Supplementary Information for

Figures

• Figure S1     Two-step model of formation of the pericentric Y-chromosome inversion observed in AMC0972. (A) Reference Y-chromosome structure and probe hybridization sites. (B) A two-step model explains the metaphase and interphase FISH results observed for AMC0972: 1) a gr/rg inversion within the AZFc region orients the IR1-b3 amplicon on Yq into inverted orientation relative to IR1 on Yp, and 2) intrachromatid crossing-over between IR on Yp and IR1-b3 on Yq results in a pericentric inversion.
• Figure S2     Inversion polymorphisms in the human Y chromosome alter the orientations of IR1 and IR4 amplicons. (A) Schematic representation of the human Y chromosome. The male-specific region of the Y chromosome, or MSY, is flanked by two pseudoautosomal regions, PAR1 and PAR2 (green), and contains blocks of heterochromatin (orange). (B) Inverted repeats IR1 and IR4 are composed of one amplicon on the short arm (Yp) and one amplicon on the long arm (Yq). In addition, segments of IR1 are repeated distally to IR1 on Yq: IR1-b3, IR1-g2, IR1-g3, and IR1-b4. (C) Inversion polymorphisms in Yp and in the AZFc region on Yq alter the orientation and arrangement of IR1 and IR4 amplicons on each chromosome arm. On Yp, the IR3/IR3 inversion changes the orientation of both IR1 and IR4. In the AZFc region, b2/b3 and gr/rg inversions change the orientations of various IR1 amplicons. (D) Six schematized dot plots, mirroring the magnified region shown in Fig. 2C. The sequence of each IR3 orientation (reference IR3/IR3, IR3/IR3 inversion) is plotted against the sequence of each of three common AZFc orientations (reference AZFc, b2/b3 inversion, gr/rg inversion) to identify putative inverted repeat pairs. Inverted repeats appear as vertical lines, direct repeats as horizontal lines. See Table 1 for sizes and sequence similarities of the 18 putative targets of homologous recombination.
• Figure S3     Fifty possible MSY structures can arise by homologous recombination between 18 pairs of IR1 or IR4 amplicons on opposing arms of the Y chromosome. (A–R) For each of 18 repeat pairs, we show: (i) a schematic of the parental Y-chromosome with the indicated orientations of IR3/IR3 and AZFc, and the sister-chromatid crossing-over event for that IR pair, resulting in the formation of a pseudoisoYp chromosome and pseudoisoYq chromosome; and (ii) a schematic of the parental Y-chromosome with the indicated orientations of IR3/IR3 and AZFc, and the intrachromatid crossing-over event for that IR pair, resulting in a pericentric inversion in that chromatid. Of a total of 54 pseudoisochromosomes and pericentric inversions, four are redundant; thus, there are 50 different Y-chromosome structures. Predicted hybridization sites of the probes used in metaphase and interphase FISH analysis are shown for each Y chromosome.

Tables