An unusual nucleosomal sequence pattern is enriched in mammalian genes

Abstract

Nucleosomal DNA sequences generally follow a well-known pattern with [~]10-bp periodic WW (where W is A or T) dinucleotides that oscillate in phase with each other and out of phase with SS (where S is G or C) dinucleotides. However, nucleosomes having a DNA sequence pattern inverse to the conventional one have not been systematically analyzed in eukaryotes. Here, we show that anti-WW/SS nucleosomes are widespread and exhibit a species- and context-specific distribution in the genomes. The enrichment of anti-WW/SS nucleosomes in mammalian genomes is positively correlated with RNA Pol II transcriptional levels, but negatively correlated with the presence of the periodic WW or SS sequence patterns. In addition, chromatin remodeling complexes have an impact on the abundance of anti-WW/SS nucleosomes. The data reveal distinct roles of cis- and trans-acting factors in the rotational positioning of nucleosomes between non-mammals and mammals. Implications of the anti-WW/SS sequence pattern for RNA Pol II transcription are discussed.