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Pseudoautosomal region 1 length polymorphism in the human population.

Mensah MA, Hestand MS, Larmuseau MH, Isrie M, Vanderheyden N, Declercq M, Souche EL, Van Houdt J, Stoeva R, Van Esch H, Devriendt K, Voet T, Decorte R, Robinson PN, Vermeesch JR - PLoS Genet. (2014)

Bottom Line: Subsequent genomic analysis demonstrated that an insertional translocation of X chromosomal sequence into the Y chromosome generates an extended PAR [corrected].The insertion is generated by non-allelic homologous recombination between a 548 bp LTR6B repeat within the Y chromosome PAR1 and a second LTR6B repeat located 105 kb from the PAR boundary on the X chromosome.The identification of the reciprocal deletion on the X chromosome in one family and the occurrence of the variant in different chromosome Y haplogroups demonstrate this is a recurrent genomic rearrangement in the human population.This finding represents a novel mechanism shaping sex chromosomal evolution.

View Article: PubMed Central - PubMed

Affiliation: KU Leuven, Department of Human Genetics, Leuven, Belgium; Institut für Medizinische Genetik und Humangenetik, Charité - Universitätsmedizin Berlin, Berlin, Germany.

ABSTRACT
The human sex chromosomes differ in sequence, except for the pseudoautosomal regions (PAR) at the terminus of the short and the long arms, denoted as PAR1 and PAR2. The boundary between PAR1 and the unique X and Y sequences was established during the divergence of the great apes. During a copy number variation screen, we noted a paternally inherited chromosome X duplication in 15 independent families. Subsequent genomic analysis demonstrated that an insertional translocation of X chromosomal sequence into the Y chromosome generates an extended PAR [corrected].The insertion is generated by non-allelic homologous recombination between a 548 bp LTR6B repeat within the Y chromosome PAR1 and a second LTR6B repeat located 105 kb from the PAR boundary on the X chromosome. The identification of the reciprocal deletion on the X chromosome in one family and the occurrence of the variant in different chromosome Y haplogroups demonstrate this is a recurrent genomic rearrangement in the human population. This finding represents a novel mechanism shaping sex chromosomal evolution.

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Related in: MedlinePlus

Sequencing to validate the insertion and demonstrate recurrence.(A) Illustrations of a reference Y chromosome, a reference X chromosome, and a Y chromosome with an X insertion. X specific sequence is indicated in red, Y specific sequence in blue, PAR1 reference sequence in purple, and LTR6B's in yellow. Arrows indicate primer pairs, with a bar representing an amplifiable product. The position of the SNPs of this study is shown in the order found in the amplicon. (B) PCRs using the Sanger.Junc primers shows bands for patients (P) and fathers (F), but not mothers (M), male controls (mc), female control (fc) or negative controls (neg), confirming the presence of an X specific insertional translocation in Y. (C) Sequenced amplicons of PCRs from part B, excluding reference upstream/downstream sequence. Red letters are from the X specific reference sequence. Yellow letters are from LTR6B reference sequence with red highlights indicating X specific LTR6B sequence and purple highlights indicating sequence specific for pseudoautosomal LTR6B. Purple letters indicate pseudoautosomal reference sequence. The gap underlined in red indicate bases missing from the X specific LTR6B. In black are annotated SNPs/Indels. In order from the beginning to the end of sequences, green boxes indicate SNP positions for rs2534625/rs12843082, rs2316283, rs2534627, and rs2857320. This Sanger sequencing identified two junction types, indicated as Junc1 and Junc2. (D) Phased haplotypes found through PacBio amplicon sequencing of the PacBio Duplication amplicons, with haplotypes assigned numbers indicated by gray boxes. Families in which both the patient and father were sequenced are color coded. No color indicates a sample in which the father was not sequenced. * Each individual has two haplotypes in the figure, except patients 10 and 15, which had a second unillustrated haplotype with many more variants that more closely resembled Y chromosome sequence.
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pgen-1004578-g002: Sequencing to validate the insertion and demonstrate recurrence.(A) Illustrations of a reference Y chromosome, a reference X chromosome, and a Y chromosome with an X insertion. X specific sequence is indicated in red, Y specific sequence in blue, PAR1 reference sequence in purple, and LTR6B's in yellow. Arrows indicate primer pairs, with a bar representing an amplifiable product. The position of the SNPs of this study is shown in the order found in the amplicon. (B) PCRs using the Sanger.Junc primers shows bands for patients (P) and fathers (F), but not mothers (M), male controls (mc), female control (fc) or negative controls (neg), confirming the presence of an X specific insertional translocation in Y. (C) Sequenced amplicons of PCRs from part B, excluding reference upstream/downstream sequence. Red letters are from the X specific reference sequence. Yellow letters are from LTR6B reference sequence with red highlights indicating X specific LTR6B sequence and purple highlights indicating sequence specific for pseudoautosomal LTR6B. Purple letters indicate pseudoautosomal reference sequence. The gap underlined in red indicate bases missing from the X specific LTR6B. In black are annotated SNPs/Indels. In order from the beginning to the end of sequences, green boxes indicate SNP positions for rs2534625/rs12843082, rs2316283, rs2534627, and rs2857320. This Sanger sequencing identified two junction types, indicated as Junc1 and Junc2. (D) Phased haplotypes found through PacBio amplicon sequencing of the PacBio Duplication amplicons, with haplotypes assigned numbers indicated by gray boxes. Families in which both the patient and father were sequenced are color coded. No color indicates a sample in which the father was not sequenced. * Each individual has two haplotypes in the figure, except patients 10 and 15, which had a second unillustrated haplotype with many more variants that more closely resembled Y chromosome sequence.

