Chromatin structure-dependent histone incorporation revealed by a genome-wide deposition assay
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Curated by eLife
Evaluation Summary:
The method presented in this article is of interest for all fields that interface with chromatin dynamics. It could provide a powerful tool to dissect the mechanisms of chromatin assembly and disassembly genome-wide, and determine how cell cycle and chromatin structure influence these dynamics. However, in the current form, the article falls short of its potential. Further validation of the data, and clarification of its implications is requested.
(This preprint has been reviewed by eLife. We include the public review from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)
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Abstract
In eukaryotes, histone variant distribution within the genome is the key epigenetic feature. To understand how each histone variant is targeted to the genome, we developed a new method, the RhIP ( R econstituted h istone complex I ncorporation into chromatin of P ermeabilized cell) assay, in which epitope-tagged histone complexes are introduced into permeabilized cells and incorporated into their chromatin. Using this method, we found that H3.1 and H3.3 were incorporated into chromatin in replication-dependent and -independent manners, respectively. We further found that the incorporation of histones H2A and H2A.Z mainly occurred at less condensed chromatin (open), suggesting that condensed chromatin (closed) is a barrier for histone incorporation. To overcome this barrier, H2A, but not H2A.Z, uses a replication-coupled deposition mechanism. Our study revealed that the combination of chromatin structure and DNA replication dictates the differential histone deposition to maintain the epigenetic chromatin states.
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Joint Public Review:
The manuscript by Tachinawa et al. presents a new method (named RhIP), to study incorporation of recombinant epitope-tagged histone dimers into permeabilized cell nuclei. Using RhIP, the authors demonstrate that both H3-H4 and H2A-H2B and their variants are incorporated in this setup. They proceed with investigating context-specific features of these events, providing evidence that ongoing replication and overall chromatin structure may influence histone dimer incorporation in RhIP. This argues for RhIP having the potential to reveal the mechanisms of chromatin assembly and disassembly genome-wide, and determine how cell cycle and chromatin structure influence these dynamics.
The system is capable of recapitulating major known chromatin assembly pathways and supports existing knowledge of histone dimer dynamics on …
Joint Public Review:
The manuscript by Tachinawa et al. presents a new method (named RhIP), to study incorporation of recombinant epitope-tagged histone dimers into permeabilized cell nuclei. Using RhIP, the authors demonstrate that both H3-H4 and H2A-H2B and their variants are incorporated in this setup. They proceed with investigating context-specific features of these events, providing evidence that ongoing replication and overall chromatin structure may influence histone dimer incorporation in RhIP. This argues for RhIP having the potential to reveal the mechanisms of chromatin assembly and disassembly genome-wide, and determine how cell cycle and chromatin structure influence these dynamics.
The system is capable of recapitulating major known chromatin assembly pathways and supports existing knowledge of histone dimer dynamics on chromatin. RhIP is also valuable in directly testing histone mutants or variants, as proven by authors.
H3.1 incorporation is shown to be exquisitely dependent on replication, demonstrating that replication itself, as well as replication-dependent chromatin assembly are successfully reconstituted with isolated nuclei, cytosolic extracts and recombinant histones.
The focus of the study is on the incorporation H2A variants, in particular H2A.Z. These data supports known notions about H2A.Z dynamics in chromatin, showing a preference for transcription start sites, and the dependence on the M6 region.
However, the major limitation of the current manuscript is that it remains unclear what properties are driving the observed RhIP effects. This is not fully elucidated and thus limits the ability of RhIP to enable the discovery of new mechanisms.
While replication-dependent mechanisms are well captured by RhIP, it is less clear if transcription and chromatin remodeling is functional in this system and thus if transcription-dependent nucleosome exchange processes are faithfully recapitulated. It is important to improve the comparison of RhIP with 'in vivo' (i.e. existing ChIP-seq datasets) localisation and explicitly develop hypotheses why in some cases the data matches the 'in vivo' situation and in others not. It would be helpful to improve the interpretation of the data to include all existing caveats to the assay setup.
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Evaluation Summary:
The method presented in this article is of interest for all fields that interface with chromatin dynamics. It could provide a powerful tool to dissect the mechanisms of chromatin assembly and disassembly genome-wide, and determine how cell cycle and chromatin structure influence these dynamics. However, in the current form, the article falls short of its potential. Further validation of the data, and clarification of its implications is requested.
(This preprint has been reviewed by eLife. We include the public review from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)
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