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Schwartz U, Németh A, Diermeier S, Exler JH, Hansch S, Maldonado R, Heizinger L, Merkl R, Längst G. Characterizing the nuclease accessibility of DNA in human cells to map higher order structures of chromatin. Nucleic Acids Res 2019; 47:1239-1254. [PMID: 30496478 PMCID: PMC6379673 DOI: 10.1093/nar/gky1203] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 11/17/2018] [Accepted: 11/22/2018] [Indexed: 12/22/2022] Open
Abstract
Packaging of DNA into chromatin regulates DNA accessibility and consequently all DNA-dependent processes. The nucleosome is the basic packaging unit of DNA forming arrays that are suggested, by biochemical studies, to fold hierarchically into ordered higher-order structures of chromatin. This organization has been recently questioned using microscopy techniques, proposing an irregular structure. To address the principles of chromatin organization, we applied an in situ differential MNase-seq strategy and analyzed in silico the results of complete and partial digestions of human chromatin. We investigated whether different levels of chromatin packaging exist in the cell. We assessed the accessibility of chromatin within distinct domains of kb to Mb genomic regions, performed statistical analyses and computer modelling. We found no difference in MNase accessibility, suggesting no difference in fiber folding between domains of euchromatin and heterochromatin or between other sequence and epigenomic features of chromatin. Thus, our data suggests the absence of differentially organized domains of higher-order structures of chromatin. Moreover, we identified only local structural changes, with individual hyper-accessible nucleosomes surrounding regulatory elements, such as enhancers and transcription start sites. The regulatory sites per se are occupied with structurally altered nucleosomes, exhibiting increased MNase sensitivity. Our findings provide biochemical evidence that supports an irregular model of large-scale chromatin organization.
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Affiliation(s)
- Uwe Schwartz
- Department of Biochemistry III, University of Regensburg, University of Regensburg, 93040 Regensburg, Germany
| | - Attila Németh
- Department of Biochemistry III, University of Regensburg, University of Regensburg, 93040 Regensburg, Germany
| | - Sarah Diermeier
- Department of Biochemistry III, University of Regensburg, University of Regensburg, 93040 Regensburg, Germany
| | - Josef H Exler
- Department of Biochemistry III, University of Regensburg, University of Regensburg, 93040 Regensburg, Germany
| | - Stefan Hansch
- Department of Biochemistry III, University of Regensburg, University of Regensburg, 93040 Regensburg, Germany
| | - Rodrigo Maldonado
- Department of Biochemistry III, University of Regensburg, University of Regensburg, 93040 Regensburg, Germany
| | - Leonhard Heizinger
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, 93040 Regensburg, Germany
| | - Rainer Merkl
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, 93040 Regensburg, Germany
| | - Gernot Längst
- Department of Biochemistry III, University of Regensburg, University of Regensburg, 93040 Regensburg, Germany
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2
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Zhang Z, Zhang Y, Gutman I. Predicting nucleosome positions in yeast: using the absolute frequency. J Biomol Struct Dyn 2012; 29:1081-8. [PMID: 22292961 DOI: 10.1080/073911012010525032] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Nucleosome is the basic structure of chromatin in eukaryotic cells, and they form the chromatin fiber interconnected by sections of linker DNA. Nucleosome positioning is of great significance for gene transcription regulation. In this paper, we consider the difference of absolute frequency of nucleotides between the nucleosome forming and nucleosome inhibiting sequences. Based on the 2-mer absolute frequency of nucleotides in genome, a new model is constructed to distinguish nucleosome DNA and linker DNA. When used to predict DNA potential for forming nucleosomes in S. cerevisiae, the model achieved a high accuracy of 96.05%. Thus, the model is very useful for predicting nucleosome positioning.
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Affiliation(s)
- Zhiqian Zhang
- School of Mathematics and Statistics, Shandong University at Weihai, Weihai 264209, China
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3
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Deniz O, Flores O, Battistini F, Pérez A, Soler-López M, Orozco M. Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast. BMC Genomics 2011; 12:489. [PMID: 21981773 PMCID: PMC3224377 DOI: 10.1186/1471-2164-12-489] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Accepted: 10/07/2011] [Indexed: 01/13/2023] Open
Abstract
Background In eukaryotic organisms, DNA is packaged into chromatin structure, where most of DNA is wrapped into nucleosomes. DNA compaction and nucleosome positioning have clear functional implications, since they modulate the accessibility of genomic regions to regulatory proteins. Despite the intensive research effort focused in this area, the rules defining nucleosome positioning and the location of DNA regulatory regions still remain elusive. Results Naked (histone-free) and nucleosomal DNA from yeast were digested by microccocal nuclease (MNase) and sequenced genome-wide. MNase cutting preferences were determined for both naked and nucleosomal DNAs. Integration of their sequencing profiles with DNA conformational descriptors derived from atomistic molecular dynamic simulations enabled us to extract the physical properties of DNA on a genomic scale and to correlate them with chromatin structure and gene regulation. The local structure of DNA around regulatory regions was found to be unusually flexible and to display a unique pattern of nucleosome positioning. Ab initio physical descriptors derived from molecular dynamics were used to develop a computational method that accurately predicts nucleosome enriched and depleted regions. Conclusions Our experimental and computational analyses jointly demonstrate a clear correlation between sequence-dependent physical properties of naked DNA and regulatory signals in the chromatin structure. These results demonstrate that nucleosome positioning around TSS (Transcription Start Site) and TTS (Transcription Termination Site) (at least in yeast) is strongly dependent on DNA physical properties, which can define a basal regulatory mechanism of gene expression.
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Affiliation(s)
- Ozgen Deniz
- Institute for Research in Biomedicine and Barcelona Supercomputing Center Joint Research Program on Computational Biology, Baldiri i Reixac 10, Barcelona 08028, Spain
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4
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Kaplan N, Hughes TR, Lieb JD, Widom J, Segal E. Contribution of histone sequence preferences to nucleosome organization: proposed definitions and methodology. Genome Biol 2010; 11:140. [PMID: 21118582 PMCID: PMC3156944 DOI: 10.1186/gb-2010-11-11-140] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2010] [Accepted: 11/26/2010] [Indexed: 01/25/2023] Open
Abstract
We propose definitions and procedures for comparing nucleosome maps and discuss current agreement and disagreement on the effect of histone sequence preferences on nucleosome organization in vivo.
