Limits...
Complex genomic rearrangements at the PLP1 locus include triplication and quadruplication.

Beck CR, Carvalho CM, Banser L, Gambin T, Stubbolo D, Yuan B, Sperle K, McCahan SM, Henneke M, Seeman P, Garbern JY, Hobson GM, Lupski JR - PLoS Genet. (2015)

Bottom Line: We investigated 17 unrelated PMD subjects with copy number gains at the PLP1 locus including triplication and quadruplication of specific genomic intervals-16/17 were found to have a DUP-TRP/INV-DUP rearrangement product.An IR distal to PLP1 facilitates DUP-TRP/INV-DUP formation as well as an inversion structural variation found frequently amongst normal individuals.Moreover, we provide evidence that quadruplication and potentially higher order amplification of a genomic interval can occur in a manner consistent with rolling circle amplification as predicted by the microhomology-mediated break induced replication (MMBIR) model.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America.

ABSTRACT
Inverted repeats (IRs) can facilitate structural variation as crucibles of genomic rearrangement. Complex duplication-inverted triplication-duplication (DUP-TRP/INV-DUP) rearrangements that contain breakpoint junctions within IRs have been recently associated with both MECP2 duplication syndrome (MIM#300260) and Pelizaeus-Merzbacher disease (PMD, MIM#312080). We investigated 17 unrelated PMD subjects with copy number gains at the PLP1 locus including triplication and quadruplication of specific genomic intervals-16/17 were found to have a DUP-TRP/INV-DUP rearrangement product. An IR distal to PLP1 facilitates DUP-TRP/INV-DUP formation as well as an inversion structural variation found frequently amongst normal individuals. We show that a homology-or homeology-driven replicative mechanism of DNA repair can apparently mediate template switches within stretches of microhomology. Moreover, we provide evidence that quadruplication and potentially higher order amplification of a genomic interval can occur in a manner consistent with rolling circle amplification as predicted by the microhomology-mediated break induced replication (MMBIR) model.

Show MeSH

Related in: MedlinePlus

Inversion discovery and frequency between A1a and A1b.A) A depiction of the PLP1 genomic region on chromosome Xq22.2. PLP1 is proximal to the LCR structures and the black horizontal arrow indicates direction of transcription. There are three IRs present at chrX:103,171,387–103,359,682: the outer C and D repeats, middle A1a and A1b repeats, and inner A2 and A3 repeats [23,24]. The gene and the IR structures are separated by ~150 kb. B) A common inversion, discovered in the HGSV resource, is depicted between the A1a and A1b repeats. This inversion was present in at least 5/9 of individuals in the fosmid resource, and is possible in three additional people (S1 Fig). C) A Southern blotting scheme to distinguish between reference and inversion alleles is depicted, with A1a, A1b, A2 and A3 represented as above. Female genomes have two alleles, and phenotypically normal males have one allele (blot quantitated in S1 Table). Digestion with BssSI (depicted by black vertical lines) and detection with a probe proximal to LCR A1a (indicated by red star) should distinguish reference (25 kb, red) from inverted (29 kb, purple) alleles. Nine individuals from the HapMap population were studied for inversion via Southern blotting. Gender of the individual is indicated by circles (female) or squares (male) above the blot. DNA identifiers (NA numbers) are consistent with Coriell names (http://ccr.coriell.org/), and fosmid libraries (ABC library identifiers) are as in Kidd et al. [49]. The population of origin for each individual and the genotypes are indicated at the bottom of the blot. H = Han Chinese, J = Japanese, Y = Yoruban, and U = unknown. Genotyping for 8 additional individuals is depicted in S3 Fig.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4352052&req=5

