The effects of histone H4 tail acetylations on cation-induced chromatin folding and self-association

Abstract

Understanding the molecular mechanisms behind regulation of chromatin folding through covalent modifications of the histone N-terminal tails is hampered by a lack of accessible chromatin containing precisely modified histones. We study the internal folding and intermolecular self-association of a chromatin system consisting of saturated 12-mer nucleosome arrays containing various combinations of completely acetylated lysines at positions 5, 8, 12 and 16 of histone H4, induced by the cations Na+, K+, Mg2+, Ca2+, cobalt-hexammine3+, spermidine3+ and spermine4+. Histones were prepared using a novel semi-synthetic approach with native chemical ligation. Acetylation of H4-K16, but not its glutamine mutation, drastically reduces cation-induced folding of the array. Neither acetylations nor mutations of all the sites K5, K8 and K12 can induce a similar degree of array unfolding. The ubiquitous K+, (as well as Rb+ and Cs+) showed an unfolding effect on unmodified arrays almost similar to that of H4-K16 acetylation. We propose that K+ (and Rb+/Cs+) binding to a site on the H2B histone (R96-L99) disrupts H4K16 ε-amino group binding to this specific site, thereby deranging H4 tail-mediated nucleosome–nucleosome stacking and that a similar mechanism operates in the case of H4-K16 acetylation. Inter-array self-association follows electrostatic behavior and is largely insensitive to the position or nature of the H4 tail charge modification.

Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains

“…Self-association of nucleosomes may be explained by the interaction of positively charged histone tails (in particular, the tail of histone H4) of one nucleosome with the acidic patch of histones H2A/H2B at an adjacent nucleosome (Luger et al 1997;Schalch et al 2005;Sinha and Shogren-Knaak 2010). Acetylation of histone tails, which is typical of active chromatin (Shahbazian and Grunstein 2007), may interfere with inter-nucleosomal associations (Shogren-Knaak et al 2006;Allahverdi et al 2011). In addition to a high level of histone acetylation, other features of active chromatin, including lower nucleosome density in inter-TADs, manifested as the decreased histone H3 occupancy (Fig.…”

“…Such inability to form contacts may be explained by the acetylation of histone tails, which is typical for active chromatin (Shahbazian and Grunstein 2007) and is known to interfere with inter-nucleosomal associations (Shogren-Knaak et al 2006;Allahverdi et al 2011). In this case, nucleosomes of inactive chromatin would form various supra-nucleosomal structures due to interactions between positively charged histone tails of one nucleosome and the acidic patch of another nucleosome (Luger et al 1997;Schalch et al 2005;Sinha and Shogren-Knaak 2010).…”

Dosage Compensation inDrosophila

“…The role of histone modifications, namely H4K16 acetylation and H2B ubiquitination, will be assessed by replacing canonical histones with multiple copies of modified histone transgenes (Gunesdogan et al 2010). Topological characteristics of dosage compensated chromatin units will be determined by biophysical experiments (Kruithof et al 2009;Allahverdi et al 2011). An important insight into the function of the MSL complex will be to determine its status during the cell cycle and how it manages to survive through DNA replication and mitosis Strukov et al 2011).…”

Regulation of the H4 tail binding and folding landscapes via Lys-16 acetylation

“…Some of the end effects of histone tail acetylations are now well known and documented (26,(28)(29)(30). However, there seems to be little if any molecular-level rationale about how the acetylation of the H4 tail induces the observed dramatic changes in the chromatin organization (12,31). Here we propose a molecular level mechanism by which the acetylations may regulate the functions of the H4 tail, which may have implications for the functional regulation of other IDPs based on similar posttranslational modification strategies.…”