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A study of strong nucleosomes in the human genome. iScience 2022; 25:104593. [PMID: 35789840 PMCID: PMC9249913 DOI: 10.1016/j.isci.2022.104593] [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: 09/09/2021] [Revised: 03/03/2022] [Accepted: 06/08/2022] [Indexed: 11/30/2022] Open
Abstract
Micrococcal nuclease (MNase) is widely used to map nucleosomes. However, nucleosomes are highly dynamic and susceptible to experimental conditions, resulting in extreme variability across nucleosome maps, which complicates the generation of accurate nucleosome organization data. We mapped nucleosomes from different individuals using improved MNase-seq. The improvements included setting different digestion levels (low, medium, high) and naked DNA correction to remove the noise caused by experimental manipulation and comparing maps to obtain the accurate position and occupancy of strong nucleosomes (SNs) in the whole genome. In addition, the characteristics of SNs were further excavated. SNs were enriched in Alu elements and near the centromere of Chr12. SNs contain some specific sequences, and the GC content of SNs is different from that of dynamic nucleosomes. The findings suggest that nucleosome location in the genome and the DNA sequence may affect nucleosome stability. Naked DNA correction improved the accuracy of nucleosome map in partial digestion Level of MNase digestion has effects on nucleosome organization A type of strong nucleosomes (SNs) exist across different nucleosome maps Nucleosome stability may be related to its location and the DNA sequence
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Ordu O, Lusser A, Dekker NH. DNA Sequence Is a Major Determinant of Tetrasome Dynamics. Biophys J 2019; 117:2217-2227. [PMID: 31521330 PMCID: PMC6895708 DOI: 10.1016/j.bpj.2019.07.055] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/13/2019] [Accepted: 07/30/2019] [Indexed: 10/26/2022] Open
Abstract
Eukaryotic genomes are hierarchically organized into protein-DNA assemblies for compaction into the nucleus. Nucleosomes, with the (H3-H4)2 tetrasome as a likely intermediate, are highly dynamic in nature by way of several different mechanisms. We have recently shown that tetrasomes spontaneously change the direction of their DNA wrapping between left- and right-handed conformations, which may prevent torque buildup in chromatin during active transcription or replication. DNA sequence has been shown to strongly affect nucleosome positioning throughout chromatin. It is not known, however, whether DNA sequence also impacts the dynamic properties of tetrasomes. To address this question, we examined tetrasomes assembled on a high-affinity DNA sequence using freely orbiting magnetic tweezers. In this context, we also studied the effects of mono- and divalent salts on the flipping dynamics. We found that neither DNA sequence nor altered buffer conditions affect overall tetrasome structure. In contrast, tetrasomes bound to high-affinity DNA sequences showed significantly altered flipping kinetics, predominantly via a reduction in the lifetime of the canonical state of left-handed wrapping. Increased mono- and divalent salt concentrations counteracted this behavior. Thus, our study indicates that high-affinity DNA sequences impact not only the positioning of the nucleosome but that they also endow the subnucleosomal tetrasome with enhanced conformational plasticity. This may provide a means to prevent histone loss upon exposure to torsional stress, thereby contributing to the integrity of chromatin at high-affinity sites.
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Affiliation(s)
- Orkide Ordu
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Alexandra Lusser
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Nynke H Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands.
