1
|
Masoudi-Sobhanzadeh Y, Li S, Peng Y, Panchenko AR. Interpretable deep residual network uncovers nucleosome positioning and associated features. Nucleic Acids Res 2024:gkae623. [PMID: 39036965 DOI: 10.1093/nar/gkae623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 05/31/2024] [Accepted: 07/04/2024] [Indexed: 07/23/2024] Open
Abstract
Nucleosomes represent elementary building units of eukaryotic chromosomes and consist of DNA wrapped around a histone octamer flanked by linker DNA segments. Nucleosomes are central in epigenetic pathways and their genomic positioning is associated with regulation of gene expression, DNA replication, DNA methylation and DNA repair, among other functions. Building on prior discoveries that DNA sequences noticeably affect nucleosome positioning, our objective is to identify nucleosome positions and related features across entire genome. Here, we introduce an interpretable framework based on the concepts of deep residual networks (NuPoSe). Trained on high-coverage human experimental MNase-seq data, NuPoSe is able to learn sequence and structural patterns associated with nucleosome organization in human genome. NuPoSe can be also applied to unseen data from different organisms and cell types. Our findings point to 43 informative features, most of them constitute tri-nucleotides, di-nucleotides and one tetra-nucleotide. Most features are significantly associated with the nucleosomal structural characteristics, namely, periodicity of nucleosomal DNA and its location with respect to a histone octamer. Importantly, we show that features derived from the 27 bp linker DNA flanking nucleosomes contribute up to 10% to the quality of the prediction model. This, along with the comprehensive training sets, deep-learning architecture, and feature selection method, may contribute to the NuPoSe's 80-89% classification accuracy on different independent datasets.
Collapse
Affiliation(s)
| | - Shuxiang Li
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, K7L3N6, Canada
| | - Yunhui Peng
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan, 430079, China
| | - Anna R Panchenko
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, K7L3N6, Canada
- Department of Biology and Molecular Sciences, Queen's University, Kingston, K7L3N6, Canada
- School of Computing, Queen's University, Kingston, K7L3N6, Canada
- Ontario Institute of Cancer Research, Toronto, M5G 0A3, Canada
| |
Collapse
|
2
|
Robert F, Jeronimo C. Transcription-coupled nucleosome assembly. Trends Biochem Sci 2023; 48:978-992. [PMID: 37657993 DOI: 10.1016/j.tibs.2023.08.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 07/21/2023] [Accepted: 08/04/2023] [Indexed: 09/03/2023]
Abstract
Eukaryotic transcription occurs on chromatin, where RNA polymerase II encounters nucleosomes during elongation. These nucleosomes must unravel for the DNA to enter the active site. However, in most transcribed genes, nucleosomes remain intact due to transcription-coupled chromatin assembly mechanisms. These mechanisms primarily involve the local reassembly of displaced nucleosomes to prevent (epi)genomic instability and the emergence of cryptic transcription. As a fail-safe mechanism, cells can assemble nucleosomes de novo, particularly in highly transcribed genes, but this may result in the loss of epigenetic information. This review examines transcription-coupled chromatin assembly, with an emphasis on studies in yeast and recent structural studies. These studies shed light on how elongation factors and histone chaperones coordinate to enable nucleosome recycling during transcription.
Collapse
Affiliation(s)
- François Robert
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada; Département de Médecine, Faculté de Médecine, Université de Montréal, 2900 Boul. Édouard-Montpetit, Montréal, QC H3T 1J4, Canada; Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC H3A 1A3, Canada.
| | - Célia Jeronimo
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| |
Collapse
|
3
|
Abstract
Nearly three-fourths of all eukaryotic DNA is occupied by nucleosomes, protein-DNA complexes comprising octameric histone core proteins and ∼150 base pairs of DNA. In addition to acting as a DNA compaction vehicle, the dynamics of nucleosomes regulate the DNA site accessibility for the nonhistone proteins, thereby controlling regulatory processes involved in determining the cell identity and cell fate. Here, we propose an analytical framework to analyze the role of nucleosome dynamics on the target search process of transcription factors through a simple discrete-state stochastic description of the search process. By considering the experimentally determined kinetic rates associated with protein and nucleosome dynamics as the only inputs, we estimate the target search time of a protein via first-passage probability calculations separately during nucleosome breathing and sliding dynamics. Although both the nucleosome dynamics permit transient access to the DNA sites that are otherwise occluded by the histone proteins, our result suggests substantial differences between the protein search mechanism on a nucleosome performing breathing and sliding dynamics. Furthermore, we identify the molecular factors that influence the search efficiency and demonstrate how these factors together portray a highly dynamic landscape of gene regulation. Our analytical results are validated using extensive Monte Carlo simulations.
Collapse
Affiliation(s)
- Sujeet Kumar Mishra
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Arnab Bhattacherjee
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| |
Collapse
|
4
|
Staneva D, Vasileva B, Podlesniy P, Miloshev G, Georgieva M. Yeast Chromatin Mutants Reveal Altered mtDNA Copy Number and Impaired Mitochondrial Membrane Potential. J Fungi (Basel) 2023; 9:jof9030329. [PMID: 36983497 PMCID: PMC10058930 DOI: 10.3390/jof9030329] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/02/2023] [Accepted: 03/04/2023] [Indexed: 03/30/2023] Open
Abstract
Mitochondria are multifunctional, dynamic organelles important for stress response, cell longevity, ageing and death. Although the mitochondrion has its genome, nuclear-encoded proteins are essential in regulating mitochondria biogenesis, morphology, dynamics and function. Moreover, chromatin structure and epigenetic mechanisms govern the accessibility to DNA and control gene transcription, indirectly influencing nucleo-mitochondrial communications. Thus, they exert crucial functions in maintaining proper chromatin structure, cell morphology, gene expression, stress resistance and ageing. Here, we present our studies on the mtDNA copy number in Saccharomyces cerevisiae chromatin mutants and investigate the mitochondrial membrane potential throughout their lifespan. The mutants are arp4 (with a point mutation in the ARP4 gene, coding for actin-related protein 4-Arp4p), hho1Δ (lacking the HHO1 gene, coding for the linker histone H1), and the double mutant arp4 hho1Δ cells with the two mutations. Our findings showed that the three chromatin mutants acquired strain-specific changes in the mtDNA copy number. Furthermore, we detected the disrupted mitochondrial membrane potential in their chronological lifespan. In addition, the expression of nuclear genes responsible for regulating mitochondria biogenesis and turnover was changed. The most pronounced were the alterations found in the double mutant arp4 hho1Δ strain, which appeared as the only petite colony-forming mutant, unable to grow on respiratory substrates and with partial depletion of the mitochondrial genome. The results suggest that in the studied chromatin mutants, hho1Δ, arp4 and arp4 hho1Δ, the nucleus-mitochondria communication was disrupted, leading to impaired mitochondrial function and premature ageing phenotype in these mutants, especially in the double mutant.
