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Palindrome-Mediated Translocations in Humans: A New Mechanistic Model for Gross Chromosomal Rearrangements.

Inagaki H, Kato T, Tsutsumi M, Ouchi Y, Ohye T, Kurahashi H - Front Genet (2016)

Bottom Line: Indeed, experiments using a plasmid-based model system showed that the formation of non-B DNA is likely the key to palindrome-mediated genomic rearrangements.Some evidence implies a new mechanism that cruciform DNAs may come close together first in nucleus and illegitimately joined.Analysis of PATRR-mediated translocations in humans will provide further understanding of gross chromosomal rearrangements in many organisms.

View Article: PubMed Central - PubMed

Affiliation: Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health UniversityToyoake, Japan; Genome and Transcriptome Analysis Center, Fujita Health UniversityToyoake, Japan.

ABSTRACT
Palindromic DNA sequences, which can form secondary structures, are widely distributed in the human genome. Although the nature of the secondary structure-single-stranded "hairpin" or double-stranded "cruciform"-has been extensively investigated in vitro, the existence of such unusual non-B DNA in vivo remains controversial. Here, we review palindrome-mediated gross chromosomal rearrangements possibly induced by non-B DNA in humans. Recent advances in next-generation sequencing have not yet overcome the difficulty of palindromic sequence analysis. However, a dozen palindromic AT-rich repeat (PATRR) sequences have been identified at the breakpoints of recurrent or non-recurrent chromosomal translocations in humans. The breakages always occur at the center of the palindrome. Analyses of polymorphisms within the palindromes indicate that the symmetry and length of the palindrome affect the frequency of the de novo occurrence of these palindrome-mediated translocations, suggesting the involvement of non-B DNA. Indeed, experiments using a plasmid-based model system showed that the formation of non-B DNA is likely the key to palindrome-mediated genomic rearrangements. Some evidence implies a new mechanism that cruciform DNAs may come close together first in nucleus and illegitimately joined. Analysis of PATRR-mediated translocations in humans will provide further understanding of gross chromosomal rearrangements in many organisms.

No MeSH data available.


(A) Translocation model system. Two plasmids, one harboring a promoter, splicing donor, and PATRR11, and the other carrying PATRR22, a splicing acceptor, and a coding region of the GFP gene, were simultaneously transfected into HEK293 cells. After 24 h, fusion molecules generated by joining of the PATRR11 and PATRR22 at the center were detected by PCR or GFP-positive cells were monitored by flow cytometry (Inagaki et al., 2013). (B) Determination of the PATRR8 sequence by next-generation sequencing. Although the depth of the coverage was low at the center of the palindrome, massive parallel sequencing was able to fill the entire region of the palindrome (Mishra et al., 2014).
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Figure 1: (A) Translocation model system. Two plasmids, one harboring a promoter, splicing donor, and PATRR11, and the other carrying PATRR22, a splicing acceptor, and a coding region of the GFP gene, were simultaneously transfected into HEK293 cells. After 24 h, fusion molecules generated by joining of the PATRR11 and PATRR22 at the center were detected by PCR or GFP-positive cells were monitored by flow cytometry (Inagaki et al., 2013). (B) Determination of the PATRR8 sequence by next-generation sequencing. Although the depth of the coverage was low at the center of the palindrome, massive parallel sequencing was able to fill the entire region of the palindrome (Mishra et al., 2014).

Mentions: To determine the involvement of DNA replication in translocation formation, we established a model system for the t(11;22) translocation in cultured cells by using plasmids harboring PATRR11 or PATRR22 (Inagaki et al., 2009). Both plasmids were transfected into the HEK293 human cell line and we monitored the fusion of the different plasmids at each PATRR using GFP expression or translocation-specific PCR (Figure 1A). The results indicated that a translocation-like reaction took place. In this reaction, both PATRRs were cleaved at the center of the palindrome and joined via non-homologous end-joining in a similar manner to the human t(11;22) translocation. Crucially, the plasmids had no replication origin for human cells, which means that the translocation took place without DNA replication.


