thomas Jefferson University, Philadelphia, PA, USA
| | - Marc Kantorow
- Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL, USA.
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29
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Back G, Walther D. Predictions of DNA mechanical properties at a genomic scale reveal potentially new functional roles of DNA flexibility. NAR Genom Bioinform 2023; 5:lqad097. [PMID: 37954573 PMCID: PMC10632188 DOI: 10.1093/nargab/lqad097] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 09/28/2023] [Accepted: 10/25/2023] [Indexed: 11/14/2023] Open
Abstract
Mechanical properties of DNA have been implied to influence many of its biological functions. Recently, a new high-throughput method, called loop-seq, which allows measuring the intrinsic bendability of DNA fragments, has been developed. Using loop-seq data, we created a deep learning model to explore the biological significance of local DNA flexibility in a range of different species from different kingdoms. Consistently, we observed a characteristic and largely dinucleotide-composition-driven change of local flexibility near transcription start sites. In the presence of a TATA-box, a pronounced peak of high flexibility can be observed. Furthermore, depending on the transcription factor investigated, flanking-sequence-dependent DNA flexibility was identified as a potential factor influencing DNA binding. Compared to randomized genomic sequences, depending on species and taxa, actual genomic sequences were observed both with increased and lowered flexibility. Furthermore, in Arabidopsis thaliana, mutation rates, both de novo and fixed, were found to be associated with relatively rigid sequence regions. Our study presents a range of significant correlations between characteristic DNA mechanical properties and genomic features, the significance of which with regard to detailed molecular relevance awaits further theoretical and experimental exploration.
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Affiliation(s)
- Georg Back
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
| | - Dirk Walther
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
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30
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Brahma P, Aggarwal R, Sanyal K. Biased eviction of variant histone H3 nucleosomes triggers biofilm growth in Candida albicans. mBio 2023; 14:e0206323. [PMID: 37768046 PMCID: PMC10653867 DOI: 10.1128/mbio.02063-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 08/09/2023] [Indexed: 09/29/2023] Open
Abstract
IMPORTANCE Candida albicans lives as a commensal in most healthy humans but can cause superficial skin infections to life-threatening systemic infections. C. albicans also forms biofilms on biotic and abiotic surfaces. Biofilm cells are difficult to treat and highly resistant to antifungals. A specific set of genes is differentially regulated in biofilm cells as compared to free-floating planktonic cells of C. albicans. In this study, we addressed how a variant histone H3VCTG, a previously identified negative regulator of biofilm formation, modulates gene expression changes. By providing compelling evidence, we show that biased eviction of H3VCTG nucleosomes at the promoters of biofilm-relevant genes facilitates the accessibility of both transcription activators and repressors to modulate gene expression. Our study is a comprehensive investigation of genome-wide nucleosome occupancy in both planktonic and biofilm states, which reveals transition to an open chromatin landscape during biofilm mode of growth in C. albicans, a medically relevant pathogen.
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Affiliation(s)
- Priya Brahma
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, Karnataka, India
| | - Rashi Aggarwal
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, Karnataka, India
| | - Kaustuv Sanyal
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, Karnataka, India
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31
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Schwartz U, Komatsu T, Huber C, Lagadec F, Baumgartl C, Silberhorn E, Nuetzel M, Rayne F, Basyuk E, Bertrand E, Rehli M, Wodrich H, Laengst G. Changes in adenoviral chromatin organization precede early gene activation upon infection. EMBO J 2023; 42:e114162. [PMID: 37641864 PMCID: PMC10548178 DOI: 10.15252/embj.2023114162] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 07/10/2023] [Accepted: 08/04/2023] [Indexed: 08/31/2023] Open
Abstract
Within the virion, adenovirus DNA associates with the virus-encoded, protamine-like structural protein pVII. Whether this association is organized, and how genome packaging changes during infection and subsequent transcriptional activation is currently unclear. Here, we combined RNA-seq, MNase-seq, ChIP-seq, and single genome imaging during early adenovirus infection to unveil the structure- and time-resolved dynamics of viral chromatin changes as well as their correlation with gene transcription. Our MNase mapping data indicates that the adenoviral genome is arranged in precisely positioned nucleoprotein particles with nucleosome-like characteristics, that we term adenosomes. We identified 238 adenosomes that are positioned by a DNA sequence code and protect about 60-70 bp of DNA. The incoming adenoviral genome is more accessible at early gene loci that undergo additional chromatin de-condensation upon infection. Histone H3.3 containing nucleosomes specifically replaces pVII at distinct genomic sites and at the transcription start sites of early genes. Acetylation of H3.3 is predominant at the transcription start sites and precedes transcriptional activation. Based on our results, we propose a central role for the viral pVII nucleoprotein architecture, which is required for the dynamic structural changes during early infection, including the regulation of nucleosome assembly prior to transcription initiation. Our study thus may aid the rational development of recombinant adenoviral vectors exhibiting sustained expression in gene therapy.
