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Church MC, Workman JL. The SWI/SNF chromatin remodeling complex: a critical regulator of metabolism. Biochem Soc Trans 2024; 52:1327-1337. [PMID: 38666605 PMCID: PMC11346436 DOI: 10.1042/bst20231141] [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: 02/06/2024] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 06/27/2024]
Abstract
The close relationship between chromatin and metabolism has been well-studied in recent years. Many metabolites have been found to be cofactors used to modify chromatin, and these modifications can in turn affect gene transcription. One chromatin-associated factor responsible for regulating transcription is the SWI/SNF complex, an ATP-dependent chromatin remodeler conserved throughout eukaryotes. SWI/SNF was originally described in yeast as regulating genes involved in carbon source metabolism and mating type switching, and its mammalian counterpart has been extensively studied for its role in diseases such as cancer. The yeast SWI/SNF complex is closely associated with activation of stress response genes, many of which have metabolic functions. It is now recognized that this is a conserved function of the complex, and recent work has shown that mammalian SWI/SNF is also a key regulator of metabolic transcription. Emerging evidence suggests that loss of SWI/SNF introduces vulnerabilities to cells due to this metabolic influence, and that this may present opportunities for treatment of SWI/SNF-deficient cancers.
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Affiliation(s)
- Michael C. Church
- Stowers Institute of Medical Research, 1000 E 50th Street, Kansas City, MO 64118, U.S.A
| | - Jerry L. Workman
- Stowers Institute of Medical Research, 1000 E 50th Street, Kansas City, MO 64118, U.S.A
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2
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Venu V, Roth C, Adikari SH, Small EM, Starkenburg SR, Sanbonmatsu KY, Steadman CR. Multi-omics analysis reveals the dynamic interplay between Vero host chromatin structure and function during vaccinia virus infection. Commun Biol 2024; 7:721. [PMID: 38862613 PMCID: PMC11166932 DOI: 10.1038/s42003-024-06389-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 05/27/2024] [Indexed: 06/13/2024] Open
Abstract
The genome folds into complex configurations and structures thought to profoundly impact its function. The intricacies of this dynamic structure-function relationship are not well understood particularly in the context of viral infection. To unravel this interplay, here we provide a comprehensive investigation of simultaneous host chromatin structural (via Hi-C and ATAC-seq) and functional changes (via RNA-seq) in response to vaccinia virus infection. Over time, infection significantly impacts global and local chromatin structure by increasing long-range intra-chromosomal interactions and B compartmentalization and by decreasing chromatin accessibility and inter-chromosomal interactions. Local accessibility changes are independent of broad-scale chromatin compartment exchange (~12% of the genome), underscoring potential independent mechanisms for global and local chromatin reorganization. While infection structurally condenses the host genome, there is nearly equal bidirectional differential gene expression. Despite global weakening of intra-TAD interactions, functional changes including downregulated immunity genes are associated with alterations in local accessibility and loop domain restructuring. Therefore, chromatin accessibility and local structure profiling provide impactful predictions for host responses and may improve development of efficacious anti-viral counter measures including the optimization of vaccine design.
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Affiliation(s)
- Vrinda Venu
- Climate, Ecology & Environment Group, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Cullen Roth
- Genomics & Bioanalytics Group, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Samantha H Adikari
- Biochemistry & Biotechnology Group, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Eric M Small
- Climate, Ecology & Environment Group, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Shawn R Starkenburg
- Genomics & Bioanalytics Group, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Karissa Y Sanbonmatsu
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, USA
- New Mexico Consortium, Los Alamos, NM, USA
| | - Christina R Steadman
- Climate, Ecology & Environment Group, Los Alamos National Laboratory, Los Alamos, NM, USA.
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3
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Mondal A, Kolomeisky AB. Role of Nucleosome Sliding in the Protein Target Search for Covered DNA Sites. J Phys Chem Lett 2023; 14:7073-7082. [PMID: 37527481 DOI: 10.1021/acs.jpclett.3c01704] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
Associations of transcription factors (TFs) with specific sites on DNA initiate major cellular processes. But DNA in eukaryotic cells is covered by nucleosomes which prevent TFs from binding. However, nucleosome structures on DNA are not static and exhibit breathing and sliding. We develop a theoretical framework to investigate the effect of nucleosome sliding on a protein target search. By analysis of a discrete-state stochastic model of nucleosome sliding, search dynamics are explicitly evaluated. It is found that for long sliding lengths the target search dynamics are faster for normal TFs that cannot enter the nucleosomal DNA. But for more realistic short sliding lengths, the so-called pioneer TFs, which can invade nucleosomal DNA, locate specific sites faster. It is also suggested that nucleosome breathing, which is a faster process, has a stronger effect on protein search dynamics than that of nucleosome sliding. Theoretical arguments to explain these observations are presented.
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Affiliation(s)
- Anupam Mondal
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Anatoly B Kolomeisky
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, United States
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4
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Santos MM, Johnson MC, Fiedler L, Zegerman P. Global early replication disrupts gene expression and chromatin conformation in a single cell cycle. Genome Biol 2022; 23:217. [PMID: 36253803 PMCID: PMC9575230 DOI: 10.1186/s13059-022-02788-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 10/10/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND The early embryonic divisions of many organisms, including fish, flies, and frogs, are characterized by a very rapid S-phase caused by high rates of replication initiation. In somatic cells, S-phase is much longer due to both a reduction in the total number of initiation events and the imposition of a temporal order of origin activation. The physiological importance of changes in the rate and timing of replication initiation in S-phase remains unclear. RESULTS Here we assess the importance of the temporal control of replication initiation using a conditional system in budding yeast to drive the early replication of the majority of origins in a single cell cycle. We show that global early replication disrupts the expression of over a quarter of all genes. By deleting individual origins, we show that delaying replication is sufficient to restore normal gene expression, directly implicating origin firing control in this regulation. Global early replication disrupts nucleosome positioning and transcription factor binding during S-phase, suggesting that the rate of S-phase is important to regulate the chromatin landscape. CONCLUSIONS Together, these data provide new insight into the role of the temporal control of origin firing during S-phase for coordinating replication, gene expression, and chromatin establishment as occurs in the early embryo.
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Affiliation(s)
- Miguel M Santos
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Mark C Johnson
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Lukáš Fiedler
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Philip Zegerman
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK.
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.
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5
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Kondalaji SG, Bowman GD. In Vitro Mapping of Nucleosome Positions at Base-Pair Resolution Using Ortho-Phenanthroline. Curr Protoc 2022; 2:e518. [PMID: 35943282 PMCID: PMC9373710 DOI: 10.1002/cpz1.518] [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] [Indexed: 06/15/2023]
Abstract
The positions of nucleosomes along genomic DNA play a role in defining patterns of gene expression and chromatin organization. Determination of nucleosome positions in vivo and in vitro, as revealed by the locations of histones on DNA, has provided insight into mechanisms of nucleosome sliding, spacing, assembly, and disassembly. Here, we describe methods for the in vitro determination of histone-DNA contacts at base-pair (bp) resolution. The protocol involves the labeling of histones with ortho-phenanthroline (OP), site-specific cleavage of nucleosomal DNA, and processing and analysis of the resulting DNA fragments. This methodology provides an efficient and high-resolution means for studying kinetics and behavior of enzymes that alter nucleosome structure and/or positioning, and can be used to identify preferred distributions of nucleosomes on natural DNA sequences. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Cysteine-specific chemical modification of folded histones with ortho-phenanthroline (OP) Basic Protocol 2: Nucleosome sliding assay adapted for OP mapping of histone-DNA contacts Basic Protocol 3: OP-mediated cleavage, processing, and analysis of DNA fragments using a sequencing gel Support Protocol 1: Preparation of dideoxy sequencing ladders Support Protocol 2: Preparation and running of a denaturing DNA sequencing gel.
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Affiliation(s)
| | - Gregory D Bowman
- T. C. Jenkins Department of Biophysics, Johns Hopkins
University, Baltimore, Maryland 21218
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6
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Distinct functions of three chromatin remodelers in activator binding and preinitiation complex assembly. PLoS Genet 2022; 18:e1010277. [PMID: 35793348 PMCID: PMC9292117 DOI: 10.1371/journal.pgen.1010277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 07/18/2022] [Accepted: 05/28/2022] [Indexed: 12/01/2022] Open
Abstract
The nucleosome remodeling complexes (CRs) SWI/SNF, RSC, and Ino80C cooperate in evicting or repositioning nucleosomes to produce nucleosome depleted regions (NDRs) at the promoters of many yeast genes induced by amino acid starvation. We analyzed mutants depleted of the catalytic subunits of these CRs for binding of transcriptional activator Gcn4 and recruitment of TATA-binding protein (TBP) during preinitiation complex (PIC) assembly. RSC and Ino80 were found to enhance Gcn4 binding to both UAS elements in NDRs upstream of promoters and to unconventional binding sites within nucleosome-occupied coding sequences; and SWI/SNF contributes to UAS binding when RSC is depleted. All three CRs are actively recruited by Gcn4 to most UAS elements and appear to enhance Gcn4 binding by reducing nucleosome occupancies at the binding motifs, indicating a positive regulatory loop. SWI/SNF acts unexpectedly in WT cells to prevent excessive Gcn4 binding at many UAS elements, indicating a dual mode of action that is modulated by the presence of RSC. RSC and SWI/SNF collaborate to enhance TBP recruitment at Gcn4 target genes, together with Ino80C, in a manner associated with nucleosome eviction at the TBP binding sites. Cooperation among the CRs in TBP recruitment is also evident at the highly transcribed ribosomal protein genes, while RSC and Ino80C act more broadly than SWI/SNF at the majority of other constitutively expressed genes to stimulate this step in PIC assembly. Our findings indicate a complex interplay among the CRs in evicting promoter nucleosomes to regulate activator binding and stimulate PIC assembly. ATP-dependent chromatin remodelers (CRs), including SWI/SNF and RSC in budding yeast, are thought to stimulate transcription by repositioning or evicting promoter nucleosomes, and we recently implicated the CR Ino80C in this process as well. The relative importance of these CRs in stimulating activator binding and recruitment of TATA-binding protein (TBP) to promoters is incompletely understood. Examining mutants depleted of the catalytic subunits of these CRs, we determined that RSC and Ino80C stimulate binding of transcription factor Gcn4 to nucleosome-depleted regions, or linkers between genic nucleosomes, at multiple target genes activated by Gcn4 in amino acid-starved cells, frequently via evicting nucleosomes from the Gcn4 binding motifs. At some genes, SWI/SNF functionally complements RSC, while opposing RSC at others to limit Gcn4 binding. The CRs in turn are recruited by Gcn4, consistent with a positive feedback loop that enhances Gcn4 binding. The three CRs also cooperate to enhance TBP recruitment, again involving nucleosome depletion, at both Gcn4 target and highly expressed ribosomal protein genes, whereas only RSC and Ino80C act broadly throughout the genome to enhance this key step in preinitiation complex assembly. Our findings illuminate functional cooperation among multiple CRs in regulating activator binding and promoter activation.
