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• W2023292879 endingPage "18039" @default.
• W2023292879 startingPage "18028" @default.
• W2023292879 abstract "We report the characterization of an in vitro chromatin assembly system derived from Artemiaembryos and its application to the study of AluI-113 satellite DNA organization in nucleosomes. The system efficiently reconstitutes chromatin templates by associating DNA, core histones, and H1. The polynucleosomal complexes show physiological spacing of repeat length 190 ± 5 base pairs, and the internucleosomal distances are modulated by energy-using activities that contribute to the dynamics of chromatin conformation. The assembly extract was used to reconstitute tandemly repeated AluI-113 sequences. The establishment of preferred histone octamer/satellite DNA interactions was observed. In vitro, AluI-113 elements dictated the same nucleosome translational localizations as foundin vivo. Specific rotational constraints seem to be the central structural requirement for nucleosome association. Satellite dinucleosomes showed decreased translational mobility compared with mononucleosomes. This could be the consequence of interactions between rotationally positioned nucleosomes separated by linker DNA of uniform length. AluI-113 DNA led to weak cooperativity of nucleosome association in the proximal flanking regions, which decreased with distance. Moreover, the structural properties of satellite chromatin can spread, thus leading to a specific organization of adjacent nucleosomes. We report the characterization of an in vitro chromatin assembly system derived from Artemiaembryos and its application to the study of AluI-113 satellite DNA organization in nucleosomes. The system efficiently reconstitutes chromatin templates by associating DNA, core histones, and H1. The polynucleosomal complexes show physiological spacing of repeat length 190 ± 5 base pairs, and the internucleosomal distances are modulated by energy-using activities that contribute to the dynamics of chromatin conformation. The assembly extract was used to reconstitute tandemly repeated AluI-113 sequences. The establishment of preferred histone octamer/satellite DNA interactions was observed. In vitro, AluI-113 elements dictated the same nucleosome translational localizations as foundin vivo. Specific rotational constraints seem to be the central structural requirement for nucleosome association. Satellite dinucleosomes showed decreased translational mobility compared with mononucleosomes. This could be the consequence of interactions between rotationally positioned nucleosomes separated by linker DNA of uniform length. AluI-113 DNA led to weak cooperativity of nucleosome association in the proximal flanking regions, which decreased with distance. Moreover, the structural properties of satellite chromatin can spread, thus leading to a specific organization of adjacent nucleosomes. Most higher eukaryotic DNA is folded into a dynamic nucleoprotein structure, which is subject to progressive and reversible modifications of its condensation state during transitions between interphasic and metaphasic chromatin. However, there are chromosomal regions that maintain cytological properties comparable with those of the metaphase chromosome throughout the cell cycle (1Heitz E. Jahrb. Wiss. Bot. 1928; 69: 726-818Google Scholar). Termed heterochromatin, these highly condensed regions consist of simple DNA sequences repeated in long tandem arrays and are typically localized around centromeres and telomeres (reviewed in Refs. 2Pardue M.L. Curr. Opin. Genet. Dev. 1994; 4: 845-850Crossref PubMed Scopus (19) Google Scholar and 3Lohe A.R. Hilliker A.J. Curr. Opin. Genet. Dev. 1995; 5: 746-755Crossref PubMed Scopus (74) Google Scholar). Heterochromatic regions are replicated late during S phase (4Lima de Faria A. Jaworska H. Nature. 1968; 217: 138-142Crossref PubMed Scopus (201) Google Scholar, 5Holmquist G.P. Am. J. Hum. Genet. 1987; 40: 151-173PubMed Google Scholar); they do not participate in meiotic recombination and are generally associated with the transcriptionally repressed state (reviewed in Ref. 6Elgin S.C.R. Curr. Opin. Genet. Dev. 1996; 6: 193-202Crossref PubMed Scopus (198) Google Scholar). These regions can influence the expression of juxtaposed genes in a manner dependent on their distance from the point of juxtaposition, a phenomenon called “position effect variegation” (7Lewis E.B. Adv. Genet. 