Precise identification of cascading alpha satellite higher order repeats in T2T-CHM13 assembly of human chromosome 3

Abstract

Aim: To precisely identify and analyze alpha-satellite higher-order repeats (HORs) in T2T-CHM13 assembly of human chromosome 3.

Methods: From the recently sequenced complete T2T-CHM13 assembly of human chromosome 3, the precise alpha satellite HOR structure was computed by using the novel high-precision GRM2023 algorithm with global repeat map (GRM) and monomer distance (MD) diagrams.

Results: The major alpha satellite HOR array in chromosome 3 revealed a novel cascading HOR, housing 17mer HOR copies with subfragments of periods 15 and 2. Within each row in the cascading HOR, the monomers were of different types, but different rows within the same cascading 17mer HOR contained more than one monomer of the same type. Each canonical 17mer HOR copy comprised 17 monomers belonging to 16 different monomer types. Another pronounced 10mer HOR array was of the regular Willard's type.

Conclusion: Our findings emphasize the complexity within the chromosome 3 centromere as well as deviations from expected highly regular patterns.

Figure 1

Global repeat map (GRM) diagram and monomer distance (MD) diagram for tandemly arranged alpha satellite monomers in complete T2T-CHM13 assembly of human chromosome 3. (A) GRM diagram. Horizontal axis: GRM periods. Vertical axis: the frequency of monomer repeats period. Identified major GRM peaks have periods 17, 15, 2, and 10, and minor peaks 15, 2, 13, 19, 5, 6. The significance of these GRM peaks (HORs or subfragment repeats) can be inferred from the MD diagram. (B) MD diagram. Horizontal axis: enumeration of tandemly organized alpha satellite monomers in order of appearance in GRM analysis of T2T assembly. Vertical axis: period (distance between the start of a monomer and of the next monomer of the same type). Two pronounced distinct regions with MD-line segments correspond to 17mer HOR (referred to as hor1) and 10mer (referred to as hor2). The additional MD-line segments at periods 15 and 2 correspond to subsegments of 17mer HOR. There also some additional weak repeats and sporadic MD points.

Figure 2

The ideogram of major alpha satellite higher-order repeats (HOR) arrays in the centromeric region of T2T-CHM13 assembly of human chromosome 3. hor1 – cascading 17mer HOR array; hor2 – Willard՚s type 10mer HOR array.

Figure 3

An aligned scheme of cascading 17mer canonical higher-order repeats (HOR) copies and some variants. (A) 17mer canonical HOR copy constituted of 17 monomers (denoted m1,… m17) of 16 different types (t1,… t16) presented in the linear monomeric scheme. The number of different types of monomers in the canonical HOR copy is denoted by τ. Each monomer is presented by a colored box. (B) A cascading aligned scheme of the canonical 17mer HOR (n = 17, τ = 16) corresponding to the linearized scheme in Figure 3A. Two monomers of the same type are aligned in the first column: monomer m1 of the type t1 in the first row and monomer m16 of the same type t1 in the second row. (C) Several examples of variant cascading HOR copies from Supplemental Figure 1(Supplementary Figure 1): 13mer, 30mer, and 7mer with respect to 17mer HOR array.

Figure 4

An aligned scheme of some segments from cascading 17mer higher-order repeat (HOR) array. (A) A segment of the first ten cascading 17mer HOR copies from position 91 779 888 to 91 811 017. Each HOR copy corresponds to cascading rows of monomers. The No.1 HOR copy is canonical, consisting of two cascading rows: the first row with 15 monomers of types t1-t15 and the second row with two monomers of types t1 and t16. The next five HOR copies, No. 2-6, are of the same canonical structure. The cascading HOR copy No. 7, starting at position 91 797 236, is a variant HOR consisting of 15 + 15 + 2 = 32 monomers (three cascading rows of 15, 15, and 2 monomers, respectively). This variant HOR copy arises from the canonical HOR copy by duplicating its first row. The next HOR copy, No.8, starting at position 91 802 681 is the same as HOR copy No. 7. The next two HOR copies, No.9 and 10, are canonical (15 + 2). (B) A segment of cascading 17mer HOR copies from position 91 813 909 to 91 854 237. This segment starts with canonical 17mer HOR copy (15 + 2 monomers). The following copy is an extended HOR copy of 2 × 15 + 2 = 32 monomers, which arises from the canonical 17mer HOR copy by multiplication of the first row in the canonical HOR copy. The next copy is an extended HOR copy of 6 × 15 + 2 = 92 monomers, which arises from the canonical 17mer HOR copy by multiple multiplication of the first row in the canonical HOR copy. The next copy is a variant HOR copy of 4 × 15 + 2 = 62 monomers, which arises from the canonical 17mer HOR copy by multiplication of the first row in the canonical HOR copy. After that follows a sequence of canonical 17mer HOR copies. (C) A segment of cascading 17mer HOR copies from position 92 087 584 to 92 110 030, giving rise to a tertiary period-2 subfragment. This graphical presentation is also presented in Table 3. The sub-tandem of (t1, t16) doublets within HOR copies gives rise to subrepeats … t2 t15 t2 t15 …, which due to distances t2-t2 and t15-t15 of 2 × 171 bp generates intra-HOR tertiary periodicity 2.

Figure 5

An aligned scheme of the entire array of cascading 36mer alpha satellite higher-order repeat (HOR). The number on the left side indicates the initial position of the first monomer in each row of HOR copy. The box colors and monomer type labels align consistently with those of the 17mer HOR. There are five canonical copies of the cascade 36mer HOR, primarily composed of the same monomers found in the 17mer HOR. Each HOR copy corresponds to cascading rows of monomers. The HOR copies No. 1, 3, 4, 5 and 7 are canonical, consisting of four cascading rows: the first row with 6 monomers of types t1, t16, t17, t2-t4; the second row with 17 monomers of types t1, t16, t17, t2-t15; the third row with 8 monomers of types t1, t16, t17, t2-t5, t18; and the forth row with 5 monomers of types t11-t15 (6 + 17 + 8+5 = 36). Between these canonical HOR copies, four-variant HOR copies with significantly fewer monomers in each HOR unit are dispersed.

Figure 6

An aligned scheme of some segments from Willard՚s type 10mer HOR array. (A) a scheme of canonical 10mer HOR copy. (B) A scheme of several variants in 10mer HOR array. (C) A cluster of canonical and variant HOR copies (2 canonical and 11 variant) at the end of 10mer HOR array.