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Affiliation(s)
- Uwe Schwartz
- Biochemie Zentrum RegensburgUniversity of RegensburgRegensburgGermany
| | - Tetsuro Komatsu
- Laboratory of Epigenetics and Metabolism, Institute for Molecular and Cellular RegulationGunma UniversityGunmaJapan
- CNRS UMR 5234, Microbiologie Fondamentale et PathogénicitéUniversité de BordeauxBordeauxFrance
| | - Claudia Huber
- Biochemie Zentrum RegensburgUniversity of RegensburgRegensburgGermany
| | - Floriane Lagadec
- CNRS UMR 5234, Microbiologie Fondamentale et PathogénicitéUniversité de BordeauxBordeauxFrance
- Department of Molecular Biology, Faculty of Medicine, Göttingen Center of Biosciences (GZMB)Georg‐August‐University GöttingenGöttingenGermany
| | | | | | - Margit Nuetzel
- Department of Internal Medicine IIIUniversity Hospital RegensburgRegensburgGermany
| | - Fabienne Rayne
- CNRS UMR 5234, Microbiologie Fondamentale et PathogénicitéUniversité de BordeauxBordeauxFrance
| | - Eugenia Basyuk
- CNRS UMR 5234, Microbiologie Fondamentale et PathogénicitéUniversité de BordeauxBordeauxFrance
| | - Edouard Bertrand
- CNRS UMR 5355Institut de Généthique Moléculaire de MontpellierMontpellierFrance
| | - Michael Rehli
- Department of Internal Medicine IIIUniversity Hospital RegensburgRegensburgGermany
- Leibniz Institute for ImmunotherapyRegensburgGermany
- University Hospital RegensburgRegensburgGermany
| | - Harald Wodrich
- CNRS UMR 5234, Microbiologie Fondamentale et PathogénicitéUniversité de BordeauxBordeauxFrance
| | - Gernot Laengst
- Biochemie Zentrum RegensburgUniversity of RegensburgRegensburgGermany
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32
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Biernat E, Khan U, Govind CK. Measuring occupancies of the nucleosome and nucleosome-interacting factors in vivo in Saccharomyces cerevisiae genome-wide. Methods 2023; 218:167-175. [PMID: 37598811 PMCID: PMC10529416 DOI: 10.1016/j.ymeth.2023.08.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 07/26/2023] [Accepted: 08/11/2023] [Indexed: 08/22/2023] Open
Abstract
Nucleosomes are the repeating units of chromatin. The presence of nucleosomes poses a major impediment to all DNA-dependent processes. As a result, access to DNA in chromatin is dynamically regulated by many factors, including ATP-dependent chromatin remodeling complexes. Digestion of chromatin by micrococcal nuclease (MNase) followed by chromatin immunoprecipitation (ChIP) and sequencing can be leveraged to determine nucleosome occupancy, positioning, and the ability of chromatin interacting factors to alter chromatin accessibility. Here we describe the procedure for performing MNase and MNase ChIP-seq in detail.
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Affiliation(s)
- Emily Biernat
- Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA
| | - Uzair Khan
- Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA
| | - Chhabi K Govind
- Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA.
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33
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Zhong B, Liao Q, Wang X, Wang X, Zhang J. The roles of epigenetic regulation in cholangiocarcinogenesis. Biomed Pharmacother 2023; 166:115290. [PMID: 37557012 DOI: 10.1016/j.biopha.2023.115290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/01/2023] [Accepted: 08/04/2023] [Indexed: 08/11/2023] Open
Abstract
Cholangiocarcinoma (CCA), a heterogeneous malignancy of bile duct epithelial cells, is characterized by aggressiveness, difficult diagnosis, and poor prognosis due to limited understanding and lack of effective therapeutic strategies. Genetic and epigenetic alterations accumulated in CCA cells can cause the aberrant regulation of oncogenes and tumor suppressors. Epigenetic alterations with histone modification, DNA methylation, and noncoding RNA modulation are associated with the carcinogenesis of CCA. Mutation or silencing of genes by various mechanisms can be a frequent event during CCA development. Alterations in histone acetylation/deacetylation at the posttranslational level, DNA methylation at promoters, and noncoding RNA regulation contribute to the heterogeneity of CCA and drive tumor development. In this review article, we mainly focus on the roles of epigenetic regulation in cholangiocarcinogenesis. Alterations in epigenetic modification can be potential targets for the therapeutic management of CCA, and epigenetic targets may become diagnostic biomarkers of CCA.
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Affiliation(s)
- Baiyin Zhong
- Department of Hepatobiliary Surgery, First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China
| | - Qicheng Liao
- Department of Hepatobiliary Surgery, First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China
| | - Xin Wang
- Department of Hepatobiliary Surgery, First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China
| | - Xiaonong Wang
- Department of Hepatobiliary Surgery, First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China
| | - Jianhong Zhang
- Department of Hepatobiliary Surgery, First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China; Ganzhou Key Laboratory of Hepatocellular Carcinoma, First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China.
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Ramalingam V, Yu X, Slaughter BD, Unruh JR, Brennan KJ, Onyshchenko A, Lange JJ, Natarajan M, Buck M, Zeitlinger J. Lola-I is a promoter pioneer factor that establishes de novo Pol II pausing during development. Nat Commun 2023; 14:5862. [PMID: 37735176 PMCID: PMC10514308 DOI: 10.1038/s41467-023-41408-1] [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: 03/15/2023] [Accepted: 08/30/2023] [Indexed: 09/23/2023] Open
Abstract
While the accessibility of enhancers is dynamically regulated during development, promoters tend to be constitutively accessible and poised for activation by paused Pol II. By studying Lola-I, a Drosophila zinc finger transcription factor, we show here that the promoter state can also be subject to developmental regulation independently of gene activation. Lola-I is ubiquitously expressed at the end of embryogenesis and causes its target promoters to become accessible and acquire paused Pol II throughout the embryo. This promoter transition is required but not sufficient for tissue-specific target gene activation. Lola-I mediates this function by depleting promoter nucleosomes, similar to the action of pioneer factors at enhancers. These results uncover a level of regulation for promoters that is normally found at enhancers and reveal a mechanism for the de novo establishment of paused Pol II at promoters.
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Affiliation(s)
- Vivekanandan Ramalingam
- Stowers Institute for Medical Research, Kansas City, MO, USA
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center----, Kansas City, KS, USA
- Department of Genetics, Stanford University, Palo Alto, CA, USA
| | - Xinyang Yu
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY, USA
| | | | - Jay R Unruh
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | | | | | - Jeffrey J Lange
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | | | - Michael Buck
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY, USA
- Department of Biomedical Informatics, Jacobs School of Medicine & Biomedical Sciences, Buffalo, NY, USA
| | - Julia Zeitlinger
- Stowers Institute for Medical Research, Kansas City, MO, USA.
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center----, Kansas City, KS, USA.