Collapse
Affiliation(s)
- Dessislava Staneva
- Laboratory of Molecular Genetics, Epigenetics and Longevity, Institute of Molecular Biology "RoumenTsanev", Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Bela Vasileva
- Laboratory of Molecular Genetics, Epigenetics and Longevity, Institute of Molecular Biology "RoumenTsanev", Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Petar Podlesniy
- CiberNed (Centro Investigacion Biomedica en Red Enfermedades Neurodegenerativas), 28029 Barcelona, Spain
| | - George Miloshev
- Laboratory of Molecular Genetics, Epigenetics and Longevity, Institute of Molecular Biology "RoumenTsanev", Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Milena Georgieva
- Laboratory of Molecular Genetics, Epigenetics and Longevity, Institute of Molecular Biology "RoumenTsanev", Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| |
Collapse
|
5
|
Ramatchandirin B, Pearah A, He L. Regulation of Liver Glucose and Lipid Metabolism by Transcriptional Factors and Coactivators. Life (Basel) 2023; 13:life13020515. [PMID: 36836874 PMCID: PMC9962321 DOI: 10.3390/life13020515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/08/2023] [Accepted: 02/10/2023] [Indexed: 02/16/2023] Open
Abstract
The prevalence of nonalcoholic fatty liver disease (NAFLD) worldwide is on the rise and NAFLD is becoming the most common cause of chronic liver disease. In the USA, NAFLD affects over 30% of the population, with similar occurrence rates reported from Europe and Asia. This is due to the global increase in obesity and type 2 diabetes mellitus (T2DM) because patients with obesity and T2DM commonly have NAFLD, and patients with NAFLD are often obese and have T2DM with insulin resistance and dyslipidemia as well as hypertriglyceridemia. Excessive accumulation of triglycerides is a hallmark of NAFLD and NAFLD is now recognized as the liver disease component of metabolic syndrome. Liver glucose and lipid metabolisms are intertwined and carbon flux can be used to generate glucose or lipids; therefore, in this review we discuss the important transcription factors and coactivators that regulate glucose and lipid metabolism.
Collapse
Affiliation(s)
| | - Alexia Pearah
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Ling He
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, 600 N. Wolfe St, Baltimore, MD 21287, USA
- Correspondence: ; Tel.: +1-410-502-5765; Fax: +1-410-502-5779
| |
Collapse
|
6
|
Gray JS, Wani SA, Campbell MJ. Epigenomic alterations in cancer: mechanisms and therapeutic potential. Clin Sci (Lond) 2022; 136:473-492. [PMID: 35383835 DOI: 10.1042/cs20210449] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 03/11/2022] [Accepted: 03/21/2022] [Indexed: 11/17/2022]
Abstract
The human cell requires ways to specify its transcriptome without altering the essential sequence of DNA; this is achieved through mechanisms which govern the epigenetic state of DNA and epitranscriptomic state of RNA. These alterations can be found as modified histone proteins, cytosine DNA methylation, non-coding RNAs, and mRNA modifications, such as N6-methyladenosine (m6A). The different aspects of epigenomic and epitranscriptomic modifications require protein complexes to write, read, and erase these chemical alterations. Reflecting these important roles, many of these reader/writer/eraser proteins are either frequently mutated or differentially expressed in cancer. The disruption of epigenetic regulation in the cell can both contribute to cancer initiation and progression, and increase the likelihood of developing resistance to chemotherapies. Development of therapeutics to target proteins involved in epigenomic/epitranscriptomic modifications has been intensive, but further refinement is necessary to achieve ideal treatment outcomes without too many off-target effects for cancer patients. Therefore, further integration of clinical outcomes combined with large-scale genomic analyses is imperative for furthering understanding of epigenomic mechanisms in cancer.
Collapse
Affiliation(s)
- Jaimie S Gray
- Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, U.S.A
| | - Sajad A Wani
- Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, U.S.A
| | - Moray J Campbell
- Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, U.S.A
- Biomedical Informatics Shared Resource, The Ohio State University, Columbus, OH 43210, U.S.A
| |
Collapse
|
7
|
Li X, Li H, Jing Q, Wang M, Hu T, Li L, Zhang Q, Liu M, Fu YV, Han J, Su D. Structural insights into multifunctionality of human FACT complex subunit hSSRP1. J Biol Chem 2021; 297:101360. [PMID: 34756889 PMCID: PMC8639466 DOI: 10.1016/j.jbc.2021.101360] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 10/14/2021] [Accepted: 10/26/2021] [Indexed: 02/05/2023] Open
Abstract
Human structure-specific recognition protein 1 (hSSRP1) is an essential component of the facilitates chromatin transcription complex, which participates in nucleosome disassembly and reassembly during gene transcription and DNA replication and repair. Many functions, including nuclear localization, histone chaperone activity, DNA binding, and interaction with cellular proteins, are attributed to hSSRP1, which contains multiple well-defined domains, including four pleckstrin homology (PH) domains and a high-mobility group domain with two flanking disordered regions. However, little is known about the mechanisms by which these domains cooperate to carry out hSSRP1’s functions. Here, we report the biochemical characterization and structure of each functional domain of hSSRP1, including the N-terminal PH1, PH2, PH3/4 tandem PH, and DNA-binding high-mobility group domains. Furthermore, two casein kinase II binding sites in hSSRP1 were identified in the PH3/4 domain and in a disordered region (Gly617–Glu709) located in the C-terminus of hSSRP1. In addition, a histone H2A–H2B binding motif and a nuclear localization signal (Lys677‒Asp687) of hSSRP1 are reported for the first time. Taken together, these studies provide novel insights into the structural basis for hSSRP1 functionality.