pgen.1005050.g001: Inversion discovery and frequency between A1a and A1b.A) A depiction of the PLP1 genomic region on chromosome Xq22.2. PLP1 is proximal to the LCR structures and the black horizontal arrow indicates direction of transcription. There are three IRs present at chrX:103,171,387–103,359,682: the outer C and D repeats, middle A1a and A1b repeats, and inner A2 and A3 repeats [23,24]. The gene and the IR structures are separated by ~150 kb. B) A common inversion, discovered in the HGSV resource, is depicted between the A1a and A1b repeats. This inversion was present in at least 5/9 of individuals in the fosmid resource, and is possible in three additional people (S1 Fig). C) A Southern blotting scheme to distinguish between reference and inversion alleles is depicted, with A1a, A1b, A2 and A3 represented as above. Female genomes have two alleles, and phenotypically normal males have one allele (blot quantitated in S1 Table). Digestion with BssSI (depicted by black vertical lines) and detection with a probe proximal to LCR A1a (indicated by red star) should distinguish reference (25 kb, red) from inverted (29 kb, purple) alleles. Nine individuals from the HapMap population were studied for inversion via Southern blotting. Gender of the individual is indicated by circles (female) or squares (male) above the blot. DNA identifiers (NA numbers) are consistent with Coriell names (http://ccr.coriell.org/), and fosmid libraries (ABC library identifiers) are as in Kidd et al. [49]. The population of origin for each individual and the genotypes are indicated at the bottom of the blot. H = Han Chinese, J = Japanese, Y = Yoruban, and U = unknown. Genotyping for 8 additional individuals is depicted in S3 Fig.

Mentions: The 186 kb genomic interval (ChrX: 103,172,000–103,358,000 in hg19) located ~150 kb distal to PLP1 contains a complex genomic architecture in the haploid reference genome. This region consists of an array of IRs, with the ~40 kb outer C and D repeats having ~93% identity, the middle A1a and A1b repeats ~20 kb in size and ~99% identical, and the innermost ~10 kb A2 and A3 repeats showing ~87% identity both with each other and with A1a and A1b (Fig. 1A) [16,23,24]. The IR architecture predicts the potential for inversion mediated by non-allelic homologous recombination (NAHR), resulting in at least two structural haplotypes, analogous to the H1 and H2 structural variant (SV) alleles at the MECP2 locus [1]. Indeed, in silico analysis of the human genome SV track from the UCSC Genome Browser (www.genome.ucsc.edu) suggests the existence of such an SV allele [25]. The browser track indicates fosmids consistent with inversions spanning both of the A1a and A1b LCRs in 5 of 9 individuals (S1 Fig) [8,26]. These data indicate that there was an inversion between A1a and A1b LCRs and that the inversion haplotype exists at a relatively high allele frequency as a non-pathogenic rearrangement in HapMap individuals (Fig. 1B). Further investigation mapped the apparent ectopic crossover for the NAHR-mediated inversion in a fosmid from the G248 library to nucleotide-level resolution (S2 Fig).


Complex genomic rearrangements at the PLP1 locus include triplication and quadruplication.

Beck CR, Carvalho CM, Banser L, Gambin T, Stubbolo D, Yuan B, Sperle K, McCahan SM, Henneke M, Seeman P, Garbern JY, Hobson GM, Lupski JR - PLoS Genet. (2015)

Inversion discovery and frequency between A1a and A1b.A) A depiction of the PLP1 genomic region on chromosome Xq22.2. PLP1 is proximal to the LCR structures and the black horizontal arrow indicates direction of transcription. There are three IRs present at chrX:103,171,387–103,359,682: the outer C and D repeats, middle A1a and A1b repeats, and inner A2 and A3 repeats [23,24]. The gene and the IR structures are separated by ~150 kb. B) A common inversion, discovered in the HGSV resource, is depicted between the A1a and A1b repeats. This inversion was present in at least 5/9 of individuals in the fosmid resource, and is possible in three additional people (S1 Fig). C) A Southern blotting scheme to distinguish between reference and inversion alleles is depicted, with A1a, A1b, A2 and A3 represented as above. Female genomes have two alleles, and phenotypically normal males have one allele (blot quantitated in S1 Table). Digestion with BssSI (depicted by black vertical lines) and detection with a probe proximal to LCR A1a (indicated by red star) should distinguish reference (25 kb, red) from inverted (29 kb, purple) alleles. Nine individuals from the HapMap population were studied for inversion via Southern blotting. Gender of the individual is indicated by circles (female) or squares (male) above the blot. DNA identifiers (NA numbers) are consistent with Coriell names (http://ccr.coriell.org/), and fosmid libraries (ABC library identifiers) are as in Kidd et al. [49]. The population of origin for each individual and the genotypes are indicated at the bottom of the blot. H = Han Chinese, J = Japanese, Y = Yoruban, and U = unknown. Genotyping for 8 additional individuals is depicted in S3 Fig.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4352052&req=5