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Rehman S, Ahmad Z, Ramakrishnan M, Kalendar R, Zhuge Q. Regulation of plant epigenetic memory in response to cold and heat stress: towards climate resilient agriculture. Funct Integr Genomics 2023; 23:298. [PMID: 37700098 DOI: 10.1007/s10142-023-01219-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 08/18/2023] [Accepted: 08/23/2023] [Indexed: 09/14/2023]
Abstract
Plants have evolved to adapt and grow in hot and cold climatic conditions. Some also adapt to daily and seasonal temperature changes. Epigenetic modifications play an important role in regulating plant tolerance under such conditions. DNA methylation and post-translational modifications of histone proteins influence gene expression during plant developmental stages and under stress conditions, including cold and heat stress. While short-term modifications are common, some modifications may persist and result in stress memory that can be inherited by subsequent generations. Understanding the mechanisms of epigenomes responding to stress and the factors that trigger stress memory is crucial for developing climate-resilient agriculture, but such an integrated view is currently limited. This review focuses on the plant epigenetic stress memory during cold and heat stress. It also discusses the potential of machine learning to modify stress memory through epigenetics to develop climate-resilient crops.
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Affiliation(s)
- Shamsur Rehman
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology, College of Biology and the Environment, Nanjing Forestry University, Ministry of Education, Nanjing, China
| | - Zishan Ahmad
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, 210037, China
| | - Muthusamy Ramakrishnan
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, 210037, China
| | - Ruslan Kalendar
- Helsinki Institute of Life Science HiLIFE, Biocenter 3, Viikinkaari 1, FI-00014 University of Helsinki, Helsinki, Finland.
- Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan.
| | - Qiang Zhuge
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology, College of Biology and the Environment, Nanjing Forestry University, Ministry of Education, Nanjing, China.
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36
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Zheng W, Wang L, He W, Hu X, Zhu Q, Gu L, Jiang C. Transcriptome profiles and chromatin states in mouse androgenetic haploid embryonic stem cells. Cell Prolif 2023; 56:e13436. [PMID: 36855927 PMCID: PMC10472531 DOI: 10.1111/cpr.13436] [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: 11/14/2022] [Revised: 02/12/2023] [Accepted: 02/17/2023] [Indexed: 03/02/2023] Open
Abstract
Haploid embryonic stem cells (haESCs) are derived from the inner cell mass of the haploid blastocyst, containing only one set of chromosomes. Extensive and accurate chromatin remodelling occurs during haESC derivation, but the intrinsic transcriptome profiles and chromatin structure of haESCs have not been fully explored. We profiled the transcriptomes, nucleosome positioning, and key histone modifications of four mouse haESC lines, and compared these profiles with those of other closely-related stem cell lines, MII oocytes, round spermatids, sperm, and mouse embryonic fibroblasts. haESCs had transcriptome profiles closer to those of naïve pluripotent stem cells. Consistent with the one X chromosome in haESCs, Xist was repressed, indicating no X chromosome inactivation. haESCs and ESCs shared a similar global chromatin structure. However, a nucleosome depletion region was identified in 2056 promoters in ESCs, which was absent in haESCs. Furthermore, three characteristic spatial relationships were formed between transcription factor motifs and nucleosomes in both haESCs and ESCs, specifically in the linker region, on the nucleosome central surface, and nucleosome borders. Furthermore, the chromatin state of 4259 enhancers was off in haESCs but active in ESCs. Functional annotation of these enhancers revealed enrichment in regulation of the cell cycle, a predominantly reported mechanism of haESC self-diploidization. Notably, the transcriptome profiles and chromatin structure of haESCs were highly preserved during passaging but different from those of differentiated cell types.
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Affiliation(s)
- Weisheng Zheng
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Liping Wang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Wenteng He
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Xinjie Hu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Qianshu Zhu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Liang Gu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Cizhong Jiang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and TechnologyTongji UniversityShanghaiChina
- Frontier Science Center for Stem Cell ResearchTongji UniversityShanghaiChina
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Kleinschmidt H, Xu C, Bai L. Using Synthetic DNA Libraries to Investigate Chromatin and Gene Regulation. Chromosoma 2023; 132:167-189. [PMID: 37184694 PMCID: PMC10542970 DOI: 10.1007/s00412-023-00796-5] [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: 02/05/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/16/2023]
Abstract
Despite the recent explosion in genome-wide studies in chromatin and gene regulation, we are still far from extracting a set of genetic rules that can predict the function of the regulatory genome. One major reason for this deficiency is that gene regulation is a multi-layered process that involves an enormous variable space, which cannot be fully explored using native genomes. This problem can be partially solved by introducing synthetic DNA libraries into cells, a method that can test the regulatory roles of thousands to millions of sequences with limited variables. Here, we review recent applications of this method to study transcription factor (TF) binding, nucleosome positioning, and transcriptional activity. We discuss the design principles, experimental procedures, and major findings from these studies and compare the pros and cons of different approaches.
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Affiliation(s)
- Holly Kleinschmidt
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Cheng Xu
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Lu Bai
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA.
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, 16802, USA.
- Department of Physics, The Pennsylvania State University, University Park, PA, 16802, USA.
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38
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Helzer KT, Sharifi MN, Sperger JM, Shi Y, Annala M, Bootsma ML, Reese SR, Taylor A, Kaufmann KR, Krause HK, Schehr JL, Sethakorn N, Kosoff D, Kyriakopoulos C, Burkard ME, Rydzewski NR, Yu M, Harari PM, Bassetti M, Blitzer G, Floberg J, Sjöström M, Quigley DA, Dehm SM, Armstrong AJ, Beltran H, McKay RR, Feng FY, O'Regan R, Wisinski KB, Emamekhoo H, Wyatt AW, Lang JM, Zhao SG. Fragmentomic analysis of circulating tumor DNA-targeted cancer panels. Ann Oncol 2023; 34:813-825. [PMID: 37330052 PMCID: PMC10527168 DOI: 10.1016/j.annonc.2023.06.001] [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: 12/09/2022] [Revised: 05/30/2023] [Accepted: 06/06/2023] [Indexed: 06/19/2023] Open
Abstract
BACKGROUND The isolation of cell-free DNA (cfDNA) from the bloodstream can be used to detect and analyze somatic alterations in circulating tumor DNA (ctDNA), and multiple cfDNA-targeted sequencing panels are now commercially available for Food and Drug Administration (FDA)-approved biomarker indications to guide treatment. More recently, cfDNA fragmentation patterns have emerged as a tool to infer epigenomic and transcriptomic information. However, most of these analyses used whole-genome sequencing, which is insufficient to identify FDA-approved biomarker indications in a cost-effective manner. PATIENTS AND METHODS We used machine learning models of fragmentation patterns at the first coding exon in standard targeted cancer gene cfDNA sequencing panels to distinguish between cancer and non-cancer patients, as well as the specific tumor type and subtype. We assessed this approach in two independent cohorts: a published cohort from GRAIL (breast, lung, and prostate cancers, non-cancer, n = 198) and an institutional cohort from the University of Wisconsin (UW; breast, lung, prostate, bladder cancers, n = 320). Each cohort was split 70%/30% into training and validation sets. RESULTS In the UW cohort, training cross-validated accuracy was 82.1%, and accuracy in the independent validation cohort was 86.6% despite a median ctDNA fraction of only 0.06. In the GRAIL cohort, to assess how this approach performs in very low ctDNA fractions, training and independent validation were split based on ctDNA fraction. Training cross-validated accuracy was 80.6%, and accuracy in the independent validation cohort was 76.3%. In the validation cohort where the ctDNA fractions were all <0.05 and as low as 0.0003, the cancer versus non-cancer area under the curve was 0.99. CONCLUSIONS To our knowledge, this is the first study to demonstrate that sequencing from targeted cfDNA panels can be utilized to analyze fragmentation patterns to classify cancer types, dramatically expanding the potential capabilities of existing clinically used panels at minimal additional cost.