Collapse
Affiliation(s)
- Xuehui Li
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, China
| | - Huiyan Li
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, China
| | - Qian Jing
- Research Laboratory of Tumor Epigenetics and Genomics, Department of General Surgery, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Mengxue Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Tingting Hu
- College of Life Sciences, Neijiang Normal University, Neijiang, Sichuan, China
| | - Li Li
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, China
| | - Qiuping Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, China
| | - Mengxin Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, China
| | - Yu Vincent Fu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Junhong Han
- Research Laboratory of Tumor Epigenetics and Genomics, Department of General Surgery, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China.
| | - Dan Su
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, China; Infectious Disease Drug Discovery Institute, Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, China.
| |
Collapse
|
8
|
Morgunova E, Taipale J. Structural insights into the interaction between transcription factors and the nucleosome. Curr Opin Struct Biol 2021; 71:171-179. [PMID: 34364091 DOI: 10.1016/j.sbi.2021.06.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/21/2021] [Accepted: 06/28/2021] [Indexed: 01/26/2023]
Abstract
In eukaryotic cells, DNA interacts with two main types of binding proteins: transcription factors and histones. Histones form the core of nucleosomes and display weak sequence preference owing to differences in bendability of different DNA sequences. By contrast, the affinity of transcription factors is highly dependent on DNA sequence - all sequences are bound with moderate affinity, but only few specific sequences are bound more tightly via molecular recognition of the DNA bases. Transcription factors can interact with nucleosomes directly by recognizing nucleosome-associated DNA and also indirectly by recruiting histone-modifying enzymes and nucleosome remodelers. These interactions result in sequence-dependent formation of a pattern of open and closed chromatin, where specific positions are occupied by transcription factors, histone-modifying enzymes, and modified histones. These patterns are then recognized by large DNA-associated macromolecular complexes such as cohesin and RNA polymerase II, which are involved in regulation of higher-order chromatin structure and transcription, respectively. Here, we review recent work that has provided structural and mechanistic insight into the interactions between all these classes of DNA-associated proteins.
Collapse
Affiliation(s)
- Ekaterina Morgunova
- Karolinska Institute, Department of Medical Biochemistry and Biophysics, Stockholm, Sweden
| | | |
Collapse
|
9
|
Chen X, Yang H, Liu G, Zhang Y. NUCOME: A comprehensive database of nucleosome organization referenced landscapes in mammalian genomes. BMC Bioinformatics 2021; 22:321. [PMID: 34120586 PMCID: PMC8201709 DOI: 10.1186/s12859-021-04239-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 06/06/2021] [Indexed: 12/02/2022] Open
Abstract
Background Nucleosome organization is involved in many regulatory activities in various organisms. However, studies integrating nucleosome organization in mammalian genomes are very limited mainly due to the lack of comprehensive data quality control (QC) assessment and uneven data quality of public data sets. Results The NUCOME is a database focused on filtering qualified nucleosome organization referenced landscapes covering various cell types in human and mouse based on QC metrics. The filtering strategy guarantees the quality of nucleosome organization referenced landscapes and exempts users from redundant data set selection and processing. The NUCOME database provides standardized, qualified data source and informative nucleosome organization features at a whole-genome scale and on the level of individual loci. Conclusions The NUCOME provides valuable data resources for integrative analyses focus on nucleosome organization. The NUCOME is freely available at http://compbio-zhanglab.org/NUCOME. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04239-9.
Collapse
Affiliation(s)
- Xiaolan Chen
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Science and Technology, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Hui Yang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Science and Technology, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Guifen Liu
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Science and Technology, Tongji University, 1239 Siping Road, Shanghai, 200092, China.
| | - Yong Zhang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Science and Technology, Tongji University, 1239 Siping Road, Shanghai, 200092, China.
| |
Collapse
|
10
|
Strohkendl I, Saifuddin FA, Gibson BA, Rosen MK, Russell R, Finkelstein IJ. Inhibition of CRISPR-Cas12a DNA targeting by nucleosomes and chromatin. SCIENCE ADVANCES 2021; 7:7/11/eabd6030. [PMID: 33692102 PMCID: PMC7946368 DOI: 10.1126/sciadv.abd6030] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 01/22/2021] [Indexed: 06/10/2023]
Abstract
Genome engineering nucleases must access chromatinized DNA. Here, we investigate how AsCas12a cleaves DNA within human nucleosomes and phase-condensed nucleosome arrays. Using quantitative kinetics approaches, we show that dynamic nucleosome unwrapping regulates target accessibility to Cas12a and determines the extent to which both steps of binding-PAM recognition and R-loop formation-are inhibited by the nucleosome. Relaxing DNA wrapping within the nucleosome by reducing DNA bendability, adding histone modifications, or introducing target-proximal dCas9 enhances DNA cleavage rates over 10-fold. Unexpectedly, Cas12a readily cleaves internucleosomal linker DNA within chromatin-like, phase-separated nucleosome arrays. DNA targeting is reduced only ~5-fold due to neighboring nucleosomes and chromatin compaction. This work explains the observation that on-target cleavage within nucleosomes occurs less often than off-target cleavage within nucleosome-depleted genomic regions in cells. We conclude that nucleosome unwrapping regulates accessibility to CRISPR-Cas nucleases and propose that increasing nucleosome breathing dynamics will improve DNA targeting in eukaryotic cells.
Collapse
Affiliation(s)
- Isabel Strohkendl
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.
| | - Fatema A Saifuddin
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA
- Department of Cell and Tissue Biology, University of California, San Francisco, 513 Parnassus Ave, San Francisco, CA 94143, USA
| | - Bryan A Gibson
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Michael K Rosen
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Rick Russell
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.
| | - Ilya J Finkelstein
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA
| |
Collapse
|
11
|
Kutuzov MM, Belousova EA, Kurgina TA, Ukraintsev AA, Vasil’eva IA, Khodyreva SN, Lavrik OI. The contribution of PARP1, PARP2 and poly(ADP-ribosyl)ation to base excision repair in the nucleosomal context. Sci Rep 2021; 11:4849. [PMID: 33649352 PMCID: PMC7921663 DOI: 10.1038/s41598-021-84351-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 02/11/2021] [Indexed: 01/31/2023] Open
Abstract
The regulation of repair processes including base excision repair (BER) in the presence of DNA damage is implemented by a cellular signal: poly(ADP-ribosyl)ation (PARylation), which is catalysed by PARP1 and PARP2. Despite ample studies, it is far from clear how BER is regulated by PARPs and how the roles are distributed between the PARPs. Here, we investigated the effects of PARP1, PARP2 and PARylation on activities of the main BER enzymes (APE1, DNA polymerase β [Polβ] and DNA ligase IIIα [LigIIIα]) in combination with BER scaffold protein XRCC1 in the nucleosomal context. We constructed nucleosome core particles with midward- or outward-oriented damage. It was concluded that in most cases, the presence of PARP1 leads to the suppression of the activities of APE1, Polβ and to a lesser extent LigIIIα. PARylation by PARP1 attenuated this effect to various degrees depending on the enzyme. PARP2 had an influence predominantly on the last stage of BER: DNA sealing. Nonetheless, PARylation by PARP2 led to Polβ inhibition and to significant stimulation of LigIIIα activities in a NAD+-dependent manner. On the basis of the obtained and literature data, we suggest a hypothetical model of the contribution of PARP1 and PARP2 to BER.