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Zhao H, Zhang F, Guo M, Xing Y, Liu G, Zhao X, Cai L. The affinity of DNA sequences containing R5Y5 motif and TA repeats with 10.5-bp periodicity to histone octamer in vitro. J Biomol Struct Dyn 2018; 37:1935-1943. [PMID: 30044196 DOI: 10.1080/07391102.2018.1477621] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Nucleosome positioning along the genome is partially determined by the intrinsic DNA sequence preferences on histone. RRRRRYYYYY (R5Y5, R = Purine and Y = Pyrimidine) motif in nucleosome DNA, which was presented based on several theoretical models by Trifonov et al., might be a facilitating sequence pattern for nucleosome assembly. However, there is not a high conformity experimental evidence to support the concept that R5Y5 motif is a key element for the determination of nucleosome positioning. In this work, the ability of the canonical, H2A.Z- and H3.3-containing octamers to assemble nucleosome on DNA templates containing R5Y5 motif and TA repeats within 10.5-bp periodicity was investigated by using salt-dialysis method in vitro. The results showed that the10.5-bp periodical distributions of both R5Y5 motif and TA repeats along DNA templates can significantly promote canonical nucleosome assembly and may be key sequence factors for canonical nucleosome assembly. Compared with TA repeats within 10.5-bp periodicity, R5Y5 motif in DNA templates did not elevate H2A.Z- and H3.3-containing nucleosome formation efficiency in vitro. This result indicates that R5Y5 motif probably isn't a pivotal factor to regulate nucleosome assembly on histone variants. It is speculated that the regulatory mechanism of nucleosome assembly is different between canonical and variant histone. These conclusions can provide a deeper insight on the mechanism of nucleosome positioning. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hongyu Zhao
- a School of Life Science and Technology , Inner Mongolia University of Science and Technology , Baotou , China.,b Inner Mongolia Key Laboratory of Functional Genome Bioinformatics , Inner Mongolia University of Science and Technology , Baotou , China
| | - Fenghui Zhang
- a School of Life Science and Technology , Inner Mongolia University of Science and Technology , Baotou , China
| | - Mingxin Guo
- a School of Life Science and Technology , Inner Mongolia University of Science and Technology , Baotou , China
| | - Yongqiang Xing
- a School of Life Science and Technology , Inner Mongolia University of Science and Technology , Baotou , China.,b Inner Mongolia Key Laboratory of Functional Genome Bioinformatics , Inner Mongolia University of Science and Technology , Baotou , China
| | - Guoqing Liu
- a School of Life Science and Technology , Inner Mongolia University of Science and Technology , Baotou , China.,b Inner Mongolia Key Laboratory of Functional Genome Bioinformatics , Inner Mongolia University of Science and Technology , Baotou , China
| | - Xiujuan Zhao
- a School of Life Science and Technology , Inner Mongolia University of Science and Technology , Baotou , China.,b Inner Mongolia Key Laboratory of Functional Genome Bioinformatics , Inner Mongolia University of Science and Technology , Baotou , China
| | - Lu Cai
- a School of Life Science and Technology , Inner Mongolia University of Science and Technology , Baotou , China.,b Inner Mongolia Key Laboratory of Functional Genome Bioinformatics , Inner Mongolia University of Science and Technology , Baotou , China
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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.
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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
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Schneider B, Božíková P, Čech P, Svozil D, Černý J. A DNA Structural Alphabet Distinguishes Structural Features of DNA Bound to Regulatory Proteins and in the Nucleosome Core Particle. Genes (Basel) 2017; 8:E278. [PMID: 29057824 PMCID: PMC5664128 DOI: 10.3390/genes8100278] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 10/06/2017] [Accepted: 10/13/2017] [Indexed: 01/21/2023] Open
Abstract
We analyzed the structural behavior of DNA complexed with regulatory proteins and the nucleosome core particle (NCP). The three-dimensional structures of almost 25 thousand dinucleotide steps from more than 500 sequentially non-redundant crystal structures were classified by using DNA structural alphabet CANA (Conformational Alphabet of Nucleic Acids) and associations between ten CANA letters and sixteen dinucleotide sequences were investigated. The associations showed features discriminating between specific and non-specific binding of DNA to proteins. Important is the specific role of two DNA structural forms, A-DNA, and BII-DNA, represented by the CANA letters AAA and BB2: AAA structures are avoided in non-specific NCP complexes, where the wrapping of the DNA duplex is explained by the periodic occurrence of BB2 every 10.3 steps. In both regulatory and NCP complexes, the extent of bending of the DNA local helical axis does not influence proportional representation of the CANA alphabet letters, namely the relative incidences of AAA and BB2 remain constant in bent and straight duplexes.
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Affiliation(s)
- Bohdan Schneider
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, CZ-252 50 Vestec, Prague West, Czech Republic.
| | - Paulína Božíková
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, CZ-252 50 Vestec, Prague West, Czech Republic.
| | - Petr Čech
- Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology Prague, Technická 5, CZ-166 28 Prague, Czech Republic.
| | - Daniel Svozil
- Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology Prague, Technická 5, CZ-166 28 Prague, Czech Republic.
| | - Jiří Černý
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, CZ-252 50 Vestec, Prague West, Czech Republic.