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Affiliation(s)
- K T Helzer
- Department of Human Oncology, University of Wisconsin, Madison
| | - M N Sharifi
- Carbone Cancer Center, University of Wisconsin, Madison; Department of Medicine, University of Wisconsin, Madison, USA
| | - J M Sperger
- Department of Medicine, University of Wisconsin, Madison, USA
| | - Y Shi
- Department of Human Oncology, University of Wisconsin, Madison
| | - M Annala
- Department of Urologic Sciences, Vancouver Prostate Centre, University of British Columbia, Vancouver, Canada; Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - M L Bootsma
- Department of Human Oncology, University of Wisconsin, Madison
| | - S R Reese
- Department of Human Oncology, University of Wisconsin, Madison; Department of Medicine, University of Wisconsin, Madison, USA
| | - A Taylor
- Department of Medicine, University of Wisconsin, Madison, USA
| | - K R Kaufmann
- Department of Medicine, University of Wisconsin, Madison, USA
| | - H K Krause
- Department of Medicine, University of Wisconsin, Madison, USA
| | - J L Schehr
- Carbone Cancer Center, University of Wisconsin, Madison
| | - N Sethakorn
- Carbone Cancer Center, University of Wisconsin, Madison; Department of Medicine, University of Wisconsin, Madison, USA
| | - D Kosoff
- Carbone Cancer Center, University of Wisconsin, Madison; Department of Medicine, University of Wisconsin, Madison, USA
| | - C Kyriakopoulos
- Carbone Cancer Center, University of Wisconsin, Madison; Department of Medicine, University of Wisconsin, Madison, USA
| | - M E Burkard
- Carbone Cancer Center, University of Wisconsin, Madison; Department of Medicine, University of Wisconsin, Madison, USA
| | - N R Rydzewski
- Department of Human Oncology, University of Wisconsin, Madison
| | - M Yu
- Carbone Cancer Center, University of Wisconsin, Madison; Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison
| | - P M Harari
- Department of Human Oncology, University of Wisconsin, Madison; Carbone Cancer Center, University of Wisconsin, Madison
| | - M Bassetti
- Department of Human Oncology, University of Wisconsin, Madison; Carbone Cancer Center, University of Wisconsin, Madison
| | - G Blitzer
- Department of Human Oncology, University of Wisconsin, Madison; Carbone Cancer Center, University of Wisconsin, Madison
| | - J Floberg
- Department of Human Oncology, University of Wisconsin, Madison; Carbone Cancer Center, University of Wisconsin, Madison
| | - M Sjöström
- Department of Radiation Oncology, University of California San Francisco, San Francisco; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco
| | - D A Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco; Departments of Epidemiology and Biostatistics; Urology, University of California San Francisco, San Francisco
| | - S M Dehm
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis
| | - A J Armstrong
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Department of Medicine, Duke University, Durham
| | - H Beltran
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston
| | - R R McKay
- Moores Cancer Center, University of California San Diego, La Jolla
| | - F Y Feng
- Department of Radiation Oncology, University of California San Francisco, San Francisco; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco; Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis; Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco
| | - R O'Regan
- Carbone Cancer Center, University of Wisconsin, Madison; Department of Medicine, University of Wisconsin, Madison, USA; Department of Medicine, University of Rochester, Rochester, USA
| | - K B Wisinski
- Carbone Cancer Center, University of Wisconsin, Madison; Department of Medicine, University of Wisconsin, Madison, USA
| | - H Emamekhoo
- Carbone Cancer Center, University of Wisconsin, Madison; Department of Medicine, University of Wisconsin, Madison, USA
| | - A W Wyatt
- Department of Urologic Sciences, Vancouver Prostate Centre, University of British Columbia, Vancouver, Canada; Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - J M Lang
- Carbone Cancer Center, University of Wisconsin, Madison; Department of Medicine, University of Wisconsin, Madison, USA
| | - S G Zhao
- Department of Human Oncology, University of Wisconsin, Madison; Carbone Cancer Center, University of Wisconsin, Madison; William S. Middleton Memorial Veterans' Hospital, Madison, USA.
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Esnault C, Magat T, Zine El Aabidine A, Garcia-Oliver E, Cucchiarini A, Bouchouika S, Lleres D, Goerke L, Luo Y, Verga D, Lacroix L, Feil R, Spicuglia S, Mergny JL, Andrau JC. G4access identifies G-quadruplexes and their associations with open chromatin and imprinting control regions. Nat Genet 2023; 55:1359-1369. [PMID: 37400615 DOI: 10.1038/s41588-023-01437-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 05/31/2023] [Indexed: 07/05/2023]
Abstract
Metazoan promoters are enriched in secondary DNA structure-forming motifs, such as G-quadruplexes (G4s). Here we describe 'G4access', an approach to isolate and sequence G4s associated with open chromatin via nuclease digestion. G4access is antibody- and crosslinking-independent and enriches for computationally predicted G4s (pG4s), most of which are confirmed in vitro. Using G4access in human and mouse cells, we identify cell-type-specific G4 enrichment correlated with nucleosome exclusion and promoter transcription. G4access allows measurement of variations in G4 repertoire usage following G4 ligand treatment, HDAC and G4 helicases inhibitors. Applying G4access to cells from reciprocal hybrid mouse crosses suggests a role for G4s in the control of active imprinting regions. Consistently, we also observed that G4access peaks are unmethylated, while methylation at pG4s correlates with nucleosome repositioning on DNA. Overall, our study provides a new tool for studying G4s in cellular dynamics and highlights their association with open chromatin, transcription and their antagonism to DNA methylation.
