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Molecular delineation of de novo small supernumerary marker chromosomes in prenatal diagnosis, a retrospective study. Taiwan J Obstet Gynecol 2023; 62:94-100. [PMID: 36720559 DOI: 10.1016/j.tjog.2022.06.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2022] [Indexed: 01/30/2023] Open
Abstract
OBJECTIVES To define the genotype-phenotype correlation of small supernumerary marker chromosomes (sSMCs) and conduct precise genetic counseling, we retrospectively searched and reviewed de novo sSMCs cases detected during prenatal diagnosis at The First Affiliated Hospital of Zhengzhou University. MATERIALS AND METHODS Chromosome karyotypes of 20,314 cases of amniotic fluid from pregnant women were performed. For 16 samples with de novo sSMCs, 10 were subjected to single-nucleotide polymorphism (SNP) array or low-coverage massively parallel copy number variation sequencing (CNV-seq) analysis. RESULTS Among the 10 sSMCs cases, two sSMCs derived from chromosome 9, and three sSMCs derived from chromosomes 12, 18 and 22. The remaining 5 cases were not identified by SNP array or CNV-seq because they lacked euchromatin or had a low proportion of mosaicism. Four of them with a karyotype of 47,XN,+mar presented normal molecular cytogenetic results (seq[hg19] 46,XN), and the remaining patient with a karyotype of 46,XN,+mar presented with Turner syndrome (seq[hg19] 45,X). Five sSMCs samples were mosaics of all 16 cases. CONCLUSION Considering the variable origins of sSMCs, further genetic testing of sSMCs should be performed by SNP array or CNV-seq. Detailed molecular characterization would allow precise genetic counseling for prenatal diagnosis.
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2
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Locarnini SA, Civitico GM, Newbold JE. Hepatitis B: New Approaches for Antiviral Chemotherapy. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/095632029600700201] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Progress in the development of effective therapeutic regimes for chronic hepatitis B has been slow, mainly due to the lack of promising lead compounds and useful assays for high throughput in-vitro screening. Nucleoside analogue chemotherapy has targeted the inhibition of the hepatitis B virus (HBV) polymerase and achieved inhibition of this unique viral enzyme. The persistence and resistance of HBV covalently closed circular (or supercoiled) DNA, the key replicative intermediate and sole transcriptional template, to existing treatments also poses challenges for the effective development of antiviral chemotherapy. In spite of these difficulties, the process of viral DNA replication, as well as supercoiled DNA generation and processing, is now being elucidated at the molecular level, presenting unique opportunities for new drug targeting and design. This review attempts to highlight these new approaches to the development of treatment regimes for this important disease.
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Affiliation(s)
- S. A. Locarnini
- Victorian Infectious Diseases Reference Laboratory, Fairfield Hospital, Fairfield, Victoria 3078, Australia
| | - G. M. Civitico
- Victorian Infectious Diseases Reference Laboratory, Fairfield Hospital, Fairfield, Victoria 3078, Australia
| | - J. E. Newbold
- Department of Microbiology & Immunology, The School of Medicine, University of North Carolina, Chapel Hill, NC27599–7290, USA
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Platonova O, Akey IV, Head JF, Akey CW. Crystal structure and function of human nucleoplasmin (npm2): a histone chaperone in oocytes and embryos. Biochemistry 2011; 50:8078-89. [PMID: 21863821 DOI: 10.1021/bi2006652] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Human Npm2 is an ortholog of Xenopus nucleoplasmin (Np), a chaperone that binds histones. We have determined the crystal structure of a truncated Npm2-core at 1.9 Å resolution and show that the N-terminal domains of Npm2 and Np form similar pentamers. This allowed us to model an Npm2 decamer which may be formed by hydrogen bonds between quasi-conserved residues in the interface between two pentamers. Interestingly, the Npm2 pentamer lacks a prototypical A1-acidic tract in each of its subunits. This feature may be responsible for the inability of Npm2-core to bind histones. However, Npm2 with a large acidic tract in its C-terminal tail (Npm2-A2) is able to bind histones and form large complexes. Fluorescence resonance energy transfer experiments and biochemical analysis of loop mutations support the premise that nucleoplasmins form decamers when they bind H2A-H2B dimers and H3-H4 tetramers simultaneously. In the absence of histone tetramers, these chaperones bind H2A-H2B dimers with a single pentamer forming the central hub. When taken together, our data provide insights into the mechanism of histone binding by nucleoplasmins.
