Abstract
It is increasingly apparent that gene function is influenced by a variety of constituents, only a few of which are effectively mimicked by in vitro analyses with linear, cloned pieces of genes. A diverse compliment of proteinacious interactions affect the structure and subsequent function of genes in the cell. The association between this compliment of proteins and the eukaryotic genome is referred to as chromatin.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsPreview
Unable to display preview. Download preview PDF.
References
Bers EP, Singh NP, Pardonen VA, Lutova LA, Zalensky AO (1992) Nucleosomal structure and histone H1 subfraction composition of pea (Pisum staivum) root nodules, radicles and callus chromatin. Plant Mol Biol 20: 1089–1096.
Church GM, Gilbert W (1984) Genomic sequencing. Proc Natl Acad Sci USA 81: 1991–1995.
Conconi A, Ryan CA (1993) DNase I and micrococcal analyses of the tomato proteinase inhibitor I gene in chromatin. J Biol Chem 268: 430–431.
Dellaporta SL, Wood J, Hicks JB (1983) A plant DNA minipreparation: Version II. Plant Mol Biol Rep 1: 19–23.
Elgin SCR (1981) Anatomy of hypersensitive sites. Cell 27: 413–415.
Ephrussi A, Chwch G, Tonegawa S, Gilbert W (1985) B lineage-specific interactions of an immunoglobin enhancer with cellular factors in vivo. Science 227: 134–140.
Ferl RJ (1985) Modulation of chromatin structure in the regulation of the maize Adhl gene. Mol Gen Genet 200: 207–210.
Ferl RJ, Laughner B (1989) In vivo detection of regulatory factor binding sites of Arabidopsis thaliana Adh. Plant Mol Biol 12: 357–366.
Ferl RJ, Nick HN (1987) In vivo detection of regulatory factor binding sites in the 5′ flanking region of maize Adh1. J Biol Chem 262: 7947–7950.
Freid M, Crothers DM (1981) Equilibria and kinetics of lac repressor operator interaction by polyacrylamide gel electrophoresis. Nucl Acids Res 9: 6505–6526.
Garrity PA, Wold B (1992) Effects of different polymerases in ligation-mediated PCR: Enhanced genomic sequencing and in vivo footprinting. Proc Natl Acad Sci USA 89: 1021–1025.
Gorz A, Schafer W, Hirasawa E, Kahl G (1988) Constitutive and light-induced DNAse I hypersensitive sites in the rbcS genes of pea (Pisum sativum). Plant Mol Biol 11: 561–573.
Green P, Kay S, Chua N-H (1987) Sequence specific interactions of a pea nuclear factor with light-responsive elements upstream of the rbcS-3A gene. EMBO J 6: 2543–2549.
Hammond-Kosack MCU, Holdsworth MJ, Bevan MW (1993) In vivo footprinting of a low molecular weight glutenin gene (LMWG-1D1) in wheat endosperm. EMBO J 12: 545–554.
Horastra IK, Yang TP (1993) In vivo footprinting and genomic sequencing by ligation mediated PCR. Anal Biochem 213 (in press).
Jensen EO, Marcker KA, Schell J, Bruijn FJ (1988) Interaction of a nodule specific, transacting factor with distinct DNA elements in the soybean leghaemoglobin 1bc3 5′ upstream region. EMBO J 7: 1265–1271.
Jofuku KD, Okamuro JK, Goldberg RB (1987) Interaction of an embryo DNA binding protein with a soybean lectin gene upstream region. Nature 328: 734–737.
Kaufman LS, Watson JC, Thompson WF (1987) Light-regulated changes in DNase I hypersensitive sites in the rRNA genes of Pisum sativum. Proc Natl Acad Sci USA 84: 1550–1554.
Lohr D, Tatchell K, Van Holde KE (1977) On the occurrence of nucleosome phasing in chromatin. Cell 12: 829–836.
Luthe DS, Quatrano RS (1980) Transcription in isolated wheat nuclei; I. Isolation of nuclei and elimination of endogeneous ribonuclease activity. Plant Physiol 65: 305–308.
Maier U-G, Brown JWS, Toloczyki C, Feix G (1987) Binding of a nuclear factor to a consensus sequence in the 5′ flanking region of zein genes from maize. EMBO J 6: 17–22.
Maxam AM, Gilbert W (1980) Sequencing end-labelled DNA with base-specific chemical cleavages. Meth Enzymol 65: 499–560.
McGhee JD, Felsenfeld G (1983) Another potential artifact in the study of nucleosome phasing by chromatin digestion with micrococcal nuclease. Cell 32: 1205–1215.
McGhee JD, Nikol JM, Felsenfeld G, Rau DC (1983) High order of chromatin orientation of nucleosomes within the 30 nm chromatin selenoid is independent of species and spacer length. Cell 33: 831–841.
Melton DA, King PA, Rebagliati MR, Maniatis T, Green MR (1984) Efficient in vitro synthesis of biologically active RNA and RNA hybridization probes from plasmids containing a bacteriophage SP6 promoter. Nucl Acids Res 12: 7035–7056.
Mikami K, Tabata T, Kawata T, Nakayama T, Iwabuchi M (1987) Nuclear protein(s) binding to the conserved DNA hexameric sequence postulated to regulate transcription of wheat histone genes. FEBS Lett 223: 273–278.