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7
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Aberrant nucleosome organization in mouse SCNT embryos revealed by ULI-MNase-seq. Stem Cell Reports 2022; 17:1730-1742. [PMID: 35750045 PMCID: PMC9287678 DOI: 10.1016/j.stemcr.2022.05.020] [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: 03/23/2022] [Revised: 05/25/2022] [Accepted: 05/26/2022] [Indexed: 11/23/2022] Open
Abstract
Somatic cell nuclear transfer (SCNT) can reprogram terminally differentiated somatic cells into totipotent embryos, but with multiple defects. The nucleosome positioning, as an important epigenetic regulator for gene expression, is largely unexplored during SCNT embryonic development. Here, we mapped genome-wide nucleosome profiles in mouse SCNT embryos using ultra-low-input MNase-seq (ULI-MNase-seq). We found that the nucleosome-depleted regions (NDRs) around promoters underwent dramatic reestablishment, which is consistent with the cell cycle. Dynamics of nucleosome position in SCNT embryos were delayed compared to fertilized embryos. Subsequently, we found that the aberrant gene expression levels in inner cell mass (ICM) were positively correlated with promoter NDRs in donor cells, which indicated that the memory of nucleosome occupancy in donor cells was a potential barrier for SCNT-mediated reprogramming. We further confirmed that the histone acetylation level of donor cells was associated with the memory of promoter NDRs. Our study provides insight into nucleosome reconfiguration during SCNT preimplantation embryonic development.
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8
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Han GS, Li Q, Li Y. Nucleosome positioning based on DNA sequence embedding and deep learning. BMC Genomics 2022; 23:301. [PMID: 35418074 PMCID: PMC9006412 DOI: 10.1186/s12864-022-08508-6] [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: 03/28/2022] [Accepted: 03/28/2022] [Indexed: 11/25/2022] Open
Abstract
Background Nucleosome positioning is the precise determination of the location of nucleosomes on DNA sequence. With the continuous advancement of biotechnology and computer technology, biological data is showing explosive growth. It is of practical significance to develop an efficient nucleosome positioning algorithm. Indeed, convolutional neural networks (CNN) can capture local features in DNA sequences, but ignore the order of bases. While the bidirectional recurrent neural network can make up for CNN's shortcomings in this regard and extract the long-term dependent features of DNA sequence. Results In this work, we use word vectors to represent DNA sequences and propose three new deep learning models for nucleosome positioning, and the integrative model NP_CBiR reaches a better prediction performance. The overall accuracies of NP_CBiR on H. sapiens, C. elegans, and D. melanogaster datasets are 86.18%, 89.39%, and 85.55% respectively. Conclusions Benefited by different network structures, NP_CBiR can effectively extract local features and bases order features of DNA sequences, thus can be considered as a complementary tool for nucleosome positioning.
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Affiliation(s)
- Guo-Sheng Han
- Department of Mathematics and Computational Science, Xiangtan University, Xiangtan, 411105, Hunan, China. .,Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education and Hunan Key Laboratory for Computation and Simulation in Science and Engineering, Xiangtan University, Xiangtan, 411105, Hunan, China.
| | - Qi Li
- Department of Mathematics and Computational Science, Xiangtan University, Xiangtan, 411105, Hunan, China.,Xiangtan Medicine Health Vocational College, Xiangtan, 411102, Hunan, China
| | - Ying Li
- Department of Mathematics and Computational Science, Xiangtan University, Xiangtan, 411105, Hunan, China.,Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education and Hunan Key Laboratory for Computation and Simulation in Science and Engineering, Xiangtan University, Xiangtan, 411105, Hunan, China
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9
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Wiles ET, Mumford CC, McNaught KJ, Tanizawa H, Selker EU. The ACF chromatin-remodeling complex is essential for Polycomb repression. eLife 2022; 11:e77595. [PMID: 35257662 PMCID: PMC9038196 DOI: 10.7554/elife.77595] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 03/03/2022] [Indexed: 11/13/2022] Open
Abstract
Establishing and maintaining appropriate gene repression is critical for the health and development of multicellular organisms. Histone H3 lysine 27 (H3K27) methylation is a chromatin modification associated with repressed facultative heterochromatin, but the mechanism of this repression remains unclear. We used a forward genetic approach to identify genes involved in transcriptional silencing of H3K27-methylated chromatin in the filamentous fungus Neurospora crassa. We found that the N. crassa homologs of ISWI (NCU03875) and ACF1 (NCU00164) are required for repression of a subset of H3K27-methylated genes and that they form an ACF chromatin-remodeling complex. This ACF complex interacts with chromatin throughout the genome, yet association with facultative heterochromatin is specifically promoted by the H3K27 methyltransferase, SET-7. H3K27-methylated genes that are upregulated when iswi or acf1 are deleted show a downstream shift of the +1 nucleosome, suggesting that proper nucleosome positioning is critical for repression of facultative heterochromatin. Our findings support a direct role of the ACF complex in Polycomb repression.
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Affiliation(s)
- Elizabeth T Wiles
- Institute of Molecular Biology, University of OregonEugeneUnited States
| | - Colleen C Mumford
- Institute of Molecular Biology, University of OregonEugeneUnited States
| | - Kevin J McNaught
- Institute of Molecular Biology, University of OregonEugeneUnited States
| | - Hideki Tanizawa
- Institute of Molecular Biology, University of OregonEugeneUnited States
| | - Eric U Selker
- Institute of Molecular Biology, University of OregonEugeneUnited States
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10
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Swygert SG, Lin D, Portillo-Ledesma S, Lin PY, Hunt DR, Kao CF, Schlick T, Noble WS, Tsukiyama T. Local chromatin fiber folding represses transcription and loop extrusion in quiescent cells. eLife 2021; 10:e72062. [PMID: 34734806 PMCID: PMC8598167 DOI: 10.7554/elife.72062] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 11/03/2021] [Indexed: 12/16/2022] Open
Abstract
A longstanding hypothesis is that chromatin fiber folding mediated by interactions between nearby nucleosomes represses transcription. However, it has been difficult to determine the relationship between local chromatin fiber compaction and transcription in cells. Further, global changes in fiber diameters have not been observed, even between interphase and mitotic chromosomes. We show that an increase in the range of local inter-nucleosomal contacts in quiescent yeast drives the compaction of chromatin fibers genome-wide. Unlike actively dividing cells, inter-nucleosomal interactions in quiescent cells require a basic patch in the histone H4 tail. This quiescence-specific fiber folding globally represses transcription and inhibits chromatin loop extrusion by condensin. These results reveal that global changes in chromatin fiber compaction can occur during cell state transitions, and establish physiological roles for local chromatin fiber folding in regulating transcription and chromatin domain formation.
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Affiliation(s)
- Sarah G Swygert
- Basic Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Dejun Lin
- Department of Genome Sciences, University of WashingtonSeattleUnited States
| | | | - Po-Yen Lin
- Institute of Cellular and Organismic Biology, Academia SinicaTaipeiTaiwan
| | - Dakota R Hunt
- Basic Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Cheng-Fu Kao
- Institute of Cellular and Organismic Biology, Academia SinicaTaipeiTaiwan
| | - Tamar Schlick
- Department of Chemistry, New York UniversityNew YorkUnited States
- Courant Institute of Mathematical Sciences, New York UniversityNew YorkUnited States
- New York University-East China Normal University Center for Computational Chemistry at New York University ShanghaiShanghaiChina
| | - William S Noble
- Department of Genome Sciences, University of WashingtonSeattleUnited States
- Paul G. Allen School of Computer Science and Engineering, University of WashingtonSeattleUnited States
| | - Toshio Tsukiyama
- Basic Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
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11
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Kumar A, Chan J, Taguchi M, Kono H. Interplay among transacting factors around promoter in the initial phases of transcription. Curr Opin Struct Biol 2021; 71:7-15. [PMID: 34111671 DOI: 10.1016/j.sbi.2021.04.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/20/2021] [Accepted: 04/27/2021] [Indexed: 10/21/2022]
Abstract
The initiation signals are raised around the promoter by one of the general transcription factors, triggering a sequence of events that lead to mRNA transcript formation from target genes. Both specific noncoding DNA regions and transacting, macromolecular assemblies are intricately involved and indispensable. The transition between the subsequent transcriptional stages is accompanied by stage-specific signals and structural changes in the macromolecular assemblies and facilitated by the recruitment/removal of other chromatin and transcription-associated elements. Here, we discuss the choreography of transacting factors around promoter in the establishment and effectuation of the initial phases of transcription such as NDR formation, +1 nucleosome positioning, promoter DNA opening, and RNAPII promoter escape from a structural viewpoint.
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Affiliation(s)
- Amarjeet Kumar
- Molecular Modeling and Simulation Group, Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 8-1-7 Umemidai, Kizugawa, Kyoto, 619-0215, Japan
| | - Justin Chan
- Molecular Modeling and Simulation Group, Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 8-1-7 Umemidai, Kizugawa, Kyoto, 619-0215, Japan
| | - Masahiko Taguchi
- Molecular Modeling and Simulation Group, Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 8-1-7 Umemidai, Kizugawa, Kyoto, 619-0215, Japan
| | - Hidetoshi Kono
- Molecular Modeling and Simulation Group, Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 8-1-7 Umemidai, Kizugawa, Kyoto, 619-0215, Japan.
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12
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Han GS, Li Q, Li Y. Comparative analysis and prediction of nucleosome positioning using integrative feature representation and machine learning algorithms. BMC Bioinformatics 2021; 22:129. [PMID: 34078256 PMCID: PMC8170966 DOI: 10.1186/s12859-021-04006-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 02/08/2021] [Indexed: 12/01/2022] Open
Abstract
Background Nucleosome plays an important role in the process of genome expression, DNA replication, DNA repair and transcription. Therefore, the research of nucleosome positioning has invariably received extensive attention. Considering the diversity of DNA sequence representation methods, we tried to integrate multiple features to analyze its effect in the process of nucleosome positioning analysis. This process can also deepen our understanding of the theoretical analysis of nucleosome positioning. Results Here, we not only used frequency chaos game representation (FCGR) to construct DNA sequence features, but also integrated it with other features and adopted the principal component analysis (PCA) algorithm. Simultaneously, support vector machine (SVM), extreme learning machine (ELM), extreme gradient boosting (XGBoost), multilayer perceptron (MLP) and convolutional neural networks (CNN) are used as predictors for nucleosome positioning prediction analysis, respectively. The integrated feature vector prediction quality is significantly superior to a single feature. After using principal component analysis (PCA) to reduce the feature dimension, the prediction quality of H. sapiens dataset has been significantly improved. Conclusions Comparative analysis and prediction on H. sapiens, C. elegans, D. melanogaster and S. cerevisiae datasets, demonstrate that the application of FCGR to nucleosome positioning is feasible, and we also found that integrative feature representation would be better.