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Affiliation(s)
- Cyril Esnault
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS-UMR 5535, Montpellier, France
| | - Talha Magat
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS-UMR 5535, Montpellier, France
| | - Amal Zine El Aabidine
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS-UMR 5535, Montpellier, France
| | - Encar Garcia-Oliver
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS-UMR 5535, Montpellier, France
| | - Anne Cucchiarini
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, Palaiseau, France
| | - Soumya Bouchouika
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS-UMR 5535, Montpellier, France
| | - David Lleres
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS-UMR 5535, Montpellier, France
| | - Lutz Goerke
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS-UMR 5535, Montpellier, France
| | - Yu Luo
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, Palaiseau, France
- Université Paris-Saclay, Institut Curie, Orsay, France
| | - Daniela Verga
- Université Paris-Saclay, Institut Curie, Orsay, France
| | - Laurent Lacroix
- Institut de Biologie de l'École Normale Supérieure, ENS, CNRS UMR8197, Inserm U1024, Paris, France
| | - Robert Feil
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS-UMR 5535, Montpellier, France
| | - Salvatore Spicuglia
- Aix-Marseille University, INSERM, TAGC, UMR 1090, Marseille, France
- Equipe Labellisée Ligue Contre le Cancer, Marseille, France
| | - Jean-Louis Mergny
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, Palaiseau, France
| | - Jean-Christophe Andrau
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS-UMR 5535, Montpellier, France.
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Wang B, Zhou X, Kettenbach AN, Mitchell HD, Markillie LM, Loros JJ, Dunlap JC. A crucial role for dynamic expression of components encoding the negative arm of the circadian clock. Nat Commun 2023; 14:3371. [PMID: 37291101 PMCID: PMC10250352 DOI: 10.1038/s41467-023-38817-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 05/17/2023] [Indexed: 06/10/2023] Open
Abstract
In the Neurospora circadian system, the White Collar Complex (WCC) drives expression of the principal circadian negative arm component frequency (frq). FRQ interacts with FRH (FRQ-interacting RNA helicase) and CKI, forming a stable complex that represses its own expression by inhibiting WCC. In this study, a genetic screen identified a gene, designated as brd-8, that encodes a conserved auxiliary subunit of the NuA4 histone acetylation complex. Loss of brd-8 reduces H4 acetylation and RNA polymerase (Pol) II occupancy at frq and other known circadian genes, and leads to a long circadian period, delayed phase, and defective overt circadian output at some temperatures. In addition to strongly associating with the NuA4 histone acetyltransferase complex, BRD-8 is also found complexed with the transcription elongation regulator BYE-1. Expression of brd-8, bye-1, histone h2a.z, and several NuA4 subunits is controlled by the circadian clock, indicating that the molecular clock both regulates the basic chromatin status and is regulated by changes in chromatin. Taken together, our data identify auxiliary elements of the fungal NuA4 complex having homology to mammalian components, which along with conventional NuA4 subunits, are required for timely and dynamic frq expression and thereby a normal and persistent circadian rhythm.
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Affiliation(s)
- Bin Wang
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA.
| | - Xiaoying Zhou
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA
| | - Arminja N Kettenbach
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA
| | - Hugh D Mitchell
- Biological Sciences Divisions, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Lye Meng Markillie
- Biological Sciences Divisions, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Jennifer J Loros
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA
| | - Jay C Dunlap
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA.
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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. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.25.541209. [PMID: 37292814 PMCID: PMC10245875 DOI: 10.1101/2023.05.25.541209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
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 exhibiting 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 demonstrate 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, NC 27710
| | - Heather K. MacAlpine
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710
| | | | - David M. MacAlpine
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710
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Pan Y, Hu C, Hou LJ, Chen YL, Shi J, Liu JC, Zhou JQ. Swc4 protects nucleosome-free rDNA, tDNA and telomere loci to inhibit genome instability. DNA Repair (Amst) 2023; 127:103512. [PMID: 37230009 DOI: 10.1016/j.dnarep.2023.103512] [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: 11/22/2022] [Revised: 04/17/2023] [Accepted: 05/11/2023] [Indexed: 05/27/2023]
Abstract
In the baker's yeast Saccharomyces cerevisiae, NuA4 and SWR1-C, two multisubunit complexes, are involved in histone acetylation and chromatin remodeling, respectively. Eaf1 is the assembly platform subunit of NuA4, Swr1 is the assembly platform and catalytic subunit of SWR1-C, while Swc4, Yaf9, Arp4 and Act1 form a functional module, and is present in both NuA4 and SWR1 complexes. ACT1 and ARP4 are essential for cell survival. Deletion of SWC4, but not YAF9, EAF1 or SWR1 results in a severe growth defect, but the underlying mechanism remains largely unknown. Here, we show that swc4Δ, but not yaf9Δ, eaf1Δ, or swr1Δ cells display defects in DNA ploidy and chromosome segregation, suggesting that the defects observed in swc4Δ cells are independent of NuA4 or SWR1-C integrity. Swc4 is enriched in the nucleosome-free regions (NFRs) of the genome, including characteristic regions of RDN5s, tDNAs and telomeres, independently of Yaf9, Eaf1 or Swr1. In particular, rDNA, tDNA and telomere loci are more unstable and prone to recombination in the swc4Δ cells than in wild-type cells. Taken together, we conclude that the chromatin associated Swc4 protects nucleosome-free chromatin of rDNA, tDNA and telomere loci to ensure genome integrity.
