Genomic and functional variation of human centromeres

Abstract

Centromeres are central to chromosome segregation and genome stability, and thus their molecular foundations are important for understanding their function and the ways in which they go awry. Human centromeres typically form at large megabase-sized arrays of alpha satellite DNA for which there is little genomic understanding due to its repetitive nature. Consequently, it has been difficult to achieve genome assemblies at centromeres using traditional next generation sequencing approaches, so that centromeres represent gaps in the current human genome assembly. The role of alpha satellite DNA has been debated since centromeres can form, albeit rarely, on non-alpha satellite DNA. Conversely, the simple presence of alpha satellite DNA is not sufficient for centromere function since chromosomes with multiple alpha satellite arrays only exhibit a single location of centromere assembly. Here, we discuss the organization of human centromeres as well as genomic and functional variation in human centromere location, and current understanding of the genomic and epigenetic mechanisms that underlie centromere flexibility in humans.

Keywords: Dicentric chromosome; Epiallele; Haplotype; Kinetochore; Repetitive DNA; Satellite DNA.

Figure 1.. Genomic organization and variation of alpha satellite DNA at human centromeres.

a. Schematic of the general organization of an alpha satellite DNA array at human centromere regions. Alpha satellite is based on ~171bp monomeric repeat units (black arrows with white numbers) that are 50–70% identical in sequence and arranged tandemly to form a HOR unit; shown here as a 12 monomer HOR (yellow array). Monomers are numbered by their position within the HOR and not based on their homology between two distinct HORs. The HORs are repeated hundreds to thousands of times to create homogenous arrays in which HOR within a given array are 97–100% identical. The HOR array is flanked by degenerate alpha satellite DNA monomers (small black arrows) that lack hierarchical structure and separate the HOR array from the chromosome arms. HOR arrays are interrupted by other repetitive elements, such as transposable elements (TEs, blue), but the extent of TE distribution across specific alpha satellite arrays is currently unclear due the lack of linear, contiguous alpha satellite assemblies. b. The number of times a chromosome-specific HOR unit is repeated to create an extensive homogenous array varies between homologs and individuals. The distribution of total array sizes from a subset of the population is shown for our distinct alpha satellite arrays, including D17Z1 and D17Z1-B, two arrays from Homo sapiens chromosome 17 (HSA17), as well as DXZ1 and DYZ3, the alpha satellite arrays from HSAX and HSAY. Each open circle represents an independent chromosome/individual. c. Individual alpha satellite monomers are distributed into five suprachromosomal groups or families, based on the concentration of specific monomer types (based on sequence homology) on distinct chromosomes. Suprachromosomal families 1 and 2 (SF1, SF2) represent the most abundant HOR configuration within human centromere regions and are defined by distinct dimeric configurations (shown as blue or yellow. HOR units on some chromosomes like HSA1 are defined by the two dimers themselves while larger HOR units on chromosomes like HSA18 are comprised of multiple alternating copies of the same two monomers. The HOR units are then repeated hundreds to thousands of times to produce a large homogenous satellite array. d. Over half of native human chromosomes contain more than one distinctive alpha satellite array. For example, HSA17 has three arrays that are ~92% identical and defined by different HOR units. D17Z1, the largest array (blue) is defined by a canonical 16 monomer (16-mer) HOR that is repeated thousands of times to produce total array sizes that range from 2.3–4.2Mb in the population. D17Z1-B (pink) and D17Z1-C (light orange) flank D17Z1 and are each defined by different 14-mer HOR units. Centromere assembly can occur at either D17Z1 or D17Z1-B.

Figure 2.. Functional centromeric epialleles on Homo sapiens chromosome 17 (HSA17) are influenced by genomic variation within alpha satellite DNA.

a. The large array D17Z1 on HSA17 is defined by a canonical (wild-type) 16-mer HOR unit. However, D17Z1 is highly polymorphic such that single and multiple monomer deletions produce HOR variants that differ in length by an integral number of monomers. In the general population, HOR variants range from 15-mers to 12-mers. Two major haplotypes (Haplotype I - wildtype; Haplotype II – variant) exist in the population, distinguished by the presence or absence of the 13-mer HOR unit. b. HSA17 exhibits centromeric epialleles (i.e. multiple sites of centromere assembly) based on the amount of variation within D17Z1. Arrays containing predominantly wild-type 16-mer HORs are preferred locations for centromere assembly, denoted by CENP-A (red circles) and other centromere proteins, and are associated with stable HSA17s. When D17Z1 arrays are composed of more than 70% variant 13-mer HORs, centromere assembly occurs on neighboring D17Z1-B (pink arrows) and chromosome stability is comparable to HSA17s with wild-type arrays. However, centromere assembly occurs on D17Z1 arrays exhibiting intermediate levels of variation (40–60%) but leads to two distinct chromosome phenotypes: stable and unstable. Variant arrays exhibiting the unstable HSA17 phenotype are associated with reduced numbers of centromere proteins.