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Affiliation(s)
- Noam Kaplan
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
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5
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Sha K, Gu SG, Pantalena-Filho LC, Goh A, Fleenor J, Blanchard D, Krishna C, Fire A. Distributed probing of chromatin structure in vivo reveals pervasive chromatin accessibility for expressed and non-expressed genes during tissue differentiation in C. elegans. BMC Genomics 2010; 11:465. [PMID: 20691096 PMCID: PMC3091661 DOI: 10.1186/1471-2164-11-465] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2010] [Accepted: 08/06/2010] [Indexed: 12/21/2022] Open
Abstract
Background Tissue differentiation is accompanied by genome-wide changes in the underlying chromatin structure and dynamics, or epigenome. By controlling when, where, and what regulatory factors have access to the underlying genomic DNA, the epigenome influences the cell's transcriptome and ultimately its function. Existing genomic methods for analyzing cell-type-specific changes in chromatin generally involve two elements: (i) a source for purified cells (or nuclei) of distinct types, and (ii) a specific treatment that partitions or degrades chromatin by activity or structural features. For many cell types of great interest, such assays are limited by our inability to isolate the relevant cell populations in an organism or complex tissue containing an intertwined mixture of other cells. This limitation has confined available knowledge of chromatin dynamics to a narrow range of biological systems (cell types that can be sorted/separated/dissected in large numbers and tissue culture models) or to amalgamations of diverse cell types (tissue chunks, whole organisms). Results Transgene-driven expression of DNA/chromatin modifying enzymes provides one opportunity to query chromatin structures in expression-defined cell subsets. In this work we combine in vivo expression of a bacterial DNA adenine methyltransferase (DAM) with high throughput sequencing to sample tissue-specific chromatin accessibility on a genome-wide scale. We have applied the method (DALEC: Direct Asymmetric Ligation End Capture) towards mapping a cell-type-specific view of genome accessibility as a function of differentiated state. Taking advantage of C. elegans strains expressing the DAM enzyme in diverse tissues (body wall muscle, gut, and hypodermis), our efforts yield a genome-wide dataset measuring chromatin accessibility at each of 538,000 DAM target sites in the C. elegans (diploid) genome. Conclusions Validating the DALEC mapping results, we observe a strong association between observed coverage by nucleosomes and low DAM accessibility. Strikingly, we observed no extended regions of inaccessible chromatin for any of the tissues examined. These results are consistent with "local choreography" models in which differential gene expression is driven by intricate local rearrangements of chromatin structure rather than gross impenetrability of large chromosomal regions.
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Affiliation(s)
- Ky Sha
- Depts, of Pathology and Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Palo Alto CA, USA
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6
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Travers A, Hiriart E, Churcher M, Caserta M, Di Mauro E. The DNA sequence-dependence of nucleosome positioning in vivo and in vitro. J Biomol Struct Dyn 2010; 27:713-24. [PMID: 20232928 PMCID: PMC2864905 DOI: 10.1080/073911010010524942] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The contribution of histone-DNA interactions to nucleosome positioning in vivo is currently a matter of debate. We argue here that certain nucleosome positions, often in promoter regions, in yeast may be, at least in part, specified by the DNA sequence. In contrast other positions may be poorly specified. Positioning thus has both statistical and DNA-determined components. We further argue that the relative affinity of the octamer for different DNA sequences can vary and therefore the interaction of histones with the DNA is a 'tunable' property.
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Affiliation(s)
- Andrew Travers
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.
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7
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Abstract
Nucleosome positioning has been the subject of intense study for many years. The properties of micrococcal nuclease, the enzyme central to these studies, are discussed. The various methods used to determine nucleosome positions in vitro and in vivo are reviewed critically. These include the traditional low resolution method of indirect end-labelling, high resolution methods such as primer extension, monomer extension and nucleosome sequencing, and the high throughput methods for genome-wide analysis (microarray hybridisation and parallel sequencing). It is established that low resolution mapping yields an averaged chromatin structure, whereas high resolution mapping reveals the weighted superposition of all the chromatin states in a cell population. Mapping studies suggest that yeast DNA contains information specifying the positions of nucleosomes and that this code is made use of by the cell. It is proposed that the positioning code facilitates nucleosome spacing by encoding information for multiple alternative overlapping nucleosomal arrays. Such a code might facilitate the shunting of nucleosomes from one array to another by ATP-dependent chromatin remodelling machines.
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Affiliation(s)
- David J Clark
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Building 6A, National Institutes of Health, 6 Center Drive, Bethesda, MD 20892, USA.
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8
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The early apoptotic DNA fragmentation targets a small number of specific open chromatin regions. PLoS One 2009; 4:e5010. [PMID: 19347039 PMCID: PMC2661134 DOI: 10.1371/journal.pone.0005010] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Accepted: 03/02/2009] [Indexed: 11/19/2022] Open
Abstract
We report here that early apoptotic DNA fragmentation, as obtained by using an entirely new approach, is the result of an attack at a small number of specific open chromatin regions of interphase nuclei. This was demonstrated as follows: (i) chicken liver was excised and kept in sterile tubes for 1 to 3 hours at 37 degrees C; (ii) this induced apoptosis (possibly because of oxygen deprivation), as shown by the electrophoretic nucleosomal ladder produced by DNA preparations; (iii) low molecular-weight DNA fragments (approximately 200 bp) were cloned, sequenced, and shown to derive predominantly from genes and surrounding 100 kb regions; (iv) a few hundred cuts were produced, very often involving the same chromosomal sites; (v) at comparable DNA degradation levels, micrococcal nuclease (MNase) also showed a general preference for genes and surrounding regions, but MNase cuts were located at sites that were quite distinct from, and less specific than, those cut by apoptosis. In conclusion, the approach presented here, which is the mildest and least intrusive approach, identifies a preferred accessibility landscape in interphase chromatin.