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Affiliation(s)
- Yue Pan
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Can Hu
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Lin-Jun Hou
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yu-Long Chen
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jiantao Shi
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jia-Cheng Liu
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Jin-Qiu Zhou
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.
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43
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Nifker G, Grunwald A, Margalit S, Tulpova Z, Michaeli Y, Har-Gil H, Maimon N, Roichman E, Schütz L, Weinhold E, Ebenstein Y. Dam Assisted Fluorescent Tagging of Chromatin Accessibility (DAFCA) for Optical Genome Mapping in Nanochannel Arrays. ACS NANO 2023; 17:9178-9187. [PMID: 37154345 DOI: 10.1021/acsnano.2c12755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Proteins and enzymes in the cell nucleus require physical access to their DNA target sites in order to perform genomic tasks such as gene activation and transcription. Hence, chromatin accessibility is a central regulator of gene expression, and its genomic profile holds essential information on the cell type and state. We utilized the E. coli Dam methyltransferase in combination with a fluorescent cofactor analogue to generate fluorescent tags in accessible DNA regions within the cell nucleus. The accessible portions of the genome are then detected by single-molecule optical genome mapping in nanochannel arrays. This method allowed us to characterize long-range structural variations and their associated chromatin structure. We show the ability to create whole-genome, allele-specific chromatin accessibility maps composed of long DNA molecules extended in silicon nanochannels.
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Affiliation(s)
- Gil Nifker
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Assaf Grunwald
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Sapir Margalit
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Zuzana Tulpova
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Yael Michaeli
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Hagai Har-Gil
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Noy Maimon
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Elad Roichman
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Leonie Schütz
- Institute of Organic Chemistry, RWTH Aachen University, D-52056 Aachen, Germany
| | - Elmar Weinhold
- Institute of Organic Chemistry, RWTH Aachen University, D-52056 Aachen, Germany
| | - Yuval Ebenstein
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
- Department of Biomedical Engineering, Faculty of Engineering, Tel Aviv University, 6997801 Tel Aviv, Israel
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44
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Turkalj S, Jakobsen NA, Groom A, Metzner M, Riva SG, Gür ER, Usukhbayar B, Salazar MA, Hentges LD, Mickute G, Clark K, Sopp P, Davies JOJ, Hughes JR, Vyas P. GTAC enables parallel genotyping of multiple genomic loci with chromatin accessibility profiling in single cells. Cell Stem Cell 2023; 30:722-740.e11. [PMID: 37146586 DOI: 10.1016/j.stem.2023.04.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 02/23/2023] [Accepted: 04/12/2023] [Indexed: 05/07/2023]
Abstract
Understanding clonal evolution and cancer development requires experimental approaches for characterizing the consequences of somatic mutations on gene regulation. However, no methods currently exist that efficiently link high-content chromatin accessibility with high-confidence genotyping in single cells. To address this, we developed Genotyping with the Assay for Transposase-Accessible Chromatin (GTAC), enabling accurate mutation detection at multiple amplified loci, coupled with robust chromatin accessibility readout. We applied GTAC to primary acute myeloid leukemia, obtaining high-quality chromatin accessibility profiles and clonal identities for multiple mutations in 88% of cells. We traced chromatin variation throughout clonal evolution, showing the restriction of different clones to distinct differentiation stages. Furthermore, we identified switches in transcription factor motif accessibility associated with a specific combination of driver mutations, which biased transformed progenitors toward a leukemia stem cell-like chromatin state. GTAC is a powerful tool to study clonal heterogeneity across a wide spectrum of pre-malignant and neoplastic conditions.
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Affiliation(s)
- Sven Turkalj
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Niels Asger Jakobsen
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK; Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Angus Groom
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Marlen Metzner
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Simone G Riva
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - E Ravza Gür
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Batchimeg Usukhbayar
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Mirian Angulo Salazar
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Lance D Hentges
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Gerda Mickute
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Kevin Clark
- Flow Cytometry Facility, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Paul Sopp
- Flow Cytometry Facility, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - James O J Davies
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK; Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Paresh Vyas
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK; Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
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45
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Chen H, Yang QL, Xu JX, Deng X, Zhang YJ, Liu T, Rots MG, Xu GL, Huang KY. Efficient methods for multiple types of precise gene-editing in Chlamydomonas. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023. [PMID: 37310200 DOI: 10.1111/tpj.16265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/20/2023] [Accepted: 04/26/2023] [Indexed: 06/14/2023]
Abstract
Precise gene-editing using CRISPR/Cas9 technology remains a long-standing challenge, especially for genes with low expression and no selectable phenotypes in Chlamydomonas reinhardtii, a classic model for photosynthesis and cilia research. Here, we developed a multi-type and precise genetic manipulation method in which a DNA break was generated by Cas9 nuclease and the repair was mediated using a homologous DNA template. The efficacy of this method was demonstrated for several types of gene editing, including inactivation of two low-expression genes (CrTET1 and CrKU80), the introduction of a FLAG-HA epitope tag into VIPP1, IFT46, CrTET1 and CrKU80 genes, and placing a YFP tag into VIPP1 and IFT46 for live-cell imaging. We also successfully performed a single amino acid substitution for the FLA3, FLA10 and FTSY genes, and documented the attainment of the anticipated phenotypes. Lastly, we demonstrated that precise fragment deletion from the 3'-UTR of MAA7 and VIPP1 resulted in a stable knock-down effect. Overall, our study has established efficient methods for multiple types of precise gene editing in Chlamydomonas, enabling substitution, insertion and deletion at the base resolution, thus improving the potential of this alga in both basic research and industrial applications.
