Chromatin techniques for plant cells.

A large number of recent studies have demonstrated that many important aspects of plant development are regulated by heritable changes in gene expression that do not involve changes in DNA sequence. Rather, these regulatory mechanisms involve modifications of chromatin structure that affect the accessibility of target genes to regulatory factors that can control their expression. The central component of chromatin is the nucleosome, containing the highly conserved histone proteins that are known to be subject to a wide range of post-translational modifications, which act as recognition codes for the binding of chromatin-associated factors. In addition to these histone modifications, DNA methylation can also have a dramatic influence on gene expression. To accommodate the burgeoning interest of the plant science community in the epigenetic control of plant development, a series of methods used routinely in our laboratories have been compiled that can facilitate the characterization of putative chromatin-binding factors at the biochemical, molecular and cellular levels.

[1]  G. H. Jones,et al.  A light microscopic atlas of meiosis inArabidopsis thaliana , 1996, Chromosome Research.

[2]  C. Pedersen,et al.  Chromosomal locations of four minor rDNA loci and a marker microsatellite sequence in barley , 2005, Chromosome Research.

[3]  Y. Chua,et al.  Microarray analysis of chromatin-immunoprecipitated DNA identifies specific regions of tobacco genes associated with acetylated histones. , 2004, The Plant journal : for cell and molecular biology.

[4]  R. Amasino,et al.  Vernalization and epigenetics: how plants remember winter. , 2004, Current opinion in plant biology.

[5]  M. Murata,et al.  Floral chromosomes of Arabidopsis thaliana for detecting low-copy DNA sequences by fluorescence in situ hybridization , 1995, Chromosoma.

[6]  M. Montagu,et al.  Distribution of the rDNA and three classes of highly repetitive DNA in the chromatin of interphase nuclei of Arabidopsis thaliana , 1991, Chromosoma.

[7]  C. P. Moehs,et al.  Chromosomal proteins of Arabidopsis thaliana , 1988, Plant Molecular Biology.

[8]  D. Zink,et al.  Comparative analysis of the functional genome architecture of animal andplant cell nuclei , 2004, Chromosome Research.

[9]  I. Schubert,et al.  Recent progress in chromosome painting of Arabidopsis and related species , 2004, Chromosome Research.

[10]  R. Amasino,et al.  Regulation of Flowering Time by Histone Acetylation in Arabidopsis , 2003, Science.

[11]  Wolfgang Fischle,et al.  Binary switches and modification cassettes in histone biology and beyond , 2003, Nature.

[12]  A. Probst,et al.  Erasure of CpG methylation in Arabidopsis alters patterns of histone H3 methylation in heterochromatin , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[13]  D. Wagner Chromatin regulation of plant development. , 2003, Current opinion in plant biology.

[14]  B. Turner,et al.  Histone modifications in Arabidopsis- high methylation of H3 lysine 9 is dispensable for constitutive heterochromatin. , 2003, The Plant journal : for cell and molecular biology.

[15]  A. Probst,et al.  Two means of transcriptional reactivation within heterochromatin. , 2003, The Plant journal : for cell and molecular biology.

[16]  P. Fransz,et al.  Chromatin dynamics in plants. , 2002, Current opinion in plant biology.

[17]  S. Jacobsen,et al.  DNA methylation controls histone H3 lysine 9 methylation and heterochromatin assembly in Arabidopsis , 2002, The EMBO journal.

[18]  E. Schäfer,et al.  Phytochrome‐mediated photoperception and signal transduction in higher plants , 2002 .

[19]  Ingo Schubert,et al.  Interphase chromosomes in Arabidopsis are organized as well defined chromocenters from which euchromatin loops emanate , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[20]  G. Benvenuto,et al.  The Photomorphogenesis Regulator DET1 Binds the Amino-Terminal Tail of Histone H2B in a Nucleosome Context , 2002, Current Biology.

[21]  Xiaofeng Cao,et al.  Interplay between Two Epigenetic Marks DNA Methylation and Histone H3 Lysine 9 Methylation , 2002, Current Biology.

[22]  R. Martienssen,et al.  Dependence of Heterochromatic Histone H3 Methylation Patterns on the Arabidopsis Gene DDM1 , 2002, Science.

[23]  Kevin Struhl,et al.  Genome-wide location and regulated recruitment of the RSC nucleosome-remodeling complex. , 2002, Genes & development.

[24]  T. Jenuwein,et al.  Higher-order structure in pericentric heterochromatin involves a distinct pattern of histone modification and an RNA component , 2002, Nature Genetics.