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Affiliation(s)
- Guo-Sheng Han
- Department of Mathematics and Computational Science, Xiangtan University, Xiangtan, 411105, Hunan, China. .,Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education and Hunan Key Laboratory for Computation and Simulation in Science and Engineering, Xiangtan University, Xiangtan, 411105, Hunan, China.
| | - Qi Li
- Department of Mathematics and Computational Science, Xiangtan University, Xiangtan, 411105, Hunan, China.,Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education and Hunan Key Laboratory for Computation and Simulation in Science and Engineering, Xiangtan University, Xiangtan, 411105, Hunan, China
| | - Ying Li
- Department of Mathematics and Computational Science, Xiangtan University, Xiangtan, 411105, Hunan, China.,Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education and Hunan Key Laboratory for Computation and Simulation in Science and Engineering, Xiangtan University, Xiangtan, 411105, Hunan, China
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13
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Abstract
Determining the effect of DNA methylation on chromatin structure and function in higher organisms is challenging due to the extreme complexity of epigenetic regulation. We studied a simpler model system, budding yeast, that lacks DNA methylation machinery making it a perfect model system to study the intrinsic role of DNA methylation in chromatin structure and function. We expressed the murine DNA methyltransferases in Saccharomyces cerevisiae and analyzed the correlation between DNA methylation, nucleosome positioning, gene expression and 3D genome organization. Despite lacking the machinery for positioning and reading methylation marks, induced DNA methylation follows a conserved pattern with low methylation levels at the 5’ end of the gene increasing gradually toward the 3’ end, with concentration of methylated DNA in linkers and nucleosome free regions, and with actively expressed genes showing low and high levels of methylation at transcription start and terminating sites respectively, mimicking the patterns seen in mammals. We also see that DNA methylation increases chromatin condensation in peri-centromeric regions, decreases overall DNA flexibility, and favors the heterochromatin state. Taken together, these results demonstrate that methylation intrinsically modulates chromatin structure and function even in the absence of cellular machinery evolved to recognize and process the methylation signal. Multi-layered epigenetic regulation in higher eukaryotes makes it challenging to disentangle the individual effects of modifications on chromatin structure and function. Here, the authors expressed mammalian DNA methyltransferases in yeast, which have no DNA methylation, to show that methylation has intrinsic effects on chromatin structure.
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14
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Tran TQ, MacAlpine HK, Tripuraneni V, Mitra S, MacAlpine DM, Hartemink AJ. Linking the dynamics of chromatin occupancy and transcription with predictive models. Genome Res 2021; 31:1035-1046. [PMID: 33893157 PMCID: PMC8168580 DOI: 10.1101/gr.267237.120] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 04/19/2021] [Indexed: 12/30/2022]
Abstract
Though the sequence of the genome within each eukaryotic cell is essentially fixed, it exists within a complex and changing chromatin state. This state is determined, in part, by the dynamic binding of proteins to the DNA. These proteins—including histones, transcription factors (TFs), and polymerases—interact with one another, the genome, and other molecules to allow the chromatin to adopt one of exceedingly many possible configurations. Understanding how changing chromatin configurations associate with transcription remains a fundamental research problem. We sought to characterize at high spatiotemporal resolution the dynamic interplay between transcription and chromatin in response to cadmium stress. Whereas gene regulatory responses to environmental stress in yeast have been studied, how the chromatin state changes and how those changes connect to gene regulation remain unexplored. By combining MNase-seq and RNA-seq data, we found chromatin signatures of transcriptional activation and repression involving both nucleosomal and TF-sized DNA-binding factors. Using these signatures, we identified associations between chromatin dynamics and transcriptional regulation, not only for known cadmium response genes, but across the entire genome, including antisense transcripts. Those associations allowed us to develop generalizable models that predict dynamic transcriptional responses on the basis of dynamic chromatin signatures.
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Affiliation(s)
- Trung Q Tran
- Department of Computer Science, Duke University, Durham, North Carolina 27708, USA
| | - Heather K MacAlpine
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Vinay Tripuraneni
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Sneha Mitra
- Department of Computer Science, Duke University, Durham, North Carolina 27708, USA
| | - David M MacAlpine
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA.,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA
| | - Alexander J Hartemink
- Department of Computer Science, Duke University, Durham, North Carolina 27708, USA.,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA
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15
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Habib O, Mohd Sakri R, Ghazalli N, Chau DM, Ling KH, Abdullah S. Limited expression of non-integrating CpG-free plasmid is associated with increased nucleosome enrichment. PLoS One 2020; 15:e0244386. [PMID: 33347482 PMCID: PMC7751972 DOI: 10.1371/journal.pone.0244386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 12/08/2020] [Indexed: 11/18/2022] Open
Abstract
CpG-free pDNA was reported to facilitate sustained transgene expression with minimal inflammation in vivo as compared to CpG-containing pDNA. However, the expression potential and impact of CpG-free pDNA in in vitro model have never been described. Hence, in this study, we analyzed the transgene expression profiles of CpG-free pDNA in vitro to determine the influence of CpG depletion from the transgene. We found that in contrast to the published in vivo studies, CpG-free pDNA expressed a significantly lower level of luciferase than CpG-rich pDNA in several human cell lines. By comparing novel CpG-free pDNA carrying CpG-free GFP (pZGFP: 0 CpG) to CpG-rich GFP (pRGFP: 60 CpGs), we further showed that the discrepancy was not influenced by external factors such as gene transfer agent, cell species, cell type, and cytotoxicity. Moreover, pZGFP exhibited reduced expression despite having equal gene dosage as pRGFP. Analysis of mRNA distribution revealed that the mRNA export of pZGFP and pRGFP was similar; however, the steady state mRNA level of pZGFP was significantly lower. Upon further investigation, we found that the CpG-free transgene in non-integrating CpG-free pDNA backbone acquired increased nucleosome enrichment as compared with CpG-rich transgene, which may explain the observed reduced level of steady state mRNA. Our findings suggest that nucleosome enrichment could regulate non-integrating CpG-free pDNA expression and has implications on pDNA design.
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Affiliation(s)
- Omar Habib
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia (UPM), Serdang, Selangor, Malaysia
- Genetics and Regenerative Medicine Research Centre, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia (UPM), Serdang, Selangor, Malaysia
| | - Rozita Mohd Sakri
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia (UPM), Serdang, Selangor, Malaysia
- Genetics and Regenerative Medicine Research Centre, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia (UPM), Serdang, Selangor, Malaysia
- Faculty of Applied Sciences, Universiti Teknologi MARA (UiTM), Shah Alam, Selangor, Malaysia
| | - Nadiah Ghazalli
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia (UPM), Serdang, Selangor, Malaysia
- Genetics and Regenerative Medicine Research Centre, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia (UPM), Serdang, Selangor, Malaysia
| | - De-Ming Chau
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia (UPM), Serdang, Selangor, Malaysia
- Genetics and Regenerative Medicine Research Centre, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia (UPM), Serdang, Selangor, Malaysia
| | - King-Hwa Ling
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia (UPM), Serdang, Selangor, Malaysia
- Genetics and Regenerative Medicine Research Centre, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia (UPM), Serdang, Selangor, Malaysia
| | - Syahril Abdullah
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia (UPM), Serdang, Selangor, Malaysia
- Genetics and Regenerative Medicine Research Centre, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia (UPM), Serdang, Selangor, Malaysia
- UPM-MAKNA Cancer Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia (UPM), Serdang, Selangor, Malaysia
- * E-mail:
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16
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Portillo-Ledesma S, Tsao LH, Wagley M, Lakadamyali M, Cosma MP, Schlick T. Nucleosome Clutches are Regulated by Chromatin Internal Parameters. J Mol Biol 2020; 433:166701. [PMID: 33181171 DOI: 10.1016/j.jmb.2020.11.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/27/2020] [Accepted: 11/02/2020] [Indexed: 01/17/2023]
Abstract
Nucleosomes cluster together when chromatin folds in the cell to form heterogeneous groups termed "clutches". These structural units add another level of chromatin regulation, for example during cell differentiation. Yet, the mechanisms that regulate their size and compaction remain obscure. Here, using our chromatin mesoscale model, we dissect clutch patterns in fibers with different combinations of nucleosome positions, linker histone density, and acetylation levels to investigate their role in clutch regulation. First, we isolate the effect of each chromatin parameter by studying systems with regular nucleosome spacing; second, we design systems with naturally-occurring linker lengths that fold onto specific clutch patterns; third, we model gene-encoding fibers to understand how these combined factors contribute to gene structure. Our results show how these chromatin parameters act together to produce different-sized nucleosome clutches. The length of nucleosome free regions (NFRs) profoundly affects clutch size, while the length of linker DNA has a moderate effect. In general, higher linker histone densities produce larger clutches by a chromatin compaction mechanism, while higher acetylation levels produce smaller clutches by a chromatin unfolding mechanism. We also show that it is possible to design fibers with naturally-occurring DNA linkers and NFRs that fold onto specific clutch patterns. Finally, in gene-encoding systems, a complex combination of variables dictates a gene-specific clutch pattern. Together, these results shed light into the mechanisms that regulate nucleosome clutches and suggest a new epigenetic mechanism by which chromatin parameters regulate transcriptional activity via the three-dimensional folded state of the genome at a nucleosome level.
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Affiliation(s)
- Stephanie Portillo-Ledesma
- Department of Chemistry, New York University, 1021 Silver, 100 Washington Square East, New York, NY, 10003, USA
| | - Lucille H Tsao
- Department of Chemistry, New York University, 1021 Silver, 100 Washington Square East, New York, NY, 10003, USA
| | - Meghna Wagley
- Department of Chemistry, New York University, 1021 Silver, 100 Washington Square East, New York, NY, 10003, USA
| | - Melike Lakadamyali
- Perelman School of Medicine, Department of Physiology, University of Pennsylvania, Clinical Research Building, 415 Curie Boulevard, Philadelphia, PA 19104, USA; Perelman School of Medicine, Department of Cell and Developmental Biology, University of Pennsylvania, Clinical Research Building, 415 Curie Boulevard, Philadelphia, PA 19104, USA
| | - Maria Pia Cosma
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain; Bioland Laboratory, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China; CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Tamar Schlick
- Department of Chemistry, New York University, 1021 Silver, 100 Washington Square East, New York, NY, 10003, USA; New York University-East China Normal University Center for Computational Chemistry at New York University Shanghai, Room 340, Geography Building, 3663 North Zhongshan Road, Shanghai, 200062, China; Courant Institute of Mathematical Sciences, New York University, 251 Mercer St, New York, NY, 10012, USA.
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17
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Capturing and Understanding the Dynamics and Heterogeneity of Gene Expression in the Living Cell. Int J Mol Sci 2020; 21:ijms21218278. [PMID: 33167354 PMCID: PMC7663833 DOI: 10.3390/ijms21218278] [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: 09/23/2020] [Revised: 10/29/2020] [Accepted: 11/03/2020] [Indexed: 11/21/2022] Open
Abstract
The regulation of gene expression is a fundamental process enabling cells to respond to internal and external stimuli or to execute developmental programs. Changes in gene expression are highly dynamic and depend on many intrinsic and extrinsic factors. In this review, we highlight the dynamic nature of transient gene expression changes to better understand cell physiology and development in general. We will start by comparing recent in vivo procedures to capture gene expression in real time. Intrinsic factors modulating gene expression dynamics will then be discussed, focusing on chromatin modifications. Furthermore, we will dissect how cell physiology or age impacts on dynamic gene regulation and especially discuss molecular insights into acquired transcriptional memory. Finally, this review will give an update on the mechanisms of heterogeneous gene expression among genetically identical individual cells. We will mainly focus on state-of-the-art developments in the yeast model but also cover higher eukaryotic systems.
