Role of DNA sequence based structural features of promoters in transcription initiation and gene expression

•We briefly review the status of sequence based promoter methods.•The role of non-B-DNA motifs in promoters and their effect on transcription is discussed.•The DNA sequence dependent structural features that are commonly observed in promoters are reviewed.•The role of the characteristic structural features on gene expression and its variability is discussed. Schematic illustrations showing (a) canonical B-DNA along with structural elements representing (b) meltable, low stability regions (c) nucleosome depleted/free region (NDR/NFR) and (d) curved DNA, that are associated with promoter sequences located upstream of transcription start sites (indicated by brown arrows). Regulatory information for transcription initiation is present in a stretch of genomic DNA, called the promoter region that is located upstream of the transcription start site (TSS) of the gene. The promoter region interacts with different transcription factors and RNA polymerase to initiate transcription and contains short stretches of transcription factor binding sites (TFBSs), as well as structurally unique elements. Recent experimental and computational analyses of promoter sequences show that they often have non-B-DNA structural motifs, as well as some conserved structural properties, such as stability, bendability, nucleosome positioning preference and curvature, across a class of organisms. Here, we briefly describe these structural features, the differences observed in various organisms and their possible role in regulation of gene expression.