Collapse
Affiliation(s)
- M. M. Kutuzov
- grid.415877.80000 0001 2254 1834Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia
| | - E. A. Belousova
- grid.415877.80000 0001 2254 1834Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia
| | - T. A. Kurgina
- grid.415877.80000 0001 2254 1834Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia ,grid.4605.70000000121896553Novosibirsk State University, Novosibirsk, Russia
| | - A. A. Ukraintsev
- grid.415877.80000 0001 2254 1834Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia
| | - I. A. Vasil’eva
- grid.415877.80000 0001 2254 1834Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia
| | - S. N. Khodyreva
- grid.415877.80000 0001 2254 1834Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia
| | - O. I. Lavrik
- grid.415877.80000 0001 2254 1834Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia ,grid.4605.70000000121896553Novosibirsk State University, Novosibirsk, Russia
| |
Collapse
|
12
|
De Benedittis S, Gaspari M, Magariello A, Spadafora P, Citrigno L, Romeo N, Qualtieri A. LC-MALDI-TOF ISD MS analysis is an effective, simple and rapid method of investigation for histones characterization: Application to EBV lymphoblastoid cell lines. JOURNAL OF MASS SPECTROMETRY : JMS 2021; 56:e4712. [PMID: 33851762 DOI: 10.1002/jms.4712] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 06/12/2023]
Abstract
This contribution is the result of our progressive engagement to develop and to apply a top-down liquid chromatography (LC) matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) (LC-MALDI-TOF) analysis for the histone post-translational modifications (PTMs) and variants characterization, mainly in order to provide comprehensive and fast results. The histone post-translational modifications and the differential expression of the histone variants play an essential role both in the DNA packaging mechanism in chromosomes and in the regulation of gene expression in different cellular processes, also in response to molecular agents of environmental origin. This epigenetic mechanism is widely studied in different field such as cellular differentiation, development and in the understanding of mechanisms underlying diseases. The characterization of histone PTMs has traditionally performed by antibodies-based assay, but immunological methods have significant limits, and today systems that use mass spectrometry are increasingly employed. We evaluated an in-source decay (ISD) analysis for the histone investigation on human lymphoblastoid cells, and by this approach, we were able to identify and quantify several PTMs such as the di-methylation in the lysine 20 and the acetylation in the lysine 16 in H4 and the mono-methylation, di-methylation and trimethylations at K9 of the histone H3.1. Moreover, we detected and quantified in the same H2B spectrum the prevalent H2B 1C/2E type but also the minor H2B 1D, 1M and 1B/1L/1N, 1O/2F, 1J/1K variants. In this work, we show that MALDI-ISD represents an excellent methodology to obtain global information on histone PTMs and variants from cells in culture, with rapidity and simplicity of execution. Finally, this is a useful approach to get label-free relative quantitative data of histone variants and PTMs.
Collapse
Affiliation(s)
- Selene De Benedittis
- National Research Council, Institute for Biomedical Research and Innovation (IRIB), Cosenza, Italy
- Department of Medical and Surgical Sciences, Magna Graecia University of Catanzaro, Catanzaro, Italy
| | - Marco Gaspari
- Research Centre for Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, Catanzaro, Italy
| | - Angela Magariello
- National Research Council, Institute for Agricultural and Forest Systems in the Mediterranean (ISAFOM), Cosenza, Italy
| | - Patrizia Spadafora
- National Research Council, Institute for Biomedical Research and Innovation (IRIB), Cosenza, Italy
| | - Luigi Citrigno
- National Research Council, Institute for Biomedical Research and Innovation (IRIB), Cosenza, Italy
| | - Nelide Romeo
- National Research Council, Institute for Agricultural and Forest Systems in the Mediterranean (ISAFOM), Cosenza, Italy
| | - Antonio Qualtieri
- National Research Council, Institute for Biomedical Research and Innovation (IRIB), Cosenza, Italy
| |
Collapse
|
13
|
Jiang Z, Zhang B. On the role of transcription in positioning nucleosomes. PLoS Comput Biol 2021; 17:e1008556. [PMID: 33417594 PMCID: PMC7819601 DOI: 10.1371/journal.pcbi.1008556] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 01/21/2021] [Accepted: 11/23/2020] [Indexed: 12/12/2022] Open
Abstract
Nucleosome positioning is crucial for the genome’s function. Though the role of DNA sequence in positioning nucleosomes is well understood, a detailed mechanistic understanding on the impact of transcription remains lacking. Using numerical simulations, we investigated the dependence of nucleosome density profiles on transcription level across multiple species. We found that the low nucleosome affinity of yeast, but not mouse, promoters contributes to the formation of phased nucleosomes arrays for inactive genes. For the active genes, a heterogeneous distribution of +1 nucleosomes, caused by a tug-of-war between two types of remodeling enzymes, is essential for reproducing their density profiles. In particular, while positioning enzymes are known to remodel the +1 nucleosome and align it toward the transcription start site (TSS), spacer enzymes that use a pair of nucleosomes as their substrate can shift the nucleosome array away from the TSS. Competition between these enzymes results in two types of nucleosome density profiles with well- and ill-positioned +1 nucleosome. Finally, we showed that Pol II assisted histone exchange, if occurring at a fast speed, can abolish the impact of remodeling enzymes. By elucidating the role of individual factors, our study reconciles the seemingly conflicting results on the overall impact of transcription in positioning nucleosomes across species. Nucleosome positioning plays a key role in the genome’s function by regulating the accessibility of protein binding sites as well as higher-order chromatin organization. Though significant progress has been made towards studying the role of DNA sequence in positioning the nucleosomes, our understanding on the impact of transcription lags behind. Our study uses kinetic simulations to explore the role of DNA sequence specificity, transcription factor binding, enzyme remodeling, and Pol II elongation in positioning nucleosomes. It suggests that the differences in nucleosome density profiles observed at various transcription levels in yeast and mouse embryonic stem cells can be understood from a tug-of-war between two types of remodeling enzymes.
Collapse
Affiliation(s)
- Zhongling Jiang
- Departments of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Bin Zhang
- Departments of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- * E-mail:
| |
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
Chereji RV, Clark DJ. Major Determinants of Nucleosome Positioning. Biophys J 2018; 114:2279-2289. [PMID: 29628211 DOI: 10.1016/j.bpj.2018.03.015] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 02/27/2018] [Accepted: 03/08/2018] [Indexed: 12/21/2022] Open
Abstract
The compact structure of the nucleosome limits DNA accessibility and inhibits the binding of most sequence-specific proteins. Nucleosomes are not randomly located on the DNA but positioned with respect to the DNA sequence, suggesting models in which critical binding sites are either exposed in the linker, resulting in activation, or buried inside a nucleosome, resulting in repression. The mechanisms determining nucleosome positioning are therefore of paramount importance for understanding gene regulation and other events that occur in chromatin, such as transcription, replication, and repair. Here, we review our current understanding of the major determinants of nucleosome positioning: DNA sequence, nonhistone DNA-binding proteins, chromatin-remodeling enzymes, and transcription. We outline the major challenges for the future: elucidating the precise mechanisms of chromatin opening and promoter activation, identifying the complexes that occupy promoters, and understanding the multiscale problem of chromatin fiber organization.