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Affiliation(s)
- Olga Platonova
- Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany St., Boston, Massachusetts 02118-2526, USA
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4
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Shechter D, Nicklay JJ, Chitta RK, Shabanowitz J, Hunt DF, Allis CD. Analysis of histones in Xenopus laevis. I. A distinct index of enriched variants and modifications exists in each cell type and is remodeled during developmental transitions. J Biol Chem 2008; 284:1064-74. [PMID: 18957438 DOI: 10.1074/jbc.m807273200] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Histone proteins contain epigenetic information that is encoded both in the relative abundance of core histones and variants and particularly in the post-translational modification of these proteins. We determined the presence of such variants and covalent modifications in seven tissue types of the anuran Xenopus laevis, including oocyte, egg, sperm, early embryo equivalent (pronuclei incubated in egg extract), S3 neurula cells, A6 kidney cells, and erythrocytes. We first developed a new robust method for isolating the stored, predeposition histones from oocytes and eggs via chromatography on heparin-Sepharose, whereas we isolated chromatinized histones via conventional acid extraction. We identified two previously unknown H1 isoforms (H1fx and H1B.Sp) present on sperm chromatin. We immunoblotted this global collection of histones with many specific post-translational modification antibodies, including antibodies against methylated histone H3 on Lys(4), Lys(9), Lys(27), Lys(79), Arg(2), Arg(17), and Arg(26); methylated histone H4 on Lys(20); methylated H2A and H4 on Arg(3); acetylated H4 on Lys(5), Lys(8), Lys(12), and Lys(16) and H3 on Lys(9) and Lys(14); and phosphorylated H3 on Ser(10) and H2A/H4 on Ser(1). Furthermore, we subjected a subset of these histones to two-dimensional gel analysis and subsequent immunoblotting and mass spectrometry to determine the global remodeling of histone modifications that occurs as development proceeds. Overall, our observations suggest that each metazoan cell type may have a unique histone modification signature correlated with its differentiation status.
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Affiliation(s)
- David Shechter
- Laboratory of Chromatin Biology, The Rockefeller University, New York, New York 10065, USA
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5
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Frehlick LJ, Eirín-López JM, Jeffery ED, Hunt DF, Ausió J. The characterization of amphibian nucleoplasmins yields new insight into their role in sperm chromatin remodeling. BMC Genomics 2006; 7:99. [PMID: 16646973 PMCID: PMC1479337 DOI: 10.1186/1471-2164-7-99] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2006] [Accepted: 04/28/2006] [Indexed: 12/04/2022] Open
Abstract
Background Nucleoplasmin is a nuclear chaperone protein that has been shown to participate in the remodeling of sperm chromatin immediately after fertilization by displacing highly specialized sperm nuclear basic proteins (SNBPs), such as protamine (P type) and protamine-like (PL type) proteins, from the sperm chromatin and by the transfer of histone H2A-H2B. The presence of SNBPs of the histone type (H type) in some organisms (very similar to the histones found in somatic tissues) raises uncertainty about the need for a nucleoplasmin-mediated removal process in such cases and poses a very interesting question regarding the appearance and further differentiation of the sperm chromatin remodeling function of nucleoplasmin and the implicit relationship with SNBP diversity The amphibians represent an unique opportunity to address this issue as they contain genera with SNBPs representative of each of the three main types: Rana (H type); Xenopus (PL type) and Bufo (P type). Results In this work, the presence of nucleoplasmin in oocyte extracts from these three organisms has been assessed using Western Blotting. We have used mass spectrometry and cloning techniques to characterize the full-length cDNA sequences of Rana catesbeiana and Bufo marinus nucleoplasmin. Northern dot blot analysis shows that nucleoplasmin is mainly transcribed in the egg of the former species. Phylogenetic analysis of nucleoplasmin family members from various metazoans suggests that amphibian nucleoplasmins group closely with mammalian NPM2 proteins. Conclusion We have shown that these organisms, in striking contrast to their SNBPs, all contain nucleoplasmins with very similar primary structures. This result has important implications as it suggests that nucleoplasmin's role in chromatin assembly during early zygote development could have been complemented by the acquisition of a new function of non-specifically removing SNBPs in sperm chromatin remodeling. This acquired function would have been strongly determined by the constraints imposed by the appearance and differentiation of SNBPs in the sperm.