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18
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Qiu H, Biernat E, Govind CK, Rawal Y, Chereji RV, Clark DJ, Hinnebusch AG. Chromatin remodeler Ino80C acts independently of H2A.Z to evict promoter nucleosomes and stimulate transcription of highly expressed genes in yeast. Nucleic Acids Res 2020; 48:8408-8430. [PMID: 32663283 DOI: 10.1093/nar/gkaa571] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 05/19/2020] [Accepted: 06/29/2020] [Indexed: 12/22/2022] Open
Abstract
The chromatin remodelers SWI/SNF and RSC function in evicting promoter nucleosomes at highly expressed yeast genes, particularly those activated by transcription factor Gcn4. Ino80 remodeling complex (Ino80C) can establish nucleosome-depleted regions (NDRs) in reconstituted chromatin, and was implicated in removing histone variant H2A.Z from the -1 and +1 nucleosomes flanking NDRs; however, Ino80C's function in transcriptional activation in vivo is not well understood. Analyzing the cohort of Gcn4-induced genes in ino80Δ mutants has uncovered a role for Ino80C on par with SWI/SNF in evicting promoter nucleosomes and transcriptional activation. Compared to SWI/SNF, Ino80C generally functions over a wider region, spanning the -1 and +1 nucleosomes, NDR and proximal genic nucleosomes, at genes highly dependent on its function. Defects in nucleosome eviction in ino80Δ cells are frequently accompanied by reduced promoter occupancies of TBP, and diminished transcription; and Ino80 is enriched at genes requiring its remodeler activity. Importantly, nuclear depletion of Ino80 impairs promoter nucleosome eviction even in a mutant lacking H2A.Z. Thus, Ino80C acts widely in the yeast genome together with RSC and SWI/SNF in evicting promoter nucleosomes and enhancing transcription, all in a manner at least partly independent of H2A.Z editing.
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Affiliation(s)
- Hongfang Qiu
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Emily Biernat
- Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA
| | - Chhabi K Govind
- Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA
| | - Yashpal Rawal
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Răzvan V Chereji
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - David J Clark
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alan G Hinnebusch
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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19
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Liu R, Ding J. Chromosomal Repositioning and Gene Regulation of Cells on a Micropillar Array. ACS APPLIED MATERIALS & INTERFACES 2020; 12:35799-35812. [PMID: 32667177 DOI: 10.1021/acsami.0c05883] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
While various cell responses on material surfaces have been examined, relatively few reports are focused on significant self-deformation of cell nuclei and corresponding chromosomal repositioning. Herein, we prepared a micropillar array of poly(lactide-co-glycolide) (PLGA) and observed significant nuclear deformation of HeLa cells on the polymeric micropillars. In particular, we detected the territory positioning of chromosomes 18 and 19 and gene expression profiles of HeLa cells on the micropillar array using fluorescence in situ hybridization and a DNA microarray. Chromosome 18 was found to be translocated closer to the nuclear periphery than chromosome 19 on the micropillar array. With the repositioning of chromosomal territories, HeLa cells changed their gene expressions on the micropillar array with 180 genes upregulated and 255 genes downregulated for all of the 23 pairs of chromosomes under the experimental conditions and the employed Bioinformatics criteria. Hence, this work deepens the understanding on cell-material interactions by revealing that material surface topography can probably influence chromosomal repositioning in the nuclei and gene expressions of cells.
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Affiliation(s)
- Ruili Liu
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200438, China
| | - Jiandong Ding
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200438, China
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20
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崔 颖, 徐 泽, 李 建. [Identification of nucleosome positioning using support vector machine method based on comprehensive DNA sequence feature]. SHENG WU YI XUE GONG CHENG XUE ZA ZHI = JOURNAL OF BIOMEDICAL ENGINEERING = SHENGWU YIXUE GONGCHENGXUE ZAZHI 2020; 37:496-501. [PMID: 32597092 PMCID: PMC10319573 DOI: 10.7507/1001-5515.201911064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Indexed: 11/03/2022]
Abstract
In this article, based on z-curve theory and position weight matrix (PWM), a model for nucleosome sequences was constructed. Nucleosome sequence dataset was transformed into three-dimensional coordinates, PWM of the nucleosome sequences was calculated and the similarity score was obtained. After integrating them, a nucleosome feature model based on the comprehensive DNA sequences was obtained and named CSeqFM. We calculated the Euclidean distance between nucleosome sequence candidates or linker sequences and CSeqFM model as the feature dataset, and put the feature datasets into the support vector machine (SVM) for training and testing by ten-fold cross-validation. The results showed that the sensitivity, specificity, accuracy and Matthews correlation coefficient (MCC) of identifying nucleosome positioning for S. cerevisiae were 97.1%, 96.9%, 94.2% and 0.89, respectively, and the area under the receiver operating characteristic curve (AUC) was 0.980 1. Compared with another z-curve method, it was found that our method had better identifying effect and each evaluation performance showed better superiority. CSeqFM method was applied to identify nucleosome positioning for other three species, including C. elegans, H. sapiens and D. melanogaster. The results showed that AUCs of the three species were all higher than 0.90, and CSeqFM method also showed better stability and effectiveness compared with iNuc-STNC and iNuc-PseKNC methods, which is further demonstrated that CSeqFM method has strong reliability and good identification performance.
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Affiliation(s)
- 颖 崔
- 黑龙江大学 电子工程学院(哈尔滨 150080)Electronic Engineering College, Heilongjiang University, Harbin 150080, P.R.China
- 哈尔滨医科大学 生物信息科学与技术学院(哈尔滨 150081)School of Bioinformatics Sciences and Technology, Harbin Medical University, Harbin 150081, P.R.China
| | - 泽龙 徐
- 黑龙江大学 电子工程学院(哈尔滨 150080)Electronic Engineering College, Heilongjiang University, Harbin 150080, P.R.China
| | - 建中 李
- 黑龙江大学 电子工程学院(哈尔滨 150080)Electronic Engineering College, Heilongjiang University, Harbin 150080, P.R.China
- 哈尔滨医科大学 生物信息科学与技术学院(哈尔滨 150081)School of Bioinformatics Sciences and Technology, Harbin Medical University, Harbin 150081, P.R.China
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21
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Fine Chromatin-Driven Mechanism of Transcription Interference by Antisense Noncoding Transcription. Cell Rep 2020; 31:107612. [DOI: 10.1016/j.celrep.2020.107612] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 03/12/2020] [Accepted: 04/14/2020] [Indexed: 01/04/2023] Open
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22
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Morrison AJ. Chromatin-remodeling links metabolic signaling to gene expression. Mol Metab 2020; 38:100973. [PMID: 32251664 PMCID: PMC7300377 DOI: 10.1016/j.molmet.2020.100973] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 03/01/2020] [Accepted: 03/03/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND ATP-dependent chromatin remodelers are evolutionarily conserved complexes that alter nucleosome positioning to influence many DNA-templated processes, such as replication, repair, and transcription. In particular, chromatin remodeling can dynamically regulate gene expression by altering accessibility of chromatin to transcription factors. SCOPE OF REVIEW This review provides an overview of the importance of chromatin remodelers in the regulation of metabolic gene expression. Particular emphasis is placed on the INO80 and SWI/SNF (BAF/PBAF) chromatin remodelers in both yeast and mammals. This review details discoveries from the initial identification of chromatin remodelers in Saccharomyces cerevisiae to recent discoveries in the metabolic requirements of developing embryonic tissues in mammals. MAJOR CONCLUSIONS INO80 and SWI/SNF (BAF/PBAF) chromatin remodelers regulate the expression of energy metabolism pathways in S. cerevisiae and mammals in response to diverse nutrient environments. In particular, the INO80 complex organizes the temporal expression of gene expression in the metabolically synchronized S. cerevisiae system. INO80-mediated chromatin remodeling is also needed to constrain cell division during metabolically favorable conditions. Conversely, the BAF/PBAF remodeler regulates tissue-specific glycolytic metabolism and is disrupted in cancers that are dependent on glycolysis for proliferation. The role of chromatin remodeling in metabolic gene expression is downstream of the metabolic signaling pathways, such as the TOR pathway, a critical regulator of metabolic homeostasis. Furthermore, the INO80 and BAF/PBAF chromatin remodelers have both been shown to regulate heart development, the tissues of which have unique requirements for energy metabolism during development. Collectively, these results demonstrate that chromatin remodelers communicate metabolic status to chromatin and are a central component of homeostasis pathways that optimize cell fitness, organismal development, and prevent disease.
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Affiliation(s)
- Ashby J Morrison
- Department of Biology, Stanford University, Stanford CA 94305, USA.
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23
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Duman M, Martinez-Moreno M, Jacob C, Tapinos N. Functions of histone modifications and histone modifiers in Schwann cells. Glia 2020; 68:1584-1595. [PMID: 32034929 DOI: 10.1002/glia.23795] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 01/24/2020] [Accepted: 01/28/2020] [Indexed: 01/25/2023]
Abstract
Schwann cells (SCs) are the main glial cells present in the peripheral nervous system (PNS). Their primary functions are to insulate peripheral axons to protect them from the environment and to enable fast conduction of electric signals along big caliber axons by enwrapping them in a thick myelin sheath rich in lipids. In addition, SCs have the peculiar ability to foster axonal regrowth after a lesion by demyelinating and converting into repair cells that secrete neurotrophic factors and guide axons back to their former target to finally remyelinate regenerated axons. The different steps of SC development and their role in the maintenance of PNS integrity and regeneration after lesion are controlled by various factors among which transcription factors and chromatin-remodeling enzymes hold major functions. In this review, we discussed how histone modifications and histone-modifying enzymes control SC development, maintenance of PNS integrity and response to injury. The functions of histone modifiers as part of chromatin-remodeling complexes are discussed in another review published in the same issue of Glia.
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Affiliation(s)
- Mert Duman
- Faculty of Biology, Institute of Developmental Biology and Neurobiology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Margot Martinez-Moreno
- Department of Neurosurgery, Molecular Neuroscience & Neuro-Oncology Laboratory, Brown University, Providence, Rhode Island
| | - Claire Jacob
- Faculty of Biology, Institute of Developmental Biology and Neurobiology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Nikos Tapinos
- Department of Neurosurgery, Molecular Neuroscience & Neuro-Oncology Laboratory, Brown University, Providence, Rhode Island
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24
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Cucinotta CE, Hildreth AE, McShane BM, Shirra MK, Arndt KM. The nucleosome acidic patch directly interacts with subunits of the Paf1 and FACT complexes and controls chromatin architecture in vivo. Nucleic Acids Res 2019; 47:8410-8423. [PMID: 31226204 PMCID: PMC6895269 DOI: 10.1093/nar/gkz549] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 06/07/2019] [Accepted: 06/11/2019] [Indexed: 12/12/2022] Open
Abstract
The nucleosome core regulates DNA-templated processes through the highly conserved nucleosome acidic patch. While structural and biochemical studies have shown that the acidic patch controls chromatin factor binding and activity, few studies have elucidated its functions in vivo. We employed site-specific crosslinking to identify proteins that directly bind the acidic patch in Saccharomyces cerevisiae and demonstrated crosslinking of histone H2A to Paf1 complex subunit Rtf1 and FACT subunit Spt16. Rtf1 bound to nucleosomes through its histone modification domain, supporting its role as a cofactor in H2B K123 ubiquitylation. An acidic patch mutant showed defects in nucleosome positioning and occupancy genome-wide. Our results provide new information on the chromatin engagement of two central players in transcription elongation and emphasize the importance of the nucleosome core as a hub for proteins that regulate chromatin during transcription.