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Affiliation(s)
- Hui Chen
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Qing-Lin Yang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Jia-Xi Xu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuan Deng
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yun-Jie Zhang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Ting Liu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Marianne G Rots
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, The Netherlands
| | - Guo-Liang Xu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- Shanghai Key Laboratory of Medical Epigenetics, Laboratory of Cancer Epigenetics, Institutes of Biomedical Sciences, Medical College of Fudan University, Chinese Academy of Medical Sciences (RU069), Shanghai, China
| | - Kai-Yao Huang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
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46
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Abril-Garrido J, Dienemann C, Grabbe F, Velychko T, Lidschreiber M, Wang H, Cramer P. Structural basis of transcription reduction by a promoter-proximal +1 nucleosome. Mol Cell 2023:S1097-2765(23)00255-1. [PMID: 37148879 DOI: 10.1016/j.molcel.2023.04.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/16/2023] [Accepted: 04/11/2023] [Indexed: 05/08/2023]
Abstract
At active human genes, the +1 nucleosome is located downstream of the RNA polymerase II (RNA Pol II) pre-initiation complex (PIC). However, at inactive genes, the +1 nucleosome is found further upstream, at a promoter-proximal location. Here, we establish a model system to show that a promoter-proximal +1 nucleosome can reduce RNA synthesis in vivo and in vitro, and we analyze its structural basis. We find that the PIC assembles normally when the edge of the +1 nucleosome is located 18 base pairs (bp) downstream of the transcription start site (TSS). However, when the nucleosome edge is located further upstream, only 10 bp downstream of the TSS, the PIC adopts an inhibited state. The transcription factor IIH (TFIIH) shows a closed conformation and its subunit XPB contacts DNA with only one of its two ATPase lobes, inconsistent with DNA opening. These results provide a mechanism for nucleosome-dependent regulation of transcription initiation.
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Affiliation(s)
- Julio Abril-Garrido
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Christian Dienemann
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Frauke Grabbe
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Taras Velychko
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Michael Lidschreiber
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Haibo Wang
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany.
| | - Patrick Cramer
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany.
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47
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Wang B, Zhou X, Kettenbach AN, Mitchell HD, Markillie LM, Loros JJ, Dunlap JC. A crucial role for dynamic expression of components encoding the negative arm of the circadian clock. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.24.538162. [PMID: 37162945 PMCID: PMC10168201 DOI: 10.1101/2023.04.24.538162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
In the Neurospora circadian system, the White Collar Complex (WCC) drives expression of the principal circadian negative arm component frequency ( frq ). FRQ interacts with FRH (FRQ-interacting helicase) and CK-1 forming a stable complex that represses its own expression by inhibiting WCC. In this study, a genetic screen identified a gene, designated as brd-8 , that encodes a conserved auxiliary subunit of the NuA4 histone acetylation complex. Loss of brd-8 reduces H4 acetylation and RNA polymerase (Pol) II occupancy at frq and other known circadian genes, and leads to a long circadian period, delayed phase, and defective overt circadian output at some temperatures. In addition to strongly associating with the NuA4 histone acetyltransferase complex, BRD-8 is also found complexed with the transcription elongation regulator BYE-1. Expression of brd-8, bye-1, histone hH2Az , and several NuA4 subunits is controlled by the circadian clock, indicating that the molecular clock both regulates the basic chromatin status and is regulated by changes in chromatin. Taken together, our data identify new auxiliary elements of the fungal NuA4 complex having homology to mammalian components, which along with conventional NuA4 subunits, are required for timely and dynamic frq expression and thereby a normal and persistent circadian rhythm.
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48
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Ma M, Zhang X, Zheng Y, Lu S, Pan X, Mao X, Pan H, Chung HL, Wang H, Guo H, Bellen HJ. The fly homolog of SUPT16H, a gene associated with neurodevelopmental disorders, is required in a cell-autonomous fashion for cell survival. Hum Mol Genet 2023; 32:984-997. [PMID: 36255738 PMCID: PMC9991001 DOI: 10.1093/hmg/ddac259] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/22/2022] [Accepted: 10/14/2022] [Indexed: 11/14/2022] Open
Abstract
SUPT16H encodes the large subunit of the FAcilitate Chromatin Transcription (FACT) complex, which functions as a nucleosome organizer during transcription. We identified two individuals from unrelated families carrying de novo missense variants in SUPT16H. The probands exhibit global developmental delay, intellectual disability, epilepsy, facial dysmorphism and brain structural abnormalities. We used Drosophila to characterize two variants: p.T171I and p.G808R. Loss of the fly ortholog, dre4, causes lethality at an early developmental stage. RNAi-mediated knockdown of dre4 in either glia or neurons causes severely reduced eclosion and longevity. Tissue-specific knockdown of dre4 in the eye or wing leads to the loss of these tissues, whereas overexpression of SUPT16H has no dominant effect. Moreover, expression of the reference SUPT16H significantly rescues the loss-of-function phenotypes in the nervous system as well as wing and eye. In contrast, expression of SUPT16H p.T171I or p.G808R rescues the phenotypes poorly, indicating that the variants are partial loss-of-function alleles. While previous studies argued that the developmental arrest caused by loss of dre4 is due to impaired ecdysone production in the prothoracic gland, our data show that dre4 is required for proper cell growth and survival in multiple tissues in a cell-autonomous manner. Altogether, our data indicate that the de novo loss-of-function variants in SUPT16H are indeed associated with developmental and neurological defects observed in the probands.
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Affiliation(s)
- Mengqi Ma
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Xi Zhang
- National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan 410008, China
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Yiming Zheng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Shenzhao Lu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Xueyang Pan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Xiao Mao
- National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan 410008, China
- Department of Medical Genetics, Maternal and Child Health Hospital of Hunan Province, Changsha, Hunan 410008, China
| | - Hongling Pan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Hyung-lok Chung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Hua Wang
- National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan 410008, China
- Department of Medical Genetics, Hunan Children’s Hospital, Changsha, Hunan 410007, China
| | - Hong Guo
- Department of Medical Genetics, Army Medical University, Chongqing 400038, China
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
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Singh VK, Kainat KM, Sharma PK. Crosstalk between epigenetics and tumor promoting androgen signaling in prostate cancer. VITAMINS AND HORMONES 2023; 122:253-282. [PMID: 36863797 DOI: 10.1016/bs.vh.2022.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Prostate cancer (PCa) is one of the major health burdens among all cancer types in men globally. Early diagnosis and efficacious treatment options are highly warranted as far as the incidence of PCa is concerned. Androgen-dependent transcriptional activation of androgen receptor (AR) is central to the prostate tumorigenesis and therefore hormonal ablation therapy remains the first line of treatment for PCa in the clinics. However, the molecular signaling engaged in AR-dependent PCa initiation and progression is infrequent and diverse. Moreover, apart from the genomic changes, non-genomic changes such as epigenetic modifications have also been suggested as critical regulator of PCa development. Among the non-genomic mechanisms, various epigenetic changes such as histones modifications, chromatin methylation and noncoding RNAs regulations etc. play decisive role in the prostate tumorigenesis. Given that epigenetic modifications are reversible using pharmacological modifiers, various promising therapeutic approaches have been designed for the better management of PCa. In this chapter, we discuss the epigenetic control of tumor promoting AR signaling that underlies the mechanism of prostate tumorigenesis and progression. In addition, we have discussed the approaches and opportunities to develop novel epigenetic modifications based therapeutic strategies for targeting PCa including castrate resistant prostate cancer (CRPC).
