Table 1

Comparison of methods for measuring chromatin dynamics

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


Deal and Henikoff Genome Biology 2010 11:218   doi:10.1186/gb-2010-11-10-218