DANPOS Reveals Dynamic Nucleosomes

Keeping track of where some nucleosomes are on chromatin can be just as tricky as keeping track of Taylor Swift’s love life. They’re on, they’re off, they’re at a new place. Well, here comes a new bioinformatics solution to help you keep score on the nucleosome front, anyway. It’s called DANPOS, and it provides single-nucleotide resolution to zero in on position shift, fuzziness change, and occupancy change.

First author Kaifu Chen and his Houston- and Philly-based researcher group found that although algorithms exist that can pinpoint the locations of nucleosomes in one condition, figuring out how nucleosome locations change with different environmental conditions is still a big challenge.

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That’s why they developed DANPOS, which uses MNase-seq data. Here’s a little of what they learned:

  • DANPOS outperformed other similar algorithms and defined accurate nucleosome maps with both simulated and real data.
  • The dynamics discovered with DANPOS reflected environmental changes. For example, changing the media that yeast grew in also changed the nucleosome positioning near key yeast genes responsible for metabolism.
  • DANPOS can distinguish functional categories of nucleosomes.
  • Even though the sequencing depth was ~200-fold, they were still finding more dynamic nucleosomes with greater sequencing depth.
  • In human hematopoietic stem cells and mouse embryonic stem cells, DANPOS found dynamic nucleosomes in promoters and in distal regions.

“We believe that DANPOS’ superior performance will greatly facilitate the understanding of the roles of chromatin, and particularly nucleosome organization, in various cellular functions and disease processes,” the team concludes.

Read all the info at Genome Research, November 2012.