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Cruciform extrusion propensity of human translocation-mediating palindromic AT-rich repeats.

Kogo H, Inagaki H, Ohye T, Kato T, Emanuel BS, Kurahashi H - Nucleic Acids Res. (2007)

Bottom Line: The resultant deletions are putatively mediated by central cleavage by the structure-specific endonuclease SbcCD, indicating the possibility of a cruciform conformation in vivo.Insertion of a short spacer at the centre of the PATRR22 greatly reduces both its cruciform extrusion in vitro and instability in vivo.Taken together, cruciform extrusion propensity depends on the length and central symmetry of the PATRR, and is likely to determine the instability that leads to recurrent translocations in humans.

View Article: PubMed Central - PubMed

Affiliation: Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan.

ABSTRACT
There is an emerging consensus that secondary structures of DNA have the potential for genomic instability. Palindromic AT-rich repeats (PATRRs) are a characteristic sequence identified at each breakpoint of the recurrent constitutional t(11;22) and t(17;22) translocations in humans, named PATRR22 (approximately 600 bp), PATRR11 (approximately 450 bp) and PATRR17 (approximately 190 bp). The secondary structure-forming propensity in vitro and the instability in vivo have been experimentally evaluated for various PATRRs that differ regarding their size and symmetry. At physiological ionic strength, a cruciform structure is most frequently observed for the symmetric PATRR22, less often for the symmetric PATRR11, but not for the other PATRRs. In wild-type E. coli, only these two PATRRs undergo extensive instability, consistent with the relatively high incidence of the t(11;22) in humans. The resultant deletions are putatively mediated by central cleavage by the structure-specific endonuclease SbcCD, indicating the possibility of a cruciform conformation in vivo. Insertion of a short spacer at the centre of the PATRR22 greatly reduces both its cruciform extrusion in vitro and instability in vivo. Taken together, cruciform extrusion propensity depends on the length and central symmetry of the PATRR, and is likely to determine the instability that leads to recurrent translocations in humans.

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Potential secondary structures formed by single-stranded PATRR sequences. Eight-hundred nucleotides containing each PATRR at the centre are analysed by mfold to demonstrate the putative stem-loop structures formed by intrastrand basepairing. The most prominent stem-loop structure for each sequence is formed by every PATRR sequence, whose length is indicated in parentheses. With regard to the PATRR22-pal and the PATRR22-quasi, sequences around the centre are indicated. The lowercase sequences are PATRR11-derived sequences in the junction fragment of the t(11;22) that provide the SnaBI site used to ligate the proximal and distal arms of the PATRR22-derived sequence. The PATRR22-pal is a perfect palindrome, whereas the PATRR22-quasi is a quasipalindrome having a spacer of 9 nt at the centre and four mismatched bases at 23, 27, 28 and 29 nt away from the hairpin tip.
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Figure 1: Potential secondary structures formed by single-stranded PATRR sequences. Eight-hundred nucleotides containing each PATRR at the centre are analysed by mfold to demonstrate the putative stem-loop structures formed by intrastrand basepairing. The most prominent stem-loop structure for each sequence is formed by every PATRR sequence, whose length is indicated in parentheses. With regard to the PATRR22-pal and the PATRR22-quasi, sequences around the centre are indicated. The lowercase sequences are PATRR11-derived sequences in the junction fragment of the t(11;22) that provide the SnaBI site used to ligate the proximal and distal arms of the PATRR22-derived sequence. The PATRR22-pal is a perfect palindrome, whereas the PATRR22-quasi is a quasipalindrome having a spacer of 9 nt at the centre and four mismatched bases at 23, 27, 28 and 29 nt away from the hairpin tip.

Mentions: We have previously cloned the PATRR sequences on human chromosomes 11 and 17 using an optimized PCR method (4,6). The PATRR11 and the PATRR17 manifest length polymorphisms; PATRR11-long (445 bp) and PATRR11-short (205 bp), and PATRR17-long (187 bp) and PATRR17-short (161 bp). The long and short PATRRs are different not only with respect to their length, but also their symmetry. The long types of both PATRR11 and PATRR17 are nearly perfect palindromes, whereas the short versions have asymmetric regions around their centres. The authentic PATRR22 has not yet been cloned to date, but is presumed to be a nearly perfect palindrome of ∼590 bp based on junction fragment sequences of the der(11) and the der(22) of the t(11;22) (4,12). For experimental analysis in the present study, we prepared two artificial PATRR22 constructs; one is a completely perfect palindrome (PATRR22-pal, 602 bp), and the other is a quasipalindrome having a short spacer at the centre and four mismatched bases near the centre (PATRR22-quasi, 593 bp). The possible secondary structures formed by these PATRRs were analysed using the DNA mfold server (http://www.bioinfo.rpi.edu/applications/mfold/old/dna/), and they are schematically shown in Figure 1.Figure 1.


Cruciform extrusion propensity of human translocation-mediating palindromic AT-rich repeats.