Collapse
Affiliation(s)
- Răzvan V Chereji
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, Maryland.
| | - David J Clark
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, Maryland.
| |
Collapse
|
16
|
Jia Y, Li H, Wang J, Meng H, Yang Z. Spectrum structures and biological functions of 8-mers in the human genome. Genomics 2018. [PMID: 29522801 DOI: 10.1016/j.ygeno.2018.03.006] [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] [Indexed: 11/30/2022]
Abstract
The spectra of k-mer frequencies can reveal the structures and evolution of genome sequences. We confirmed that the trimodal spectrum of 8-mers in human genome sequences is distinguished only by CG2, CG1 and CG0 8-mer sets, containing 2,1 or 0 CpG, respectively. This phenomenon is called independent selection law. The three types of CG 8-mers were considered as different functional elements. We conjectured that (1) nucleosome binding motifs are mainly characterized by CG1 8-mers and (2) the core structural units of CpG island sequences are predominantly characterized by CG2 8-mers. To validate our conjectures, nucleosome occupied sequences and CGI sequences were extracted, then the sequence parameters were constructed through the information of the three CG 8-mer sets respectively. ROC analysis showed that CG1 8-mers are more preference in nucleosome occupied segments (AUC > 0.7) and CG2 8-mers are more preference in CGI sequences (AUC > 0.99). This validates our conjecture in principle.
Collapse
Affiliation(s)
- Yun Jia
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China; College of Science, Inner Mongolia University of Technology, Hohhot 010051, China
| | - Hong Li
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China.
| | - Jingfeng Wang
- College of Science, Inner Mongolia University of Technology, Hohhot 010051, China
| | - Hu Meng
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
| | - Zhenhua Yang
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
| |
Collapse
|
17
|
Chereji RV, Ramachandran S, Bryson TD, Henikoff S. Precise genome-wide mapping of single nucleosomes and linkers in vivo. Genome Biol 2018; 19:19. [PMID: 29426353 PMCID: PMC5807854 DOI: 10.1186/s13059-018-1398-0] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 01/24/2018] [Indexed: 11/10/2022] Open
Abstract
We developed a chemical cleavage method that releases single nucleosome dyad-containing fragments, allowing us to precisely map both single nucleosomes and linkers with high accuracy genome-wide in yeast. Our single nucleosome positioning data reveal that nucleosomes occupy preferred positions that differ by integral multiples of the DNA helical repeat. By comparing nucleosome dyad positioning maps to existing genomic and transcriptomic data, we evaluated the contributions of sequence, transcription, and histones H1 and H2A.Z in defining the chromatin landscape. We present a biophysical model that neglects DNA sequence and shows that steric occlusion suffices to explain the salient features of nucleosome positioning.
Collapse
Affiliation(s)
- Răzvan V Chereji
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Srinivas Ramachandran
- Howard Hughes Medical Institute and Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Terri D Bryson
- Howard Hughes Medical Institute and Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Steven Henikoff
- Howard Hughes Medical Institute and Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA.
| |
Collapse
|
18
|
Djordjevic M, Djordjevic M, Zdobnov E. Scoring Targets of Transcription in Bacteria Rather than Focusing on Individual Binding Sites. Front Microbiol 2017; 8:2314. [PMID: 29213263 PMCID: PMC5702782 DOI: 10.3389/fmicb.2017.02314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 11/09/2017] [Indexed: 11/13/2022] Open
Abstract
Reliable identification of targets of bacterial regulators is necessary to understand bacterial gene expression regulation. These targets are commonly predicted by searching for high-scoring binding sites in the upstream genomic regions, which typically leads to a large number of false positives. In contrast to the common approach, here we propose a novel concept, where overrepresentation of the scoring distribution that corresponds to the entire searched region is assessed, as opposed to predicting individual binding sites. We explore two implementations of this concept, based on Kolmogorov-Smirnov (KS) and Anderson-Darling (AD) tests, which both provide straightforward P-value estimates for predicted targets. This approach is implemented for pleiotropic bacterial regulators, including σ70 (bacterial housekeeping σ factor) target predictions, which is a classical bioinformatics problem characterized by low specificity. We show that KS based approach is both faster and more accurate, departing from the current paradigm of AD being slower, but more accurate. Moreover, KS approach leads to a significant increase in the search accuracy compared to the standard approach, while at the same time straightforwardly assigning well established P-values to each potential target. Consequently, the new KS based method proposed here, which assigns P-values to fixed length upstream regions, provides a fast and accurate approach for predicting bacterial transcription targets.
Collapse
Affiliation(s)
- Marko Djordjevic
- Institute of Physiology and Biochemistry, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | | | - Evgeny Zdobnov
- Swiss Institute of Bioinformatics and Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
| |
Collapse
|
19
|
Gibson MD, Brehove M, Luo Y, North J, Poirier MG. Methods for Investigating DNA Accessibility with Single Nucleosomes. Methods Enzymol 2017; 581:379-415. [PMID: 27793287 DOI: 10.1016/bs.mie.2016.08.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Nucleosomes are the fundamental organizing unit of all eukaryotic genomes. Understanding how proteins gain access to DNA-binding sites located within nucleosomes is important for understanding DNA processing including transcription, replication, and repair. Single-molecule total internal reflection fluorescence (smTIRF) microscopy measurements can provide key insight into how proteins gain and maintain access to DNA sites within nucleosomes. Here, we describe methods for smTIRF experiments including the preparation of fluorophore-labeled nucleosomes, the smTIRF system, data acquisition, analysis, and controls. These methods are presented for investigating transcription factor binding within nucleosomes. However, they are applicable for investigating the binding of any site-specific DNA-binding protein within nucleosomes.
