Zoya Avramova

Nested retrotransposons in the intergenic regions of the maize genome

The relative organization of genes and repetitive DNAs in complex eukaryotic genomes is not well understood. Diagnostic sequencing indicated that a 280-kilobase region containing the maize Adh1-F and u22 genes is composed primarily of retrotransposons inserted within each other. Ten retroelement families were discovered, with reiteration frequencies ranging from 10 to 30,000 copies per haploid genome. These retrotransposons accounted for more than 60 percent of the Adh1-F region and at least 50 percent of the nuclear DNA of maize. These elements were largely intact and are dispersed throughout the gene-containing regions of the maize genome.

MATRIX ATTACHMENT REGIONS AND TRANSCRIBED SEQUENCES WITHIN A LONG CHROMOSOMAL CONTINUUM CONTAINING MAIZE ADH1

We provide evidence for the location of matrix attachment sites along a contiguous region of 280 kb on maize chromosome 1. We define nine potential loops that vary in length from 6 kb to > 75 kb. The distribution of the different classes of DNA within this continuum with respect to the predicted structural loops reveals an interesting correlation: the long stretches of mixed classes of highly repetitive DNAs are often segregated into topologically sequestered units, whereas low-copy-number DNAs (including the alcohol dehydrogenase1 [adh1] gene) are positioned in separate loops. Contrary to expectations, several classes of highly repeated elements with representatives in this region were found to be transcribed, and some of these exhibited tissue-specific patterns of expression.

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.

Two Arabidopsis homologs of the animal trithorax genes: a new structural domain is a signature feature of the trithorax gene family

Two Arabidopsis genes have been characterized as first examples of plant genes homologous to the animal trithorax genes. The Arabidopsis genes are highly similar but display different tissue and development expression patterns. One of them was ubiquitously expressed, with highest levels registered in young seedlings. The other gene was less active in all tested tissues, was not expressed in mature leaves but was highly expressed in roots. A new structural motif common to all TRX-related proteins has been identified. This new architectural element was found only in genes of multicellular species and is present in all genes belonging to the trithorax family. Along with the SET domain and the PHD fingers, this new element is a signature feature for the trithorax gene family.

Isolation of matrices from maize leaf nuclei: identification of a matrix-binding site adjacent to theAdh1 gene

Nuclear matrices were isolated from maize leaves by the two conventional methods usually employed for the preparation of the corresponding structures of animal origin. It is demonstrated that functionally competent matrices, recognizing and specifically binding the MAR-containing DNA of the mousek-immunoglobulin gene may be prepared by both 2 M NaCl and LIS extractions of maize nuclei.A DNA region with a high affinity for the nuclear matrix was identified at the 5′ end of the maizeAdh1-S gene, distal to the promoter region. The presence of sites of reported altered chromatin structure in this particular region is discussed. While the proximity and the cohabitation of MARs with different regulatory elements is a common feature of matrix association regions in animal systems, this is the first plant MAR identified in a region of known significance for gene regulation.

Commonalities and Contrasts in the Organization of the Maize and Sorghum Nuclear Genomes

Analysis of plant genome organization has long been the realm of plant geneticists and cytogeneticists. The multipartite (several chromosome) nature of the nuclear genome, heritable and line-specific variations in the cytology or number of chromosomes (Blakeslee, 1922; Randolph and McClintock, 1926; Stadler, 1928; Kostoff, 1929; Philip and Huskins, 1931; McClintock, 1932; Creighton, 1934; Sears, 1939; Swanson, 1940), the linear order of genes whose linkage could be determined by analysis of crossover exchanges in meiosis, the physical exchange of chromosomal segments associated with recombination (Creighton and McClintock, 1931), the properties of telomeres (McClintock, 1941), the behavior of primary and secondary constrictions as centromeres in mitosis and meiosis (Prakken and Muntzing, 1942; Rhoades and Vilkomerson, 1942), the contribution of a particular chromosomal segment (the nucleolar organizer, NOR) to formation of the nucleolus (McClintock, 1934), the existence and preferential transmission of supernumerary (B) chromosomes (Longley, 1927; Darlington and Thomas, 1941; Roman, 1947), the biology of one class of highly repetitive DNA (the knob satellite) (Rhoades and Dempsey, 1966; Peacock et al., 1981), and the properties of a key class of middle repetitive DNAs (transposable elements) (McClintock, 1950) were all identified in plants concurrent with, or prior to, their discovery in other species. Much of this initial work was performed with maize, partly due to the early and excellent characterization of its karyotypic properties (Longley, 1924).