Species-specific patterns of DNA bending and sequence

Abstract

Nucleotide sequences in the GenEMBL database were analyzed using strategies designed to reveal species-specific patterns of DNA bending and DNA sequence. The results uncovered striking species-dependent patterns of bending with more variations among individual organisms than between prokaryotes and eukaryotes. The frequency of bent sites in sequences from different bacteria was related to genomic A + T content and this relationship was confirmed by electrophoretic analysis of genomic DNA. However, base composition was not an accurate predictor for DNA bending in eukaryotes. Sequences from C. elegans exhibited the highest frequency of bent sites in the database and the RNA polymerase II locus from the nematode was the most bent gene in GenEMBL. Bent DNA extended throughout most introns and gene flanking segments from C.elegans while exon regions lacked A-tract bending characteristics. Independent evidence for the strong bending character of this genome was provided by electrophoretic studies which revealed that a large number of the fragments from C.elegans DNA exhibited anomalous gel mobilities when compared to genomic fragments from over 20 other organisms. The prevalence of bent sites in this genome enabled us to detect selectively C.elegans sequences in a computer search of the database using as probes C.elegans introns, bending elements, and a 20 nucleotide consensus sequence for bent DNA. This approach was also used to provide additional examples of species-specific sequence patterns in eukaryotes where it was shown that (A) greater than or equal to 10 and (A.T) greater than or equal to 5 tracts are prevalent throughout the untranslated DNA of D.discodium and P.falciparum, respectively. These results provide new insight into the organization of eukaryotic DNA because they show that species-specific patterns of simple sequences are found in introns and in other untranslated regions of the genome.

Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin

“…5B) is consistent with two possible explanations, the first of which is operational (a bias in preparation or amplification/sequencing of nucleosome cores that might recapitulate the strong underlying 10.n periodicity in the C. elegans genome) (McGhee and Felsenfeld 1983) and the second of which is fundamental (significant rotational constraint of nucleosomes on the DNA template). As the parameters for rotational and translational constraint in positioning of nucleosomes become clear, it will be of particular interest to compare these with the large number of potential nucleosome positioning guide sequences that have been detected bioinformatically in the C. elegans genome (VanWye et al 1991;Widom 1996;Fukushima et al 2002;Cohanim et al 2006;Kumar et al 2006). …”

“…In addition, the C. elegans genome can be readily modified by transgenesis (introduction of foreign DNA in a variety of contexts) or by mutation. These manipulations, combined with an unusually high incidence of putative nucleosomal positioning cues in a fraction of the genome (e.g., VanWye et al 1991;Widom 1996;Fukushima et al 2002;Cohanim et al 2006;Fire et al 2006;Kumar et al 2006;MorenoHerrero et al 2006) should eventually facilitate the experimental analysis of connections between DNA sequence, nucleosome dynamics, and genetic function.…”

Unusual DNA Structures Associated With Germline Genetic Activity in Caenorhabditis elegans

“…From this perspective, well-characterized model systems such as Caenorhabditis elegans provide a tool of considerable value. C. elegans has been reported to exhibit a strong $10-base periodicity signal (e.g., VanWye et al 1991;Widom 1996;Fukushima et al 2002) and is among the most extensively characterized both in structure (a complete sequence) and function (both individual genetic studies and whole-genome expression/phenotype analysis).…”

Intrinsic bent DNA sites in the chromosomal replication origin of Xylella fastidiosa 9a5c

“…ENDS ratio values of 1.15 or higher were defined as indicative of bent DNA elements in the Bacillus thuringiensis chromosome, for which an average of eight ENDS ratio values yielding a mean greater than 1.2 for each 10-kb segment has been reported (35). However, ENDS ratio values lower than 1.10 were reported for the Xenopus laevis ribosomal intergenic sequence (36).…”