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Affiliation(s)
- Lindsay J Frehlick
- Department of Biochemistry and Microbiology, University of Victoria, Petch Building, Victoria, BC, V8W 3P6, Canada
| | - José María Eirín-López
- Department of Biochemistry and Microbiology, University of Victoria, Petch Building, Victoria, BC, V8W 3P6, Canada
- Departamento de Biología Celular y Molecular, Universidade da Coruña, Campus de A Zapateira s/n, E-15071, Spain
| | - Erin D Jeffery
- Department of Chemistry and Pathology, University of Virginia, Charlottesville, VA 22901, USA
| | - Donald F Hunt
- Department of Chemistry and Pathology, University of Virginia, Charlottesville, VA 22901, USA
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Petch Building, Victoria, BC, V8W 3P6, Canada
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6
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Rodriguez P, Ruiz MT, Price GB, Zannis-Hadjopoulos M. NAP-2 is part of multi-protein complexes in Hela cells. J Cell Biochem 2004; 93:398-408. [PMID: 15368365 DOI: 10.1002/jcb.20163] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We previously reported that a complex of nuclear proteins from HeLa cells, among them histone H1 and casein kinase 2 co-eluted from immobilized nucleosome assembly protein 2 (NAP-2)-Sepharose. Here, using HeLa cell nuclear extracts, we found NAP-2 migrates in a blue-native polyacrylamide gel with an apparent molecular weight of 300 kDa. HeLa cell NAP-2, labeled in vivo with radioactive orthophosphate, co-precipitated with at least two phosphoproteins, with an apparent mass of 100 and 175 kDa, respectively, as determined by SDS-PAGE. NAP-2 from total HeLa cell extract co-purified with other proteins through two sequential chromatographic steps: first, a positively charged resin, Q-Sepharose, was used, which purified NAP-2 more easily with other proteins that eluted as a single peak at 0.5 M NaCl. This fraction possessed both relaxing and supercoiling activities, and it was able to assemble regularly spaced nucleosomes onto naked DNA in an ATP-dependent manner. Second, a negatively charged resin (heparin) was used, which retained small amounts of NAP-2 (a very acidic polypeptide) and topoisomerase I. This fraction, although able to supercoil relaxed DNA, did so to a lesser extent than the Q-Sepharose fraction. The data suggest that NAP-2 is in complex(es) with other proteins, which are distinct from histones.
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Affiliation(s)
- Pedro Rodriguez
- McGill Cancer Center, McGill University, Montreal, Quebec, Canada H3G 1Y6
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7
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Abstract
Recent structures of the nucleosome core particle reveal details of histone-histone and histone-DNA interactions. These structures have now set the stage for understanding chromatin assembly and dynamics during replication and transcription. Histone chaperones and chromatin remodeling complexes are important in both of these processes. The nucleosome and its protein core, the histone octamer, have twofold symmetry, which histone chaperones may use to bind core histones. Recent studies suggest that the nucleoplasmin pentamer may mediate histone storage, sperm chromatin decondensation and nucleosome assembly, by dimerizing to form a decamer. In this model, histone binding on the lateral surface of the chaperone involves stereospecific interactions and a shared twofold axis.
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Affiliation(s)
- Christopher W Akey
- Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, MA 02118-2526, USA.
