H2A.Z contributes to the unique 3D structure of the centromere

Abstract

Mammalian centromere function depends upon a specialized chromatin organization where distinct domains of CENP-A and dimethyl K4 histone H3, forming centric chromatin, are uniquely positioned on or near the surface of the chromosome. These distinct domains are embedded in pericentric heterochromatin (characterized by H3 methylated at K9). The mechanisms that underpin this complex spatial organization are unknown. Here, we identify the essential histone variant H2A.Z as a new structural component of the centromere. Along linear chromatin fibers H2A.Z is distributed nonuniformly throughout heterochromatin, and centric chromatin where regions of nucleosomes containing H2A.Z and dimethylated K4 H3 are interspersed between subdomains of CENP-A. At metaphase, using the inactive X chromosome centromere as a model, complex folding of this fiber produces spatially positioned domains where H2A.Z/dimethylated K4 H3 chromatin juxtaposes one side of CENP-A chromatin, whereas a region of H2A/trimethyl K9 H3 borders the other side. A second region of H2A.Z is found, with trimethyl K9 H3 at the inner centromere. We therefore propose that H2A.Z plays an integral role in organizing centromere structure.centromere organization ͉ chromosome structure ͉ histone variants A ll active centromeres contain an evolutionary conserved variant of histone H3 (CENP-A in mammals). Although poorly understood, fundamental to centromere function is the 3D organization of CENP-A containing chromatin, so that it is presented on the poleward face of a chromosome while being embedded in pericentric heterochromatin. This heterochromatin has a role in the cohesion of sister chromatids (1). The complex nature of this organization was demonstrated by showing that, whereas blocks of human CENP-A (and the Drosophila counterpart CID) and H3 nucleosomes (Ϸ15-40 kb) are interspersed along an extended chromatin fiber, the folding of this fiber in mitotic chromosomes yields separate CENP-A-and H3-containing domains, with the H3 domain located toward the inner chromatid region (together, these domains have been referred to as centric chromatin; ref. 2). Most interestingly, this H3-containing domain is enriched with a euchromatic mark, H3 dimethylated at K4 and not K9 H3 methylation associated with the flanking heterochromatin (3). Therefore, it was postulated that this distinct histone modification pattern might contribute to centromere structure and/or identity (3).Our recent studies have demonstrated that another histone variant, H2A.Z, has a role in mitosis (4). When H2A.Z is depleted in mammalian cells, major defects in chromosome segregation (and cytokinesis) are observed with a corresponding loss of HP1␣ from pericentric heterochromatin, indicating this domain is severely disrupted. The mechanism responsible for this defect remains unresolved. Although others (5) and we (6) have shown that the concentration of H2A.Z can dynamically increase at pericentric heterochromatin under different physiological contexts, whether H2A.Z is a core component of this domai...

An epichromatin epitope: Persistence in the cell cycle and conservation in evolution

“…For example, mammalian centromeric regions contain H2A.Z in many of the nucleosomes. 40 Indeed, the present study documents include specific variants that might preserve a unique chromatin conformation by epigenetic mechanisms. In many respects, our view of interphase epichromatin resembles that of van Steensel and co-workers.…”

Random deposition of histone variants: A cellular mistake or a novel regulatory mechanism?

“…[23][24][25] Having so many different locations for a histone variant is very intriguing. Here, we review recent work suggesting that multiple routes can be used to incorporate H2A.Z in the genome and propose that this may lead to different functions for the histone variant.…”

“…At centromeres, H2A.Z integrates several nucleosomes and it has been proposed that these arrays of H2A.Z-containing nucleosomes are important for the architecture of the centromeres and their attachment to the kinetochore during M phase. 25 Accumulation of H2A.Z over large domains in facultative heterochromatin may favor further compaction of the chromatin fiber via inter-nucleosomal interactions, analogously to what occurs at the centromere. At promoters, where H2A.Z occupies only one or two nucleosomes, it may not be able to condense chromatin allowing it to fulfill a different role (Fig.…”

“…25 Therefore, H2A.Z and CENP-A do not appear to co-occupy nucleosomes but are rather present in neighboring nucleosomes. If the two variants mediate a shared function at centromeres, it is likely to be via internucleosomes interactions.…”

Regulation of ISWI chromatin remodelling activity

“…H2A.Z proteins are essential for establishing proper chromatin structure in many organisms (Raisner and Madhani 2006). Mammalian H2A.Z contributes to the unique structure of centromere (Greaves et al 2007) as well as to maintain genome integrity (Rangasamy et al 2004). In plants, H2A.Z has been shown to be enriched in nucleosomes localized at transcriptional control regions and to regulate both silencing and activation (Coleman-Derr and Zilberman 2012).…”