Computational analysis of base composition pattern and promoter elements in the putative promoter regions in relation to expression profiles of 682 human genes on chromosome 22

The base composition pattern (BCP) in the putative promoter region (PPRs) up to 5 Kb lengths of 682 human genes on Chromosome 22 (Chr22) was examined. Two-dimensional (2D) and three-dimensional (3D) functions were designed to delineate the DNA base composition, with four major patterns identified. It is found that 17.6% genes include TATA box, 28.0% GC box, 18.9% CAAT box and 38.4% CpG islands, and approximately 10% genes have one of four putative initiator (Inr) motifs. The occurrence of the promoter elements is tightly associated with the base composition features in the promoter regions, and the associations of the base composition features with occurrence of the promoter elements in the promoter regions mediate tissue-wide expression of the genes in human. The occurrence of two or more promoter elements in the promoter regions is required for the medium- and wide-range expression profiles of the human genes on Chr22. Thus, the reported data shed light on the characteristics of the PPRs of the human genes on Chr22, which may improve our understanding of regulatory roles of the PPRs with occurrence of the promoter elements in gene expression.

Atomic composition profile change of SiGe islands during Si capping

The 6% Ge isocomposition profile change of individual SiGe islands during Si capping at 640 degrees C is investigated by atomic force microscopy combined with a selective etching procedure. The island shape transforms from a dome to a {103}-faceted pyramid at a Si capping thickness of 0.32 nm, followed by the decreasing of pyramid facet inclination with increasing Si capping layer thickness. The 6% Ge isocomposition profiles show that the island with more highly Si enriched at its one base corner before Si capping becomes to be more highly Si intermixed along pyramid base diagonals during Si capping. This Si enrichment evolution inside an island during Si capping can be attributed to the exchange of capped Si atoms that aggregated to the island by surface diffusion with Ge atoms from inside the island by both atomic surface segregation and interdiffusion rather than to the atomic interdiffusion at the interface between the island and the Si substrate. In addition, the observed Si enrichment along the island base diagonals is attempted to be explained on the basis of the elastic constant anisotropy of the Si and Ge materials in (001) plane. (c) 2006 American Institute of Physics.