No abstract

Background: SNPs are abundant, codominantly inherited, and sequence-tagged markers. They are highly adaptable to large-scale automated genotyping, and therefore, are most suitable for association studies and applicable to comparative genome analysis. However, discovery of SNPs requires genome sequencing efforts through whole genome sequencing or deep sequencing of reduced representation libraries. Such genome resources are not yet available for many species including catfish. A large resource of ESTs is to become available in catfish allowing identification of large number of SNPs, but reliability of EST-derived SNPs are relatively low because of sequencing errors. This project was designed to answer some of the questions relevant to quality assessment of EST-derived SNPs.

The mammalian genome contains tens of thousands of CG and TG repeat sequences that have high potential to form the nonclassical left-handed double-helical Z-DNA structure. Previously we showed that activation of the colony-stimulating factor 1 (CSF1) gene by the chromatin remodeling enzyme, BRG1, results in formation of Z-DNA at the TG repeat sequence located within the promoter. In this report, we show that the TG repeats are assembled in a positioned nucleosome in the silent CSF1 promoter and that activation by BRG1 disrupts this nucleosome and results in Z-DNA formation. Active transcription is not required for the formation of Z-DNA but does result in an expanded region of Z-DNA. Formation of sequences by both BRG1 and the Z-DNA is required for effective chromatin remodeling of the CSF1 promoter. We propose the Z-DNA formation induced by BRG1 promotes a transition from a transient and partial remodeling to a more extensive disruption of the canonical nucleosomal structure. The data presented in this report establish that Z-DNA formation is an important mechanism in modulating chromatin structure, in similarity to the activities of ATP-dependent remodelers and posttranslational histone modifications.DNA sequences with high potential for forming an alternate DNA structure, Z-DNA, are found frequently throughout the mammalian genome (6, 39). Despite extensive investigations over the past two decades, the biological function of Z-DNA structure has not been well established (34). Z-DNA-forming sequences, such as TG or GC repeats, are detected more frequently in the 5Ј regulatory region of a gene than in other regions (36), suggesting that Z-DNA structure may play a role in the regulation of transcription. The formation of Z-DNA structure is well correlated with the transcriptional activity of the c-Myc gene (42). Studies of Saccharomyces cerevisiae with an artificial promoter suggest that Z-DNA structure in the promoter region can act as a cis element in gene regulation (33,35). An analysis of human chromosome 22 indicates that Z-DNA-forming regions and the nuclear factor I (NFI) target sites are well correlated with the locations of known and predicted genes across the chromosome and accumulate around the transcription start sites (3). It was reported recently that the Z-DNA-binding activity of the E3L gene of the vaccinia virus product may regulate its pathogenicity, possibly by regulating transcription from cellular genes involved in fighting viral infection (17). We have previously shown that Z-DNA formation at the promoter of the colony-stimulating factor 1 (CSF1) gene is accompanied by transcriptional activation by a chromatin remodeling complex (25).Mammalian DNA is organized in a highly ordered chromatin structure, with the nucleosome as its basic repeat unit. The local chromatin architecture affects the accessibility of regulatory sequences and, thus, the expression potential of a gene.Structural changes result from posttranslational histone modifications (1,4,20,21,37,38,44) and from the activity of ATP...