Structural Domains and Matrix Attachment Regions along Colinear Chromosomal Segments of Maize and Sorghum

Although a gene’s location can greatly influence its expression, genome sequencing has shown that orthologous genes may exist in very different environments in the genomes of closely related species. Four genes in the maize alcohol dehydrogenase (adh1) region represent solitary genes dispersed among large repetitive blocks, whereas the orthologous genes in sorghum are located in a different setting surrounded by low-copy-number DNAs. A specific class of DNA sequences, matrix attachment regions (MARs), was found to be in comparable positions in the two species, often flanking individual genes. If these MARs define structural domains, then the orthologous genes in maize and sorghum should experience similar chromatin environments. In addition, MARs were divided into two groups, based on the competitive affinity of their association with the matrix. The “durable” MARs retained matrix associations at the highest concentrations of competitor DNA. Most of the durable MARs mapped outside genes, defining the borders of putative chromatin loops. The “unstable” MARs lost their association with the matrix under similar competitor conditions and mapped mainly within introns. These results suggest that MARs possess both domain-defining and regulatory roles. Miniature inverted repeat transposable elements (MITEs) often were found on the same fragments as the MARs. Our studies showed that many MITEs can bind to isolated nuclear matrices, suggesting that MITEs may function as MARs in vivo.

[1]  J. Bennetzen,et al.  Colinearity and its exceptions in orthologous adh regions of maize and sorghum. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[2]  Paul Christou,et al.  Matrix attachment regions increase transgene expression levels and stability in transgenic rice plants and their progeny , 1999 .

[3]  B. Charrier,et al.  Bigfoot. a new family of MITE elements characterized from the Medicago genus. , 1999, The Plant journal : for cell and molecular biology.

[4]  W. F. Thompson,et al.  A tobacco matrix attachment region reduces the loss of transgene expression in the progeny of transgenic tobacco plants , 1999 .

[5]  Z. Avramova,et al.  Are scs and scs′ ‘neutral’ chromatin domain boundaries of the 87A7 locus in vivo? , 1999 .

[6]  S. Gasser,et al.  Nuclear compartments and gene regulation. , 1999, Current opinion in genetics & development.

[7]  R. Ferl,et al.  Higher Order Chromatin Structures in Maize and Arabidopsis , 1998, Plant Cell.

[8]  S. Henikoff,et al.  Trans-Sensing Effects: The Ups and Downs of Being Together , 1998, Cell.

[9]  A. Lamond,et al.  Structure and function in the nucleus. , 1998, Science.

[10]  M. Matzke,et al.  Position effects and epigenetic silencing of plant transgenes. , 1998, Current opinion in plant biology.

[11]  L. Comai,et al.  Nuclear matrix attachment regions and plant gene expression , 1998 .

[12]  J. Bennetzen,et al.  Matrix attachment regions and structural colinearity in the genomes of two grass species. , 1998, Nucleic acids research.

[13]  J. Bennetzen,et al.  Sequence organization and conservation in sh2/a1-homologous regions of sorghum and rice. , 1998, Genetics.

[14]  C. Benham,et al.  Stress-induced duplex DNA destabilization in scaffold/matrix attachment regions. , 1997, Journal of molecular biology.

[15]  P. Weisbeek,et al.  Analysis of the chromatin domain organisation around the plastocyanin gene reveals an MAR-specific sequence element in Arabidopsis thaliana. , 1997, Nucleic acids research.

[16]  T. Eickbush.  Telomerase and Retrotransposons: Which Came First? , 1997, Science.

[17]  M. Matzke,et al.  Molecular and cytogenetic analyses of stably and unstably expressed transgene loci in tobacco. , 1997, The Plant cell.

[18]  P. Geyer,et al.  The role of insulator elements in defining domains of gene expression. , 1997, Current opinion in genetics & development.

[19]  J. Bennetzen,et al.  Gene identification in a complex chromosomal continuum by local genomic cross-referencing. , 1996, The Plant journal : for cell and molecular biology.

