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Discovery and characterization of Alu repeat sequences via precise local read assembly.

Wildschutte JH, Baron A, Diroff NM, Kidd JM - Nucleic Acids Res. (2015)

Bottom Line: In our assembled sequences, we find evidence of premature insertion mechanisms and observe 5' truncation in 16% of AluYa5 and AluYb8 insertions.The sites of truncation coincide with stem-loop structures and SRP9/14 binding sites in the Alu RNA, implicating L1 ORF2p pausing in the generation of 5' truncations.Additionally, we identified variable AluJ and AluS elements that likely arose due to non-retrotransposition mechanisms.

View Article: PubMed Central - PubMed

Affiliation: Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA.

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Length distribution of assembled AluYa5 and AluYb8 insertions. (A) Scaled representation of the AluYa5 and AluYb8 consensus and element properties. The Alu is comprised of two arms (left, blue; right, grey) joined by an A-rich region and having a 3′ poly-A tail. The A and B boxes indicate promoter regions. A 31 bp insertion distinguishes the arms. AluYb8 has a 3′ 7 bp insertion relative to Ya5; the sequences are otherwise structurally conserved. The gold bar shows bases within SRP/14 binding sites. (B) The size distribution of 351 AluYa5 and 215 AluYb8 assembled insertions relative to the respective subfamily consensus. The red dashed lines indicate peaks in truncation near 45 bp and 170 bp. The number of assembled insertions containing an aligned nucleotide is shown against the corresponding position in the consensus.
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Figure 3: Length distribution of assembled AluYa5 and AluYb8 insertions. (A) Scaled representation of the AluYa5 and AluYb8 consensus and element properties. The Alu is comprised of two arms (left, blue; right, grey) joined by an A-rich region and having a 3′ poly-A tail. The A and B boxes indicate promoter regions. A 31 bp insertion distinguishes the arms. AluYb8 has a 3′ 7 bp insertion relative to Ya5; the sequences are otherwise structurally conserved. The gold bar shows bases within SRP/14 binding sites. (B) The size distribution of 351 AluYa5 and 215 AluYb8 assembled insertions relative to the respective subfamily consensus. The red dashed lines indicate peaks in truncation near 45 bp and 170 bp. The number of assembled insertions containing an aligned nucleotide is shown against the corresponding position in the consensus.

Mentions: To assess the length distribution of non-reference Alu variants from our call set, we focused on insertions assembled from the AluYa5 and AluYb8 subfamilies. We reasoned that analysis of these particular subfamilies should provide the most informative resource for comparison given their representation as the majority of identified variants. We further limited analysis to those Alu that were suitable for genotyping, as insertions that do not meet our criteria for genotyping may erroneously appear to be truncated due to an incomplete breakpoint assembly. This resulted in an analysis set of 351 AluYa5 and 215 AluYb8 insertions. Based on nucleotide alignments of the assembled insertions against their respective consensus, we examined the collective coverage of assembled elements, per subfamily, in comparison to the nucleotide positions relative to their respective consensus (also refer to the plots in Figure 3A and B).


Discovery and characterization of Alu repeat sequences via precise local read assembly.

Wildschutte JH, Baron A, Diroff NM, Kidd JM - Nucleic Acids Res. (2015)

Length distribution of assembled AluYa5 and AluYb8 insertions. (A) Scaled representation of the AluYa5 and AluYb8 consensus and element properties. The Alu is comprised of two arms (left, blue; right, grey) joined by an A-rich region and having a 3′ poly-A tail. The A and B boxes indicate promoter regions. A 31 bp insertion distinguishes the arms. AluYb8 has a 3′ 7 bp insertion relative to Ya5; the sequences are otherwise structurally conserved. The gold bar shows bases within SRP/14 binding sites. (B) The size distribution of 351 AluYa5 and 215 AluYb8 assembled insertions relative to the respective subfamily consensus. The red dashed lines indicate peaks in truncation near 45 bp and 170 bp. The number of assembled insertions containing an aligned nucleotide is shown against the corresponding position in the consensus.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4666360&req=5

Figure 3: Length distribution of assembled AluYa5 and AluYb8 insertions. (A) Scaled representation of the AluYa5 and AluYb8 consensus and element properties. The Alu is comprised of two arms (left, blue; right, grey) joined by an A-rich region and having a 3′ poly-A tail. The A and B boxes indicate promoter regions. A 31 bp insertion distinguishes the arms. AluYb8 has a 3′ 7 bp insertion relative to Ya5; the sequences are otherwise structurally conserved. The gold bar shows bases within SRP/14 binding sites. (B) The size distribution of 351 AluYa5 and 215 AluYb8 assembled insertions relative to the respective subfamily consensus. The red dashed lines indicate peaks in truncation near 45 bp and 170 bp. The number of assembled insertions containing an aligned nucleotide is shown against the corresponding position in the consensus.
Mentions: To assess the length distribution of non-reference Alu variants from our call set, we focused on insertions assembled from the AluYa5 and AluYb8 subfamilies. We reasoned that analysis of these particular subfamilies should provide the most informative resource for comparison given their representation as the majority of identified variants. We further limited analysis to those Alu that were suitable for genotyping, as insertions that do not meet our criteria for genotyping may erroneously appear to be truncated due to an incomplete breakpoint assembly. This resulted in an analysis set of 351 AluYa5 and 215 AluYb8 insertions. Based on nucleotide alignments of the assembled insertions against their respective consensus, we examined the collective coverage of assembled elements, per subfamily, in comparison to the nucleotide positions relative to their respective consensus (also refer to the plots in Figure 3A and B).

Bottom Line: In our assembled sequences, we find evidence of premature insertion mechanisms and observe 5' truncation in 16% of AluYa5 and AluYb8 insertions.The sites of truncation coincide with stem-loop structures and SRP9/14 binding sites in the Alu RNA, implicating L1 ORF2p pausing in the generation of 5' truncations.Additionally, we identified variable AluJ and AluS elements that likely arose due to non-retrotransposition mechanisms.

View Article: PubMed Central - PubMed

Affiliation: Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA.

Show MeSH
Related in: MedlinePlus