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8
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Alexiadis V, Waldmann T, Andersen J, Mann M, Knippers R, Gruss C. The protein encoded by the proto-oncogene DEK changes the topology of chromatin and reduces the efficiency of DNA replication in a chromatin-specific manner. Genes Dev 2000. [DOI: 10.1101/gad.14.11.1308] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The structure of chromatin regulates the genetic activity of the underlying DNA sequence. We report here that the protein encoded by the proto-oncogene DEK, which is involved in acute myelogenous leukemia, induces alterations of the superhelical density of DNA in chromatin. The change in topology is observed with chromatin but not with naked DNA and does not involve dissociation of core histones from chromatin. Moreover, these effects require histone H2A/H2B dimers in addition to histone H3/H4. We additionally tested whether the DEK protein affects DNA-utilizing processes and found that the DEK protein substantially reduces the replication efficiency of chromatin but not of naked DNA templates.
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9
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Vestner B, Waldmann T, Gruss C. Histone octamer dissociation is not required for in vitro replication of simian virus 40 minichromosomes. J Biol Chem 2000; 275:8190-5. [PMID: 10713143 DOI: 10.1074/jbc.275.11.8190] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Replication of chromosomal templates requires the passage of the replication machinery through nucleosomally organized DNA. To gain further insights into these processes we have used chromatin that was reconstituted with dimethyl suberimidate-cross-linked histone octamers as template in the SV40 in vitro replication system. By supercoiling analysis we found that cross-linked histone octamers were reconstituted with the same kinetic and efficiency as control octamers. Minichromosomes with cross-linked nucleosomes were completely replicated, although the efficiency of replication was lower compared with control chromatin. Analysis of the chromatin structure of the replicated DNA revealed that the cross-linked octamer is transferred to the daughter strands. Thus, our data imply that histone octamer dissociation is not a prerequisite for the passage of the replication machinery and the transfer of the parental nucleosomes.
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Affiliation(s)
- B Vestner
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Federal Republic of Germany
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10
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Di Croce L, Koop R, Venditti P, Westphal HM, Nightingale KP, Corona DF, Becker PB, Beato M. Two-step synergism between the progesterone receptor and the DNA-binding domain of nuclear factor 1 on MMTV minichromosomes. Mol Cell 1999; 4:45-54. [PMID: 10445026 DOI: 10.1016/s1097-2765(00)80186-0] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
In contrast to its behavior as naked DNA, the MMTV promoter assembled in minichromosomes can be activated synergistically by the progesterone receptor and NF1 in a process involving ATP-dependent chromatin remodeling. The DNA-binding domain of NF1 is required and sufficient for stable occupancy of all receptor-binding sites and for functional synergism. Activation of purified minichromosomes is observed in the absence of SWI/SNF and can be enhanced by recombinant ISWI. Receptor binding to minichromosomes recruits ISWI and NURF38, but not brahma. We propose a two-step synergism in which the receptor triggers a chromatin remodeling event that facilitates access of NF1, which in turn stabilizes an open nucleosomal conformation required for efficient binding of further receptor molecules and full transactivation.
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Affiliation(s)
- L Di Croce
- IMT, Institut für Molekularbiologie und Tumorforschung Philipps-Universität Marburg, Germany
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11
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Affiliation(s)
- D J Tremethick
- John Curtin School of Medical Research, Australian National University, Australian Capital Territory, Australia
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12
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Nightingale KP, Becker PB. Structural and functional analysis of chromatin assembled from defined histones. Methods 1998; 15:343-53. [PMID: 9740722 DOI: 10.1006/meth.1998.0638] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
In this review we describe how the extract-mediated chromatin assembly system derived from preblastoderm Drosophila embryos can be modified to assemble chromatin from defined histones. This approach combines the advantages of assembling (i) chromatin templates from homogeneous histones with (ii) an assembly system that generates chromatin with physiological nucleosome spacing and density and that contains the biological complexity of in vivo chromatin. We have used this technique to assemble nonacetylated and hyperacetylated histones into chromatin (K. P. Nightingale, R. Wellinger, J. Sogo, and P. B. Becker, 1998, EMBO J. 17, 2865-2876; W. A. Krajewski and P. B. Becker, 1998, Proc. Natl. Acad. Sci. USA 95, 1540-1545), and use this as an example to detail the structural and transcriptional assays used to compare and characterize these chromatin templates. The application of this procedure to assemble chromatin from recombinant histones should facilitate a wide variety of studies on the role(s) of histone mutants and variants.
