Single-molecule kinetic analysis of HP1-chromatin binding reveals a dynamic network of histone modification and DNA interactions

Abstract

Chromatin recruitment of effector proteins involved in gene regulation depends on multivalent interaction with histone post-translational modifications (PTMs) and structural features of the chromatin fiber. Due to the complex interactions involved, it is currently not understood how effectors dynamically sample the chromatin landscape. Here, we dissect the dynamic chromatin interactions of a family of multivalent effectors, heterochromatin protein 1 (HP1) proteins, using single-molecule fluorescence imaging and computational modeling. We show that the three human HP1 isoforms are recruited and retained on chromatin by a dynamic exchange between histone PTM and DNA bound states. These interactions depend on local chromatin structure, the HP1 isoforms as well as on PTMs on HP1 itself. Of the HP1 isoforms, HP1α exhibits the longest residence times and fastest binding rates due to DNA interactions in addition to PTM binding. HP1α phosphorylation further increases chromatin retention through strengthening of multivalency while reducing DNA binding. As DNA binding in combination with specific PTM recognition is found in many chromatin effectors, we propose a general dynamic capture mechanism for effector recruitment. Multiple weak protein and DNA interactions result in a multivalent interaction network that targets effectors to a specific chromatin modification state, where their activity is required.

Heterochromatin Protein HP1α Gelation Dynamics Revealed by Solid‐State NMR Spectroscopy

“…Reaching agel state after 7days (Supporting Information, Figure S2), the total CP signal increased 3.3 fold, the INEPT signal decreased 1. 35 fold, and the 13 CDPsignal remained unchanged. We interpret the dramatic change in total CP intensity to arise from an expanding cross-linking network during gelation that restricts the motion of individual pHP1a dimers and shifts their overall dynamics to as lower timescale where dipolar-based polarization transfer mechanisms are more efficient.…”

“…[35] Nevertheless,the preservation of mobility in chromatin-containing pHP1a dense phases has important implications for heterochromatin compaction and regulation in the cell where access to genetic information is preserved and can be granted on demand. [35] Nevertheless,the preservation of mobility in chromatin-containing pHP1a dense phases has important implications for heterochromatin compaction and regulation in the cell where access to genetic information is preserved and can be granted on demand.…”

“…Zuschriften and states have been reported. [35] Nevertheless,the preservation of mobility in chromatin-containing pHP1a dense phases has important implications for heterochromatin compaction and regulation in the cell where access to genetic information is preserved and can be granted on demand. We expect that implementing the full suite of solid-state NMR spectroscopy experiments will help illuminate the specific intermolecular interactions and structural ensembles of biomolecules in condensed environments.…”

KAP1 is an antiparallel dimer with a natively functional asymmetry

“…off,2 , Table 1). It was previously shown that the slow exponential phase is attributed to bivalent chromatin binding by HP1α dimers 76 . KAP1 addition indeed stabilized HP1α chromatin binding, exhibiting a larger percentage of bound molecules at times >1s (Figure 6d).…”

“…The asymmetric KAP1 structure has in fact only one HP1BD fully exposed for HP1 interaction, while the second is mostly interacting with the RBCC domain (Figures 2c, 3d and 5d). imaging approaches can directly observe the chromatin interaction kinetics of individual chromatin binders 76,77 . We used this technique to determine how KAP1 alters the interaction dynamics of HP1α with chromatin fibers, trimethylated at lysine 9 on histone H3 (H3K9me3) to observe the behavior of the complex in the context of chromatin (Figure 6a).…”