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Pondugula S, Kladde MP. Single-molecule analysis of chromatin: changing the view of genomes one molecule at a time. J Cell Biochem 2009; 105:330-7. [PMID: 18615586 DOI: 10.1002/jcb.21849] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Wrapping DNA into chromatin provides a wealth of regulatory mechanisms that ensure normal growth and development in eukaryotes. Our understanding of chromatin structure, including nucleosomes and non-histone protein-DNA interactions, has benefited immensely from nuclease and chemical digestion techniques. DNA-bound proteins, such as histones or site-specific factors, protect DNA against nuclease cleavage and generate large nucleosomal or small regulatory factor footprints. Chromatin subject to distinct modes of regulation often coincides with sites of nuclease hypersensitivity or nucleosome positioning. An inherent limitation of cleavage-based analyses has been the inability to reliably analyze regions of interest when levels of digestion depart from single-hit kinetics. Moreover, cleavage-based techniques provide views that are averaged over all the molecules in a sample population. Therefore, in cases of occupancy of multiple regulatory elements by factors, one cannot define whether the factors are bound to the same or different molecules in the population. The recent development of DNA methyltransferase-based, single-molecule MAP-IT technology overcomes limitations of ensemble approaches and has opened numerous new avenues in chromatin research. Here, we review the strengths, limitations, applications and future prospects of MAP-IT ranging from structural issues to mechanistic questions in eukaryotic chromatin regulation.
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Affiliation(s)
- Santhi Pondugula
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, Florida 32610-3633, USA
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10
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Sequence-dependent nucleosome positioning. J Mol Biol 2008; 386:1411-22. [PMID: 19070622 DOI: 10.1016/j.jmb.2008.11.049] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2008] [Revised: 11/17/2008] [Accepted: 11/21/2008] [Indexed: 01/11/2023]
Abstract
Eukaryotic DNA is organized into a macromolecular structure called chromatin. The basic repeating unit of chromatin is the nucleosome, which consists of two copies of each of the four core histones and DNA. The nucleosomal organization and the positions of nucleosomes have profound effects on all DNA-dependent processes. Understanding the factors that influence nucleosome positioning is therefore of general interest. Among the many determinants of nucleosome positioning, the DNA sequence has been proposed to have a major role. Here, we analyzed more than 860,000 nucleosomal DNA sequences to identify sequence features that guide the formation of nucleosomes in vivo. We found that both a periodic enrichment of AT base pairs and an out-of-phase oscillating enrichment of GC base pairs as well as the overall preference for GC base pairs are determinants of nucleosome positioning. The preference for GC pairs can be related to a lower energetic cost required for deformation of the DNA to wrap around the histones. In line with this idea, we found that only incorporation of both signal components into a sequence model for nucleosome formation results in maximal predictive performance on a genome-wide scale. In this manner, one achieves greater predictive power than published approaches. Our results confirm the hypothesis that the DNA sequence has a major role in nucleosome positioning in vivo.
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11
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Kim Y, Shen CH, Clark DJ. Purification and nucleosome mapping analysis of native yeast plasmid chromatin. Methods 2004; 33:59-67. [PMID: 15039088 DOI: 10.1016/j.ymeth.2003.10.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/30/2003] [Indexed: 10/26/2022] Open
Abstract
There is much evidence indicating the importance in gene regulation of the positions of nucleosomes with respect to DNA sequence. Low resolution chromatin structures have been described for many genes, but there is a dearth of detailed high resolution chromatin structures. In the cases where they are available, high resolution maps have revealed much more complex chromatin structures, with multiple alternative nucleosome positions. The discovery that ATP-dependent chromatin remodelling machines are recruited to genes, with their ability to mobilise nucleosomes on DNA and to alter nucleosomal conformation, emphasises the necessity for obtaining high resolution nucleosome maps, so that the details of these remodelling reactions can be defined in vivo. Here, we describe protocols for purifying plasmid chromatin from cells of the yeast Saccharomyces cerevisiae and for mapping nucleosome positions on the plasmid using the monomer extension mapping method. This method requires purified chromatin, but is capable of mapping relatively long stretches of chromatin in great detail. Typically, it reveals very complex chromatin structures.
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Affiliation(s)
- Yeonjung Kim
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Building 50 Room 3148, 50 South Drive MSC 8028, Bethesda, MD 20892-8028, USA
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12
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Jabbari K, Bernardi G. Cytosine methylation and CpG, TpG (CpA) and TpA frequencies. Gene 2004; 333:143-9. [PMID: 15177689 DOI: 10.1016/j.gene.2004.02.043] [Citation(s) in RCA: 157] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2003] [Accepted: 02/10/2004] [Indexed: 11/19/2022]
Abstract
An analysis of dinucleotide frequencies was carried out on DNAs from insects and mammals, as well as on large DNA sequences from the genomes of Drosophila melanogaster, Anopheles gambiae, puffer fish (Takifugu rubripes), zebra fish (Danio rerio) and human. These organisms were chosen because Drosophila and Anopheles DNAs have an extremely low level of methylation, human DNA a high level and fish DNA a two-fold higher level compared to human. The results indicate that: (i) CpG deficiency and the corresponding TpG (CpA) excess show no correlation with the level of DNA methylation; indeed, genomes endowed with strikingly different levels of DNA methylation (such as those of Drosophila and human) exhibited similar TpG (CpA) levels; (ii) the correlation between GC levels of large (50 kb) DNA sequences and TpA or CpG shortage levels do not appear to be due to CpG methylation followed by deamination; (iii) CpG dinucleotides are more frequent in fishes than in mammals; interestingly, the monotreme Ornitorhinchus anatinus shows an intermediate CpG frequency. The implications of these results are discussed.
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Affiliation(s)
- Kamel Jabbari
- Laboratoire de Génétique Moléculaire, Institut Jacques Monod, 2 Place Jussieu, F-75005 Paris, France
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13
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Serna-Rico A, Muñoz-Espín D, Villar L, Salas M, Meijer WJJ. The integral membrane protein p16.7 organizes in vivo phi29 DNA replication through interaction with both the terminal protein and ssDNA. EMBO J 2003; 22:2297-306. [PMID: 12727895 PMCID: PMC156093 DOI: 10.1093/emboj/cdg221] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Remarkably little is known about the in vivo organization of membrane-associated prokaryotic DNA replication or the proteins involved. We have studied this fundamental process using the Bacillus subtilis phage phi29 as a model system. Previously, we demonstrated that the phi29-encoded dimeric integral membrane protein p16.7 binds to ssDNA and is involved in the organization of membrane-associated phi29 DNA replication. Here we demonstrate that p16.7 forms multimers, both in vitro and in vivo, and interacts with the phi29 terminal protein. In addition, we show that in vitro multimerization is enhanced in the presence of ssDNA and that the C-terminal region of p16.7 is required for multimerization but not for ssDNA binding or interaction with the terminal protein. Moreover, we provide evidence that the ability of p16.7 to form multimers is crucial for its ssDNA-binding mode. These and previous results indicate that p16.7 encompasses four distinct modules. An integrated model of the structural and functional domains of p16.7 in relation to the organization of in vivo phi29 DNA replication is presented.
