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A New Class of SINEs with snRNA Gene-Derived Heads.

Kojima KK - Genome Biol Evol (2015)

Bottom Line: SINEU-2 is the only SINE family that was active after the split of crocodiles and gharials.All SINEU families, especially SINEU-3, are preferentially inserted into a family of Mariner DNA transposon, Mariner-N4_AMi.A group of Tx1 non-long terminal repeat retrotransposons designated Tx1-Mar also show target preference for Mariner-N4_AMi, indicating that SINEU was mobilized by Tx1-Mar.

View Article: PubMed Central - PubMed

Affiliation: Genetic Information Research Institute, Los Altos, CA kojima@girinst.org.

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Alignment of SINEU-2_Crp copies with the 5′ extension sequences similar to U1 snRNA genes. The consensus sequences of SINEU-2_Crp subfamilies and also two representative U1 snRNA gene sequences (in scaffold-20780 and scaffold-27) are shown. The regions distinguishing different SINEU-2_Crp subfamilies are boxed. The 5′ extension sequences are colored in red and the downstream SINEU-2_Crp sequences are in blue. Nucleotides different among SINEU-2_Crp subfamilies are highlighted by either green or yellow. Nucleotides that can be aligned as either the 5′ extension sequences or the downstream SINEU-2_Crp sequences are shaded. If the sequence corresponds to a specific SINEU-2_Crp subfamily or subfamilies, it is indicated.
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evv100-F4: Alignment of SINEU-2_Crp copies with the 5′ extension sequences similar to U1 snRNA genes. The consensus sequences of SINEU-2_Crp subfamilies and also two representative U1 snRNA gene sequences (in scaffold-20780 and scaffold-27) are shown. The regions distinguishing different SINEU-2_Crp subfamilies are boxed. The 5′ extension sequences are colored in red and the downstream SINEU-2_Crp sequences are in blue. Nucleotides different among SINEU-2_Crp subfamilies are highlighted by either green or yellow. Nucleotides that can be aligned as either the 5′ extension sequences or the downstream SINEU-2_Crp sequences are shaded. If the sequence corresponds to a specific SINEU-2_Crp subfamily or subfamilies, it is indicated.

Mentions: Twenty-six SINEU-2 copies have 5′ extensions similar to U1 snRNA genes (fig. 4). The 5′ extension sequences show some nucleotide variations. The variations of SINEU-2 head sequences and CpG decay can explain most variations of 5′ extension sequences, but it does not exclude the possibility that they are derived from variations of U2 snRNA genes. The downstream SINEU-2 sequences also show variations and belong to different subfamilies. Even when the 5′ extension sequence corresponds to one subfamily of SINEU-2, the subfamilies of the 5′ extension and of the downstream SINEU-2 are often different; for example, a SINEU-2A copy in the scaffold-2275 has a 5′ extension identical to the heads of SINEU-2B and C. Thus, template slippage and partial duplication can be excluded as the main mechanism of this extension. The positions of 3′ truncation of the 5′ extension sequences are different by at most 22 nucleotides. Short sequence homology between the extension sequences and SINEU-2 sequences is occasionally observed at the junctions. These observations clearly show that SINEU-2 heads were generated through multiple events of 5′ sequence addition onto SINEU-2 copies, not by the retrotransposition of a single master copy.Fig. 4.—


A New Class of SINEs with snRNA Gene-Derived Heads.

Kojima KK - Genome Biol Evol (2015)

Alignment of SINEU-2_Crp copies with the 5′ extension sequences similar to U1 snRNA genes. The consensus sequences of SINEU-2_Crp subfamilies and also two representative U1 snRNA gene sequences (in scaffold-20780 and scaffold-27) are shown. The regions distinguishing different SINEU-2_Crp subfamilies are boxed. The 5′ extension sequences are colored in red and the downstream SINEU-2_Crp sequences are in blue. Nucleotides different among SINEU-2_Crp subfamilies are highlighted by either green or yellow. Nucleotides that can be aligned as either the 5′ extension sequences or the downstream SINEU-2_Crp sequences are shaded. If the sequence corresponds to a specific SINEU-2_Crp subfamily or subfamilies, it is indicated.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4494074&req=5

evv100-F4: Alignment of SINEU-2_Crp copies with the 5′ extension sequences similar to U1 snRNA genes. The consensus sequences of SINEU-2_Crp subfamilies and also two representative U1 snRNA gene sequences (in scaffold-20780 and scaffold-27) are shown. The regions distinguishing different SINEU-2_Crp subfamilies are boxed. The 5′ extension sequences are colored in red and the downstream SINEU-2_Crp sequences are in blue. Nucleotides different among SINEU-2_Crp subfamilies are highlighted by either green or yellow. Nucleotides that can be aligned as either the 5′ extension sequences or the downstream SINEU-2_Crp sequences are shaded. If the sequence corresponds to a specific SINEU-2_Crp subfamily or subfamilies, it is indicated.
Mentions: Twenty-six SINEU-2 copies have 5′ extensions similar to U1 snRNA genes (fig. 4). The 5′ extension sequences show some nucleotide variations. The variations of SINEU-2 head sequences and CpG decay can explain most variations of 5′ extension sequences, but it does not exclude the possibility that they are derived from variations of U2 snRNA genes. The downstream SINEU-2 sequences also show variations and belong to different subfamilies. Even when the 5′ extension sequence corresponds to one subfamily of SINEU-2, the subfamilies of the 5′ extension and of the downstream SINEU-2 are often different; for example, a SINEU-2A copy in the scaffold-2275 has a 5′ extension identical to the heads of SINEU-2B and C. Thus, template slippage and partial duplication can be excluded as the main mechanism of this extension. The positions of 3′ truncation of the 5′ extension sequences are different by at most 22 nucleotides. Short sequence homology between the extension sequences and SINEU-2 sequences is occasionally observed at the junctions. These observations clearly show that SINEU-2 heads were generated through multiple events of 5′ sequence addition onto SINEU-2 copies, not by the retrotransposition of a single master copy.Fig. 4.—

Bottom Line: SINEU-2 is the only SINE family that was active after the split of crocodiles and gharials.All SINEU families, especially SINEU-3, are preferentially inserted into a family of Mariner DNA transposon, Mariner-N4_AMi.A group of Tx1 non-long terminal repeat retrotransposons designated Tx1-Mar also show target preference for Mariner-N4_AMi, indicating that SINEU was mobilized by Tx1-Mar.

View Article: PubMed Central - PubMed

Affiliation: Genetic Information Research Institute, Los Altos, CA kojima@girinst.org.

Show MeSH