NET-Seq
CATCH-IT
CATCH-IT is a direct method for measuring nucleosome turnover dynamics genome-wide. In this method, cells are treated briefly with the methionine surrogate azidohomoalanine (Aha), which couples biotin to nucleosomes containing newly incorporated histones. The labeled chromatin is affinity-purified with streptavidin, washed stringently to remove nonhistone proteins, and analyzed using tiling microarrays.
Pros:
- Can determine differences in nucleosome turnover across the genome
Cons:
- Potential artifacts
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- Skene P. J., Hernandez A. E., Groudine M. and Henikoff S. The nucleosomal barrier to promoter escape by RNA polymerase II is overcome by the chromatin remodeler Chd1. Elife. 2014;3:e02042
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- Teves S. S. and Henikoff S. Transcription-generated torsional stress destabilizes nucleosomes. Nat Struct Mol Biol. 2014;21:88-94
- Yildirim O., Hung J. H., Cedeno R. J., Weng Z., Lengner C. J. and Rando O. J. A system for genome-wide histone variant dynamics in ES cells reveals dynamic MacroH2A2 replacement at promoters. PLoS Genet. 2014;10:e1004515