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Affiliation(s)
- Alejandro Serna-Rico
- Instituto de Biología Molecular 'Eladio Viñuela' (CSIC), Centro de Biología Molecular 'Severo Ochoa' (CSIC-UAM), Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
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14
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Brown J, Brown T, Fox KR. Cleavage of fragments containing DNA mismatches by enzymic and chemical probes. Biochem J 2003; 371:697-708. [PMID: 12558499 PMCID: PMC1223340 DOI: 10.1042/bj20021847] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2002] [Revised: 01/06/2003] [Accepted: 01/31/2003] [Indexed: 11/17/2022]
Abstract
We prepared synthetic 50-mer DNA duplexes, each containing four mismatched base-pairs in similar positions. We examined their cleavage by DNases I and II, micrococcal nuclease (MNase), methidiumpropyl-EDTA-Fe(II) [MPE-Fe(II)] and hydroxyl radicals. We find that single mismatches only produce subtle changes in the DNase I-cleavage pattern, the most common of which is attenuated cleavage at locations 2-3 bases on the 3'-side of the mismatch. Subtle changes are also observed in most of the DNase II-cleavage patterns, although GT and GG inhibit the cleavage over longer regions and generate patterns that resemble footprints. MNase cleaves the heteroduplexes at the mismatches themselves (except for CC), and in some cases cleaves CpG and CpC steps. None of the mismatches causes any change in the cleavage patterns produced by hydroxyl radicals or MPE-Fe(II). We also examined the cleavage patterns of fragments containing tandem GA mismatches in the sequences RGAY/RGAY and YGAR/YGAR (R, purine; Y, pyrimidine). RGAY causes only subtle changes in the cleavage patterns, which are similar to those seen with single mismatches, except that there are no changes in MNase cleavage. However, YGAR inhibits DNases I and II cleavage over 4-6 bases, and attenuates MPE-Fe(II) and hydroxyl radical cleavage at 2 bases. These changes suggest that this mismatch has a more pronounced effect on the local DNA structure. These changes are discussed in terms of the structural and dynamic effects of each mismatch.
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Affiliation(s)
- James Brown
- Division of Biochemistry and Molecular Biology, School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK
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15
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Weiss K, Simpson RT. Cell type-specific chromatin organization of the region that governs directionality of yeast mating type switching. EMBO J 1997; 16:4352-60. [PMID: 9250679 PMCID: PMC1170061 DOI: 10.1093/emboj/16.14.4352] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Switching of mating type in Saccharomyces cerevisiae is directional; MAT alpha cells recombine to transfer information from HMRa while MATa cells switch using the silent cassette at HML alpha. Genetic analysis recently has defined a 700 bp recombination enhancer approximately 29 kb from the left end of chromosome III that is necessary for directionality. The chromatin structure of this region differs strikingly in a- and alpha-cells. Mat alpha2p organizes a 3.7 kb chromatin domain that opposes interaction of trans-acting proteins with the enhancer. In a-cells lacking the alpha2 repressor, two footprinted regions flank an approximately 100 bp section having a unique DNA structure. This structural signature probably reflects interactions of proteins that result in directional mating type switching.
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Affiliation(s)
- K Weiss
- Department of Biochemistry and Molecular Biology and Center for Gene Regulation, Penn State University, University Park 16802, USA
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16
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Gerlach VL, Whitehall SK, Geiduschek EP, Brow DA. TFIIIB placement on a yeast U6 RNA gene in vivo is directed primarily by TFIIIC rather than by sequence-specific DNA contacts. Mol Cell Biol 1995; 15:1455-66. [PMID: 7862139 PMCID: PMC230370 DOI: 10.1128/mcb.15.3.1455] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The Saccharomyces cerevisiae U6 RNA gene (SNR6), which is transcribed by RNA polymerase III, has an unusual combination of promoter elements: an upstream TATA box, an intragenic A block, and a downstream B block. In tRNA genes, the A and B blocks are binding sites for the transcription initiation factor TFIIIC, which positions TFIIIB a fixed distance upstream of the A block. However, in vitro transcription of SNR6 with purified components requires neither TFIIIC nor the A and B blocks, presumably because TFIIIB recognizes the upstream sequences directly. Here we demonstrate that TFIIIB placement on SNR6 in vivo is directed primarily by the TFIIIC-binding elements rather than by upstream sequences. We show that the A block is a stronger start site determinant than the upstream sequences when the two are uncoupled by an insertion mutation. Furthermore, while TFIIIC-independent in vitro transcription of SNR6 is highly sensitive to TATA box point mutations, in vivo initiation on SNR6 is only marginally sensitive to such mutations unless the A block is mutated. Intriguingly, a deletion downstream of the U6 RNA coding region that reduces A-to-B block spacing also increases in vivo dependence on the TATA box. Moreover, this deletion results in the appearance of micrococcal nuclease-hypersensitive sites in the TFIIIB chromatin footprint, indicating that TFIIIB binding is disrupted by a mutation 150 bp distant. This and additional chromatin footprinting data suggest that SNR6 is assembled into a nucleoprotein complex that facilitates the TFIIIC-dependent binding of TFIIIB.