pgen.1005050.g001: Inversion discovery and frequency between A1a and A1b.A) A depiction of the PLP1 genomic region on chromosome Xq22.2. PLP1 is proximal to the LCR structures and the black horizontal arrow indicates direction of transcription. There are three IRs present at chrX:103,171,387–103,359,682: the outer C and D repeats, middle A1a and A1b repeats, and inner A2 and A3 repeats [23,24]. The gene and the IR structures are separated by ~150 kb. B) A common inversion, discovered in the HGSV resource, is depicted between the A1a and A1b repeats. This inversion was present in at least 5/9 of individuals in the fosmid resource, and is possible in three additional people (S1 Fig). C) A Southern blotting scheme to distinguish between reference and inversion alleles is depicted, with A1a, A1b, A2 and A3 represented as above. Female genomes have two alleles, and phenotypically normal males have one allele (blot quantitated in S1 Table). Digestion with BssSI (depicted by black vertical lines) and detection with a probe proximal to LCR A1a (indicated by red star) should distinguish reference (25 kb, red) from inverted (29 kb, purple) alleles. Nine individuals from the HapMap population were studied for inversion via Southern blotting. Gender of the individual is indicated by circles (female) or squares (male) above the blot. DNA identifiers (NA numbers) are consistent with Coriell names (http://ccr.coriell.org/), and fosmid libraries (ABC library identifiers) are as in Kidd et al. [49]. The population of origin for each individual and the genotypes are indicated at the bottom of the blot. H = Han Chinese, J = Japanese, Y = Yoruban, and U = unknown. Genotyping for 8 additional individuals is depicted in S3 Fig.
Mentions: The 186 kb genomic interval (ChrX: 103,172,000–103,358,000 in hg19) located ~150 kb distal to PLP1 contains a complex genomic architecture in the haploid reference genome. This region consists of an array of IRs, with the ~40 kb outer C and D repeats having ~93% identity, the middle A1a and A1b repeats ~20 kb in size and ~99% identical, and the innermost ~10 kb A2 and A3 repeats showing ~87% identity both with each other and with A1a and A1b (Fig. 1A) [16,23,24]. The IR architecture predicts the potential for inversion mediated by non-allelic homologous recombination (NAHR), resulting in at least two structural haplotypes, analogous to the H1 and H2 structural variant (SV) alleles at the MECP2 locus [1]. Indeed, in silico analysis of the human genome SV track from the UCSC Genome Browser (www.genome.ucsc.edu) suggests the existence of such an SV allele [25]. The browser track indicates fosmids consistent with inversions spanning both of the A1a and A1b LCRs in 5 of 9 individuals (S1 Fig) [8,26]. These data indicate that there was an inversion between A1a and A1b LCRs and that the inversion haplotype exists at a relatively high allele frequency as a non-pathogenic rearrangement in HapMap individuals (Fig. 1B). Further investigation mapped the apparent ectopic crossover for the NAHR-mediated inversion in a fosmid from the G248 library to nucleotide-level resolution (S2 Fig).

Bottom Line: We investigated 17 unrelated PMD subjects with copy number gains at the PLP1 locus including triplication and quadruplication of specific genomic intervals-16/17 were found to have a DUP-TRP/INV-DUP rearrangement product.An IR distal to PLP1 facilitates DUP-TRP/INV-DUP formation as well as an inversion structural variation found frequently amongst normal individuals.Moreover, we provide evidence that quadruplication and potentially higher order amplification of a genomic interval can occur in a manner consistent with rolling circle amplification as predicted by the microhomology-mediated break induced replication (MMBIR) model.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America.

ABSTRACT
Inverted repeats (IRs) can facilitate structural variation as crucibles of genomic rearrangement. Complex duplication-inverted triplication-duplication (DUP-TRP/INV-DUP) rearrangements that contain breakpoint junctions within IRs have been recently associated with both MECP2 duplication syndrome (MIM#300260) and Pelizaeus-Merzbacher disease (PMD, MIM#312080). We investigated 17 unrelated PMD subjects with copy number gains at the PLP1 locus including triplication and quadruplication of specific genomic intervals-16/17 were found to have a DUP-TRP/INV-DUP rearrangement product. An IR distal to PLP1 facilitates DUP-TRP/INV-DUP formation as well as an inversion structural variation found frequently amongst normal individuals. We show that a homology-or homeology-driven replicative mechanism of DNA repair can apparently mediate template switches within stretches of microhomology. Moreover, we provide evidence that quadruplication and potentially higher order amplification of a genomic interval can occur in a manner consistent with rolling circle amplification as predicted by the microhomology-mediated break induced replication (MMBIR) model.

Show MeSH
Related in: MedlinePlus