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Affiliation(s)
- Christine E Cucinotta
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - A Elizabeth Hildreth
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Brendan M McShane
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Margaret K Shirra
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Karen M Arndt
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
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25
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Buitrago D, Codó L, Illa R, de Jorge P, Battistini F, Flores O, Bayarri G, Royo R, Del Pino M, Heath S, Hospital A, Gelpí JL, Heath IB, Orozco M. Nucleosome Dynamics: a new tool for the dynamic analysis of nucleosome positioning. Nucleic Acids Res 2019; 47:9511-9523. [PMID: 31504766 PMCID: PMC6765203 DOI: 10.1093/nar/gkz759] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/23/2019] [Accepted: 08/22/2019] [Indexed: 02/03/2023] Open
Abstract
We present Nucleosome Dynamics, a suite of programs integrated into a virtual research environment and created to define nucleosome architecture and dynamics from noisy experimental data. The package allows both the definition of nucleosome architectures and the detection of changes in nucleosomal organization due to changes in cellular conditions. Results are displayed in the context of genomic information thanks to different visualizers and browsers, allowing the user a holistic, multidimensional view of the genome/transcriptome. The package shows good performance for both locating equilibrium nucleosome architecture and nucleosome dynamics and provides abundant useful information in several test cases, where experimental data on nucleosome position (and for some cases expression level) have been collected for cells under different external conditions (cell cycle phase, yeast metabolic cycle progression, changes in nutrients or difference in MNase digestion level). Nucleosome Dynamics is a free software and is provided under several distribution models.
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Affiliation(s)
- Diana Buitrago
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, Barcelona 08028, Spain
| | - Laia Codó
- Barcelona Supercomputing Center (BSC), Jordi Girona 31, Barcelona 08028. Spain
| | - Ricard Illa
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, Barcelona 08028, Spain
| | - Pau de Jorge
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, Barcelona 08028, Spain
| | - Federica Battistini
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, Barcelona 08028, Spain
| | - Oscar Flores
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, Barcelona 08028, Spain
| | - Genis Bayarri
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, Barcelona 08028, Spain
| | - Romina Royo
- Barcelona Supercomputing Center (BSC), Jordi Girona 31, Barcelona 08028. Spain
| | - Marc Del Pino
- Barcelona Supercomputing Center (BSC), Jordi Girona 31, Barcelona 08028. Spain
| | - Simon Heath
- Centro Nacional de Análisis Genómico (CNAG-CRG), Centre de Regulacio Genómico (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Adam Hospital
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, Barcelona 08028, Spain
| | - Josep Lluís Gelpí
- Barcelona Supercomputing Center (BSC), Jordi Girona 31, Barcelona 08028. Spain.,Departament de Bioquímica i Biomedicina. Facultat de Biologia, Universitat de Barcelona, Avgda Diagonal 647, Barcelona 08028, Spain
| | - Isabelle Brun Heath
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, Barcelona 08028, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, Barcelona 08028, Spain.,Departament de Bioquímica i Biomedicina. Facultat de Biologia, Universitat de Barcelona, Avgda Diagonal 647, Barcelona 08028, Spain
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26
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Soudet J, Stutz F. Regulation of Gene Expression and Replication Initiation by Non‐Coding Transcription: A Model Based on Reshaping Nucleosome‐Depleted Regions. Bioessays 2019; 41:e1900043. [DOI: 10.1002/bies.201900043] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 08/19/2019] [Indexed: 12/24/2022]
Affiliation(s)
- Julien Soudet
- Department of Cell BiologyUniversity of Geneva 1211 Geneva Switzerland
| | - Françoise Stutz
- Department of Cell BiologyUniversity of Geneva 1211 Geneva Switzerland
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27
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ZCMM: A Novel Method Using Z-Curve Theory- Based and Position Weight Matrix for Predicting Nucleosome Positioning. Genes (Basel) 2019; 10:genes10100765. [PMID: 31569414 PMCID: PMC6827144 DOI: 10.3390/genes10100765] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 09/25/2019] [Accepted: 09/26/2019] [Indexed: 02/04/2023] Open
Abstract
Nucleosomes are the basic units of eukaryotes. The accurate positioning of nucleosomes plays a significant role in understanding many biological processes such as transcriptional regulation mechanisms and DNA replication and repair. Here, we describe the development of a novel method, termed ZCMM, based on Z-curve theory and position weight matrix (PWM). The ZCMM was trained and tested using the nucleosomal and linker sequences determined by support vector machine (SVM) in Saccharomyces cerevisiae (S. cerevisiae), and experimental results showed that the sensitivity (Sn), specificity (Sp), accuracy (Acc), and Matthews correlation coefficient (MCC) values for ZCMM were 91.40%, 96.56%, 96.75%, and 0.88, respectively, and the average area under the receiver operating characteristic curve (AUC) value was 0.972. A ZCMM predictor was developed to predict nucleosome positioning in Homo sapiens (H. sapiens), Caenorhabditis elegans (C. elegans), and Drosophila melanogaster (D. melanogaster) genomes, and the accuracy (Acc) values were 77.72%, 85.34%, and 93.62%, respectively. The maximum AUC values of the four species were 0.982, 0.861, 0.912 and 0.911, respectively. Another independent dataset for S. cerevisiae was used to predict nucleosome positioning. Compared with the results of Wu's method, it was found that the Sn, Sp, Acc, and MCC of ZCMM results for S. cerevisiae were all higher, reaching 96.72%, 96.54%, 94.10%, and 0.88. Compared with the Guo's method 'iNuc-PseKNC', the results of ZCMM for D. melanogaster were better. Meanwhile, the ZCMM was compared with some experimental data in vitro and in vivo for S. cerevisiae, and the results showed that the nucleosomes predicted by ZCMM were highly consistent with those confirmed by these experiments. Therefore, it was further confirmed that the ZCMM method has good accuracy and reliability in predicting nucleosome positioning.
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Kubik S, Bruzzone MJ, Challal D, Dreos R, Mattarocci S, Bucher P, Libri D, Shore D. Opposing chromatin remodelers control transcription initiation frequency and start site selection. Nat Struct Mol Biol 2019; 26:744-754. [PMID: 31384063 DOI: 10.1038/s41594-019-0273-3] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 06/28/2019] [Indexed: 12/31/2022]
Abstract
Precise nucleosome organization at eukaryotic promoters is thought to be generated by multiple chromatin remodeler (CR) enzymes and to affect transcription initiation. Using an integrated analysis of chromatin remodeler binding and nucleosome occupancy following rapid remodeler depletion, we investigated the interplay between these enzymes and their impact on transcription in yeast. We show that many promoters are affected by multiple CRs that operate in concert or in opposition to position the key transcription start site (TSS)-associated +1 nucleosome. We also show that nucleosome movement after CR inactivation usually results from the activity of another CR and that in the absence of any remodeling activity, +1 nucleosomes largely maintain their positions. Finally, we present functional assays suggesting that +1 nucleosome positioning often reflects a trade-off between maximizing RNA polymerase recruitment and minimizing transcription initiation at incorrect sites. Our results provide a detailed picture of fundamental mechanisms linking promoter nucleosome architecture to transcription initiation.
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Affiliation(s)
- Slawomir Kubik
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), Geneva, Switzerland
| | - Maria Jessica Bruzzone
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), Geneva, Switzerland
| | - Drice Challal
- Institut Jacques Monod, CNRS-Université Paris Diderot, Paris, France
| | - René Dreos
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Stefano Mattarocci
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), Geneva, Switzerland
| | - Philipp Bucher
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Domenico Libri
- Institut Jacques Monod, CNRS-Université Paris Diderot, Paris, France
| | - David Shore
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), Geneva, Switzerland.
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INO80 Chromatin Remodeling Coordinates Metabolic Homeostasis with Cell Division. Cell Rep 2019; 22:611-623. [PMID: 29346761 PMCID: PMC5949282 DOI: 10.1016/j.celrep.2017.12.079] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 12/19/2017] [Accepted: 12/21/2017] [Indexed: 12/13/2022] Open
Abstract
Adaptive survival requires the coordination of nutrient availability with expenditure of cellular resources. For example, in nutrient-limited environments, 50% of all S. cerevisiae genes synchronize and exhibit periodic bursts of expression in coordination with respiration and cell division in the yeast metabolic cycle (YMC). Despite the importance of metabolic and proliferative synchrony, the majority of YMC regulators are currently unknown. Here, we demonstrate that the INO80 chromatin-remodeling complex is required to coordinate respiration and cell division with periodic gene expression. Specifically, INO80 mutants have severe defects in oxygen consumption and promiscuous cell division that is no longer coupled with metabolic status. In mutant cells, chromatin accessibility of periodic genes, including TORC1-responsive genes, is relatively static, concomitant with severely attenuated gene expression. Collectively, these results reveal that the INO80 complex mediates metabolic signaling to chromatin to restrict proliferation to metabolically optimal states.
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Lu Z, Lin Z. Pervasive and dynamic transcription initiation in Saccharomyces cerevisiae. Genome Res 2019; 29:1198-1210. [PMID: 31076411 PMCID: PMC6633255 DOI: 10.1101/gr.245456.118] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 05/07/2019] [Indexed: 12/15/2022]
Abstract
Transcription initiation is finely regulated to ensure proper expression and function of genes. The regulated transcription initiation in response to various environmental stimuli in a classic model organism Saccharomyces cerevisiae has not been systematically investigated. In this study, we generated quantitative maps of transcription start sites (TSSs) at a single-nucleotide resolution for S. cerevisiae grown in nine different conditions using no-amplification nontagging Cap analysis of gene expression (nAnT-iCAGE) sequencing. We mapped ∼1 million well-supported TSSs, suggesting highly pervasive transcription initiation in the compact genome of the budding yeast. The comprehensive TSS maps allowed us to identify core promoters for ∼96% verified protein-coding genes. We corrected misannotation of translation start codon for 122 genes and suggested an alternative start codon for 57 genes. We found that 56% of yeast genes are controlled by multiple core promoters, and alternative core promoter usage by a gene is widespread in response to changing environments. Most core promoter shifts are coupled with altered gene expression, indicating that alternative core promoter usage might play an important role in controlling gene transcriptional activities. Based on their activities in responding to environmental cues, we divided core promoters into constitutive class (55%) and inducible class (45%). The two classes of core promoters display distinctive patterns in transcriptional abundance, chromatin structure, promoter shape, and sequence context. In summary, our study improved the annotation of the yeast genome and demonstrated a much more pervasive and dynamic nature of transcription initiation in yeast than previously recognized.
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Affiliation(s)
- Zhaolian Lu
- Department of Biology, Saint Louis University, St. Louis, Missouri 63104, USA
| | - Zhenguo Lin
- Department of Biology, Saint Louis University, St. Louis, Missouri 63104, USA
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31
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Hesketh A, Oliver SG. High-energy guanine nucleotides as a signal capable of linking growth to cellular energy status via the control of gene transcription. Curr Genet 2019; 65:893-897. [PMID: 30937517 PMCID: PMC6620469 DOI: 10.1007/s00294-019-00963-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 03/21/2019] [Accepted: 03/26/2019] [Indexed: 12/31/2022]
Abstract
This mini-review considers the idea that guanylate nucleotide energy charge acts as an integrative signal for the regulation of gene expression in eukaryotic cells and discusses possible routes for that signal's transduction. Gene expression is intimately linked with cell nutrition and diverse signaling systems serve to coordinate the synthesis of proteins required for growth and proliferation with the prevailing cellular nutritional status. Using short pathways for the inducible and futile consumption of ATP or GTP in engineered cells of Saccharomyces cerevisiae, we have recently shown that GTP levels can also play a role in determining how genes act to respond to changes in cellular energy supply. This review aims to interpret the importance of GTP as an integrative signal in the context of an increasing body of evidence indicating the spatio-temporal complexity of cellular de novo purine nucleotide biosynthesis.
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Affiliation(s)
- Andy Hesketh
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Huxley Building, Lewes Road, Brighton, BN2 4GJ, UK
| | - Stephen G Oliver
- Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK.