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Affiliation(s)
- K P Nightingale
- Gene Expression Programme, European Molecular Biology Laboratory, Heidelberg, Germany
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13
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Chang L, Loranger SS, Mizzen C, Ernst SG, Allis CD, Annunziato AT. Histones in transit: cytosolic histone complexes and diacetylation of H4 during nucleosome assembly in human cells. Biochemistry 1997; 36:469-80. [PMID: 9012662 DOI: 10.1021/bi962069i] [Citation(s) in RCA: 130] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The organization and acetylation of nascent histones prior to their stable incorporation into chromatin were examined. Through sedimentation and immunoprecipitation analyses of HeLa cytosolic extracts, two somatic non-nucleosomal histone complexes were detected: one containing nascent H3 and H4, and a second containing H2A (and probably H2B) in association with the nonhistone protein NAP-1. The H3/H4 complex has a sedimentation coefficient of 5-6S, consistent with the presence of one or more escort proteins. H4 in the cytosolic H3/H4 complex is diacetylated, fully in accord with the acetylation state of newly synthesized H4 in chromatin. The diacetylation of nascent human H4 is therefore completed prior to nucleosome assembly. As part of our studies of the nascent H3/H4 complex, the cytoplasmic histone acetyltransferase most likely responsible for acetylating newly synthesized H4 was also investigated. HeLa histone acetyltransferase B (HAT B) acetylates H4 but not H3 in vitro, and maximally diacetylates H4 even in the presence of sodium butyrate. Human HAT B acetylates H4 exclusively on the lysine residues at positions 5 and 12, in complete agreement with the highly conserved acetylation pattern of nascent nucleosomal H4 (Sobel et al., 1995), and has a native molecular weight of approximately 100 kDa. Based on our findings a model is presented for the involvement of histone acetylation and NAP-1 in H2A/H2B deposition and exchange, during nucleosome assembly and chromatin remodeling in vivo.
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Affiliation(s)
- L Chang
- Department of Biology, Boston College, Chestnut Hill, Massachusetts 02167, USA
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14
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Ruiz-Lara SA, Cornudella L, Rodríguez-Campos A. Dissociation of protamine-DNA complexes by Xenopus nucleoplasmin and minichromosome assembly in vitro. EUROPEAN JOURNAL OF BIOCHEMISTRY 1996; 240:186-94. [PMID: 8797853 DOI: 10.1111/j.1432-1033.1996.0186h.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Nucleoplasmin, an acidic thermostable protein abundant in the nucleus of Xenopus laevis oocytes, has been found to dissociate complexes of pUC19 DNA and protein phi 1, an intermediate protamine present in ripe sperm from the mollusc Mytilus edulis. Cruder preparations of nucleoplasmin, such as the amphibian oocyte S150 extract and its thermostable fraction, also dissociate the heterologous DNA-phi 1 complexes and, in addition, promote the assembly of plasmid DNA into a minichromosome displaying regular nucleosomal periodicity, as revealed by micrococcal nuclease digestion. In contrast, purified nucleoplasmin complemented with rat hepatocyte core histone octamers in the presence of DNA topoisomerase I, although capable of inducing nucleoprotein formation onto the complexed DNA, fails to position nucleosomes at the native spacings seen in chromatin in vivo. These data favour the existence of a general mechanism to bring about, in a concerted manner, removal of sperm-specific nuclear proteins and reconstitution of somatic chromatin following fertilization.