Mentions: Upon closer scrutiny of the aligned reads, the PAB region featured three different types of reads: reference Y-PAB reads, reference X-PAB reads, and SNP containing X-PAB reads. The PAB also showed three stretches of heterozygous SNPs: a 33% allele frequency region flanked by two 50% allele frequency regions (Figure 1 D). Since males should have no heterozygous SNPs in their hemizygous X-specific sequences and pseudoautosomal SNPs should show allele ratios of 50% we hypothesized that one portion of the pseudoautosomal region was duplicated. Indeed, the 33% allele frequency region and the proximal 50% allele frequency region represent a duplication event while the distal 50% allele frequency region represents the normal pseudoautosomal SNPs. The breakpoint was delineated by selecting the most proximal (chrX:2,694,303) SNP with an allele frequency of 50% and the most distal (chrX:2,694,429) SNP with an allele frequency of 30%. Interestingly, those SNPs both lie in a long terminal repeat, LTR6B, chrX:2,694,151-2,694,702 (551bp). The most proximal 50% allele frequency SNP was also near a second LTR6B repeat, chrX:2,808,549-2,809,097 (548 bp). These repeats explain that more than 99% of the reads mapping around the SNP frequency changes feature a mapping quality of 0, an indication of reads that map to multiple locations. The presence of these repeats at both sides of the duplicon also explain the absence of chimeric pairs and split reads. The duplicon thus comprises 110 kb of X-specific sequences as well as 5 kb proximal PAR1, resulting in the construct illustrated in Figure 2 A. The 5 kb sequence is present as three copies in the patient (once on his normal X chromosome and twice on his Y chromosome with the X insertion), which explains the 33% SNP ratio profile as well as the presence of three different kinds of reads at the PAB.


Pseudoautosomal region 1 length polymorphism in the human population.

Mensah MA, Hestand MS, Larmuseau MH, Isrie M, Vanderheyden N, Declercq M, Souche EL, Van Houdt J, Stoeva R, Van Esch H, Devriendt K, Voet T, Decorte R, Robinson PN, Vermeesch JR - PLoS Genet. (2014)

Sequencing to validate the insertion and demonstrate recurrence.(A) Illustrations of a reference Y chromosome, a reference X chromosome, and a Y chromosome with an X insertion. X specific sequence is indicated in red, Y specific sequence in blue, PAR1 reference sequence in purple, and LTR6B's in yellow. Arrows indicate primer pairs, with a bar representing an amplifiable product. The position of the SNPs of this study is shown in the order found in the amplicon. (B) PCRs using the Sanger.Junc primers shows bands for patients (P) and fathers (F), but not mothers (M), male controls (mc), female control (fc) or negative controls (neg), confirming the presence of an X specific insertional translocation in Y. (C) Sequenced amplicons of PCRs from part B, excluding reference upstream/downstream sequence. Red letters are from the X specific reference sequence. Yellow letters are from LTR6B reference sequence with red highlights indicating X specific LTR6B sequence and purple highlights indicating sequence specific for pseudoautosomal LTR6B. Purple letters indicate pseudoautosomal reference sequence. The gap underlined in red indicate bases missing from the X specific LTR6B. In black are annotated SNPs/Indels. In order from the beginning to the end of sequences, green boxes indicate SNP positions for rs2534625/rs12843082, rs2316283, rs2534627, and rs2857320. This Sanger sequencing identified two junction types, indicated as Junc1 and Junc2. (D) Phased haplotypes found through PacBio amplicon sequencing of the PacBio Duplication amplicons, with haplotypes assigned numbers indicated by gray boxes. Families in which both the patient and father were sequenced are color coded. No color indicates a sample in which the father was not sequenced. * Each individual has two haplotypes in the figure, except patients 10 and 15, which had a second unillustrated haplotype with many more variants that more closely resembled Y chromosome sequence.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4222609&req=5

