DNA-protein interactions and bacterial chromosome architecture

Bacteria, like eukaryotic organisms, must compact the DNA molecule comprising their genome and form a functional chromosome. Yet, bacteria do it differently. A number of factors contribute to genome compaction and organization in bacteria, including entropic effects, supercoiling and DNA-protein interactions. A gamut of new experimental techniques have allowed new advances in the investigation of these factors, and spurred much interest in the dynamic response of the chromosome to environmental cues, segregation, and architecture, during both exponential and stationary phases. We review these recent developments with emphasis on the multifaceted roles that DNA-protein interactions play.     

Recurrent HSR in the centromeric region of chromosome 8 in breast cancer

In a sample of 44 human breast cancers, the presence of HSRs was detected in 15 cases (36%). The occurrence of HSRs seems correlated poorly with tumor progression, but the number of HSRs per cell certainly does. Chromosome 8 was the most frequently involved, and the HSRs were always located near its centromere, suggesting that an amplification of gene(s) located in this region has occurred. Among these, LHRH is a candidate, but further studies are needed to confirm or reject this hypothesis.     

Unusual chromosome 9 polymorphism and reproductive failure

Partial inversion of an unusually large 9qh variant is reported in a 28-year-old normal female with reproductive failure (karyotype: 46,XX,9[qh +,inv(p11;q12)]mat).     

Cohesin in determining chromosome architecture

Cells use ring-like structured protein complexes for various tasks in DNA dynamics. The tripartite cohesin ring is particularly suited to determine chromosome architecture, for it is large and dynamic, may acquire different forms, and is involved in several distinct nuclear processes. This review focuses on cohesin's role in structuring chromosomes during mitotic and meiotic cell divisions and during interphase.     

Meiotic drive in female mice heterozygous for the HSR inserts on chromosome 1

Chromosome 1 with one or two long insertions has been previously found in natural mouse populations. The inheritance of chromosome 1 with two insertions from the Yakutsk population is analysed in this paper. It was demonstrated that heterozygous females transmit this chromosome to 80-85% of offspring. The observations made at M II, in conjunction with the recombination data, allowed us to conclude that preferential passage of the chromosome 1 with insertions to the oocyte and egg, rather than to the first and second polar bodies at meiosis, is the causative factor of the distorted segregation. A meiotic drive of such potency has not been previously reported for female mammals. The possible mechanism of the drive is discussed.     

Genomics tools for unraveling chromosome architecture

The spatial organization of chromosomes inside the cell nucleus is still poorly understood. This organization is guided by intra- and interchromosomal contacts and by interactions of specific chromosomal loci with relatively fixed nuclear 'landmarks' such as the nuclear envelope and the nucleolus. Researchers have begun to use new molecular genome-wide mapping techniques to uncover both types of molecular interactions, providing insights into the fundamental principles of interphase chromosome folding.     

Rye B chromosome behaviour at first and second pollen mitosis and its relationship with anther maturity

Summary Rye plants carrying B chromosomes with different nuclear and cytoplasmic constitutions have been analyzed at first pollen mitosis. No differences of B chromosome behaviour have been detected. It has been concluded that non-disjunction and preferential distribution are processes controlled by Bs themselves.At second pollen anaphase, B laggards have been observed. Both non-disjunction and B laggards occurred with higher frequency in younger anthers.     

Phragmites australis at an extreme altitude: Rhizome architecture and its modelling

In central EuropePhragmites australis is a lowland plant, occurring rarely up to the tree line. In the Velká Kotlina cirque (Jeseníky mountains, NE Czech Republic), where it reaches its maximum altitude at about 1350 m a.s.l., its culms are 0.5–0.7 m high and the plants flower only in some years. During the last decade no germinable seeds have been observed. The architecture ofPhragmites rhizomes from this site was studied on seven randomly selected clonal fragments. They consisted of 3 to 10 partial tussocks (clumps) and 4 to 17 green shoots. The total length of the rhizomes was 9.7 to 50 m per plant. The number of nodes per plant was 96 to 431 and the longest internodes were 83 mm long. The number of side branches was 31 to 105 per plant. The branching angle depended on the type of branched rhizome. The mean angles of horizontal rhizomes, which connect individual tussocks, were relatively wide (modus 45°, arithmetic mean 37°), whereas within a tussock much sharper angles of branching prevailed (modal value 5°, arithmetic mean 15°). The mean internode-to-internode angle on continuing rhizomes was about 8°, with a wide variation. An architectural, spatially-explicit model ofPhragmites rhizome growth has been developed, showing that thePhragmites population in the studied locality can be maintained by vegetative multiplication, and seedling recruitment is not needed for its long-term persistence.     

Unusual DNA structures at the integration site of an HIV provirus

Supercoiled pHXBc2 DNA (containing the genome of the human immunodeficiency virus type 1 and human sequences) migrated more slowly than linear DNA in native and ethidium bromide agarose gel electrophoresis at 4.5 volts/cm, suggesting the presence of unusual DNA structures. S1 nuclease analysis of pHXBc2 revealed two S1 hypersensitive sites. Site I was located within a 25 bp direct repeat in host DNA 0.6 kB upstream from the 5' LTR. Site II was mapped 0.2 kB upstream from the vif gene start site. Sequence analysis showed that Site I sequences could assume different unusual DNA structures, whereas sequences at Site II could assume either slipped or H-DNA forms. Unusual DNA structures in host DNA may be associated with active chromatin regions and may favor proviral integration.     

Unusual sequence element found at the end of an amplicon.

In a polyomavirus-transformed rat cell line, designated LPT, the polyomavirus DNA is integrated into a single chromosomal site. Treatment of LPT cells with carcinogens induces amplification of the integrated virus DNA and flanking cellular sequences. We show that the amplification is arrested within a specific cell DNA segment that maps 1.3 to 1.85 kilobases beyond one virus-cell DNA junction, defined as the left junction. We also present the sequence of an 897-base-pair fragment spanning the arrest site. This fragment contains an unusual sequence element, which consists of two contiguous components, a potential cruciform with stems of 6 base pairs and a d(G-A)27 X d(T-C)27 tract, and maps 1,497 to 1,564 nucleotides beyond the left junction. The possibility that this unusual sequence plays a role in the arrest of the amplification process is discussed.