Isodicentric Y chromosomes and sex disorders as byproducts of homologous recombination that maintains palindromes

Abstract

Massive palindromes in the human Y chromosome harbor mirror-image gene pairs essential for spermatogenesis. During evolution, these gene pairs have been maintained by intrapalindrome, arm-to-arm recombination. The mechanism of intrapalindrome recombination and risk of harmful effects are unknown. We report 51 patients with isodicentric Y (idicY) chromosomes formed by homologous crossing over between opposing arms of palindromes on sister chromatids. These ectopic recombination events occur at nearly all Y-linked palindromes. Based on our findings, we propose that intrapalindrome sequence identity is maintained via noncrossover pathways of homologous recombination. DNA double-strand breaks that initiate these pathways can be alternatively resolved by crossing over between sister chromatids to form idicY chromosomes, with clinical consequences ranging from spermatogenic failure to sex reversal and Turner syndrome. Our observations imply that crossover and noncrossover pathways are active in nearly all Y-linked palindromes, exposing an Achilles' heel in the mechanism that preserves palindrome-borne genes.

Figure 1. Hypothesized mechanism of idicY formation by homologous recombination in MSY palindrome

(A) Schematic representation of chrY. MSY is flanked by pseudoautosomal regions PAR1 and PAR2 (green) and contains heterochromatic blocks (orange). Yp, short arm. Yq, long arm. (B) Expanded view of MSY euchromatin, with palindromes P1 through P8 and inverted repeats IR2 and IR3. (C) Conventional recombination between homologous chromosomes: DSB resolution by NCO and CO pathways yielding, respectively, gene conversion and crossing over. Second chromatid not shown for each of the two homologs. (D) Model of homologous recombination in MSY palindromes: DSB resolution by NCO pathways yields gene conversion. Resolution by crossing over between sister chromatids can produce an idicY (and an acentric fragment), while crossing over within a chromatid yields an inversion.

Figure 2. STS content of structurally anomalous Y chromosomes in 85 patients with deletion breakpoints in Yq or centromere

(A) Locations of three STSs assayed in initial screen for Yq or centromeric breakpoints. (B) Expanded view of centromere and Yq, with palindromes P1 - P8, inverted repeat IR2, and heterochromatic blocks (orange). (C) STSs employed in fine mapping breakpoints. These include boundary and spacer-flanking markers for each palindrome and inverted repeat, and markers around each heterochromatic block. (D) Results of testing DNAs from 85 patients for presence or absence of STSs. Solid black bars encompass STSs found to be present. Gray bars indicate breakpoint intervals that could not be further narrowed due to cross-amplification at other loci. See Figure S2 for identifiers of patients tested. (E) Predicted molecular signature of idicYp formed by homologous recombination between sister chromatids at palindrome P5. Thirteen individuals with this molecular signature are shown in Figure 2D.

Figure 3. IdicYp and isoYp chromosomes confirmed by metaphase FISH

(A) Probe hybridization sites shown below chrY schematic. At right: Hybridization to chrY of normal male control produced expected pattern of red and green signals. Chromosome counterstained with DAPI (blue). (B) Hybridizations to presumed idicYp chromosomes with breakpoints in Yq palindromes P8, P6, P5, P4, P3 and P1, or in IR2 inverted repeat. Hybridization sites shown below schematic of each predicted idicYp; targeted palindrome or inverted repeat lies at center of each schematic. At right: FISH produced predicted red-green-green-red patterns. (C) Hybridization to presumed isoYp or idicYp chromosomes with breakpoints in heterochromatin. All FISH micrographs at same magnification.

Figure 4. Duplication in idicYp chromosomes of sequences immediately proximal to targeted palindromes

(A) Two models of idicYp formation can be distinguished by determining copy numbers of sequences immediately proximal to targeted palindrome. (B) Probe hybridization sites shown below chrY schematic. Hybridizations to chrY of normal male produced expected signals; 15485/15486 and 15469/15470 on interphase spreads, and co-hybridization of 1136L22 and 242E13 on metaphase spreads. (C) Interphase FISH demonstrates duplication of 15485/15486 on idicYp with breakpoint in palindrome P5. (D) Interphase FISH demonstrates duplication of 15469/15470 on idicYp with breakpoint in inverted repeat IR2. (E) Metaphase FISH demonstrates duplication of 1136L22 on idicYp with breakpoint in DYZ18/DYZ1/DYZ2 heterochromatin. Co-hybridization of 1136L22, in red, with 242E13, in green, produced predicted red-green-red pattern. All micrographs at same magnification. In each interphase FISH experiment, ≥100 nuclei were scored (Figures S3, S4, and S5).