1950; 3: 73-115Crossref PubMed Scopus (193) Google Scholar, 8Spofford J.B. Ashburner M. Novitski E. The Genetics and Biology of Drosophila. 1. Academic Press, Inc., New York1976: 955-1018Google Scholar, 9Henikoff S. Genetics. 1994; 138: 1-5PubMed Google Scholar). Position effect variegation is thought to take place either by compartmentalization within transcriptionally inactive nuclear regions or by virtue of the spread of the heterochromatic structure (reviewed in Refs. 10Locke J. Kotarski M.A. Tartof K.D. Genetics. 1988; 120: 181-198Crossref PubMed Google Scholar and 11Orlando V. Paro R. Curr. Opin. Genet. Dev. 1995; 5: 174-179Crossref PubMed Scopus (137) Google Scholar).Heterochromatin is generally defined as highly organized chromatin structures stabilized by multiprotein complexes and is functionally correlated with diffusible transcription repressing properties (11Orlando V. Paro R. Curr. Opin. Genet. Dev. 1995; 5: 174-179Crossref PubMed Scopus (137) Google Scholar). Genetic and molecular studies have shown that the process of heterochromatinization involves the spread of particular chromatin structures in the cases of pericentric insertions of euchromatic genes in Drosophila (12Wallrath L.L. Elgin S.C.R. Genes Dev. 1995; 9: 1263-1277Crossref PubMed Scopus (406) Google Scholar), centromeric insertion of theura4 gene in Schizosaccharomyces pombe (13Allshire R.C. Javerzat J.P. Redhead N.J. Cranston G. Cell. 1994; 76: 157-169Abstract Full Text PDF PubMed Scopus (273) Google Scholar), and the silencing of the HML and HMR loci in S. cerevisiae (14Loo S. Rhine J. Science. 1994; 264: 1768-1771Crossref PubMed Scopus (185) Google Scholar). Analysis of the silencing processes in the yeast mating type loci indicates a fundamental role for histones H3 and H4 in the stabilization of the repressed state of yeast telomeric heterochromatin (15Johnson L.M. Kayne P.S. Kahn E.S. Grunstein M. Proc. Natl. Acad. Sci. U. S. A. 1990; 87: 6286-6290Crossref PubMed Scopus (276) Google Scholar, 16Hecht A. Laroche T. Strahl-Bolsinger S. Gasser S.M. Grunstein M. Cell. 1995; 80: 583-592Abstract Full Text PDF PubMed Scopus (692) Google Scholar). Nucleosome arrangement therefore appears to be an important structural element that allows specific silencing proteins to assemble packed, repressive chromatin structures.The study of the role of heterochromatic DNA on chromatin structure may help to clarify how specific heterochromatic structures are maintained. To this end, we reconstituted and characterized the chromatin features of chromosomal regions that are cytologically distinguishable asArtemia franciscana (Crustacea Phyllopoda) heterochromatin. These regions are mainly composed of satellite DNA with a repeat unit length of 113 bp 1The abbreviation used is: bp, base pair(s). 1The abbreviation used is: bp, base pair(s).(AluI-113). AluI-113 DNA has already been characterized by electrophoretic analysis and electron microscopy (17Benfante R. Landsberger N. Tubiello G. Badaracco G. Nucleic Acids Res. 1989; 17: 8273-8282Crossref PubMed Scopus (24) Google Scholar).AluI-113, like other satellite DNAs (18Barsacchi-Pilone G. Batistoni R. Andronico F. Vitelli L. Nardi I. Chromosoma. 1986; 93: 435-446Crossref PubMed Scopus (33) Google Scholar, 19Kodama H. Saitoh H. Tone M. Kuhara S. Sakaki Y. Mizuno S. Chromosoma. 1987; 96: 18-25Crossref PubMed Scopus (100) Google Scholar, 20Radic M.Z. Lundgren K. Hamkalo B.A. Cell. 1987; 50: 1101-1108Abstract Full Text PDF PubMed Scopus (170) Google Scholar, 21Martinez-Balbas A. Rodriguez-Campos A. Garcia-Ramirez M. Sainz J. Carrera P. Aymami J. Azorin F. Biochemistry. 1990; 29: 2342-2348Crossref PubMed Scopus (85) Google Scholar, 22Saitoh Y. Saitoh H. Ohtomo K. Mizuno S. Chromosoma. 1991; 101: 32-40Crossref PubMed Scopus (74) Google Scholar, 23Carrera P. Martinez-Balbas M.A. Portugal J. Azorin F. Nucleic Acids Res. 1991; 19: 5639-5644Crossref PubMed Scopus (14) Google Scholar), shows an intrinsic curvature of the longitudinal axis of the double helix, the structural basis of which is determined by adenine blocks positioned in phase with the pitch of the double helix. The structural properties of satellite DNAs are widely considered to be fundamental for the organization of highly condensed nucleoprotein complexes. Extensive evidence of in vivo nucleosome positioning along various satellite DNAs (reviewed in Ref. 24Simpson R.T. Prog. Nucleic Acids Res. Mol. Biol. 1991; 40: 143-184Crossref PubMed Scopus (202) Google Scholar) has suggested a role for specific chromatin structures in heterochromatin condensation (25Fitzgerald D.J. Dryden