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Affiliation(s)
- Vipendra Kumar Singh
- Environmental Carcinogenesis Lab, Food Drug and Chemical Toxicology Group, CSIR-Indian Institute of Toxicology Research, Lucknow, Uttar Pradesh, India
| | - K M Kainat
- Environmental Carcinogenesis Lab, Food Drug and Chemical Toxicology Group, CSIR-Indian Institute of Toxicology Research, Lucknow, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Pradeep Kumar Sharma
- Environmental Carcinogenesis Lab, Food Drug and Chemical Toxicology Group, CSIR-Indian Institute of Toxicology Research, Lucknow, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.
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50
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De Sarkar N, Patton RD, Doebley AL, Hanratty B, Adil M, Kreitzman AJ, Sarthy JF, Ko M, Brahma S, Meers MP, Janssens DH, Ang LS, Coleman IM, Bose A, Dumpit RF, Lucas JM, Nunez TA, Nguyen HM, McClure HM, Pritchard CC, Schweizer MT, Morrissey C, Choudhury AD, Baca SC, Berchuck JE, Freedman ML, Ahmad K, Haffner MC, Montgomery RB, Corey E, Henikoff S, Nelson PS, Ha G. Nucleosome Patterns in Circulating Tumor DNA Reveal Transcriptional Regulation of Advanced Prostate Cancer Phenotypes. Cancer Discov 2023; 13:632-653. [PMID: 36399432 PMCID: PMC9976992 DOI: 10.1158/2159-8290.cd-22-0692] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 10/01/2022] [Accepted: 11/16/2022] [Indexed: 11/19/2022]
Abstract
Advanced prostate cancers comprise distinct phenotypes, but tumor classification remains clinically challenging. Here, we harnessed circulating tumor DNA (ctDNA) to study tumor phenotypes by ascertaining nucleosome positioning patterns associated with transcription regulation. We sequenced plasma ctDNA whole genomes from patient-derived xenografts representing a spectrum of androgen receptor active (ARPC) and neuroendocrine (NEPC) prostate cancers. Nucleosome patterns associated with transcriptional activity were reflected in ctDNA at regions of genes, promoters, histone modifications, transcription factor binding, and accessible chromatin. We identified the activity of key phenotype-defining transcriptional regulators from ctDNA, including AR, ASCL1, HOXB13, HNF4G, and GATA2. To distinguish NEPC and ARPC in patient plasma samples, we developed prediction models that achieved accuracies of 97% for dominant phenotypes and 87% for mixed clinical phenotypes. Although phenotype classification is typically assessed by IHC or transcriptome profiling from tumor biopsies, we demonstrate that ctDNA provides comparable results with diagnostic advantages for precision oncology. SIGNIFICANCE This study provides insights into the dynamics of nucleosome positioning and gene regulation associated with cancer phenotypes that can be ascertained from ctDNA. New methods for classification in phenotype mixtures extend the utility of ctDNA beyond assessments of somatic DNA alterations with important implications for molecular classification and precision oncology. This article is highlighted in the In This Issue feature, p. 517.
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Affiliation(s)
- Navonil De Sarkar
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington
- Department of Pathology and Prostate Cancer Center of Excellence, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Robert D. Patton
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Anna-Lisa Doebley
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington
- Medical Scientist Training Program, University of Washington, Seattle, Washington
| | - Brian Hanratty
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Mohamed Adil
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Adam J. Kreitzman
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Jay F. Sarthy
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Minjeong Ko
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Sandipan Brahma
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Michael P. Meers
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Derek H. Janssens
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Lisa S. Ang
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Ilsa M. Coleman
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Arnab Bose
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Ruth F. Dumpit
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Jared M. Lucas
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Talina A. Nunez
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Holly M. Nguyen
- Department of Urology, University of Washington, Seattle, Washington
| | | | - Colin C. Pritchard
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
| | - Michael T. Schweizer
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Oncology, Department of Medicine, University of Washington, Seattle, Washington
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, Washington
| | - Atish D. Choudhury
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Sylvan C. Baca
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | - Matthew L. Freedman
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Kami Ahmad
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Michael C. Haffner
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
| | - R. Bruce Montgomery
- Division of Oncology, Department of Medicine, University of Washington, Seattle, Washington
| | - Eva Corey
- Department of Urology, University of Washington, Seattle, Washington
| | - Steven Henikoff
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
- Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - Peter S. Nelson
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington
- Department of Urology, University of Washington, Seattle, Washington
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
- Division of Oncology, Department of Medicine, University of Washington, Seattle, Washington
- Corresponding Authors: Gavin Ha, Fred Hutchinson Cancer Center, 1100 Fairview Avenue North, Seattle, WA 98109. Phone: 206-667-2802; E-mail: ; and Peter S. Nelson, Fred Hutchinson Cancer Center, 1100 Fairview Avenue North, Seattle, WA 98109. Phone: 206-667-3377; E-mail:
| | - Gavin Ha
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
- Department of Genome Sciences, University of Washington, Seattle, Washington
- Corresponding Authors: Gavin Ha, Fred Hutchinson Cancer Center, 1100 Fairview Avenue North, Seattle, WA 98109. Phone: 206-667-2802; E-mail: ; and Peter S. Nelson, Fred Hutchinson Cancer Center, 1100 Fairview Avenue North, Seattle, WA 98109. Phone: 206-667-3377; E-mail:
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