Vertebrate centromere architecture: from chromatin threads to functional structures

Abstract

Centromeres are chromatin structures specialized in sister chromatid cohesion, kinetochore assembly, and microtubule attachment during chromosome segregation. The regional centromere of vertebrates consists of long regions of highly repetitive sequences occupied by the Histone H3 variant CENP-A, and which are flanked by pericentromeres. The three-dimensional organization of centromeric chromatin is paramount for its functionality and its ability to withstand spindle forces. Alongside CENP-A, key contributors to the folding of this structure include components of the Constitutive Centromere-Associated Network (CCAN), the protein CENP-B, and condensin and cohesin complexes. Despite its importance, the intricate architecture of the regional centromere of vertebrates remains largely unknown. Recent advancements in long-read sequencing, super-resolution and cryo-electron microscopy, and chromosome conformation capture techniques have significantly improved our understanding of this structure at various levels, from the linear arrangement of centromeric sequences and their epigenetic landscape to their higher-order compaction. In this review, we discuss the latest insights on centromere organization and place them in the context of recent findings describing a bipartite higher-order organization of the centromere.

Keywords: CENP-A; Centromere; Chromatin organization; Epigenetics; Kinetochore.

Fig. 1

Genetic and epigenetic features of the centromere. Schematic of the genetic and epigenetic elements that compose the core centromere and pericentromere, indicating the inactive and active HOR arrays, and the CENP-A-binding domain. αSat monomers are portrayed as smaller arrows within the HORs. The DNA methylation pattern of the active array is shown in blue, and the centromere dip region (CDR) is indicated. Euchromatic (green) and heterochromatic (red) epigenetic marks present at the core centromere and pericentromere are depicted as circles located on top of the CENP-A (yellow) and H3 (gray) nucleosomes

Fig. 2

Centromeric organization by centromeric proteins. a Cartoon representing a CENP-A nucleosome bound to a CCAN complex (PDB 7QOO), not including CENP-C. b CENP-A nucleosomes organized by the oligomerization of CENP-C dimers (indicated in two shades of green). A homo-dimer of Cupin domains (PDB 7X85) is highlighted in the box. c CENP-A nucleosome-stacking driven by CENP-N (PDB 7U46). d α-satellite DNA (indicated in yellow) looping driven by CENP-B dimers (indicated in two shades of blue). The DNA binding (PDB 1HLV) and dimerization domains (PDB 1UFI) of CENP-B are indicated

Fig. 3

Bipartite higher-order organization of centromeric chromatin. Cartoon representing the centromeric region of a mitotic chromosome. Each subdomain of the bipartite centromere (yellow blobs) is associated with the flanking pericentromere, folded as a bottlebrush. Condensin (purple) extends along the central axis of the pericentromere and is enriched at each of the core centromere subdomains. The two pools of cohesin, one at the boundary of the pericentromere and one proximal to the core centromere are indicated in blue. A bipartite kinetochore (green) is bound by independent microtubule bundles