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MESH Headings
- Base Sequence
- Binding Sites
- DNA Primers
- DNA, Fungal/genetics
- DNA, Fungal/metabolism
- Genes, Fungal
- Molecular Sequence Data
- Mutagenesis, Site-Directed
- Oligodeoxyribonucleotides
- Plasmids
- Polymerase Chain Reaction
- RNA, Fungal/biosynthesis
- RNA, Fungal/genetics
- RNA, Small Nuclear/genetics
- Regulatory Sequences, Nucleic Acid
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Sequence Deletion
- Structure-Activity Relationship
- TATA Box
- Transcription Factor TFIIB
- Transcription Factors/isolation & purification
- Transcription Factors/metabolism
- Transcription Factors, TFIII
- Transcription, Genetic
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Affiliation(s)
- V L Gerlach
- Department of Biomolecular Chemistry, University of Wisconsin Medical School, Madison 53706-1532
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17
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Abstract
It has been proposed that yeast MATa cell-specific genes are repressed in MAT alpha cells by the Mat alpha 2p repressor-directed placement of a nucleosome in a position that incorporates the TATA box of the MATa-specific gene close to the nucleosomal pseudodyad. In this study, we address this proposal directly with a series of plasmids designed to place the MATa-specific STE6 TATA box at different locations in a nucleosome and in the internucleosomal linker. These plasmids contain different lengths of synthetic random DNA between the Mat alpha 2p operator and the TATA box of the STE6 promoter, which is located upstream of a lacZ reporter gene in a multicopy plasmid. We show that in MAT alpha cells, a nucleosome is retained in an identical translational frame relative to the Mat alpha 2p operator in all the constructs investigated, irrespective of the sequence of the DNA wrapped onto the histone octamer. This result shows that the nucleosomal organization of the STE6 promoter in MAT alpha cells is not conferred by the sequence of the promoter itself. No expression of the lacZ reporter gene was detectable in MAT alpha cells in any of the constructs, even with the TATA box located in a short internucleosomal linker. These data indicate that repression of MATa-specific genes in MAT alpha cells does not require the precise translational placement of the TATA box close to the nucleosomal pseudodyad; the gene remains repressed when the TATA box is located within the investigated 250-bp region in the organized chromatin domain abutting the Mat alpha 2p operator in MAT alpha cells and may remain repressed with the TATA box located anywhere within this organized repression domain.
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18
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Patterton HG, Simpson RT. Nucleosomal location of the STE6 TATA box and Mat alpha 2p-mediated repression. Mol Cell Biol 1994; 14:4002-10. [PMID: 8196639 PMCID: PMC358766 DOI: 10.1128/mcb.14.6.4002-4010.1994] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
It has been proposed that yeast MATa cell-specific genes are repressed in MAT alpha cells by the Mat alpha 2p repressor-directed placement of a nucleosome in a position that incorporates the TATA box of the MATa-specific gene close to the nucleosomal pseudodyad. In this study, we address this proposal directly with a series of plasmids designed to place the MATa-specific STE6 TATA box at different locations in a nucleosome and in the internucleosomal linker. These plasmids contain different lengths of synthetic random DNA between the Mat alpha 2p operator and the TATA box of the STE6 promoter, which is located upstream of a lacZ reporter gene in a multicopy plasmid. We show that in MAT alpha cells, a nucleosome is retained in an identical translational frame relative to the Mat alpha 2p operator in all the constructs investigated, irrespective of the sequence of the DNA wrapped onto the histone octamer. This result shows that the nucleosomal organization of the STE6 promoter in MAT alpha cells is not conferred by the sequence of the promoter itself. No expression of the lacZ reporter gene was detectable in MAT alpha cells in any of the constructs, even with the TATA box located in a short internucleosomal linker. These data indicate that repression of MATa-specific genes in MAT alpha cells does not require the precise translational placement of the TATA box close to the nucleosomal pseudodyad; the gene remains repressed when the TATA box is located within the investigated 250-bp region in the organized chromatin domain abutting the Mat alpha 2p operator in MAT alpha cells and may remain repressed with the TATA box located anywhere within this organized repression domain.
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Affiliation(s)
- H G Patterton
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
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19
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Rowland GC, Lim PP, Glass RE. 'Stop-codon-specific' restriction endonucleases: their use in mapping and gene manipulation. Gene 1992; 116:21-6. [PMID: 1628840 DOI: 10.1016/0378-1119(92)90624-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Certain restriction endonucleases recognise target sequences that contain the stop triplet TAG and are commonly either 4 or 6 bp in length. Interestingly, these restriction targets do not occur at the frequency expected on the basis of base composition and size. For example, the tetranucleotide MaeI recognition sequence (CTAG) occurs considerably less commonly (5-8-fold) in the genome of Escherichia coli (and many other eubacteria) than expected from mononucleotide frequencies. This surprising rarity is particularly evident in protein-encoding genes and is largely dictated by codon usage. Thus, amber (TAG) nonsense mutations frequently give rise to novel MaeI (CTAG) sites which are unique within a translated region. Such amber/MaeI sites, whether arising spontaneously or created in vitro by site-directed mutagenesis, act as a useful physical marker for the presence of the nonsense mutation and are a convenient startpoint for a range of diverse procedures. These features provide a useful supplement to protein engineering methods which use nonsense suppression to mediate amino acid replacements.
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Affiliation(s)
- G C Rowland
- Department of Biochemistry, University of Nottingham Medical School, Queen's Medical Centre, UK
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20
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Plouvier B, Bailly C, Houssin R, Rao KE, Lown WJ, Hénichart JP, Waring MJ. DNA-sequence specific recognition by a thiazole analogue of netropsin: a comparative footprinting study. Nucleic Acids Res 1991; 19:5821-9. [PMID: 1658746 PMCID: PMC329033 DOI: 10.1093/nar/19.21.5821] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Four different footprinting techniques have been used to probe the DNA sequence selectivity of Thia-Net, a bis-cationic analogue of the minor groove binder netropsin in which the N-methylpyrrole moieties are replaced by thiazole groups. In Thia-Net the ring nitrogen atoms are directed into the minor groove where they could accept hydrogen bonds from the exocyclic 2-amino group of guanine. Three nucleases (DNAase I, DNAase II, and micrococcal nuclease) were employed to detect binding sites on the 160bp tyr T fragment obtained from plasmid pKM delta-98, and further experiments were performed with 117mer and 253mer fragments cut out of the plasmid pBS. MPE.Fe(II) was used to footprint binding sites on an EcoRI/HindIII fragment from pBR322. Thia-Net binds to sites in the minor groove containing 4 or 5 base pairs which are predominantly composed of alternating A and T residues, but with significant acceptance of intrusive GC base pairs. Unlike the parent antibiotic netropsin, Thia-Net discriminates against homooligomeric runs of A and T. The evident preference of Thia-Net for AT-rich sites, despite its containing thiazole nitrogens capable of accepting GC sites by hydrogen bonding, supports the view that the biscationic nature of the ligand imposes a bias due to the electrostatic potential differences in the receptor which favour the ligand reading alternating AT sequences.