Collapse
Affiliation(s)
- M D Gibson
- The Ohio State University, Columbus, OH, United States
| | - M Brehove
- The Ohio State University, Columbus, OH, United States
| | - Y Luo
- The Ohio State University, Columbus, OH, United States
| | - J North
- The Ohio State University, Columbus, OH, United States
| | - M G Poirier
- The Ohio State University, Columbus, OH, United States.
| |
Collapse
|
20
|
Chen F, Ding X, Feng Y, Seebeck T, Jiang Y, Davis GD. Targeted activation of diverse CRISPR-Cas systems for mammalian genome editing via proximal CRISPR targeting. Nat Commun 2017; 8:14958. [PMID: 28387220 PMCID: PMC5385574 DOI: 10.1038/ncomms14958] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 02/16/2017] [Indexed: 02/08/2023] Open
Abstract
Bacterial CRISPR–Cas systems comprise diverse effector endonucleases with different targeting ranges, specificities and enzymatic properties, but many of them are inactive in mammalian cells and are thus precluded from genome-editing applications. Here we show that the type II-B FnCas9 from Francisella novicida possesses novel properties, but its nuclease function is frequently inhibited at many genomic loci in living human cells. Moreover, we develop a proximal CRISPR (termed proxy-CRISPR) targeting method that restores FnCas9 nuclease activity in a target-specific manner. We further demonstrate that this proxy-CRISPR strategy is applicable to diverse CRISPR–Cas systems, including type II-C Cas9 and type V Cpf1 systems, and can facilitate precise gene editing even between identical genomic sites within the same genome. Our findings provide a novel strategy to enable use of diverse otherwise inactive CRISPR–Cas systems for genome-editing applications and a potential path to modulate the impact of chromatin microenvironments on genome modification. Bacteria possess a diverse collection of CRISPR-Cas systems but many do not function in mammalian cells, precluding their use in genome editing. Here the authors show that by manipulating local chromatin structures, inhibited Cas9s can have their activity restored in human cells.
Collapse
Affiliation(s)
- Fuqiang Chen
- MilliporeSigma, 2909 Laclede Avenue, Saint Louis, Missouri 63103, USA.,A Business of Merck KGaA, 64293 Darmstadt, Germany
| | - Xiao Ding
- MilliporeSigma, 2909 Laclede Avenue, Saint Louis, Missouri 63103, USA.,A Business of Merck KGaA, 64293 Darmstadt, Germany
| | - Yongmei Feng
- MilliporeSigma, 2909 Laclede Avenue, Saint Louis, Missouri 63103, USA.,A Business of Merck KGaA, 64293 Darmstadt, Germany
| | - Timothy Seebeck
- MilliporeSigma, 2909 Laclede Avenue, Saint Louis, Missouri 63103, USA.,A Business of Merck KGaA, 64293 Darmstadt, Germany
| | - Yanfang Jiang
- MilliporeSigma, 2909 Laclede Avenue, Saint Louis, Missouri 63103, USA.,A Business of Merck KGaA, 64293 Darmstadt, Germany
| | - Gregory D Davis
- MilliporeSigma, 2909 Laclede Avenue, Saint Louis, Missouri 63103, USA.,A Business of Merck KGaA, 64293 Darmstadt, Germany
| |
Collapse
|
21
|
Zheng Y, Li H, Wang Y, Meng H, Zhang Q, Zhao X. Evolutionary mechanism and biological functions of 8-mers containing CG dinucleotide in yeast. Chromosome Res 2017; 25:173-189. [PMID: 28181048 DOI: 10.1007/s10577-017-9554-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 12/27/2016] [Accepted: 01/27/2017] [Indexed: 01/01/2023]
Abstract
The rules of k-mer non-random usage and the biological functions are worthy of special attention. Firstly, the article studied human 8-mer spectra and found that only the spectra of cytosine-guanine (CG) dinucleotide classification formed independent unimodal distributions when the 8-mers were classified into three subsets under 16 dinucleotide classifications. Secondly, the distribution rules were reproduced by other seven species including yeast, which showed that the evolution phenomenon had species universality. It followed that we proposed two theoretical conjectures: (1) CG1 motifs (8-mers including 1 CG) are the nucleosome-binding motifs. (2) CG2 motifs (8-mers including two or more than two CG) are the modular units of CpG islands. Our conjectures were confirmed in yeast by the following results: a maximum of average area under the receiver operating characteristic (AUC) resulted from CG1 information during nucleosome core sequences, and linker sequences were distinguished by three CG subsets; there was a one-to-one relationship between abundant CG1 signal regions and histone positions; the sequence changing of squeezed nucleosomes was relevant with the strength of CG1 signals; and the AUC value of 0.986 was based on CG2 information when CpG islands and non-CpG islands were distinguished by the three CG subsets.
Collapse
Affiliation(s)
- Yan Zheng
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China
| | - Hong Li
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China. .,, No.235, West University Street, Hohhot, Inner Mongolia, China.
| | - Yue Wang
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China
| | - Hu Meng
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China
| | - Qiang Zhang
- College of Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Xiaoqing Zhao
- Biotechnology research centre, Inner Mongolia Academy of Agricultural and Animal Husbandry Science, Hohhot, 010021, China
| |
Collapse
|
22
|
Jeffers TE, Lieb JD. Nucleosome fragility is associated with future transcriptional response to developmental cues and stress in C. elegans. Genome Res 2016; 27:75-86. [PMID: 27979995 PMCID: PMC5204346 DOI: 10.1101/gr.208173.116] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Accepted: 11/14/2016] [Indexed: 02/03/2023]
Abstract
Nucleosomes have structural and regulatory functions in all eukaryotic DNA-templated processes. The position of nucleosomes on DNA and the stability of the underlying histone–DNA interactions affect the access of regulatory proteins to DNA. Both stability and position are regulated through DNA sequence, histone post-translational modifications, histone variants, chromatin remodelers, and transcription factors. Here, we explored the functional implications of nucleosome properties on gene expression and development in Caenorhabditis elegans embryos. We performed a time-course of micrococcal nuclease (MNase) digestion and measured the relative sensitivity or resistance of nucleosomes throughout the genome. Fragile nucleosomes were defined by nucleosomal DNA fragments that were recovered preferentially in early MNase-digestion time points. Nucleosome fragility was strongly and positively correlated with the AT content of the underlying DNA sequence. There was no correlation between promoter nucleosome fragility and the levels of histone modifications or histone variants. Genes with fragile nucleosomes in their promoters tended to be lowly expressed and expressed in a context-specific way, operating in neuronal response, the immune system, and stress response. In addition to DNA-encoded nucleosome fragility, we also found fragile nucleosomes at locations where we expected to find destabilized nucleosomes, for example, at transcription factor binding sites where nucleosomes compete with DNA-binding factors. Our data suggest that in C. elegans promoters, nucleosome fragility is in large part DNA-encoded and that it poises genes for future context-specific activation in response to environmental stress and developmental cues.