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32
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Kubik S, O'Duibhir E, de Jonge WJ, Mattarocci S, Albert B, Falcone JL, Bruzzone MJ, Holstege FCP, Shore D. Sequence-Directed Action of RSC Remodeler and General Regulatory Factors Modulates +1 Nucleosome Position to Facilitate Transcription. Mol Cell 2019; 71:89-102.e5. [PMID: 29979971 DOI: 10.1016/j.molcel.2018.05.030] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 01/17/2018] [Accepted: 05/24/2018] [Indexed: 12/12/2022]
Abstract
Accessible chromatin is important for RNA polymerase II recruitment and transcription initiation at eukaryotic promoters. We investigated the mechanistic links between promoter DNA sequence, nucleosome positioning, and transcription. Our results indicate that positioning of the transcription start site-associated +1 nucleosome in yeast is critical for efficient TBP binding and is driven by two key factors, the essential chromatin remodeler RSC and a small set of ubiquitous general regulatory factors (GRFs). Our findings indicate that the strength and directionality of RSC action on promoter nucleosomes depends on the arrangement and proximity of two specific DNA motifs. This, together with the effect on nucleosome position observed in double depletion experiments, suggests that, despite their widespread co-localization, RSC and GRFs predominantly act through independent signals to generate accessible chromatin. Our results provide mechanistic insight into how the promoter DNA sequence instructs trans-acting factors to control nucleosome architecture and stimulate transcription initiation.
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Affiliation(s)
- Slawomir Kubik
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva (iGE3), 30 quai Ernest-Ansermet, 1211 Geneva 4, Switzerland
| | - Eoghan O'Duibhir
- Molecular Cancer Research, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Wim J de Jonge
- Molecular Cancer Research, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands; Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Stefano Mattarocci
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva (iGE3), 30 quai Ernest-Ansermet, 1211 Geneva 4, Switzerland
| | - Benjamin Albert
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva (iGE3), 30 quai Ernest-Ansermet, 1211 Geneva 4, Switzerland
| | - Jean-Luc Falcone
- Center for Advanced Modeling Sciences, Computer Science Department, University of Geneva, 7 route de Drize, 1227 Carouge, Switzerland
| | - Maria Jessica Bruzzone
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva (iGE3), 30 quai Ernest-Ansermet, 1211 Geneva 4, Switzerland
| | - Frank C P Holstege
- Molecular Cancer Research, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands; Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - David Shore
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva (iGE3), 30 quai Ernest-Ansermet, 1211 Geneva 4, Switzerland.
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Determination of the Global Pattern of Gene Expression in Yeast Cells by Intracellular Levels of Guanine Nucleotides. mBio 2019; 10:mBio.02500-18. [PMID: 30670615 PMCID: PMC6343037 DOI: 10.1128/mbio.02500-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
This paper investigates whether, independently of the supply of any specific nutrient, gene transcription responds to the energy status of the cell by monitoring ATP and GTP levels. Short pathways for the inducible and futile consumption of ATP or GTP were engineered into the yeast Saccharomyces cerevisiae, and the effect of an increased demand for these purine nucleotides on gene transcription was analyzed. The resulting changes in transcription were most consistently associated with changes in GTP and GEC levels, although the reprogramming in gene expression during glucose repression is sensitive to adenine nucleotide levels. The results show that GTP levels play a central role in determining how genes act to respond to changes in energy supply and that any comprehensive understanding of the control of eukaryotic gene expression requires the elucidation of how changes in guanine nucleotide abundance are sensed and transduced to alter the global pattern of transcription. Correlations between gene transcription and the abundance of high-energy purine nucleotides in Saccharomyces cerevisiae have often been noted. However, there has been no systematic investigation of this phenomenon in the absence of confounding factors such as nutrient status and growth rate, and there is little hard evidence for a causal relationship. Whether transcription is fundamentally responsive to prevailing cellular energetic conditions via sensing of intracellular purine nucleotides, independently of specific nutrition, remains an important question. The controlled nutritional environment of chemostat culture revealed a strong correlation between ATP and GTP abundance and the transcription of genes required for growth. Short pathways for the inducible and futile consumption of ATP or GTP were engineered into S. cerevisiae, permitting analysis of the transcriptional effect of an increased demand for these nucleotides. During steady-state growth using the fermentable carbon source glucose, the futile consumption of ATP led to a decrease in intracellular ATP concentration but an increase in GTP and the guanylate energy charge (GEC). Expression of transcripts encoding proteins involved in ribosome biogenesis, and those controlled by promoters subject to SWI/SNF-dependent chromatin remodelling, was correlated with these nucleotide pool changes. Similar nucleotide abundance changes were observed using a nonfermentable carbon source, but an effect on the growth-associated transcriptional programme was absent. Induction of the GTP-cycling pathway had only marginal effects on nucleotide abundance and gene transcription. The transcriptional response of respiring cells to glucose was dampened in chemostats induced for ATP cycling, but not GTP cycling, and this was primarily associated with altered adenine nucleotide levels.
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Catabolic repression in early-diverging anaerobic fungi is partially mediated by natural antisense transcripts. Fungal Genet Biol 2018; 121:1-9. [PMID: 30223087 DOI: 10.1016/j.fgb.2018.09.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 09/10/2018] [Accepted: 09/11/2018] [Indexed: 12/16/2022]
Abstract
Early-diverging anaerobic fungi (order: Neocallimastigomycota), lignocelluolytic chytrid-like fungi central to fiber degradation in the digestive tracts of large herbivores, are attractive sources of cellulases and hemicellulases for biotechnology. Enzyme expression is tightly regulated and coordinated through mechanisms that remain unelucidated to optimize hydrolytic efficiency. Our analysis of anaerobic fungal transcriptomes reveals hundreds of cis-natural antisense transcripts (cis-NATs), which we hypothesize play an integral role in this regulation. Through integrated genomic and transcriptomic sequencing on a range of catabolic substrates, we validate these NATs in three species (Anaeromyces robustus, Neocallimasix californiae, and Piromyces finnis), and analyze their expression patterns and prevalence to gain insight into their function. NAT function was diverse and conserved across the three fungal genomes studied, with 10% of all metabolic process NATs associated with lignocellulose hydrolysis. Despite these similarities, however, only eleven gene targets were conserved orthologs. Several NATs were dynamically regulated by lignocellulosic substrates while their gene targets were unregulated. This observation is consistent with a hypothesized, but untested, regulatory mechanism where selected genes are exclusively regulated at the transcriptional/post-transcriptional level by NATs. However, only genes with high NAT relative expression levels displayed this phenomenon, suggesting a selection mechanism that favors larger dynamic ranges for more precise control of gene expression. In addition to this mode, we observed two other possible regulatory fates: canonical transcriptional regulation with no NAT response, and positive co-regulation of target mRNA and cognate NAT, which we hypothesize is a fine-tuning strategy to locally negate control outputs from global regulators. Our work reveals the complex contributions of antisense RNA to the catabolic response in anaerobic fungi, highlighting its importance in understanding lignocellulolytic activity for bioenergy applications. More importantly, the relative expression of NAT to target may form a critical determinant of transcriptional vs post-transcriptional (NAT) control of gene expression in primitive anaerobic fungi.
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Xu Y, Lee JH, Li Z, Wang L, Ordog T, Bailey RC. A droplet microfluidic platform for efficient enzymatic chromatin digestion enables robust determination of nucleosome positioning. LAB ON A CHIP 2018; 18:2583-2592. [PMID: 30046796 PMCID: PMC6103843 DOI: 10.1039/c8lc00599k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The first step in chromatin-based epigenetic assays involves the fragmentation of chromatin to facilitate precise genomic localization of the associated DNA. Here, we report the development of a droplet microfluidic device that can rapidly and efficiently digest chromatin into single nucleosomes starting from whole-cell input material offering simplified and automated processing compared to conventional manual preparation. We demonstrate the digestion of chromatin from 2500-125 000 Jurkat cells using micrococcal nuclease for enzymatic processing. We show that the yield of mononucleosomal DNA can be optimized by controlling enzyme concentration and incubation time, with resulting mononucleosome yields exceeding 80%. Bioinformatic analysis of sequenced mononucleosomal DNA (MNase-seq) indicated a high degree of reproducibility and concordance (97-99%) compared with conventionally processed preparations. Our results demonstrate the feasibility of robust and automated nucleosome preparation using a droplet microfluidic platform for nucleosome positioning and downstream epigenomic assays.
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Affiliation(s)
- Yi Xu
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA.
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36
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Rawal Y, Chereji RV, Qiu H, Ananthakrishnan S, Govind CK, Clark DJ, Hinnebusch AG. SWI/SNF and RSC cooperate to reposition and evict promoter nucleosomes at highly expressed genes in yeast. Genes Dev 2018; 32:695-710. [PMID: 29785963 PMCID: PMC6004078 DOI: 10.1101/gad.312850.118] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 04/12/2018] [Indexed: 12/30/2022]
Abstract
The nucleosome remodeling complex RSC functions throughout the yeast genome to set the positions of -1 and +1 nucleosomes and thereby determines the widths of nucleosome-depleted regions (NDRs). The related complex SWI/SNF participates in nucleosome remodeling/eviction and promoter activation at certain yeast genes, including those activated by transcription factor Gcn4, but did not appear to function broadly in establishing NDRs. By analyzing the large cohort of Gcn4-induced genes in mutants lacking the catalytic subunits of SWI/SNF or RSC, we uncovered cooperation between these remodelers in evicting nucleosomes from different locations in the promoter and repositioning the +1 nucleosome downstream to produce wider NDRs-highly depleted of nucleosomes-during transcriptional activation. SWI/SNF also functions on a par with RSC at the most highly transcribed constitutively expressed genes, suggesting general cooperation by these remodelers for maximal transcription. SWI/SNF and RSC occupancies are greatest at the most highly expressed genes, consistent with their cooperative functions in nucleosome remodeling and transcriptional activation. Thus, SWI/SNF acts comparably with RSC in forming wide nucleosome-free NDRs to achieve high-level transcription but only at the most highly expressed genes exhibiting the greatest SWI/SNF occupancies.
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Affiliation(s)
- Yashpal Rawal
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Răzvan V Chereji
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Hongfang Qiu
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Sudha Ananthakrishnan
- Department of Biological Science, Oakland University, Rochester, Michigan 48309, USA
| | - Chhabi K Govind
- Department of Biological Science, Oakland University, Rochester, Michigan 48309, USA
| | - David J Clark
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Alan G Hinnebusch
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
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Brown T, Howe FS, Murray SC, Wouters M, Lorenz P, Seward E, Rata S, Angel A, Mellor J. Antisense transcription-dependent chromatin signature modulates sense transcript dynamics. Mol Syst Biol 2018; 14:e8007. [PMID: 29440389 PMCID: PMC5810148 DOI: 10.15252/msb.20178007] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 01/13/2018] [Accepted: 01/16/2018] [Indexed: 12/22/2022] Open
Abstract
Antisense transcription is widespread in genomes. Despite large differences in gene size and architecture, we find that yeast and human genes share a unique, antisense transcription-associated chromatin signature. We asked whether this signature is related to a biological function for antisense transcription. Using quantitative RNA-FISH, we observed changes in sense transcript distributions in nuclei and cytoplasm as antisense transcript levels were altered. To determine the mechanistic differences underlying these distributions, we developed a mathematical framework describing transcription from initiation to transcript degradation. At GAL1, high levels of antisense transcription alter sense transcription dynamics, reducing rates of transcript production and processing, while increasing transcript stability. This relationship with transcript stability is also observed as a genome-wide association. Establishing the antisense transcription-associated chromatin signature through disruption of the Set3C histone deacetylase activity is sufficient to similarly change these rates even in the absence of antisense transcription. Thus, antisense transcription alters sense transcription dynamics in a chromatin-dependent manner.