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Gent JI, Wang N, Dawe RK. Stable centromere positioning in diverse sequence contexts of complex and satellite centromeres of maize and wild relatives. Genome Biol 2017. [PMID: 28637491 PMCID: PMC5480163 DOI: 10.1186/s13059-017-1249-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Background Paradoxically, centromeres are known both for their characteristic repeat sequences (satellite DNA) and for being epigenetically defined. Maize (Zea mays mays) is an attractive model for studying centromere positioning because many of its large (~2 Mb) centromeres are not dominated by satellite DNA. These centromeres, which we call complex centromeres, allow for both assembly into reference genomes and for mapping short reads from ChIP-seq with antibodies to centromeric histone H3 (cenH3). Results We found frequent complex centromeres in maize and its wild relatives Z. mays parviglumis, Z. mays mexicana, and particularly Z. mays huehuetenangensis. Analysis of individual plants reveals minor variation in the positions of complex centromeres among siblings. However, such positional shifts are stochastic and not heritable, consistent with prior findings that centromere positioning is stable at the population level. Centromeres are also stable in multiple F1 hybrid contexts. Analysis of repeats in Z. mays and other species (Zea diploperennis, Zea luxurians, and Tripsacum dactyloides) reveals tenfold differences in abundance of the major satellite CentC, but similar high levels of sequence polymorphism in individual CentC copies. Deviation from the CentC consensus has little or no effect on binding of cenH3. Conclusions These data indicate that complex centromeres are neither a peculiarity of cultivation nor inbreeding in Z. mays. While extensive arrays of CentC may be the norm for other Zea and Tripsacum species, these data also reveal that a wide diversity of DNA sequences and multiple types of genetic elements in and near centromeres support centromere function and constrain centromere positions. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1249-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jonathan I Gent
- Department of Plant Biology, University of Georgia, Athens, USA
| | - Na Wang
- Department of Plant Biology, University of Georgia, Athens, USA
| | - R Kelly Dawe
- Department of Plant Biology, University of Georgia, Athens, USA. .,Department of Genetics, University of Georgia, Athens, USA.
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Ordu O, Lusser A, Dekker NH. Recent insights from in vitro single-molecule studies into nucleosome structure and dynamics. Biophys Rev 2016; 8:33-49. [PMID: 28058066 PMCID: PMC5167136 DOI: 10.1007/s12551-016-0212-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 06/17/2016] [Indexed: 01/04/2023] Open
Abstract
Eukaryotic DNA is tightly packed into a hierarchically ordered structure called chromatin in order to fit into the micron-scaled nucleus. The basic unit of chromatin is the nucleosome, which consists of a short piece of DNA wrapped around a core of eight histone proteins. In addition to their role in packaging DNA, nucleosomes impact the regulation of essential nuclear processes such as replication, transcription, and repair by controlling the accessibility of DNA. Thus, knowledge of this fundamental DNA-protein complex is crucial for understanding the mechanisms of gene control. While structural and biochemical studies over the past few decades have provided key insights into both the molecular composition and functional aspects of nucleosomes, these approaches necessarily average over large populations and times. In contrast, single-molecule methods are capable of revealing features of subpopulations and dynamic changes in the structure or function of biomolecules, rendering them a powerful complementary tool for probing mechanistic aspects of DNA-protein interactions. In this review, we highlight how these single-molecule approaches have recently yielded new insights into nucleosomal and subnucleosomal structures and dynamics.
