Coexistence of different base periodicities in prokaryotic genomes as related to DNA curvature, supercoiling, and transcription

We analyzed the periodic patterns in E. coli promoters and compared the distributions of the corresponding patterns in promoters and in the complete genome to elucidate their function. Except the three-base periodicity, coincident with that in the coding regions and growing stronger in the region downstream from the transcriptions start (TS), all other salient periodicities are peaked upstream of TS. We found that helical periodicities with the lengths about B-helix pitch ~10.2-10.5 bp and A-helix pitch ~10.8-11.1 bp coexist in the genomic sequences. We mapped the distributions of stretches with A-, B-, and Z- like DNA periodicities onto E.coli genome. All three periodicities tend to concentrate within non-coding regions when their intensity becomes stronger and prevail in the promoter sequences. The comparison with available experimental data indicates that promoters with the most pronounced periodicities may be related to the supercoiling-sensitive genes.Comment: 23 pages, 6 figures, 2 table

Nucleosomes in gene regulation: theoretical approaches

This work reviews current theoretical approaches of biophysics and bioinformatics for the description of nucleosome arrangements in chromatin and transcription factor binding to nucleosomal organized DNA. The role of nucleosomes in gene regulation is discussed from molecular-mechanistic and biological point of view. In addition to classical problems of this field, actual questions of epigenetic regulation are discussed. The authors selected for discussion what seem to be the most interesting concepts and hypotheses. Mathematical approaches are described in a simplified language to attract attention to the most important directions of this field

Active faults in the Eastern hemisphere.

The Project ‘‘World Map of Major Active Faults’’ was initiated in 1989 and was approved by the International Lithosphere Commission in 1990 under the chairmanship of Vladimir G. Trifonov (Russia) as Project II-2 of the International Lithosphere Program (ILP). The Project was supported by UNESCO as a contribution of the ILP to the UN International Decade of Natural Disaster Reduction. In 1991, the Project was separated for better management into two sub-projects including correspondingly representatives from the Eastern and Western Hemispheres. Dr. M.S. Machette (USGS, Denver, USA) was approved as a co-chairman for the Western Hemisphere sub-project. Because knowledge of location, parameters and contemporary behavior of active faults is important and even necessary not only for studying recent geodynamics and rock deformation, but also for estimating various natural hazards and especially seismic ones, the ILP Project II-2 was included in 1993 in the ILP Global Seismic Hazard Assessment Program