Skip to main content

Table 1 Comparison of methods for measuring chromatin dynamics

From: Capturing the dynamic epigenome

Method Utility Benefits Drawbacks
Fluorescence recovery after photobleaching (FRAP) Measurement of chromatin protein binding kinetics 1. Can be used for nucleosomes as well as other chromatin binding proteins
2. Allows observation of protein location within the nucleus
1. Cannot determine the specific genomic sites that are bound
2. Requires an epitope-tagged protein that may not behave exactly like the native form
MS-based kinetic methods Measurements of histone modification kinetics Can be used for nucleosomes as well as other chromatin-binding proteins Cannot determine the kinetics at specific genomic sites
Inducible transgene-based methods Measurement of nucleosome turnover kinetics as well as binding of other chromatin proteins Can be used for nucleosomes as well as other chromatin-binding proteins 1. Requires an epitope-tagged protein
2. Time lag during induction limits time resolution
Recombination-induced tag exchange (RITE) Measurement of nucleosome turnover kinetics as well as binding of other chromatin proteins Can be used for nucleosomes as well as other chromatin-binding proteins 1. Requires an epitope-tagged protein that may not behave exactly like the native form
2. Time lag during recombination limits time resolution
Covalent attachment of tags to capture histones and identify turnover (CATCH-IT) Measurement of nucleosome turnover kinetics 1. No transgenes or antibodies are required
2. Excellent time resolution
3. Can be used on many different cell types
Only (H3/H4)2 tetramer incorporation kinetics can be measured easily