Kogo H, Inagaki H, Ohye T, Kato T, Emanuel BS, Kurahashi H - Nucleic Acids Res. (2007)

Potential secondary structures formed by single-stranded PATRR sequences. Eight-hundred nucleotides containing each PATRR at the centre are analysed by mfold to demonstrate the putative stem-loop structures formed by intrastrand basepairing. The most prominent stem-loop structure for each sequence is formed by every PATRR sequence, whose length is indicated in parentheses. With regard to the PATRR22-pal and the PATRR22-quasi, sequences around the centre are indicated. The lowercase sequences are PATRR11-derived sequences in the junction fragment of the t(11;22) that provide the SnaBI site used to ligate the proximal and distal arms of the PATRR22-derived sequence. The PATRR22-pal is a perfect palindrome, whereas the PATRR22-quasi is a quasipalindrome having a spacer of 9 nt at the centre and four mismatched bases at 23, 27, 28 and 29 nt away from the hairpin tip.
© Copyright Policy - openaccess
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1851657&req=5

Figure 1: Potential secondary structures formed by single-stranded PATRR sequences. Eight-hundred nucleotides containing each PATRR at the centre are analysed by mfold to demonstrate the putative stem-loop structures formed by intrastrand basepairing. The most prominent stem-loop structure for each sequence is formed by every PATRR sequence, whose length is indicated in parentheses. With regard to the PATRR22-pal and the PATRR22-quasi, sequences around the centre are indicated. The lowercase sequences are PATRR11-derived sequences in the junction fragment of the t(11;22) that provide the SnaBI site used to ligate the proximal and distal arms of the PATRR22-derived sequence. The PATRR22-pal is a perfect palindrome, whereas the PATRR22-quasi is a quasipalindrome having a spacer of 9 nt at the centre and four mismatched bases at 23, 27, 28 and 29 nt away from the hairpin tip.
Mentions: We have previously cloned the PATRR sequences on human chromosomes 11 and 17 using an optimized PCR method (4,6). The PATRR11 and the PATRR17 manifest length polymorphisms; PATRR11-long (445 bp) and PATRR11-short (205 bp), and PATRR17-long (187 bp) and PATRR17-short (161 bp). The long and short PATRRs are different not only with respect to their length, but also their symmetry. The long types of both PATRR11 and PATRR17 are nearly perfect palindromes, whereas the short versions have asymmetric regions around their centres. The authentic PATRR22 has not yet been cloned to date, but is presumed to be a nearly perfect palindrome of ∼590 bp based on junction fragment sequences of the der(11) and the der(22) of the t(11;22) (4,12). For experimental analysis in the present study, we prepared two artificial PATRR22 constructs; one is a completely perfect palindrome (PATRR22-pal, 602 bp), and the other is a quasipalindrome having a short spacer at the centre and four mismatched bases near the centre (PATRR22-quasi, 593 bp). The possible secondary structures formed by these PATRRs were analysed using the DNA mfold server (http://www.bioinfo.rpi.edu/applications/mfold/old/dna/), and they are schematically shown in Figure 1.Figure 1.

Bottom Line: The resultant deletions are putatively mediated by central cleavage by the structure-specific endonuclease SbcCD, indicating the possibility of a cruciform conformation in vivo.Insertion of a short spacer at the centre of the PATRR22 greatly reduces both its cruciform extrusion in vitro and instability in vivo.Taken together, cruciform extrusion propensity depends on the length and central symmetry of the PATRR, and is likely to determine the instability that leads to recurrent translocations in humans.

View Article: PubMed Central - PubMed

Affiliation: Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan.

ABSTRACT
There is an emerging consensus that secondary structures of DNA have the potential for genomic instability. Palindromic AT-rich repeats (PATRRs) are a characteristic sequence identified at each breakpoint of the recurrent constitutional t(11;22) and t(17;22) translocations in humans, named PATRR22 (approximately 600 bp), PATRR11 (approximately 450 bp) and PATRR17 (approximately 190 bp). The secondary structure-forming propensity in vitro and the instability in vivo have been experimentally evaluated for various PATRRs that differ regarding their size and symmetry. At physiological ionic strength, a cruciform structure is most frequently observed for the symmetric PATRR22, less often for the symmetric PATRR11, but not for the other PATRRs. In wild-type E. coli, only these two PATRRs undergo extensive instability, consistent with the relatively high incidence of the t(11;22) in humans. The resultant deletions are putatively mediated by central cleavage by the structure-specific endonuclease SbcCD, indicating the possibility of a cruciform conformation in vivo. Insertion of a short spacer at the centre of the PATRR22 greatly reduces both its cruciform extrusion in vitro and instability in vivo. Taken together, cruciform extrusion propensity depends on the length and central symmetry of the PATRR, and is likely to determine the instability that leads to recurrent translocations in humans.

Show MeSH
Related in: MedlinePlus