Collapse
Affiliation(s)
- Tess E Jeffers
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
| | - Jason D Lieb
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
| |
Collapse
|
23
|
Le JV, Luo Y, Darcy MA, Lucas CR, Goodwin MF, Poirier MG, Castro CE. Probing Nucleosome Stability with a DNA Origami Nanocaliper. ACS NANO 2016; 10:7073-84. [PMID: 27362329 PMCID: PMC5460529 DOI: 10.1021/acsnano.6b03218] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The organization of eukaryotic DNA into nucleosomes and chromatin undergoes dynamic structural changes to regulate genome processing, including transcription and DNA repair. Critical chromatin rearrangements occur over a wide range of distances, including the mesoscopic length scale of tens of nanometers. However, there is a lack of methodologies that probe changes over this mesoscopic length scale within chromatin. We have designed, constructed, and implemented a DNA-based nanocaliper that probes this mesoscopic length scale. We developed an approach of integrating nucleosomes into our nanocaliper at two attachment points with over 50% efficiency. Here, we focused on attaching the two DNA ends of the nucleosome to the ends of the two nanocaliper arms, so the hinge angle is a readout of the nucleosome end-to-end distance. We demonstrate that nucleosomes integrated with 6, 26, and 51 bp linker DNA are partially unwrapped by the nanocaliper by an amount consistent with previously observed structural transitions. In contrast, the nucleosomes integrated with the longer 75 bp linker DNA remain fully wrapped. We found that the nanocaliper angle is a sensitive measure of nucleosome disassembly and can read out transcription factor (TF) binding to its target site within the nucleosome. Interestingly, the nanocaliper not only detects TF binding but also significantly increases the probability of TF occupancy at its site by partially unwrapping the nucleosome. These studies demonstrate the feasibility of using DNA nanotechnology to both detect and manipulate nucleosome structure, which provides a foundation of future mesoscale studies of nucleosome and chromatin structural dynamics.
Collapse
Affiliation(s)
- Jenny V. Le
- Biophysics Graduate Program, The Ohio State University, Columbus OH 43214
| | - Yi Luo
- Biophysics Graduate Program, The Ohio State University, Columbus OH 43214
| | - Michael A. Darcy
- Department of Physics, The Ohio State University, Columbus OH 43214
| | | | | | - Michael G. Poirier
- Biophysics Graduate Program, The Ohio State University, Columbus OH 43214
- Department of Physics, The Ohio State University, Columbus OH 43214
- Corresponding authors: ,
| | - Carlos E. Castro
- Biophysics Graduate Program, The Ohio State University, Columbus OH 43214
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus OH 43214
- Corresponding authors: ,
| |
Collapse
|
24
|
Chereji RV, Kan TW, Grudniewska MK, Romashchenko AV, Berezikov E, Zhimulev IF, Guryev V, Morozov AV, Moshkin YM. Genome-wide profiling of nucleosome sensitivity and chromatin accessibility in Drosophila melanogaster. Nucleic Acids Res 2016; 44:1036-51. [PMID: 26429969 PMCID: PMC4756854 DOI: 10.1093/nar/gkv978] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 08/27/2015] [Accepted: 09/16/2015] [Indexed: 01/09/2023] Open
Abstract
Nucleosomal DNA is thought to be generally inaccessible to DNA-binding factors, such as micrococcal nuclease (MNase). Here, we digest Drosophila chromatin with high and low concentrations of MNase to reveal two distinct nucleosome types: MNase-sensitive and MNase-resistant. MNase-resistant nucleosomes assemble on sequences depleted of A/T and enriched in G/C-containing dinucleotides, whereas MNase-sensitive nucleosomes form on A/T-rich sequences found at transcription start and termination sites, enhancers and DNase I hypersensitive sites. Estimates of nucleosome formation energies indicate that MNase-sensitive nucleosomes tend to be less stable than MNase-resistant ones. Strikingly, a decrease in cell growth temperature of about 10°C makes MNase-sensitive nucleosomes less accessible, suggesting that observed variations in MNase sensitivity are related to either thermal fluctuations of chromatin fibers or the activity of enzymatic machinery. In the vicinity of active genes and DNase I hypersensitive sites nucleosomes are organized into periodic arrays, likely due to 'phasing' off potential barriers formed by DNA-bound factors or by nucleosomes anchored to their positions through external interactions. The latter idea is substantiated by our biophysical model of nucleosome positioning and energetics, which predicts that nucleosomes immediately downstream of transcription start sites are anchored and recapitulates nucleosome phasing at active genes significantly better than sequence-dependent models.
Collapse
Affiliation(s)
- Răzvan V Chereji
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tsung-Wai Kan
- Department of Biochemistry, Erasmus Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Magda K Grudniewska
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, 9713AD, The Netherlands
| | | | - Eugene Berezikov
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, 9713AD, The Netherlands
| | - Igor F Zhimulev
- Institute of Molecular and Cellular Biology, Siberian Branch of RAS, Novosibirsk 630090, Russia
| | - Victor Guryev
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, 9713AD, The Netherlands
| | - Alexandre V Morozov
- Department of Physics and Astronomy and BioMaPS Institute for Quantitative Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Yuri M Moshkin
- Department of Biochemistry, Erasmus Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk 630090, Russia Institute of Molecular and Cellular Biology, Siberian Branch of RAS, Novosibirsk 630090, Russia
| |
Collapse
|
25
|
Ocampo J, Chereji RV, Eriksson PR, Clark DJ. The ISW1 and CHD1 ATP-dependent chromatin remodelers compete to set nucleosome spacing in vivo. Nucleic Acids Res 2016; 44:4625-35. [PMID: 26861626 PMCID: PMC4889916 DOI: 10.1093/nar/gkw068] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 01/28/2016] [Indexed: 12/17/2022] Open
Abstract
Adenosine triphosphate-dependent chromatin remodeling machines play a central role in gene regulation by manipulating chromatin structure. Most genes have a nucleosome-depleted region at the promoter and an array of regularly spaced nucleosomes phased relative to the transcription start site. In vitro, the three known yeast nucleosome spacing enzymes (CHD1, ISW1 and ISW2) form arrays with different spacing. We used genome-wide nucleosome sequencing to determine whether these enzymes space nucleosomes differently in vivo We find that CHD1 and ISW1 compete to set the spacing on most genes, such that CHD1 dominates genes with shorter spacing and ISW1 dominates genes with longer spacing. In contrast, ISW2 plays a minor role, limited to transcriptionally inactive genes. Heavily transcribed genes show weak phasing and extreme spacing, either very short or very long, and are depleted of linker histone (H1). Genes with longer spacing are enriched in H1, which directs chromatin folding. We propose that CHD1 directs short spacing, resulting in eviction of H1 and chromatin unfolding, whereas ISW1 directs longer spacing, allowing H1 to bind and condense the chromatin. Thus, competition between the two remodelers to set the spacing on each gene may result in a highly dynamic chromatin structure.