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Affiliation(s)
- S A Ruiz-Lara
- Departamento de Biología Molecular y Celular, Centro de Investigación y Desarrollo del CSIC, Barcelona, Spain
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15
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Abstract
Topological knots can be formed in vitro by incubating covalently closed double stranded DNA and purified topoisomerase II from the yeast Saccharomyces cerevisiae in an ATP-dependent reaction. Knotting production requires a starting enzyme/DNA mass ratio of 1. Analysis of knotted DNA was carried out by using both one- and two-dimensional agarose gel electrophoresis. The knots generated are efficiently untied, and give relaxed DNA rings, by catalytic amounts of topoisomerase II, but not by topoisomerase I. Time course analysis shows the knotting formation over relaxed and supercoiled DNA. When supercoiled DNA was used as a susbtrate, knots appear immediately whereas no transient relaxed rings were observed. The cell-free extract from Xenopus oocytes S-150 cannot assemble nucleosomes on knotted DNA templates as revealed by topological and micrococcal nuclease analysis. Nevertheless, the presence of knotted DNA templates does not inhibit the assembly over the relaxed plasmid. Finally, a pretreatment of knotted DNA with trace amounts of topoisomerase II before the addition of the S-150 yields a canonical minichromosome assembled in vitro. Taking into account these results, I suggest a mechanism of chromatin assembly regulation directed by topoisomerase II.
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Affiliation(s)
- A Rodríguez-Campos
- Departamento de Biología Molecular y Celular, Centro de Investigación y Desarrollo, CSIC, Jordi Girona, 18 E-08034, Barcelona, Spain
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16
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Tremethick DJ, Hyman L. High mobility group protein 14 and 17 can prevent the close packing of nucleosomes by increasing the strength of protein contacts in the linker DNA. J Biol Chem 1996; 271:12009-16. [PMID: 8662614 DOI: 10.1074/jbc.271.20.12009] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
High mobility group (HMG) proteins 14 and 17 are abundant chromatin-associated proteins found in all higher eukaryotic nuclei. This observation demonstrates that HMGs 14 and 17 must have an important and universal function with regard to the structure and function of chromatin. What this function is, including how they interact with a nucleosomal array in vivo, is not known. Recently, we have demonstrated that HMGs 14 and 17 can organize nucleosomes into a regular array and increase the repeat length from 145 to about 160-165 base pairs in vitro. In addition, they can increase the apparent repeat length of chromatin deficient in histones H2A/H2B from 125 to approximately 145 base pairs. Importantly, this template was transcriptionally active. In this study, we report five new observations that begin to address the mechanism by which HMGs 14 and 17 space nucleosomal particles. First, we demonstrate that both human placenta HMG 14 and HMG 17 can space nucleosomes to produce a chromatin template with a repeat length around 160 base pairs. This result further highlights the similarity between these proteins in terms of protein structure and perhaps function. Second, we show that digestion of HMG containing chromatin with micrococcal nuclease produces DNA fragments that were approximately 10 and 20 base pairs longer than nucleosome core-particle DNA. This suggests that HMG 14 or HMG 17 can protect, directly or indirectly, at least an additional 10 base pairs of linker DNA from micrococcal digestion. However, this HMG-containing particle does not produce a strong kinetic block, and further digestion results in the eventual accumulation of DNA fragments 145 base pairs in length. Third, by comparing the full-length protein with different domains, we demonstrate that the acidic carboxyl-terminal domain is absolutely required for nucleosome spacing, neither the nucleosome binding domain of HMG 14 or HMG 17 nor the amino-terminal domain plus the nucleosome binding domain of HMG 14 could space nucleosomes. Fourth, we demonstrate that extensive micrococcal nuclease digestion of chromatin deficient in histones H2A/H2B led to the accumulation of DNA fragments about 110 base pairs in length, which is presumably the length of DNA associated with a nucleosomal particle deficient in one H2A/H2B dimer. Incorporation of either HMG 14 or HMG 17 into this chromatin results in the disappearance of this band and increase in the accumulation of fragments around 140-150 base pairs in length. Finally, in contrast to spacing of complete nucleosomes, we find that the nucleosome binding domain of HMG 17 (but not the nucleosome binding of HMG 14) is the only domain required for spacing of H2A/H2B-deficient chromatin.