pgen-1004578-g002: Sequencing to validate the insertion and demonstrate recurrence.(A) Illustrations of a reference Y chromosome, a reference X chromosome, and a Y chromosome with an X insertion. X specific sequence is indicated in red, Y specific sequence in blue, PAR1 reference sequence in purple, and LTR6B's in yellow. Arrows indicate primer pairs, with a bar representing an amplifiable product. The position of the SNPs of this study is shown in the order found in the amplicon. (B) PCRs using the Sanger.Junc primers shows bands for patients (P) and fathers (F), but not mothers (M), male controls (mc), female control (fc) or negative controls (neg), confirming the presence of an X specific insertional translocation in Y. (C) Sequenced amplicons of PCRs from part B, excluding reference upstream/downstream sequence. Red letters are from the X specific reference sequence. Yellow letters are from LTR6B reference sequence with red highlights indicating X specific LTR6B sequence and purple highlights indicating sequence specific for pseudoautosomal LTR6B. Purple letters indicate pseudoautosomal reference sequence. The gap underlined in red indicate bases missing from the X specific LTR6B. In black are annotated SNPs/Indels. In order from the beginning to the end of sequences, green boxes indicate SNP positions for rs2534625/rs12843082, rs2316283, rs2534627, and rs2857320. This Sanger sequencing identified two junction types, indicated as Junc1 and Junc2. (D) Phased haplotypes found through PacBio amplicon sequencing of the PacBio Duplication amplicons, with haplotypes assigned numbers indicated by gray boxes. Families in which both the patient and father were sequenced are color coded. No color indicates a sample in which the father was not sequenced. * Each individual has two haplotypes in the figure, except patients 10 and 15, which had a second unillustrated haplotype with many more variants that more closely resembled Y chromosome sequence.
Mentions: Upon closer scrutiny of the aligned reads, the PAB region featured three different types of reads: reference Y-PAB reads, reference X-PAB reads, and SNP containing X-PAB reads. The PAB also showed three stretches of heterozygous SNPs: a 33% allele frequency region flanked by two 50% allele frequency regions (Figure 1 D). Since males should have no heterozygous SNPs in their hemizygous X-specific sequences and pseudoautosomal SNPs should show allele ratios of 50% we hypothesized that one portion of the pseudoautosomal region was duplicated. Indeed, the 33% allele frequency region and the proximal 50% allele frequency region represent a duplication event while the distal 50% allele frequency region represents the normal pseudoautosomal SNPs. The breakpoint was delineated by selecting the most proximal (chrX:2,694,303) SNP with an allele frequency of 50% and the most distal (chrX:2,694,429) SNP with an allele frequency of 30%. Interestingly, those SNPs both lie in a long terminal repeat, LTR6B, chrX:2,694,151-2,694,702 (551bp). The most proximal 50% allele frequency SNP was also near a second LTR6B repeat, chrX:2,808,549-2,809,097 (548 bp). These repeats explain that more than 99% of the reads mapping around the SNP frequency changes feature a mapping quality of 0, an indication of reads that map to multiple locations. The presence of these repeats at both sides of the duplicon also explain the absence of chimeric pairs and split reads. The duplicon thus comprises 110 kb of X-specific sequences as well as 5 kb proximal PAR1, resulting in the construct illustrated in Figure 2 A. The 5 kb sequence is present as three copies in the patient (once on his normal X chromosome and twice on his Y chromosome with the X insertion), which explains the 33% SNP ratio profile as well as the presence of three different kinds of reads at the PAB.

Bottom Line: Subsequent genomic analysis demonstrated that an insertional translocation of X chromosomal sequence into the Y chromosome generates an extended PAR [corrected].The insertion is generated by non-allelic homologous recombination between a 548 bp LTR6B repeat within the Y chromosome PAR1 and a second LTR6B repeat located 105 kb from the PAR boundary on the X chromosome.The identification of the reciprocal deletion on the X chromosome in one family and the occurrence of the variant in different chromosome Y haplogroups demonstrate this is a recurrent genomic rearrangement in the human population.This finding represents a novel mechanism shaping sex chromosomal evolution.

View Article: PubMed Central - PubMed

Affiliation: KU Leuven, Department of Human Genetics, Leuven, Belgium; Institut für Medizinische Genetik und Humangenetik, Charité - Universitätsmedizin Berlin, Berlin, Germany.

ABSTRACT
The human sex chromosomes differ in sequence, except for the pseudoautosomal regions (PAR) at the terminus of the short and the long arms, denoted as PAR1 and PAR2. The boundary between PAR1 and the unique X and Y sequences was established during the divergence of the great apes. During a copy number variation screen, we noted a paternally inherited chromosome X duplication in 15 independent families. Subsequent genomic analysis demonstrated that an insertional translocation of X chromosomal sequence into the Y chromosome generates an extended PAR [corrected].The insertion is generated by non-allelic homologous recombination between a 548 bp LTR6B repeat within the Y chromosome PAR1 and a second LTR6B repeat located 105 kb from the PAR boundary on the X chromosome. The identification of the reciprocal deletion on the X chromosome in one family and the occurrence of the variant in different chromosome Y haplogroups demonstrate this is a recurrent genomic rearrangement in the human population. This finding represents a novel mechanism shaping sex chromosomal evolution.

Show MeSH
Related in: MedlinePlus