G.L. Bronson E.C. Williams J.S. Anderson J.N. J. Biol. Chem. 1994; 269: 21303-21314Abstract Full Text PDF PubMed Google Scholar). However, in vitro studies of interactions between histones and satellite DNAs are few. The only examples of in vitroreconstitution aimed at the analysis of nucleosome positioning on satellite DNAs are studies of histone octamer assembly on 200–250-bp-long fragments by dialysis (26Linxweiler W. Hörz W. Cell. 1985; 42: 281-290Abstract Full Text PDF PubMed Scopus (66) Google Scholar, 27Neubauer B. Linxweiler W. Hörz W. J. Mol. Biol. 1986; 190: 639-645Crossref PubMed Scopus (36) Google Scholar).In order to determine the structural properties of polynucleosomal complexes on multimeric AluI-113 fragments, we developed and characterized a cell-free assembly system from Artemia at the nauplius embryo stage. We have used this to analyze: (i) the organization of bent AluI-113 DNA into nucleosomes; (ii) the effects of interactions between consecutive physiologically spacedAluI-113 nucleosomes; and (iii) how AluI-113 sequences could affect the chromatin structure of non-satellite flanking regions. Most higher eukaryotic DNA is folded into a dynamic nucleoprotein structure, which is subject to progressive and reversible modifications of its condensation state during transitions between interphasic and metaphasic chromatin. However, there are chromosomal regions that maintain cytological properties comparable with those of the metaphase chromosome throughout the cell cycle (1Heitz E. Jahrb. Wiss. Bot. 1928; 69: 726-818Google Scholar). Termed heterochromatin, these highly condensed regions consist of simple DNA sequences repeated in long tandem arrays and are typically localized around centromeres and telomeres (reviewed in Refs. 2Pardue M.L. Curr. Opin. Genet. Dev. 1994; 4: 845-850Crossref PubMed Scopus (19) Google Scholar and 3Lohe A.R. Hilliker A.J. Curr. Opin. Genet. Dev. 1995; 5: 746-755Crossref PubMed Scopus (74) Google Scholar). Heterochromatic regions are replicated late during S phase (4Lima de Faria A. Jaworska H. Nature. 1968; 217: 138-142Crossref PubMed Scopus (201) Google Scholar, 5Holmquist G.P. Am. J. Hum. Genet. 1987; 40: 151-173PubMed Google Scholar); they do not participate in meiotic recombination and are generally associated with the transcriptionally repressed state (reviewed in Ref. 6Elgin S.C.R. Curr. Opin. Genet. Dev. 1996; 6: 193-202Crossref PubMed Scopus (198) Google Scholar). These regions can influence the expression of juxtaposed genes in a manner dependent on their distance from the point of juxtaposition, a phenomenon called “position effect variegation” (7Lewis E.B. Adv. Genet. 1950; 3: 73-115Crossref PubMed Scopus (193) Google Scholar, 8Spofford J.B. Ashburner M. Novitski E. The Genetics and Biology of Drosophila. 1. Academic Press, Inc., New York1976: 955-1018Google Scholar, 9Henikoff S. Genetics. 1994; 138: 1-5PubMed Google Scholar). Position effect variegation is thought to take place either by compartmentalization within transcriptionally inactive nuclear regions or by virtue of the spread of the heterochromatic structure (reviewed in Refs. 10Locke J. Kotarski M.A. Tartof K.D. Genetics. 1988; 120: 181-198Crossref PubMed Google Scholar and 11Orlando V. Paro R. Curr. Opin. Genet. Dev. 1995; 5: 174-179Crossref PubMed Scopus (137) Google Scholar). Heterochromatin is generally defined as highly organized chromatin structures stabilized by multiprotein complexes and is functionally correlated with diffusible transcription repressing properties (11Orlando V. Paro R. Curr. Opin. Genet. Dev. 1995; 5: 174-179Crossref PubMed Scopus (137) Google Scholar). Genetic and molecular studies have shown that the process of heterochromatinization involves the spread of particular chromatin structures in the cases of pericentric insertions of euchromatic genes in Drosophila (12Wallrath L.L. Elgin S.C.R. Genes Dev. 1995; 9: 1263-1277Crossref PubMed Scopus (406) Google Scholar), centromeric insertion of theura4 gene in Schizosaccharomyces pombe (13Allshire R.C. Javerzat J.P. Redhead N.J. Cranston G. Cell. 1994; 76: 157-169Abstract Full Text PDF PubMed Scopus (273) Google Scholar), and the silencing of the HML and HMR loci in S. cerevisiae (14Loo S. Rhine J. Science. 