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Affiliation(s)
- D J Tremethick
- John Curtin School of Medical Research, Australian National University, Canberra, Australia
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17
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Affiliation(s)
- D Poccia
- Department of Biology, Amherst College, Massachusetts 01002, USA
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18
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Gruss C, Knippers R. Structure of replicating chromatin. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1996; 52:337-65. [PMID: 8821265 DOI: 10.1016/s0079-6603(08)60971-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- C Gruss
- Fakultät für Biologie, Universität Konstanz, Germany
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19
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Yoon HW, Kim MC, Lee SY, Hwang I, Bahk JD, Hong JC, Ishimi Y, Cho MJ. Molecular cloning and functional characterization of a cDNA encoding nucleosome assembly protein 1 (NAP-1) from soybean. MOLECULAR & GENERAL GENETICS : MGG 1995; 249:465-73. [PMID: 8544812 DOI: 10.1007/bf00290572] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
NAP-1, a protein first isolated from mammalian cells, can introduce supercoils into relaxed circular DNA in the presence of purified core histones. Based on its in vitro activity, it has been suggested that NAP-1 may be involved in nucleosome assembly in vivo. We isolated a cDNA clone encoding a soybean NAP-1 homolog, SNAP-1. The SNAP-1 cDNA contains an open reading frame of 358 amino acids residues with a calculated molecular weight of 41 kDa. The deduced amino acid sequence of SNAP-1 shares sequence similarity with yeast NAP-1 (38%) and human hNRP (32%). Notable features of the deduced sequence are two extended acidic regions thought to be involved in histone binding. SNAP-1 expressed in Escherichia coli induces supercoiling in relaxed circular DNA, suggesting that SNAP-1 may have nucleosome assembly activity. The specific activity of SNAP-1 is comparable to that of HeLa NAP-1 in an in vitro assay. Western analysis reveals that SNAP-1 is expressed in the immature and young tissues that were examined, while mature tissues such as old leaves and roots, show very little or no expression. NAP-1 homologs also appear to be present in other plant species.
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Affiliation(s)
- H W Yoon
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Chinju, Korea
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20
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[7] The SV40 minichromosome. ACTA ACUST UNITED AC 1995. [DOI: 10.1016/s1067-2389(06)80039-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
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21
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Tremethick DJ. High mobility group proteins 14 and 17 can space nucleosomal particles deficient in histones H2A and H2B creating a template that is transcriptionally active. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(18)46946-3] [Citation(s) in RCA: 5] [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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Kaufman PD, Botchan MR. Assembly of nucleosomes: do multiple assembly factors mean multiple mechanisms? Curr Opin Genet Dev 1994; 4:229-35. [PMID: 8032200 DOI: 10.1016/s0959-437x(05)80049-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
In eukaryotic cells, transcription and DNA replication occur on DNA templates associated with chromatin proteins, most notably histone octamers. Protein factors that can assemble these units have been isolated from many sources. In particular, one factor from human cells is associated with ongoing DNA synthesis; other known assembly factors are not obligately coupled to the replication process. The wide variety of histone chaperones suggests that multiple pathways for the remodeling of chromatin structure have evolved.