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Affiliation(s)
- Orkide Ordu
- Bionanoscience Department, Kavli Institute of Nanoscience,, Delft University of Technology, Van der Maasweg 9,, 2629 HZ Delft, The Netherlands
| | - Alexandra Lusser
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Nynke H. Dekker
- Bionanoscience Department, Kavli Institute of Nanoscience,, Delft University of Technology, Van der Maasweg 9,, 2629 HZ Delft, The Netherlands
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Kensche PR, Hoeijmakers WAM, Toenhake CG, Bras M, Chappell L, Berriman M, Bártfai R. The nucleosome landscape of Plasmodium falciparum reveals chromatin architecture and dynamics of regulatory sequences. Nucleic Acids Res 2015; 44:2110-24. [PMID: 26578577 PMCID: PMC4797266 DOI: 10.1093/nar/gkv1214] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 10/28/2015] [Indexed: 11/13/2022] Open
Abstract
In eukaryotes, the chromatin architecture has a pivotal role in regulating all DNA-associated processes and it is central to the control of gene expression. For Plasmodium falciparum, a causative agent of human malaria, the nucleosome positioning profile of regulatory regions deserves particular attention because of their extreme AT-content. With the aid of a highly controlled MNase-seq procedure we reveal how positioning of nucleosomes provides a structural and regulatory framework to the transcriptional unit by demarcating landmark sites (transcription/translation start and end sites). In addition, our analysis provides strong indications for the function of positioned nucleosomes in splice site recognition. Transcription start sites (TSSs) are bordered by a small nucleosome-depleted region, but lack the stereotypic downstream nucleosome arrays, highlighting a key difference in chromatin organization compared to model organisms. Furthermore, we observe transcription-coupled eviction of nucleosomes on strong TSSs during intraerythrocytic development and demonstrate that nucleosome positioning and dynamics can be predictive for the functionality of regulatory DNA elements. Collectively, the strong nucleosome positioning over splice sites and surrounding putative transcription factor binding sites highlights the regulatory capacity of the nucleosome landscape in this deadly human pathogen.
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Affiliation(s)
- Philip Reiner Kensche
- Department of Molecular Biology, Radboud University, 6525GA Nijmegen, The Netherlands
| | | | | | - Maaike Bras
- Department of Molecular Biology, Radboud University, 6525GA Nijmegen, The Netherlands
| | - Lia Chappell
- Parasite Genomics Group, Wellcome Trust Sanger Institute, CB10 1SA Hinxton, UK
| | - Matthew Berriman
- Parasite Genomics Group, Wellcome Trust Sanger Institute, CB10 1SA Hinxton, UK
| | - Richárd Bártfai
- Department of Molecular Biology, Radboud University, 6525GA Nijmegen, The Netherlands
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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.
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Abstract
Lowary and Widom selected from random sequences those which form exceptionally stable nucleosomes, including clone 601, the current champion of strong nucleosome (SN) sequences. This unique sequence database (LW sequences) carries sequence elements which confer stability on the nucleosomes formed on the sequences, and, thus, may serve as source of information on the structure of "ideal" or close to ideal nucleosome DNA sequence. An important clue is also provided by crystallographic study of Vasudevan and coauthors on clone 601 nucleosomes. It demonstrated that YR·YR dinucleotide stacks (primarily TA·TA) follow one another at distances 10 or 11 bases or multiples thereof, such that they all are located on the interface between DNA and histone octamer. Combining this important information with alignment of the YR-containing 10-mers and 11-mers from LW sequences, the bendability matrices of the stable nucleosome DNA are derived. The matrices suggest that the periodically repeated TA (YR), RR, and YY dinucleotides are the main sequence features of the SNs. This consensus coincides with the one for recently discovered SNs with visibly periodic DNA sequences. Thus, the experimentally observed stable LW nucleosomes and SNs derived computationally appear to represent the same entity - exceptionally stable SNs.
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Affiliation(s)
- Edward N Trifonov
- a Institute of Evolution , University of Haifa , Mount Carmel, 31905 Haifa , Israel
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Abstract
The bulk of strong nucleosomes (SNs, with visibly periodic DNA sequences) is described by consensus pattern of 5 or 6 base runs of purines alternating with similar runs of pyrimidines - RR/YY SNs. Yet, the strongest known nucleosome positioning sequence, the 601 clone of Lowary and Widom, is rather periodic repetition of TA dinucleotides following one another every 10 bases. We located "601"-like TA-periodic sequences in the genome of A. thaliana. Several families of such sequences are discovered repeating almost exclusively in centromeres. Thus, while A. thaliana SNs of RR/YY type have strong affinity to pericentromeric regions, as it has been previously found, the SNs of TA periodic type concentrate rather in centromeres.
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Affiliation(s)
- Reshma Nibhani
- a Genome Diversity Center, Institute of Evolution , University of Haifa , Haifa , Israel
| | - Edward N Trifonov
- a Genome Diversity Center, Institute of Evolution , University of Haifa , Haifa , Israel
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