Collapse
Affiliation(s)
- Josefina Ocampo
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute for 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 for Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter R Eriksson
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute for 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 for Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| |
Collapse
|
26
|
Aranda-Anzaldo A. The interphase mammalian chromosome as a structural system based on tensegrity. J Theor Biol 2016; 393:51-9. [PMID: 26780650 DOI: 10.1016/j.jtbi.2016.01.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Revised: 12/11/2015] [Accepted: 01/04/2016] [Indexed: 10/22/2022]
Abstract
Each mammalian chromosome is constituted by a DNA fiber of macroscopic length that needs to be fitted in a microscopic nucleus. The DNA fiber is subjected at physiological temperature to random thermal bending and looping that must be constrained so as achieve structural stability thus avoiding spontaneous rupturing of the fiber. Standard textbooks assume that chromatin proteins are primarily responsible for the packaging of DNA and so of its protection against spontaneous breakage. Yet the dynamic nature of the interactions between chromatin proteins and DNA is unlikely to provide the necessary long-term structural stability for the chromosomal DNA. On the other hand, longstanding evidence indicates that stable interactions between DNA and constituents of a nuclear compartment commonly known as the nuclear matrix organize the chromosomal DNA as a series of topologically constrained, supercoiled loops during interphase. This results in a primary level of DNA condensation and packaging within the nucleus, as well as in protection against spontaneous DNA breakage, independently of chromatin proteins which nevertheless increase and dynamically modulate the degree of DNA packaging and its role in the regulation of DNA function. Thus current evidence, presented hereunder, supports a model for the organization of the interphase chromosome as resilient system that satisfies the principles of structural tensegrity.
Collapse
Affiliation(s)
- Armando Aranda-Anzaldo
- Laboratorio de Biología Molecular y Neurociencias, Facultad de Medicina, Universidad Autónoma del Estado de México, Paseo Tollocan y Jesús Carranza s/n, Toluca, 50180 Edo. Méx., México.
| |
Collapse
|
27
|
Iuso D, Czernik M, Toschi P, Fidanza A, Zacchini F, Feil R, Curtet S, Buchou T, Shiota H, Khochbin S, Ptak GE, Loi P. Exogenous Expression of Human Protamine 1 (hPrm1) Remodels Fibroblast Nuclei into Spermatid-like Structures. Cell Rep 2015; 13:1765-71. [PMID: 26628361 PMCID: PMC4675893 DOI: 10.1016/j.celrep.2015.10.066] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 09/04/2015] [Accepted: 10/21/2015] [Indexed: 11/26/2022] Open
Abstract
Protamines confer a compact structure to the genome of male gametes. Here, we find that somatic cells can be remodeled by transient expression of protamine 1 (Prm1). Ectopically expressed Prm1 forms scattered foci in the nuclei of fibroblasts, which coalescence into spermatid-like structures, concomitant with a loss of histones and a reprogramming barrier, H3 lysine 9 methylation. Protaminized nuclei injected into enucleated oocytes efficiently underwent protamine to maternal histone TH2B exchange and developed into normal blastocyst stage embryos in vitro. Altogether, our findings present a model to study male-specific chromatin remodeling, which can be exploited for the improvement of somatic cell nuclear transfer. In vitro protaminization of somatic cell nuclei Conversion of interphase somatic nuclei into “spermatid-like” structures Protaminization of somatic nuclei that is reversed upon injection into enucleated oocytes A simplified model of nuclear remodeling and reprogramming in vitro
Collapse
Affiliation(s)
- Domenico Iuso
- Faculty of Veterinary Medicine, University of Teramo, Renato Balzarini Street 1, Campus Coste Sant'Agostino, 64100 Teramo, Italy
| | - Marta Czernik
- Faculty of Veterinary Medicine, University of Teramo, Renato Balzarini Street 1, Campus Coste Sant'Agostino, 64100 Teramo, Italy
| | - Paola Toschi
- Faculty of Veterinary Medicine, University of Teramo, Renato Balzarini Street 1, Campus Coste Sant'Agostino, 64100 Teramo, Italy
| | - Antonella Fidanza
- Faculty of Veterinary Medicine, University of Teramo, Renato Balzarini Street 1, Campus Coste Sant'Agostino, 64100 Teramo, Italy
| | - Federica Zacchini
- Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, Postepu 36A, Jastrzębiec, 05-552 Magdalenka, Poland
| | - Robert Feil
- Institute of Molecular Genetics (IGMM), CNRS UMR-5535 and University of Montpellier, 1919 route de Mende, 34293 Montpellier, France
| | - Sandrine Curtet
- INSERM, U823, Institut Albert Bonniot, Université Grenoble Alpes, 38700 Grenoble, France
| | - Thierry Buchou
- INSERM, U823, Institut Albert Bonniot, Université Grenoble Alpes, 38700 Grenoble, France
| | - Hitoshi Shiota
- INSERM, U823, Institut Albert Bonniot, Université Grenoble Alpes, 38700 Grenoble, France
| | - Saadi Khochbin
- INSERM, U823, Institut Albert Bonniot, Université Grenoble Alpes, 38700 Grenoble, France
| | - Grazyna Ewa Ptak
- Faculty of Veterinary Medicine, University of Teramo, Renato Balzarini Street 1, Campus Coste Sant'Agostino, 64100 Teramo, Italy; Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, Postepu 36A, Jastrzębiec, 05-552 Magdalenka, Poland; National Research Institute of Animal Production 1, Krakowska Street, 32-083 Balice n/Krakow, Poland
| | - Pasqualino Loi
- Faculty of Veterinary Medicine, University of Teramo, Renato Balzarini Street 1, Campus Coste Sant'Agostino, 64100 Teramo, Italy.
| |
Collapse
|
28
|
Abstract
Nucleosome positioning is an important process required for proper genome packing and its accessibility to execute the genetic program in a cell-specific, timely manner. In the recent years hundreds of papers have been devoted to the bioinformatics, physics and biology of nucleosome positioning. The purpose of this review is to cover a practical aspect of this field, namely, to provide a guide to the multitude of nucleosome positioning resources available online. These include almost 300 experimental datasets of genome-wide nucleosome occupancy profiles determined in different cell types and more than 40 computational tools for the analysis of experimental nucleosome positioning data and prediction of intrinsic nucleosome formation probabilities from the DNA sequence. A manually curated, up to date list of these resources will be maintained at http://generegulation.info.
Collapse
|
29
|
Bussemaker HJ. Recent progress in understanding transcription factor binding specificity. Brief Funct Genomics 2015; 14:1-2. [DOI: 10.1093/bfgp/elu050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
|
30
|
|