A Game of Thrones at Human Centromeres II. A new molecular/evolutionary model

Abstract

Human centromeres are remarkable in four ways: they are i) defined epigenetically by an elevated concentration of the histone H3 variant CENP-A, ii) inherited epigenetically by trans-generational cary-over of nucleosomes containing CENP-A, iii) formed over unusually long and complex tandem repeats (Higher Order Repeats, HORs) that extend over exceptionally long arrays of DNA (up to 8 Mb), and iv) evolve in such a rapid and punctuated manner that most HORs on orthologous chimp and human chromosomes are in different clades. What molecular and evolutionary processes generated these distinctive characteristics? Here I motivate and construct a new model for the formation, expansion/contraction, homogenization and rapid evolution of human centromeric repeat arrays that is based on fork-collapse during DNA replication (in response to proteins bound to DNA and/or collisions between DNA and RNA polymerases) followed by out-of-register re-initiation of replication via Break-Induced Repair (BIR). The model represents a new form of molecular drive. It predicts rapid and sometimes punctuated evolution of centromeric HORs due to a new form of intragenomic competition that is based on two features: i) the rate of tandem copy number expansion, and ii) resistance to invasion by pericentric heterochromatin within a centromere's HOR array. These features determine which variant array elements will eventually occupy a pivotal region within a centromeric repeat array (switch-point) that gradually expands to populate the entire array. In humans, continuous HOR turnover is predicted due to intra-array competition between three repeat types with an intransitive hierarchy: A < B < C < A, where A = short, single-dimer HORs containing one monomer that binds centromere protein-B (CENP-B) and another that does not, B = moderately longer HORs composed of ≥ 2 dimers, and C = substantially longer HORs that lose their dimeric modular structure. Continuous turnover of proteins that bind centromeric DNA (but these proteins are not constituents of the kinetochore) and polygenic variation influencing position-effect variegation are predicted to cause rapid turnover of centromeric repeats in species lacking HORs and/or CENP-B binding at centromeres. Evolution at centromeres is a molecular 'Game-of-Thrones' because centromeric sequences 'reign' due to an epigenetic 'crown' of CENP-A that is perpetually 'usurped' by new sequences that more rapidly assemble large 'armies' of tandem repeats and/or resist 'invasion' from a surrounding 'frontier' of percentric heterochromatin. These 'regal transitions' occur in a backdrop of slashing and decapitation (fork-collapse generating truncated sister chromatids) in the context of promiscuous sex that is frequently incestuous (out-of-register BIR between sibling chromatids).

Sequence, Chromatin and Evolution of Satellite DNA

“…Dover and colleagues argued that concerted evolution occurs via molecular drive, an evolutionary process emerging from the activities of a number of ubiquitous mechanisms of DNA turnover, such as gene conversion, unequal crossing over, replication slippage, rolling circle replication, and multiple TE insertions [ 295 , 296 , 297 ]. A specific molecular drive mechanism based on known properties of centromeric chromatin was recently proposed by Rice, who argued that collapse of the replication fork when it encounters CENP-A nucleosome-associated complexes and/or tightly bound CENP-B results in DNA breaks that are repaired by out-of-register reinitiations [ 298 ]. Such break-induced recombination (BIR) had been described for expansions and contractions of rDNA arrays, induced by fork collisions with RNA Polymerases [ 299 ].…”

A Game of Thrones at Human Centromeres I. Multifarious structure necessitates a new molecular/evolutionary model

“…Previous studies in humans indicate that the b/nbox dimeric structure strongly influences the positioning of nucleosomes (Tanaka et al 2005;Hasson et al 2013;Fujita et al 2015;Henikoff et al 2015). Each dimer winds around two neighboring histone cores leading to an a l t e r n a t i n g p a t t e r n o f l i n k e r s b e t w e e n nucleosomes: one with a b-box and the next with an n-box (see Supplemental Figure S12 in the companion paper [Rice 2019] where I will discuss the potential significance of this alternation pattern).…”

“…These questions I address in the companion paper (Rice 2019). Fishman-Lobell et al 1992;Schildkraut et al 2005. Missing from the Smith model (because it had not yet been discovered) is repair of DSBs via the Single Strand Annealing pathway (SSA; no crossing over).…”

“…BIR repair of collapsed replication forks has been studied extensively in the rDNA repeats of budding yeast and found to be biased toward array expansion rather than contraction (Kobayashi 2014). Empirical evidence indicates that fork-stalling/collapse is common during the replication of centromeric DNA in humans (Crosetto et al 2013;Aze et al 2016) and nonhumans (Greenfeder and Newlon 1992;Mitra et al 2014), as described in more detail in the companion paper (Rice 2019). BIR repair of collapsed DNA replication forks would feasibly have two results: i) it generates length variation that increases with more mitoses per generation (as occurs on the Y compared to the X), and ii) it could feasibly counterbalance array shrinkage due to SSA repair of DSBs due to its bias toward array expansion over contraction (as indicated at yeast rDNA arrays; Kobayashi 2014).…”

CENP-A chromatin prevents replication stress at centromeres to avoid structural aneuploidy

“…Human centromeres span ~0.3-5 Mb with repetitive alpha-satellite DNA arranged in tandem and then reiterated as homogenous higher order repeat (HOR) blocks (4). Evolution of centromere repeats has been modelled by short and long-range recombination events such as gene conversion, break-induced replication, crossing over and other mutagenic processes (2,3,5,6).…”