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Affiliation(s)
- Thomas Brown
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - Struan C Murray
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - Philipp Lorenz
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Emily Seward
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Scott Rata
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Andrew Angel
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Jane Mellor
- Department of Biochemistry, University of Oxford, Oxford, UK
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Watanabe K, Kokubo T. SAGA mediates transcription from the TATA-like element independently of Taf1p/TFIID but dependent on core promoter structures in Saccharomyces cerevisiae. PLoS One 2017; 12:e0188435. [PMID: 29176831 PMCID: PMC5703507 DOI: 10.1371/journal.pone.0188435] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 11/07/2017] [Indexed: 11/21/2022] Open
Abstract
In Saccharomyces cerevisiae, core promoters of class II genes contain a TATA element, either a TATA box (TATA[A/T]A[A/T][A/G]) or TATA-like element (1 or 2 bp mismatched version of the TATA box). The TATA element directs the assembly of the preinitiation complex (PIC) to ensure accurate transcriptional initiation. It has been proposed the PIC is assembled by two distinct pathways in which TBP is delivered by TFIID or SAGA, leading to the widely accepted model that these complexes mediate transcription mainly from TATA-like element- or TATA box-containing promoters, respectively. Although both complexes are involved in transcription of nearly all class II genes, it remains unclear how efficiently SAGA mediates transcription from TATA-like element-containing promoters independently of TFIID. We found that transcription from the TATA box-containing AGP1 promoter was greatly stimulated in a Spt3p-dependent manner after inactivation of Taf1p/TFIID. Thus, this promoter provides a novel experimental system in which to evaluate SAGA-mediated transcription from TATA-like element(s). We quantitatively measured transcription from various TATA-like elements in the Taf1p-dependent CYC1 promoter and Taf1p-independent AGP1 promoter. The results revealed that SAGA could mediate transcription from at least some TATA-like elements independently of Taf1p/TFIID, and that Taf1p-dependence or -independence is highly robust with respect to variation of the TATA sequence. Furthermore, chimeric promoter mapping revealed that Taf1p-dependence or independence was conferred by the upstream activating sequence (UAS), whereas Spt3p-dependent transcriptional stimulation after inactivation of Taf1p/TFIID was specific to the AGP1 promoter and dependent on core promoter regions other than the TATA box. These results suggest that TFIID and/or SAGA are regulated in two steps: the UAS first specifies TFIID or SAGA as the predominant factor on a given promoter, and then the core promoter structure guides the pertinent factor to conduct transcription in an appropriate manner.
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Affiliation(s)
- Kiyoshi Watanabe
- Molecular and Cellular Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Tetsuro Kokubo
- Molecular and Cellular Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, Japan
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Joo YJ, Ficarro SB, Soares LM, Chun Y, Marto JA, Buratowski S. Downstream promoter interactions of TFIID TAFs facilitate transcription reinitiation. Genes Dev 2017; 31:2162-2174. [PMID: 29203645 PMCID: PMC5749164 DOI: 10.1101/gad.306324.117] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 11/09/2017] [Indexed: 11/24/2022]
Abstract
TFIID binds promoter DNA to recruit RNA polymerase II and other basal factors for transcription. Although the TATA-binding protein (TBP) subunit of TFIID is necessary and sufficient for in vitro transcription, the TBP-associated factor (TAF) subunits recognize downstream promoter elements, act as coactivators, and interact with nucleosomes. In yeast nuclear extracts, transcription induces stable TAF binding to downstream promoter DNA, promoting subsequent activator-independent transcription reinitiation. In vivo, promoter responses to TAF mutations correlate with the level of downstream, rather than overall, Taf1 cross-linking. We propose a new model in which TAFs function as reinitiation factors, accounting for the differential responses of promoters to various transcription factor mutations.
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Affiliation(s)
- Yoo Jin Joo
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Scott B Ficarro
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, Massachusetts 02115, USA
- Blais Proteomics Center, Dana Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Luis M Soares
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Yujin Chun
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Jarrod A Marto
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, Massachusetts 02115, USA
- Blais Proteomics Center, Dana Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Stephen Buratowski
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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40
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Machné R, Murray DB, Stadler PF. Similarity-Based Segmentation of Multi-Dimensional Signals. Sci Rep 2017; 7:12355. [PMID: 28955039 PMCID: PMC5617875 DOI: 10.1038/s41598-017-12401-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 08/30/2017] [Indexed: 11/25/2022] Open
Abstract
The segmentation of time series and genomic data is a common problem in computational biology. With increasingly complex measurement procedures individual data points are often not just numbers or simple vectors in which all components are of the same kind. Analysis methods that capitalize on slopes in a single real-valued data track or that make explicit use of the vectorial nature of the data are not applicable in such scenaria. We develop here a framework for segmentation in arbitrary data domains that only requires a minimal notion of similarity. Using unsupervised clustering of (a sample of) the input yields an approximate segmentation algorithm that is efficient enough for genome-wide applications. As a showcase application we segment a time-series of transcriptome sequencing data from budding yeast, in high temporal resolution over ca. 2.5 cycles of the short-period respiratory oscillation. The algorithm is used with a similarity measure focussing on periodic expression profiles across the metabolic cycle rather than coverage per time point.
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Affiliation(s)
- Rainer Machné
- Institute for Synthetic Microbiology, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University Düsseldorf, Universitätsstraße 1, D-40225, Düsseldorf, Germany. .,Department of Theoretical Chemistry of the University of Vienna, Währingerstrasse 17, Vienna, A-1090, Austria.
| | - Douglas B Murray
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0017, Japan
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Competence Center for Scalable Data Services and Solutions, and Leipzig Research Center for Civilization Diseases, University Leipzig, Härtelstrasse 16-18, D-04107, Leipzig, Germany. .,Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103, Leipzig, Germany. .,Fraunhofer Institute for Cell Therapy and Immunology, Perlickstrasse 1, D-04103, Leipzig, Germany. .,Department of Theoretical Chemistry of the University of Vienna, Währingerstrasse 17, Vienna, A-1090, Austria. .,Center for RNA in Technology and Health, Univ. Copenhagen, Grønneg ardsvej 3, Frederiksberg C, Denmark. .,Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM, 87501, USA.
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41
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Lu X, Batugedara G, Lee M, Prudhomme J, Bunnik EM, Le Roch K. Nascent RNA sequencing reveals mechanisms of gene regulation in the human malaria parasite Plasmodium falciparum. Nucleic Acids Res 2017; 45:7825-7840. [PMID: 28531310 PMCID: PMC5737683 DOI: 10.1093/nar/gkx464] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 05/08/2017] [Accepted: 05/10/2017] [Indexed: 12/18/2022] Open
Abstract
Gene expression in Plasmodium falciparum is tightly regulated to ensure successful propagation of the parasite throughout its complex life cycle. The earliest transcriptomics studies in P. falciparum suggested a cascade of transcriptional activity over the course of the 48-hour intraerythrocytic developmental cycle (IDC); however, the just-in-time transcriptional model has recently been challenged by findings that show the importance of post-transcriptional regulation. To further explore the role of transcriptional regulation, we performed the first genome-wide nascent RNA profiling in P. falciparum. Our findings indicate that the majority of genes are transcribed simultaneously during the trophozoite stage of the IDC and that only a small subset of genes is subject to differential transcriptional timing. RNA polymerase II is engaged with promoter regions prior to this transcriptional burst, suggesting that Pol II pausing plays a dominant role in gene regulation. In addition, we found that the overall transcriptional program during gametocyte differentiation is surprisingly similar to the IDC, with the exception of relatively small subsets of genes. Results from this study suggest that further characterization of the molecular players that regulate stage-specific gene expression and Pol II pausing will contribute to our continuous search for novel antimalarial drug targets.
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MESH Headings
- Animals
- Epigenesis, Genetic
- Gene Expression Profiling
- Gene Expression Regulation, Developmental
- Genes, Protozoan
- Humans
- Malaria, Falciparum/blood
- Malaria, Falciparum/parasitology
- Plasmodium falciparum/genetics
- Plasmodium falciparum/growth & development
- Plasmodium falciparum/pathogenicity
- Promoter Regions, Genetic
- RNA Polymerase II/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Protozoan/genetics
- RNA, Protozoan/metabolism
- Sequence Analysis, RNA
- Transcription, Genetic
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Affiliation(s)
- Xueqing Maggie Lu
- Department of Cell Biology and Neuroscience, University of California, Riverside, CA, USA
| | - Gayani Batugedara
- Department of Cell Biology and Neuroscience, University of California, Riverside, CA, USA
| | - Michael Lee
- Department of Cell Biology and Neuroscience, University of California, Riverside, CA, USA
| | - Jacques Prudhomme
- Department of Cell Biology and Neuroscience, University of California, Riverside, CA, USA
| | - Evelien M. Bunnik
- Department of Cell Biology and Neuroscience, University of California, Riverside, CA, USA
- Department of Microbiology, Immunology and Molecular Genetics, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Karine G. Le Roch
- Department of Cell Biology and Neuroscience, University of California, Riverside, CA, USA
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42
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A comparison of nucleosome organization in Drosophila cell lines. PLoS One 2017; 12:e0178590. [PMID: 28570602 PMCID: PMC5453549 DOI: 10.1371/journal.pone.0178590] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 05/16/2017] [Indexed: 01/25/2023] Open
Abstract
Changes in the distribution of nucleosomes along the genome influence chromatin structure and impact gene expression by modulating the accessibility of DNA to transcriptional machinery. However, the role of genome-wide nucleosome positioning in gene expression and in maintaining differentiated cell states remains poorly understood. Drosophila melanogaster cell lines represent distinct tissue types and exhibit cell-type specific gene expression profiles. They thus could provide a useful tool for investigating cell-type specific nucleosome organization of an organism's genome. To evaluate this possibility, we compared genome-wide nucleosome positioning and occupancy in five different Drosophila tissue-specific cell lines, and in reconstituted chromatin, and then tested for correlations between nucleosome positioning, transcription factor binding motifs, and gene expression. Nucleosomes in all cell lines were positioned in accordance with previously known DNA-nucleosome interactions, with helically repeating A/T di-nucleotide pairs arranged within nucleosomal DNAs and AT-rich pentamers generally excluded from nucleosomal DNA. Nucleosome organization in all cell lines differed markedly from in vitro reconstituted chromatin, with highly expressed genes showing strong nucleosome organization around transcriptional start sites. Importantly, comparative analysis identified genomic regions that exhibited cell line-specific nucleosome enrichment or depletion. Further analysis of these regions identified 91 out of 16,384 possible heptamer sequences that showed differential nucleosomal occupation between cell lines, and 49 of the heptamers matched one or more known transcription factor binding sites. These results demonstrate that there is differential nucleosome positioning between these Drosophila cell lines and therefore identify a system that could be used to investigate the functional significance of differential nucleosomal positioning in cell type specification.
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43
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Mellor J. The molecular basis of metabolic cycles and their relationship to circadian rhythms. Nat Struct Mol Biol 2017; 23:1035-1044. [PMID: 27922609 DOI: 10.1038/nsmb.3311] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 09/23/2016] [Indexed: 12/12/2022]
Abstract
Metabolic cycles result from the partitioning of oxidative and reductive metabolism into rhythmic phases of gene expression and oscillating post-translational protein modifications. Relatively little is known about how these switches in gene expression are controlled, although recent studies have suggested that transcription itself may play a central role. This review explores the molecular basis of the metabolic and gene-expression oscillations in the yeast Saccharomyces cerevisiae, as well as how they relate to other biological time-keeping mechanisms, such as circadian rhythms.