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Affiliation(s)
- B Plouvier
- Institut de Chimie Pharmaceutique, Faculté de Pharmacie, Lille, France
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21
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Abstract
The DNA sequence data for Escherichia coli deposited in the EMBL library (release 27), together with miscellaneous data obtained from several laboratories, have been localized on an updated and corrected version of the restriction map of the chromosome generated by Kohara et al. (1987) and modified by others. This second update adds a further 500 kbp, increasing the amount of the E. coli chromosome sequenced to about one third of the total: 1510 kbp of sequenced DNA is included in the present data base. The accuracy of the map is assessed, and allows us to propose a precise genetic map position for every sequenced gene. The location of rare-cutting sites such as AvrII, NotI and SfiI have also been included in the update in order to combine the data obtained from different sources into one single file. The distribution of palindromic sequences (to which most restriction sites belong) has been studied in coding sequences. There appears to be a significant counter-selection against several such sequences in E. coli coding sequences (but not in other organisms such as Saccharomyces cerevisiae), suggesting the existence of constraints on DNA structure in E. coli, perhaps indicative of a functional role for horizontal gene transfer, preserving coding sequences, in this type of bacteria.
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Affiliation(s)
- C Médigue
- Section Physique-Chimie, Institut Curie, Paris, France
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22
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Waterloh K, Fox KR. The effects of actinomycin on the structure of dAn.dTn and (dA-dT)n regions surrounding its GC binding site. A footprinting study. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)38129-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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23
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Fox KR, Sansom CE, Stevens MF. Footprinting studies on the sequence-selective binding of pentamidine to DNA. FEBS Lett 1990; 266:150-4. [PMID: 2365063 DOI: 10.1016/0014-5793(90)81527-u] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The sequence-selective binding of pentamidine, an antimicrobial aromatic diamidine, has been investigated by footprinting studies on two different DNA fragments using DNase I, micrococcal nuclease and hydroxyl radical as probes. Each probe reveals drug-induced protection from cleavage in AT-rich regions. The best binding sites consist of at least 5 consecutive AT base pairs. Three or less AT pairs do not constitute a pentamidine binding site.
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Affiliation(s)
- K R Fox
- Department Physiology and Pharmacology, University of Southampton, UK
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24
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Luisi BF, Sigler PB. The stereochemistry and biochemistry of the trp repressor-operator complex. BIOCHIMICA ET BIOPHYSICA ACTA 1990; 1048:113-26. [PMID: 2182120 DOI: 10.1016/0167-4781(90)90047-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- B F Luisi
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 66511
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25
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Yoon C, Kuwabara MD, Spassky A, Sigman DS. Sequence specificity of the deoxyribonuclease activity of 1,10-phenanthroline-copper ion. Biochemistry 1990; 29:2116-21. [PMID: 2328244 DOI: 10.1021/bi00460a022] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A statistical analysis of a data set composed of over 1600 scission events of DNA produced by the 2:1 1,10-phenanthroline-copper complex (OP-Cu) has demonstrated that the nucleotide 5' to the site of phosphodiester bond scission is a primary influence in the kinetics of cleavage at any sequence position. The scission was less affected by the 3' neighbor. For each of the sixteen possible dinucleotides, a kinetic parameter can be computed reflecting scission at the 3' nucleotide. When used to predict the scission pattern of a DNA sequence not part of the present data set, correlation coefficients of about 0.6 between predicted and observed patterns were obtained.
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Affiliation(s)
- C Yoon
- Department of Biological Chemistry, School of Medicine, University of California, Los Angeles 90024
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26
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Veal JM, Rill RL. Sequence specificity of DNA cleavage by bis(1,10-phenanthroline)copper(I): effects of single base pair transitions on the cleavage of preferred pyrimidine-purine-pyrimidine triplets. Biochemistry 1989; 28:3243-50. [PMID: 2545253 DOI: 10.1021/bi00434a019] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The cleavage of DNA restriction fragments by bis(1,10-phenanthroline)copper(I) [[(OP)2CuI]+] is sequence dependent: the trimer TAT is most strongly preferred, while the trimer TGT and tetramers TAAT, TAGT, and CAGT are strongly to moderately preferred [Veal, J. M., & R. L. (1988) Biochemistry 27, 1822-1827]. [(OP)2CuI]+ cleavage of a series of oligonucleotide duplexes of the type 5'-CCCTPyPuPyCCCC-3'/3'-GGGAPuPyPuGGGG-5' (Py = pyrimidine; Pu = purine) was examined to determine the effects of purine substituents in the central triplet on specificity. The relative cleavage rates of different PyPuPy triplets in oligomers were similar to those observed for restriction fragments. The undecamer duplex containing the trimer TAT (TTATC) was most preferentially cleaved, predominantly at the central adenosine and the adjacent 3'-thymidine. Duplexes differing from TTATC by a single A.T----G.C transition in the central triplet were cleaved at significantly reduced rates relative to TTATC, the order of preference being TAT greater than TGT greater than TAC greater than CAT. By contrast, duplexes differing from TTATC by a single A.T----I.C transition were cleaved at rates similar to those for TTATC when the transition occurred at the 5'-pyrimidine or central purine [i.e., C(.I)AT and TIT]. A duplex containing the trimer TAC(.I) was cleaved at a reduced rate similar to the duplex containing TAC(.G). The guanine 2-amino group at positions 1 and 2, but not position 3, of a 5'-PyPuPy-3' trimer is therefore implicated as a strong inhibitor of DNA binding by the copper-phenanthroline complex.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- J M Veal
- Department of Chemistry, Florida State University, Tallahassee 32306-3006
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27
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Hunter WN, D'Estaintot BL, Kennard O. Structural variation in d(CTCTAGAG). Implications for protein-DNA interactions. Biochemistry 1989; 28:2444-51. [PMID: 2730875 DOI: 10.1021/bi00432a015] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Single-crystal X-ray diffraction techniques have been used to characterize the structure of the self-complementary DNA oligomer d(CTCTAGAG). The structure was refined to an R factor of 14.7% using data to 2.15-A resolution. The tetragonal unit cell, space group P4(3)2(1)2, has dimensions a = 42.53 and c = 24.33 A. The asymmetric unit consists of a single strand or four base pairs. Two strands, related by a crystallographic dyad axis, coil about each other to form a right-handed duplex. This octamer duplex has a mean helix rotation of 32 degrees, 11.3 base pairs per turn, an average rise of 3.1 A, C3'-endo furanose conformations, a shallow minor groove, and a deep major groove. Such averaged parameters suggest classification of the octamer as a member of the A-DNA family. However, the global parameters tend to mask variations in conformational parameters observed at the level of the base pairs. In particular, the central TpA (= TpA) step displays extensive interstrand purine-purine overlap and an unusual sugar-phosphate backbone conformation. These structural features may be directly related to certain sequence-specific protein-DNA interactions involving nucleases and repressors.