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23
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Svaren J, Klebanow E, Sealy L, Chalkley R. Analysis of the competition between nucleosome formation and transcription factor binding. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)37113-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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24
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Perry CA, Dadd CA, Allis CD, Annunziato AT. Analysis of nucleosome assembly and histone exchange using antibodies specific for acetylated H4. Biochemistry 1993; 32:13605-14. [PMID: 7504954 DOI: 10.1021/bi00212a028] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Using antibodies that specifically recognize the acetylated forms of histone H4, we show that it is possible to immunoprecipitate newly assembled (acetylated) nucleosomes. Newly replicated HeLa cell chromatin was labeled for 5-30 min with [3H]thymidine in the presence of sodium butyrate (thus inhibiting the deacetylation of newly deposited H4); bulk chromatin DNA was labeled for 24 h with [14C]thymidine. When soluble nucleosomes were incubated with immobilized antibodies, a comparison of the bound and unbound fractions showed up to a 65-fold enrichment for new chromatin DNA in the immunoprecipitate (bound), relative to the supernatant (unbound). No enrichment for new DNA was observed when preimmune control serum was used in a similar fashion. The enrichment for new DNA in the immunopellet was paralleled by a similar enrichment for all four newly synthesized histones. Acetylation was required for antibody recognition: When chromatin was replicated in the absence of butyrate (permitting histone deacetylation and chromatin maturation), equally low levels of new and old chromatin were immunoprecipitated, and no enrichment for new DNA was observed. Competition experiments confirmed these results. Analyses of histone deposition during the inhibition of DNA replication established that acetylated chromatin is the preferential target for H2A/H2B exchange. These experiments provide evidence for the highly selective assembly of newly synthesized H3, H2A, and H2B with acetylated H4, and for the involvement of histone acetylation in dynamic chromatin remodeling. In addition, immunoprecipitations of radiolabeled cytosolic extracts identified a possible somatic chromatin preassembly complex, containing newly synthesized H3 and new (acetylated) H4.
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Affiliation(s)
- C A Perry
- Department of Biology, Boston College, Chestnut Hill, Massachusetts 02167
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25
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Fujii-Nakata T, Ishimi Y, Okuda A, Kikuchi A. Functional analysis of nucleosome assembly protein, NAP-1. The negatively charged COOH-terminal region is not necessary for the intrinsic assembly activity. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(19)36785-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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26
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Partial purification, from Xenopus laevis oocytes, of an ATP-dependent activity required for nucleosome spacing in vitro. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(18)42143-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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27
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Abstract
Just as the faithful replication of DNA is an essential process for the cell, chromatin structures of active and inactive genes have to be copied accurately. Under certain circumstances, however, the activity pattern has to be changed in specific ways. Although analysis of specific aspects of these complex processes, by means of model systems, has led to their further elucidation, the mechanisms of chromatin replication in vivo are still controversial and far from being understood completely. Progress has been achieved in understanding: 1. The initiation of chromatin replication, indicating that a nucleosome-free origin is necessary for the initiation of replication; 2. The segregation of the parental nucleosomes, where convincing data support the model of random distribution of the parental nucleosomes to the daughter strands; and 3. The assembly of histones on the newly synthesized strands, where growing evidence is emerging for a two-step mechanism of nucleosome assembly, starting with the deposition of H3/H4 tetramers onto the DNA, followed by H2A/H2B dimers.
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Affiliation(s)
- C Gruss
- Institute for Cell Biology, ETH Zürich, Switzerland
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28
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Abstract
Previous investigations of topoisomer distributions of simian virus 40 (SV40) DNA from monkey cells have revealed that these circular mini-chromosomes, like relaxed, naked, closed circular DNA, exist as a Gaussian distribution of topoisomers. I have extended this comparison by measuring topoisomer distributions for a variety of plasmid episomes that are stably propagated in cells of the yeast Saccharomyces cerevisiae. The breadth of the topoisomer distributions for plasmid chromatin, including SV40, is approximately constant when normalized for DNA length, as is the breadth of distribution for naked DNA. However, the distributions for plasmid chromatin are substantially broader than those for the corresponding relaxed, naked DNAs. The breath is constant for plasmids differing in transcriptional activity, and varies only slightly between synchronized and unsynchronized populations of yeast cells, suggesting that variation in plasmid linking number with transcription or replication does not account for the observed heterogeneity in linking number. Topoisomer heterogeneity for plasmid chromatin in vivo may be due to heterogeneity in the number of nucleosomes on each plasmid, which could reflect either the nature of the assembly process or the dynamics of nucleosomes within the cell.
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Affiliation(s)
- R H Morse
- Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892
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29
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Identification and molecular cloning of yeast homolog of nucleosome assembly protein I which facilitates nucleosome assembly in vitro. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(20)89604-5] [Citation(s) in RCA: 138] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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