Palindrome-Mediated Translocations in Humans: A New Mechanistic Model for Gross Chromosomal Rearrangements.

Inagaki H, Kato T, Tsutsumi M, Ouchi Y, Ohye T, Kurahashi H - Front Genet (2016)

(A) Translocation model system. Two plasmids, one harboring a promoter, splicing donor, and PATRR11, and the other carrying PATRR22, a splicing acceptor, and a coding region of the GFP gene, were simultaneously transfected into HEK293 cells. After 24 h, fusion molecules generated by joining of the PATRR11 and PATRR22 at the center were detected by PCR or GFP-positive cells were monitored by flow cytometry (Inagaki et al., 2013). (B) Determination of the PATRR8 sequence by next-generation sequencing. Although the depth of the coverage was low at the center of the palindrome, massive parallel sequencing was able to fill the entire region of the palindrome (Mishra et al., 2014).
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4940405&req=5

Figure 1: (A) Translocation model system. Two plasmids, one harboring a promoter, splicing donor, and PATRR11, and the other carrying PATRR22, a splicing acceptor, and a coding region of the GFP gene, were simultaneously transfected into HEK293 cells. After 24 h, fusion molecules generated by joining of the PATRR11 and PATRR22 at the center were detected by PCR or GFP-positive cells were monitored by flow cytometry (Inagaki et al., 2013). (B) Determination of the PATRR8 sequence by next-generation sequencing. Although the depth of the coverage was low at the center of the palindrome, massive parallel sequencing was able to fill the entire region of the palindrome (Mishra et al., 2014).
Mentions: To determine the involvement of DNA replication in translocation formation, we established a model system for the t(11;22) translocation in cultured cells by using plasmids harboring PATRR11 or PATRR22 (Inagaki et al., 2009). Both plasmids were transfected into the HEK293 human cell line and we monitored the fusion of the different plasmids at each PATRR using GFP expression or translocation-specific PCR (Figure 1A). The results indicated that a translocation-like reaction took place. In this reaction, both PATRRs were cleaved at the center of the palindrome and joined via non-homologous end-joining in a similar manner to the human t(11;22) translocation. Crucially, the plasmids had no replication origin for human cells, which means that the translocation took place without DNA replication.

Bottom Line: Indeed, experiments using a plasmid-based model system showed that the formation of non-B DNA is likely the key to palindrome-mediated genomic rearrangements.Some evidence implies a new mechanism that cruciform DNAs may come close together first in nucleus and illegitimately joined.Analysis of PATRR-mediated translocations in humans will provide further understanding of gross chromosomal rearrangements in many organisms.

View Article: PubMed Central - PubMed

Affiliation: Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health UniversityToyoake, Japan; Genome and Transcriptome Analysis Center, Fujita Health UniversityToyoake, Japan.

ABSTRACT
Palindromic DNA sequences, which can form secondary structures, are widely distributed in the human genome. Although the nature of the secondary structure-single-stranded "hairpin" or double-stranded "cruciform"-has been extensively investigated in vitro, the existence of such unusual non-B DNA in vivo remains controversial. Here, we review palindrome-mediated gross chromosomal rearrangements possibly induced by non-B DNA in humans. Recent advances in next-generation sequencing have not yet overcome the difficulty of palindromic sequence analysis. However, a dozen palindromic AT-rich repeat (PATRR) sequences have been identified at the breakpoints of recurrent or non-recurrent chromosomal translocations in humans. The breakages always occur at the center of the palindrome. Analyses of polymorphisms within the palindromes indicate that the symmetry and length of the palindrome affect the frequency of the de novo occurrence of these palindrome-mediated translocations, suggesting the involvement of non-B DNA. Indeed, experiments using a plasmid-based model system showed that the formation of non-B DNA is likely the key to palindrome-mediated genomic rearrangements. Some evidence implies a new mechanism that cruciform DNAs may come close together first in nucleus and illegitimately joined. Analysis of PATRR-mediated translocations in humans will provide further understanding of gross chromosomal rearrangements in many organisms.

No MeSH data available.