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Resources » Paper

Wright GM et al. (2019) Nucleic Acids Res "The nucleosome position-encoding WW/SS sequence pattern is depleted in mammalian genes relative to other eukaryotes."

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  • Comments on Wright GM et al. (2019) Nucleic Acids Res "The nucleosome position-encoding WW/SS sequence pattern is depleted in mammalian genes relative to other eukaryotes." (0)

  • Overview

    PMID:
    31216031
    DOI:
    10.1093/nar/gkz544
    Status:
    Publication type:
    Journal_article
    WormBase ID:
    WBPaper00059458

    Wright GM, & Cui F (2019). The nucleosome position-encoding WW/SS sequence pattern is depleted in mammalian genes relative to other eukaryotes. Nucleic Acids Res, 47, 7942-7954. doi:10.1093/nar/gkz544

    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 with other DNA patterns have not been systematically analyzed. Here, we focus on an opposite pattern, namely anti-WW/SS pattern, in which WW dinucleotides preferentially occur at DNA sites that bend into major grooves and SS (where S is G or C) dinucleotides are often found at sites that bend into minor grooves. Nucleosomes with the anti-WW/SS pattern are widespread and exhibit a species- and context-specific distribution in eukaryotic genomes. Unlike non-mammals (yeast, nematode and fly), there is a positive correlation between the enrichment of anti-WW/SS nucleosomes and RNA Pol II transcriptional levels in mammals (mouse and human). Interestingly, such enrichment is not due to underlying DNA sequence. In addition, chromatin remodeling complexes have an impact on the abundance but not on the distribution of anti-WW/SS nucleosomes in yeast. Our 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.


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