Mueller PR, Wold B (1989) In vivo footprinting of a muscle specific enhancer by ligation mediated PCR. Science 246: 780–786.
Murray MG, Kennard WC (1984) Altered chromatin conformation in plant gene phaseolin. Biochem 23: 4225–4232.
Nick H, Bowen B, Ferl RJ, Gilbert W (1986) Detection of cytosine methylation in the maize alcohol dehydrogenase gene by genomic sequencing. Nature 319: 243–246.
Nick H, Gilbert W (1985) Detection in vivo of protein-DNA interactions within the lac operon of Escherichia coli. Nature 313: 795–798.
Paul A-L, Vasil V, Vasil IU, Ferl RJ (1987) Constitutive and anaerobically induced DNase I hypersensitive sites in the 5′ region of the maize Adh1 gene. Proc Natl Acad Sci USA 84: 799–803.
Paul A-L, Ferl RJ (1991) In vivo footprinting reveals unique cis elements and different modes of hypoxic induction in maize Adhl and Adh2. Plant Cell 3: 159–168
Paul A-L, Ferl RJ (1993) Osmium tetroxide footprinting of a scaffold attachment region in the maize Adhl promoter. Plant Mol Biol Plant Mol Biol 22: 1145–1151.
Riven CJ, Zimmer EA, Walbot V (1982) Isolation of DNA and DNA recombinants from maize. In: Sheridan WF (ed) Maize for Biological Research, pp. 161–165. Grand Forks, ND: University Press, University of North Dakota.
Saluz HP, Feavers IM, Jiricny J, Jost JP (1988) Genomic sequencing and in vivo footprinting of an expression-specific DNase I-hypersensitive site of avian vitellogenin II promoter reveal a demethylation of a mCpG and a change in specific interactions of proteins with DNA. Proc Natl Acad Sci USA 85: 6697–6700.
Saluz HP, Jiricny J, Jost JP (1986) Genomic sequencing reveals a positive correlation between the kinetics of strand-specific DNA demethylation of the overlapping estradiol/ glucocorticoid-receptor binding sites and the rate of avian vitellogenin mRNA synthesis. Proc Natl Acad Sci USA 83: 7167–7171.
Schulze-Lefert P, Dangl JL, Becker-André M, Hahlbrock K, Schulz W (1989) Inducible in vivo DNA footprints define sequences necessary for UV light activation of the parsley chalcone synthase gene. EMBO J 8: 651–656.
Shure M, Wessler S, Fedoroff N (1983) Molecular identification and isolation of the waxy locus in maize. Cell 35: 225–233.
Sorensen MB (1992) Methylation of B-hordein genes in the barley endosperm is inversely correlated with gene activity and affected by the regulatory gene Lys3. Proc Natl Acad Sci USA 89: 4119–4123.
Southern EM (1975) Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol 98: 503–507.
Spiker S, Murray MG, Thompson WF (1983) DNase I sensitivity of transcriptionally active genes in intact nuclei and isolated chromatin of plants. Proc Natl Acad Sci USA 80: 815–819.80
Thomas GH, Elgin SCR (1988) Protein/DNA architecture of the DNase I hypersensitive region of the Drosophila hsp26 promoter. EMBO J 7: 2191–2201.
Thomas GH, Siegfried E, Elgin SCR (1985) DNase I hypersensitive sites: A structural feature of chromatin associated with gene expression. In: Reeck G, Goodwin G, Puig-domench P (ed) Chromosomal Proteins and Gene Expression, pp. 77–101. New York, NY: Plenum Press.
Ull MA, Franco L (1986) The nucleosomal repeat length of pea (Pisum sativum) chromatin changes during germination. Plant Mol Biol 7: 25–31.
Vayda ME, Freeling M (1986) Insertion of the Mu 1 transposable element into the first intron of maize Adh 1 interferes with transcript elongation but does not disrupt chromatin structure. Plant Mol Biol 6: 441–454.
Watson AJ, Hankinson O (1992) Dioxin-and Ah receptor-dependent protein binding to xenobiotic responsive elements and G-rich DNA studied by in vivo footprinting. J Biol Chem 267: 6874–6878.
Weintraub H, Groudine H (1976) Chromosome subunits in active genes have an altered conformation. Science 193: 848–856.
Weisbrod S (1982) Active chromatin. Nature 297: 289–295.
Wu C (1980) The 5′ ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase I. Nature 286: 854–869.
Wu C (1984) Two protein-binding sites in chromatin implicated in the activation of heat chock genes. Nature 309: 229–233.
Wurtzel ET, Burr FA, Burr B (1987) DNase I hypersensitivity and expression of the Shrynken-1 gene of maize. Plant Mol Biol 8: 251–264.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 1994 Springer Science+Business Media Dordrecht
About this chapter
Cite this chapter
Paul, AL., Ferl, R.J. (1994). Analyses of plant chromatin and in vivo protein-DNA interactions. In: Gelvin, S.B., Schilperoort, R.A. (eds) Plant Molecular Biology Manual. Springer, Dordrecht. https://doi.org/10.1007/978-94-011-0511-8_30
Download citation
DOI: https://doi.org/10.1007/978-94-011-0511-8_30
Publisher Name: Springer, Dordrecht
Print ISBN: 978-94-011-7654-5
Online ISBN: 978-94-011-0511-8
eBook Packages: Springer Book Archive