[25]  S. Tweedie,et al.  Remembrance of things past: chromatin remodeling in plant development. , 2002, Annual review of cell and developmental biology.

[26]  H. Ali,et al.  Chromosome painting in Arabidopsis thaliana. , 2002, The Plant journal : for cell and molecular biology.

[27]  C. Allis,et al.  Translating the Histone Code , 2001, Science.

[28]  R. Martienssen,et al.  DNA methylation and epigenetic inheritance in plants and filamentous fungi. , 2001, Science.

[29]  T. Fischer,et al.  The centromere1 (CEN1) region of Arabidopsis thaliana: architecture and functional impact of chromatin. , 2001, The Plant journal : for cell and molecular biology.

[30]  B. Nal,et al.  Location analysis of DNA-bound proteins at the whole-genome level: untangling transcriptional regulatory networks. , 2001, BioEssays : news and reviews in molecular, cellular and developmental biology.

[31]  C. Allis,et al.  Histone methylation versus histone acetylation: new insights into epigenetic regulation. , 2001, Current opinion in cell biology.

[32]  A. Meister,et al.  Chromatin organization and its relation to replication and histone acetylation during the cell cycle in barley , 2001, Chromosoma.

[33]  Y. Chua,et al.  Targeted Histone Acetylation and Altered Nuclease Accessibility over Short Regions of the Pea Plastocyanin Gene , 2001, Plant Cell.

[34]  D. Botstein,et al.  Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF , 2001, Nature.

[35]  G. Schnitzler Isolation of Histones and Nucleosome Cores from Mammalian Cells , 2000, Current protocols in molecular biology.

[36]  C. Dean,et al.  Integrated Cytogenetic Map of Chromosome Arm 4S of A. thaliana Structural Organization of Heterochromatic Knob and Centromere Region , 2000, Cell.

[37]  C. Allis,et al.  The language of covalent histone modifications , 2000, Nature.

[38]  H. Tsukaya,et al.  Cell cycling and cell enlargement in developing leaves of Arabidopsis. , 1999, Developmental biology.

[39]  Robert Ascenzi,et al.  Subnuclear distribution of the entire complement of linker histone variants in Arabidopsis thaliana , 1999, Chromosoma.

[40]  A. Bird,et al.  DNA methylation and chromatin modification. , 1999, Current opinion in genetics & development.

[41]  M. Grunstein,et al.  Mapping DNA interaction sites of chromosomal proteins using immunoprecipitation and polymerase chain reaction. , 1999, Methods in enzymology.

[42]  P. Shaw,et al.  Transcription Sites Are Not Correlated with Chromosome Territories in Wheat Nuclei , 1998, The Journal of cell biology.

[43]  S. Armstrong,et al.  Cytogenetics for the model system Arabidopsis thaliana. , 1998, The Plant journal : for cell and molecular biology.

[44]  T. Richmond,et al.  Crystal structure of the nucleosome core particle at 2.8 Å resolution , 1997, Nature.

[45]  R. Paro,et al.  Analysis of chromatin structure by in vivo formaldehyde cross-linking. , 1997, Methods.

[46]  N. Lapitan,et al.  An optimized fluorescence in situ hybridization procedure for detecting rye chromosomes in wheat. , 1993, Genome.

[47]  J. Davie,et al.  Western blotting and immunochemical detection of histones electrophoretically resolved on acid-urea-triton- and sodium dodecyl sulfate-polyacrylamide gels. , 1992, Analytical biochemistry.

[48]  N. Chua,et al.  Analysis of protein/DNA interactions. , 1992 .

[49]  P. Dupree,et al.  A scaffold-associated DNA region is located downstream of the pea plastocyanin gene. , 1991, The Plant cell.

[50]  J. S. Heslop-Harrison,et al.  Localization of tandemly repeated DMA sequences inArabidopsis thaliana , 1991 .

[51]  R. Harrington,et al.  Histone variants and acetylated species from the alfalfa plant Medicago sativa. , 1987, Archives of biochemistry and biophysics.

[52]  T. Boulikas Electrophoretic separation of histones and high-mobility-group proteins on acid-urea-Triton gels. , 1985, Analytical biochemistry.

[53]  S. Spiker Histone variants in plants. Evidence for primary structure variants differing in molecular weight. , 1982, The Journal of biological chemistry.

[54]  A. Zweidler Resolution of histones by polyacrylamide gel electrophoresis in presence of nonionic detergents. , 1978, Methods in cell biology.

[55]  B. Wakim,et al.  Identification and fractionation of plant histones. , 1976, Archives of biochemistry and biophysics.