[20]  J. Bennetzen,et al.  Nested Retrotransposons in the Intergenic Regions of the Maize Genome , 1996, Science.

[21]  Howard Cedar,et al.  A role for nuclear NF–κB in B–cell–specific demethylation of the Igκ locus , 1996, Nature Genetics.

[22]  T. Schlake,et al.  Scaffold/matrix-attached regions: topological switches with multiple regulatory functions. , 1996, Critical reviews in eukaryotic gene expression.

[23]  S. Wessler,et al.  LTR-retrotransposons and MITEs: important players in the evolution of plant genomes. , 1995, Current opinion in genetics & development.

[24]  J. Bennetzen,et al.  Matrix attachment regions and transcribed sequences within a long chromosomal continuum containing maize Adh1. , 1995, The Plant cell.

[25]  G. Schroth,et al.  Occurrence of potential cruciform and H-DNA forming sequences in genomic DNA. , 1995, Nucleic acids research.

[26]  W. J. Stiekema,et al.  The MAR-Mediated Reduction in Position Effect Can Be Uncoupled from Copy Number-Dependent Expression in Transgenic Plants. , 1995, The Plant cell.

[27]  A. Paterson,et al.  Construction and characterization of a bacterial artificial chromosome library of Sorghum bicolor. , 1994, Nucleic acids research.

[28]  T. Hall,et al.  The β‐phaseolin gene is flanked by matrix attachment regions , 1994 .

[29]  P. Schnable,et al.  The relationship between genetic and physical distances in the cloned a1-sh2 interval of the Zea mays L. genome. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[30]  S. Wessler,et al.  Stowaway: a new family of inverted repeat elements associated with the genes of both monocotyledonous and dicotyledonous plants. , 1994, The Plant cell.

[31]  R. Flavell.  Inactivation of gene expression in plants as a consequence of specific sequence duplication. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[32]  C. Milstein,et al.  Elements regulating somatic hypermutation of an immunoglobulin κ gene: Critical role for the intron enhancer/matrix attachment region , 1994, Cell.

[33]  M. S. Patil,et al.  Characterisation of two intronic nuclear-matrix-attachment regions in the human DNA topoisomerase I gene. , 1994, European journal of biochemistry.

[34]  J. Bennetzen,et al.  DNA class organization on maize Adh1 yeast artificial chromosomes. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[35]  T. Boulikas,et al.  Multitude of inverted repeats characterizes a class of anchorage sites of chromatin loops to the nuclear matrix , 1993, Journal of cellular biochemistry.

[36]  W F Thompson,et al.  Scaffold attachment regions increase reporter gene expression in stably transformed plant cells. , 1993, The Plant cell.

[37]  S. Wessler,et al.  Tourist: a large family of small inverted repeat elements frequently associated with maize genes. , 1992, The Plant cell.

[38]  M. Van Montagu,et al.  Characterization of a plant scaffold attachment region in a DNA fragment that normalizes transgene expression in tobacco. , 1992, The Plant cell.

[39]  Z. Avramova,et al.  Matrix attachment sites in the murine α-globin gene , 1992 .

[40]  W F Thompson,et al.  Nuclear scaffolds and scaffold-attachment regions in higher plants. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[41]  J. Bode,et al.  Hierarchical binding of DNA fragments derived from scaffold-attached regions: correlation of properties in vitro and function in vivo. , 1990, Biochemistry.

[42]  U. K. Laemmli,et al.  Interaction of DNA with nuclear scaffolds in vitro. , 1988, Journal of molecular biology.

[43]  P. Cockerill,et al.  Chromosomal loop anchorage sites appear to be evolutionarily conserved , 1986, FEBS letters.

[44]  P. Cockerill,et al.  Chromosomal loop anchorage of the kappa immunoglobulin gene occurs next to the enhancer in a region containing topoisomerase II sites , 1986, Cell.

[45]  D. Laurie,et al.  Nuclear DNA content in the genera Zea and Sorghum. Intergeneric, interspecific and intraspecific variation , 1985, Heredity.