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Affiliation(s)
- W N Hunter
- University Chemical Laboratory, Cambridge, U.K
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28
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Telford DJ, Stewart BW. Micrococcal nuclease: its specificity and use for chromatin analysis. THE INTERNATIONAL JOURNAL OF BIOCHEMISTRY 1989; 21:127-37. [PMID: 2663558 DOI: 10.1016/0020-711x(89)90100-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- D J Telford
- Children's Leukaemia and Cancer Research Unit, Prince of Wales Children's Hospital, Randwick, NSW, Australia
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29
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Widmer RM, Koller T, Sogo JM. Analysis of the psoralen-crosslinking pattern in chromatin DNA by exonuclease digestion. Nucleic Acids Res 1988; 16:7013-24. [PMID: 2841647 PMCID: PMC338348 DOI: 10.1093/nar/16.14.7013] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
When chromatin is photoreacted with psoralen, crosslinks occur preferentially in the linker DNA between nucleosomes. The pattern of these crosslinks can be analysed by exonuclease digestion of random DNA fragments, since the exonucleases tested stop at sites of psoralen-crosslinks. Further digestion of these fragments with S1-nuclease leads to DNA fragments of nucleosomal and polynucleosomal size, which presumably carry psoralen-crosslinks at both ends. This method of analysis of chromatin structure complements the classical micrococcal nuclease digestion analysis, since it can be performed in vitro as well as in vivo, and since it is independent of pH and ionic conditions.
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Affiliation(s)
- R M Widmer
- Institut für Zellbiologie, Eidgenössische Technische Hochschule, ETHZ, Zürich, Switzerland
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30
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Grimwade JE, Cullinan EB, Beerman TA. Neocarzinostatin and auromomycin preferentially cleave simian virus 40 DNA and chromosomes at a number of discrete locations. BIOCHIMICA ET BIOPHYSICA ACTA 1988; 950:102-12. [PMID: 2838085 DOI: 10.1016/0167-4781(88)90002-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Neocarzinostatin and auromomycin were shown to cleave simian virus 40 (SV40) DNA with preference for distinct regions of the viral genome. The positions cut by neocarzinostatin and auromomycin were similar, while micrococcal nuclease cleaved at positions other than those recognized by neocarzinostatin and auromomycin. Breaks were distributed throughout the viral genome and were not associated with any single type of genetic element. The limited number of locations in SV40 DNA that were preferentially cut by neocarzinostatin and auromomycin suggests that drug attack is directed by DNA structures other than the known trinucleotide sequence specificity of the drugs. Neocarzinostatin and auromomycin cut purified, cell-free, nuclear and intracellular chromosomal SV40 DNA at similar regions. The data indicate that there are regions in DNA that are hypersensitive to the drugs; the hypersensitivity may be determined by the microstructure of the DNA. The conformational change associated with the packing of the DNA into nucleosomes did not affect the microstructure of the sensitive region, nor did the shielding effect of nuclear proteins affect the drug's access to it. In addition, intracellular drug metabolism or other cellular factors did not alter the ability of drugs to interact at these sensitive regions.
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Affiliation(s)
- J E Grimwade
- Department of Experimental Therapeutics, Grace Cancer Drug Center, Roswell Park Memorial Institute, Buffalo, NY 14263
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31
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Drew HR, McCall MJ. Structural analysis of a reconstituted DNA containing three histone octamers and histone H5. J Mol Biol 1987; 197:485-511. [PMID: 3441008 DOI: 10.1016/0022-2836(87)90560-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Previous work has shown that DNA and the histone proteins will combine to form structures of a complex, yet definite nature. Here, we describe three experiments aimed at a better understanding of the interactions of DNA with the histone octamer and with histone H5. First, there has been some question as to whether the methylation of DNA could influence its folding about the histone octamer. To address this point, we reconstituted the histone octamer onto a 440 base-pair DNA of defined sequence at various levels of cytosine methylation, and also onto the unmethylated DNA. The reconstituted structures were probed by digestion with two different enzymes, micrococcal nuclease and DNase I. All samples were found to contain what appear to be three histone octamers, bound in close proximity on the 440 base-pair DNA. The cutting patterns of micrococcal nuclease and DNase I remain the same in all cases, even if the DNA has been extensively methylated. The results show, therefore, that methylation has little, or no, influence on the folding of this particular DNA about the histone octamer. Second, there has been concern as to whether the base sequence of DNA could determine its folding in a long molecule containing several nucleosomes, just as it does within any single, isolated nucleosome core. In order to deal with this problem, we cut the 440 base-pair DNA into three short fragments, each of nucleosomal length; we reconstituted each separately with the histone octamer; and then we digested the reconstituted complexes with DNase I for comparison with similar data from the intact 440 base-pair molecule. The results show that the folding of this DNA is influenced strongly by its base sequence, both in the three short fragments and in the long molecule. The rotational setting of the DNA within each of the three short fragments is as predicted from a computer algorithm, which measures its homology to 177 known examples of nucleosome core DNA. The rotational setting of the DNA in the 440 base-pair molecule remains the same as in two of the three short fragments, but changes slightly in a third case, apparently because of steric requirements when the nucleosomes pack closely against one another. Finally, there has been little direct evidence of where histone H5 binds within a DNA-octamer complex.(ABSTRACT TRUNCATED AT 400 WORDS)
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Affiliation(s)
- H R Drew
- CSIRO Division of Molecular Biology, North Ryde, Australia
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32
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Szekeres M, Matveyev AV. Cleavage and sequence recognition of 2,6-diaminopurine-containing DNA by site-specific endonucleases. FEBS Lett 1987; 222:89-94. [PMID: 2820801 DOI: 10.1016/0014-5793(87)80197-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The susceptibility of 2,6-diaminopurine (DAP)-containing bacteriophage DNA to several restriction and other endonucleases was examined. With the only exception of TaqI, these enzymes did not accept the modified base as a substitute for adenine. The phage DNA was extensively fragmented by the restriction endonucleases which recognize only G and C-containing sites. 5'-terminal analysis of the MspI and SmaI fragments revealed that d(DAP-T) basepairs can be mistaken by some enzymes for d(G-C) pairs.
