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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.

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DUP-TRP/INV-DUP structures at the PLP1 locus.A) The aCGH results from patient P1407 showing a duplication of PLP1 and a distal triplication-duplication structure are shown at the top, with duplications in red and triplication in blue. The relative genomic regions are labeled with letters to distinguish their relative positions within the CGR. The IRs flanking segment e (A1a and A1b) are denoted by inverted blue and purple triangles, respectively. B) Two potential structures of the generalized DUP-TRP/INV-DUP rearrangement that are consistent with Jct2 sequencing are shown in the lower panel of the figure in relation to the canonical genomic structure at the top. Here, the unique proximal breakpoint junction location that differs between patients, the LCR-mediated distal inversion breakpoint junction, and the inverted triplication region are seen. Letters followed by a prime symbol indicate duplicated segments. Two prime symbols indicate the triplicated segment.
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pgen.1005050.g004: DUP-TRP/INV-DUP structures at the PLP1 locus.A) The aCGH results from patient P1407 showing a duplication of PLP1 and a distal triplication-duplication structure are shown at the top, with duplications in red and triplication in blue. The relative genomic regions are labeled with letters to distinguish their relative positions within the CGR. The IRs flanking segment e (A1a and A1b) are denoted by inverted blue and purple triangles, respectively. B) Two potential structures of the generalized DUP-TRP/INV-DUP rearrangement that are consistent with Jct2 sequencing are shown in the lower panel of the figure in relation to the canonical genomic structure at the top. Here, the unique proximal breakpoint junction location that differs between patients, the LCR-mediated distal inversion breakpoint junction, and the inverted triplication region are seen. Letters followed by a prime symbol indicate duplicated segments. Two prime symbols indicate the triplicated segment.

Mentions: The DUP-TRP/INV-DUP structure hypothesized for these 16 individuals postulates that although there are 4 copy number transitions in these patients, there are only two breakpoint junctions (Fig. 4A). We have sequenced Jct2 in all 16 patients; Southern blotting and quantitative PCR were used to determine Jct1, and direct junction sequencing was successful for BAB1612/P374 (Figs. 3, 4 and S6). Additionally, due to the small size (~ 254 bp) of the triplication in P255/298, a PCR approach using one primer at the proximal duplication junction and one within the LCR validated the overall structure of this rearrangement as DUP-TRP/INV-DUP.


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)

DUP-TRP/INV-DUP structures at the PLP1 locus.A) The aCGH results from patient P1407 showing a duplication of PLP1 and a distal triplication-duplication structure are shown at the top, with duplications in red and triplication in blue. The relative genomic regions are labeled with letters to distinguish their relative positions within the CGR. The IRs flanking segment e (A1a and A1b) are denoted by inverted blue and purple triangles, respectively. B) Two potential structures of the generalized DUP-TRP/INV-DUP rearrangement that are consistent with Jct2 sequencing are shown in the lower panel of the figure in relation to the canonical genomic structure at the top. Here, the unique proximal breakpoint junction location that differs between patients, the LCR-mediated distal inversion breakpoint junction, and the inverted triplication region are seen. Letters followed by a prime symbol indicate duplicated segments. Two prime symbols indicate the triplicated segment.
© Copyright Policy
Related In: Results  -  Collection

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

pgen.1005050.g004: DUP-TRP/INV-DUP structures at the PLP1 locus.A) The aCGH results from patient P1407 showing a duplication of PLP1 and a distal triplication-duplication structure are shown at the top, with duplications in red and triplication in blue. The relative genomic regions are labeled with letters to distinguish their relative positions within the CGR. The IRs flanking segment e (A1a and A1b) are denoted by inverted blue and purple triangles, respectively. B) Two potential structures of the generalized DUP-TRP/INV-DUP rearrangement that are consistent with Jct2 sequencing are shown in the lower panel of the figure in relation to the canonical genomic structure at the top. Here, the unique proximal breakpoint junction location that differs between patients, the LCR-mediated distal inversion breakpoint junction, and the inverted triplication region are seen. Letters followed by a prime symbol indicate duplicated segments. Two prime symbols indicate the triplicated segment.
Mentions: The DUP-TRP/INV-DUP structure hypothesized for these 16 individuals postulates that although there are 4 copy number transitions in these patients, there are only two breakpoint junctions (Fig. 4A). We have sequenced Jct2 in all 16 patients; Southern blotting and quantitative PCR were used to determine Jct1, and direct junction sequencing was successful for BAB1612/P374 (Figs. 3, 4 and S6). Additionally, due to the small size (~ 254 bp) of the triplication in P255/298, a PCR approach using one primer at the proximal duplication junction and one within the LCR validated the overall structure of this rearrangement as DUP-TRP/INV-DUP.

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