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Affiliation(s)
- Jane Mellor
- Department of Biochemistry, University of Oxford, Oxford, UK
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44
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Platt JL, Kent NA, Kimmel AR, Harwood AJ. Regulation of nucleosome positioning by a CHD Type III chromatin remodeler and its relationship to developmental gene expression in Dictyostelium. Genome Res 2017; 27:591-600. [PMID: 28330902 PMCID: PMC5378177 DOI: 10.1101/gr.216309.116] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Accepted: 02/27/2017] [Indexed: 01/14/2023]
Abstract
Nucleosome placement and repositioning can direct transcription of individual genes; however, the precise interactions of these events are complex and largely unresolved at the whole-genome level. The Chromodomain-Helicase-DNA binding (CHD) Type III proteins are a subfamily of SWI2/SNF2 proteins that control nucleosome positioning and are associated with several complex human disorders, including CHARGE syndrome and autism. Type III CHDs are required for multicellular development of animals and Dictyostelium but are absent in plants and yeast. These CHDs can mediate nucleosome translocation in vitro, but their in vivo mechanism is unknown. Here, we use genome-wide analysis of nucleosome positioning and transcription profiling to investigate the in vivo relationship between nucleosome positioning and gene expression during development of wild-type (WT) Dictyostelium and mutant cells lacking ChdC, a Type III CHD protein ortholog. We demonstrate major nucleosome positional changes associated with developmental gene regulation in WT. Loss of chdC caused an increase of intragenic nucleosome spacing and misregulation of gene expression, affecting ∼50% of the genes that are repositioned during WT development. These analyses demonstrate active nucleosome repositioning during Dictyostelium multicellular development, establish an in vivo function of CHD Type III chromatin remodeling proteins in this process, and reveal the detailed relationship between nucleosome positioning and gene regulation, as cells transition between developmental states.
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Affiliation(s)
- James L Platt
- School of Biosciences, Cardiff University, Cardiff, CF10 3AX, United Kingdom.,Laboratory of Cellular and Developmental Biology, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Nicholas A Kent
- School of Biosciences, Cardiff University, Cardiff, CF10 3AX, United Kingdom
| | - Alan R Kimmel
- Laboratory of Cellular and Developmental Biology, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Adrian J Harwood
- School of Biosciences, Cardiff University, Cardiff, CF10 3AX, United Kingdom.,Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, CF24 4HQ, United Kingdom
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45
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Bonifer C, Cockerill PN. Chromatin priming of genes in development: Concepts, mechanisms and consequences. Exp Hematol 2017; 49:1-8. [PMID: 28185904 DOI: 10.1016/j.exphem.2017.01.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 01/19/2017] [Accepted: 01/21/2017] [Indexed: 01/06/2023]
Abstract
During ontogeny, cells progress through multiple alternate differentiation states by activating distinct gene regulatory networks. In this review, we highlight the important role of chromatin priming in facilitating gene activation during lineage specification and in maintaining an epigenetic memory of previous gene activation. We show that chromatin priming is part of a hugely diverse repertoire of regulatory mechanisms that genes use to ensure that they are expressed at the correct time, in the correct cell type, and at the correct level, but also that they react to signals. We also emphasize how increasing our knowledge of these principles could inform our understanding of developmental failure and disease.
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Affiliation(s)
- Constanze Bonifer
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham, UK.
| | - Peter N Cockerill
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham, UK.
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46
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Rademacher A, Erdel F, Trojanowski J, Schumacher S, Rippe K. Real-time observation of light-controlled transcription in living cells. J Cell Sci 2017. [DOI: 10.1242/jcs.205534] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023] Open
Abstract
Gene expression is tightly regulated in space and time. To dissect this process with high temporal resolution, we introduce an optogenetic tool termed BLInCR (Blue Light-Induced Chromatin Recruitment) that combines rapid and reversible light-dependent recruitment of effector proteins with a real-time readout for transcription. We used BLInCR to control the activity of a reporter gene cluster in the human osteosarcoma cell line U2OS by reversibly recruiting the viral transactivator VP16. RNA production was detectable ∼2 minutes after VP16 recruitment and readily decreased when VP16 dissociated from the cluster in the absence of light. Quantitative assessment of the activation process revealed biphasic activation kinetics with a pronounced early phase in cells treated with the histone deacetylase inhibitor SAHA. Comparison with kinetic models for transcription activation suggests that the gene cluster undergoes a maturation process when activated. We anticipate that BLInCR will facilitate the study of transcription dynamics in living cells.
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Affiliation(s)
- Anne Rademacher
- German Cancer Research Center (DKFZ) and Bioquant, Division of Chromatin Networks, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Fabian Erdel
- German Cancer Research Center (DKFZ) and Bioquant, Division of Chromatin Networks, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Jorge Trojanowski
- German Cancer Research Center (DKFZ) and Bioquant, Division of Chromatin Networks, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Sabrina Schumacher
- German Cancer Research Center (DKFZ) and Bioquant, Division of Chromatin Networks, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Karsten Rippe
- German Cancer Research Center (DKFZ) and Bioquant, Division of Chromatin Networks, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
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47
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de Jonge WJ, O'Duibhir E, Lijnzaad P, van Leenen D, Groot Koerkamp MJ, Kemmeren P, Holstege FC. Molecular mechanisms that distinguish TFIID housekeeping from regulatable SAGA promoters. EMBO J 2016; 36:274-290. [PMID: 27979920 PMCID: PMC5286361 DOI: 10.15252/embj.201695621] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 10/18/2016] [Accepted: 11/01/2016] [Indexed: 11/28/2022] Open
Abstract
An important distinction is frequently made between constitutively expressed housekeeping genes versus regulated genes. Although generally characterized by different DNA elements, chromatin architecture and cofactors, it is not known to what degree promoter classes strictly follow regulatability rules and which molecular mechanisms dictate such differences. We show that SAGA‐dominated/TATA‐box promoters are more responsive to changes in the amount of activator, even compared to TFIID/TATA‐like promoters that depend on the same activator Hsf1. Regulatability is therefore an inherent property of promoter class. Further analyses show that SAGA/TATA‐box promoters are more dynamic because TATA‐binding protein recruitment through SAGA is susceptible to removal by Mot1. In addition, the nucleosome configuration upon activator depletion shifts on SAGA/TATA‐box promoters and seems less amenable to preinitiation complex formation. The results explain the fundamental difference between housekeeping and regulatable genes, revealing an additional facet of combinatorial control: an activator can elicit a different response dependent on core promoter class.
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Affiliation(s)
- Wim J de Jonge
- Molecular Cancer Research, University Medical Center Utrecht, Utrecht, The Netherlands.,Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Eoghan O'Duibhir
- Molecular Cancer Research, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Philip Lijnzaad
- Molecular Cancer Research, University Medical Center Utrecht, Utrecht, The Netherlands.,Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Dik van Leenen
- Molecular Cancer Research, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marian Ja Groot Koerkamp
- Molecular Cancer Research, University Medical Center Utrecht, Utrecht, The Netherlands.,Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Patrick Kemmeren
- Molecular Cancer Research, University Medical Center Utrecht, Utrecht, The Netherlands.,Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Frank Cp Holstege
- Molecular Cancer Research, University Medical Center Utrecht, Utrecht, The Netherlands .,Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
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48
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Ball DA, Mehta GD, Salomon-Kent R, Mazza D, Morisaki T, Mueller F, McNally JG, Karpova TS. Single molecule tracking of Ace1p in Saccharomyces cerevisiae defines a characteristic residence time for non-specific interactions of transcription factors with chromatin. Nucleic Acids Res 2016; 44:e160. [PMID: 27566148 PMCID: PMC5137432 DOI: 10.1093/nar/gkw744] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 08/05/2016] [Accepted: 08/15/2016] [Indexed: 12/26/2022] Open
Abstract
In vivo single molecule tracking has recently developed into a powerful technique for measuring and understanding the transient interactions of transcription factors (TF) with their chromatin response elements. However, this method still lacks a solid foundation for distinguishing between specific and non-specific interactions. To address this issue, we took advantage of the power of molecular genetics of yeast. Yeast TF Ace1p has only five specific sites in the genome and thus serves as a benchmark to distinguish specific from non-specific binding. Here, we show that the estimated residence time of the short-residence molecules is essentially the same for Hht1p, Ace1p and Hsf1p, equaling 0.12-0.32 s. These three DNA-binding proteins are very different in their structure, function and intracellular concentration. This suggests that (i) short-residence molecules are bound to DNA non-specifically, and (ii) that non-specific binding shares common characteristics between vastly different DNA-bound proteins and thus may have a common underlying mechanism. We develop new and robust procedure for evaluation of adverse effects of labeling, and new quantitative analysis procedures that significantly improve residence time measurements by accounting for fluorophore blinking. Our results provide a framework for the reliable performance and analysis of single molecule TF experiments in yeast.
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Affiliation(s)
- David A Ball
- CCR/LRBGE Optical Microscopy Core, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gunjan D Mehta
- CCR/LRBGE Optical Microscopy Core, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ronit Salomon-Kent
- CCR/LRBGE Optical Microscopy Core, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Davide Mazza
- Istituto Scientifico Ospedale San Raffaele, Centro di Imaging Sperimentale e Università Vita-Salute San Raffaele, Milan 20132, Italy
| | - Tatsuya Morisaki
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Florian Mueller
- Institut Pasteur, Computation Imaging and Modeling Unit, CNRS, URA 2582, Paris 75015, France
| | - James G McNally
- Institute for Soft Matter and Functional Materials, Helmholtz Center Berlin, Berlin 12489, Germany
| | - Tatiana S Karpova
- CCR/LRBGE Optical Microscopy Core, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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49
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Fennessy RT, Owen-Hughes T. Establishment of a promoter-based chromatin architecture on recently replicated DNA can accommodate variable inter-nucleosome spacing. Nucleic Acids Res 2016; 44:7189-203. [PMID: 27106059 PMCID: PMC5009725 DOI: 10.1093/nar/gkw331] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 04/15/2016] [Indexed: 12/18/2022] Open
Abstract
Nucleosomes, the fundamental subunits of eukaryotic chromatin, are organized with respect to transcriptional start sites. A major challenge to the persistence of this organization is the disassembly of nucleosomes during DNA replication. Here, we use complimentary approaches to map the locations of nucleosomes on recently replicated DNA. We find that nucleosomes are substantially realigned with promoters during the minutes following DNA replication. As a result, the nucleosomal landscape is largely re-established before newly replicated chromosomes are partitioned into daughter cells and can serve as a platform for the re-establishment of gene expression programmes. When the supply of histones is disrupted through mutation of the chaperone Caf1, a promoter-based architecture is generated, but with increased inter-nucleosomal spacing. This indicates that the chromatin remodelling enzymes responsible for spacing nucleosomes are capable of organizing nucleosomes with a range of different linker DNA lengths.
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Affiliation(s)
- Ross T Fennessy
- Centre for Gene Regulation and Expression, School of Life Sceinces, University of Dundee, Dundee, DD1 5EH, UK
| | - Tom Owen-Hughes
- Centre for Gene Regulation and Expression, School of Life Sceinces, University of Dundee, Dundee, DD1 5EH, UK
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