Figure 5. IdicYq chromosomes formed by crossing over between sister chromatids at Yp inverted repeat: STS content and FISH analyses

(A) Schematic representation of Yp and centromeric region. (B) STSs employed in mapping deletion breakpoints in two individuals in whom sY14 (SRY) was absent, and sY78 and sY1273 (Figure 2) were present. These STSs include boundary and spacer-flanking markers for IR3 inverted repeat and a marker in Yp pericentromeric euchromatin. (C) Results of testing DNAs from two patients for presence or absence of STSs. Solid black bars encompass STSs found to be present. Gray bars indicate breakpoint intervals within IR3's distal arm that could not be further narrowed due to cross-amplification of identical sequences in IR3's proximal arm. See Figure S6 for identifiers of patients tested. (D) Hybridization of probes pDP97 (to centromeric DYZ3 repeats), in green, and 242E13 (to DYZ1 repeats in distal Yq heterochromatin), in red, to metaphase chrY of normal male (above) and to idicYq with breakpoint in IR3 (below). (Metaphase FISH precludes resolution of two centromeric signals in this idicYq.) All images at same magnification. (E) Interphase FISH demonstrates duplication of sequences proximal to IR3 in idicYq. Hybridization of probes 15499/15500 (proximal to IR3), in red, and pDP97, in green, produced expected patterns of red-green on chrY of normal male (above) and green-red-red-green on idicYq with breakpoint in IR3 (below). All images at same magnification. Two hundred nuclei were scored (Figure S7).

Figure 6. Correlates of intercentromeric distance in idicYp chromosomes: centromere inactivation and sex reversal

(A) Active chrY centromeres identified by immunofluorescence followed by FISH (IF-FISH). Anti-CENP-E antibody staining, in red, identifies all active centromeres. FISH probe pDP97 (to DYZ3 alpha satellite repeats), in green, identifies chrY centromeric DNA. IF-FISH to chrY of normal male control produced expected signals at single centromere. (B) IF-FISH to idicYp case with breakpoint in palindrome P6 demonstrates cell-to-cell mosaicism for functionally dicentric (left) or functionally monocentric (right) chromosomes. (C) IF-FISH to idicYp cases with breakpoints in palindrome P1 (left) or in DYZ18/DYZ1/DYZ2 heterochromatin (right) demonstrates functional inactivation of one Y centromere. (D) Plots of recombination sites in 13 idicYp cases assayed by IF-FISH and displaying either cell-to-cell mosaicism for functionally dicentric and monocentric idicYp chromosomes (three cases, above) or exclusively functionally monocentric idicYp chromosomes (ten cases, below). For each cell line, ≥20 idicYp-bearing spreads of good morphology were scored. Among the three cases with cell-to-cell variation, fraction of cells displaying functionally dicentric idicYp chromosomes ranged from 41% to 77%. See Figure S8 for additional data. (E) Plots of intercentromeric distances in SRY-positive idicYp or isoYp chromosomes in 18 feminized individuals (above) and 40 males (below). Dotted lines indicate mean intercentromeric distances for the two groups; 95% confidence intervals calculated by bootstrapping method.

Figure 7. Model of DSB resolution in MSY direct and inverted repeats (palindromes) by NCO and CO pathways

Sequence identity between palindrome arms or inverted repeats, and between direct repeats, is maintained by NCO resolution of DSBs; such gene conversion could occur between sister chromatids or within a single chromatid. In the case of palindromes or inverted repeats, CO resolution between sister chromatids can generate an idicY and an acentric fragment, while CO resolution within a chromatid results in inversion. In the case of direct repeats, CO resolution between sister chromatids can generate a duplication and an interstitial deletion, while CO resolution within a chromatid yields an interstitial deletion and an acentric fragment.