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Affiliation(s)
- M Szekeres
- Institute of Plant Physiology, Biological Research Center, Szeged, Hungary
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33
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Grimwade JE, Cason EB, Beerman TA. Site specificity of bleomycin cleavage in purified and intracellular simian virus 40 DNA. Nucleic Acids Res 1987; 15:6315-29. [PMID: 2442726 PMCID: PMC306108 DOI: 10.1093/nar/15.16.6315] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The sites of bleomycin-induced cleavage of purified and intracellular simian virus 40 DNA were examined. Breaks in purified DNA were mapped to several discrete sites that were distributed throughout the viral genome, but were not associated with a common genetic element. Double-stranded breaks were made in positions of the first single-stranded nick, and regions of cuts were unaffected by changes in DNA superhelicity. Bleomycin cut intracellular chromosomes at the same sites that were cleaved in purified DNA. These results indicate that SV40 DNA contains DNA secondary structures that are highly preferred sites for BLM cleavage. These conformations appear to be unaffected by nucleoproteins bound to DNA.
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34
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Abstract
Histone octamers were reconstituted on plasmids carrying the alternating nucleotide sequence (G-C)15. The plasmids, radioactively labeled at one of two neighboring sites near the (G-C) insert, were digested with micrococcal nuclease. Nucleosome core particles were isolated and the monomer DNA subjected to restriction analysis. Quite different results are obtained if the reconstitution is carried out with relaxed plasmids, in which the (G-C) insert is in the B form, or with supercoiled plasmids, where it is in the Z form. With supercoiled plasmids, there is a marked reduction (compared with relaxed plasmids) in the abundance of labeled monomers, the result of a large decrease in core particles carrying any (G-C) sequence. Some core particles formed on supercoiled (Z) plasmids are positioned either just outside the (G-C) sequence, or with the sequence occupying the terminal position within the core particle. In contrast, monomers obtained from relaxed plasmids incorporate the (G-C) sequence in the B form more or less randomly in the interior of the core particle; species showing discrete positioning make only a minor contribution. We conclude that DNA in the Z form cannot be incorporated within core particles, except at their termini, and that a transition from the B to the Z form in vivo might result in a significantly altered local placement of nucleosomes.
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Affiliation(s)
- M M Garner
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892
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35
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Fox KR, Waring MJ. The use of micrococcal nuclease as a probe for drug-binding sites on DNA. BIOCHIMICA ET BIOPHYSICA ACTA 1987; 909:145-55. [PMID: 3593730 DOI: 10.1016/0167-4781(87)90036-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The cutting pattern produced by micrococcal nuclease on three DNA fragments has been determined in the absence and presence of various DNA-binding drugs. The enzyme itself cuts almost exclusively at pA and pT bonds, showing a greater activity at (A-T)n than in homopolymeric runs of A and T. Each drug produces distinct changes in the cleavage pattern. The protected regions can not be pinpointed with sufficient precision to assess the exact drug-binding sites on account of the sequence selectivity of the enzyme, although where a direct comparison is possible these include most of those seen as DNAase I footprints. The enzyme is most useful for assessing the selectivity of drugs which bind to AT-rich regions. Several drugs protect the DNA from micrococcal nuclease attack in regions which do not contain their acknowledged best binding sites. It appears that micrococcal nuclease is sensitive to the existence of secondary drug-binding sites which are not evident with other footprinting techniques.
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36
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Drew HR, Calladine CR. Sequence-specific positioning of core histones on an 860 base-pair DNA. Experiment and theory. J Mol Biol 1987; 195:143-73. [PMID: 3656408 DOI: 10.1016/0022-2836(87)90333-0] [Citation(s) in RCA: 110] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Previous experiments have shown that the locations of the histone octamer on DNA molecules of 140 to 240 base-pairs (bp) are influenced strongly by the nucleotide sequence. Here we have studied the locations of the histone octamer on a relatively long DNA molecule of 860 bp, using two different nucleases, micrococcal and DNAase I. Data were obtained from both the protein--DNA complexes and from the naked DNA at single-bond resolution, and then were analyzed by densitometry to yield plots of differential cleavage, which show clearly the changes in cutting due to the addition of protein. Our results show that the placement of core histones on the 860 bp molecule is definitely non-random. The digestion data provide evidence for five nucleosome cores, the centers of which lie in defined locations. In all but one of these protein--DNA complexes, the DNA adopts a unique, highly preferred rotational setting with respect to the protein surface. Another protein--DNA complex is unusual in that it protects 200 bp from digestion, yet is cut in its very center as if it were split into two parts. The apparent average twist of the DNA within all of these protein--DNA complexes is 10.2(+/- 0.1) bp, as measured by the periodicity of DNAase I digestion. This value is in excellent agreement with the twist of 10.21(+/- 0.05) bp deduced from the periodicity of sequence content in chicken nucleosome core DNA. In addition, we observe a discontinuity in the periodic cutting by DNAase I of about -1 to -3 bonds in going from any nucleosome core to the next. The most plausible interpretation of this discontinuity is that it reflects the angle by which adjacent protein--DNA complexes are aligned. Thus, any nucleosome may be related to its neighbor by a left-handed rotation in space of -1/10.2 to -3/10.2 helix turns, or -35 degrees to -105 degrees. Repeated many times, this operation would build a long, left-handed helix of nucleosomes similar to that described by many workers for the packing of nucleosomes in chromatin. In order to look for any long-range influences on the positioning of the histone octamer in the 860 bp molecule (as would be expected if the nucleosomes have to fit into some higher-order structure), we have examined the locations of the histone octamer on five different isolated short fragments of the 860-mer, all of nucleosomal length.(ABSTRACT TRUNCATED AT 400 WORDS)
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Affiliation(s)
- H R Drew
- M.R.C. Laboratory of Molecular Biology, Cambridge, U.K
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37
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Abstract
The binding of phleomycin and bleomycin to DNA has been investigated by studying their effects on cleavage by DNAase I and micrococcal nuclease. In the presence of cobalt, cleavage of DNA by the antibiotics is suppressed, yet they still provide protection from nuclease attack in regions surrounding the drug cleavage sites. We conclude that cleavage by phleomycin occurs at bonds around which the antibiotic is already selectively bound.
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Affiliation(s)
- K R Fox
- Department of Pharmacology, University of Cambridge, U.K
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