1994; 264: 1768-1771Crossref PubMed Scopus (185) Google Scholar). Analysis of the silencing processes in the yeast mating type loci indicates a fundamental role for histones H3 and H4 in the stabilization of the repressed state of yeast telomeric heterochromatin (15Johnson L.M. Kayne P.S. Kahn E.S. Grunstein M. Proc. Natl. Acad. Sci. U. S. A. 1990; 87: 6286-6290Crossref PubMed Scopus (276) Google Scholar, 16Hecht A. Laroche T. Strahl-Bolsinger S. Gasser S.M. Grunstein M. Cell. 1995; 80: 583-592Abstract Full Text PDF PubMed Scopus (692) Google Scholar). Nucleosome arrangement therefore appears to be an important structural element that allows specific silencing proteins to assemble packed, repressive chromatin structures. The study of the role of heterochromatic DNA on chromatin structure may help to clarify how specific heterochromatic structures are maintained. To this end, we reconstituted and characterized the chromatin features of chromosomal regions that are cytologically distinguishable asArtemia franciscana (Crustacea Phyllopoda) heterochromatin. These regions are mainly composed of satellite DNA with a repeat unit length of 113 bp 1The abbreviation used is: bp, base pair(s). 1The abbreviation used is: bp, base pair(s).(AluI-113). AluI-113 DNA has already been characterized by electrophoretic analysis and electron microscopy (17Benfante R. Landsberger N. Tubiello G. Badaracco G. Nucleic Acids Res. 1989; 17: 8273-8282Crossref PubMed Scopus (24) Google Scholar).AluI-113, like other satellite DNAs (18Barsacchi-Pilone G. Batistoni R. Andronico F. Vitelli L. Nardi I. Chromosoma. 1986; 93: 435-446Crossref PubMed Scopus (33) Google Scholar, 19Kodama H. Saitoh H. Tone M. Kuhara S. Sakaki Y. Mizuno S. Chromosoma. 1987; 96: 18-25Crossref PubMed Scopus (100) Google Scholar, 20Radic M.Z. Lundgren K. Hamkalo B.A. Cell. 1987; 50: 1101-1108Abstract Full Text PDF PubMed Scopus (170) Google Scholar, 21Martinez-Balbas A. Rodriguez-Campos A. Garcia-Ramirez M. Sainz J. Carrera P. Aymami J. Azorin F. Biochemistry. 1990; 29: 2342-2348Crossref PubMed Scopus (85) Google Scholar, 22Saitoh Y. Saitoh H. Ohtomo K. Mizuno S. Chromosoma. 1991; 101: 32-40Crossref PubMed Scopus (74) Google Scholar, 23Carrera P. Martinez-Balbas M.A. Portugal J. Azorin F. Nucleic Acids Res. 1991; 19: 5639-5644Crossref PubMed Scopus (14) Google Scholar), shows an intrinsic curvature of the longitudinal axis of the double helix, the structural basis of which is determined by adenine blocks positioned in phase with the pitch of the double helix. The structural properties of satellite DNAs are widely considered to be fundamental for the organization of highly condensed nucleoprotein complexes. Extensive evidence of in vivo nucleosome positioning along various satellite DNAs (reviewed in Ref. 24Simpson R.T. Prog. Nucleic Acids Res. Mol. Biol. 1991; 40: 143-184Crossref PubMed Scopus (202) Google Scholar) has suggested a role for specific chromatin structures in heterochromatin condensation (25Fitzgerald D.J. Dryden G.L. Bronson E.C. Williams J.S. Anderson J.N. J. Biol. Chem. 1994; 269: 21303-21314Abstract Full Text PDF PubMed Google Scholar). However, in vitro studies of interactions between histones and satellite DNAs are few. The only examples of in vitroreconstitution aimed at the analysis of nucleosome positioning on satellite DNAs are studies of histone octamer assembly on 200–250-bp-long fragments by dialysis (26Linxweiler W. Hörz W. Cell. 1985; 42: 281-290Abstract Full Text PDF PubMed Scopus (66) Google Scholar, 27Neubauer B. Linxweiler W. Hörz W. J. Mol. Biol. 1986; 190: 639-645Crossref PubMed Scopus (36) Google Scholar). In order to determine the structural properties of polynucleosomal complexes on multimeric AluI-113 fragments, we developed and characterized a cell-free assembly system from Artemia at the nauplius embryo stage. We have used this to analyze: (i) the organization of bent AluI-113 DNA into nucleosomes; (ii) the effects of interactions between consecutive physiologically spacedAluI-113 nucleosomes; and (iii) how AluI-113 sequences could affect the chromatin structure of non-satellite flanking regions. We are grateful to Ida Ruberti for helpful suggestions in setting up the Artemia chromatin assembly system; G. Camilloni and E. Di Mauro for the protocols to map translational nucleosome positioning; and A. P. MacCabe and R. Mantovani for critical reading of the manuscript." @default.
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• W2023292879 date "1998-07-01" @default.
• W2023292879 modified "2023-10-16" @default.
• W2023292879 title "In Vitro Reconstitution of Artemia Satellite Chromatin" @default.
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• W2023292879 doi "https://doi.org/10.1074/jbc.273.29.18028" @default.
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