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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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Phylogeny of Tx1 non-LTR retrotransposons. Only Tx1 families whose targets are known were analyzed with crocodilian Tx1 families. Bootstrap values of 1,000 replicates are shown at nodes if they are over 500. Names of crocodilian families are in bold. Three lineages of crocodilian Tx1 families are indicated by asterisks. Target sequences are shown in parentheses after names. The transposon superfamilies are shown when the targets are transposon, while the repeat units are shown when the targets are microsatellites. U2, U2 snRNA; Sat, satellites; U5, U5 snRNA; 5S, 5S rRNA.
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evv100-F3: Phylogeny of Tx1 non-LTR retrotransposons. Only Tx1 families whose targets are known were analyzed with crocodilian Tx1 families. Bootstrap values of 1,000 replicates are shown at nodes if they are over 500. Names of crocodilian families are in bold. Three lineages of crocodilian Tx1 families are indicated by asterisks. Target sequences are shown in parentheses after names. The transposon superfamilies are shown when the targets are transposon, while the repeat units are shown when the targets are microsatellites. U2, U2 snRNA; Sat, satellites; U5, U5 snRNA; 5S, 5S rRNA.

Mentions: Some families of Tx1 non-LTR retrotransposons from crocodilians are also preferentially inserted into Mariner-N4_AMi. On the basis of the phylogeny of RT sequences, crocodilian Tx1 families are classified into three groups (fig. 3, asterisks). One group is coclustered with Keno. Most crocodilian Tx1 families in this group are preferentially inserted into Mariner-N4_AMi and its related transposons (supplementary figs. S3 and S4, Supplementary Material online). This Tx1 group was designated “Tx1-Mar.” Exceptions are Tx1-8_Crp and Tx1-4_AMi, preferentially inserted into specific groups of LTR retrotransposons.Fig. 3.—


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

Kojima KK - Genome Biol Evol (2015)

Phylogeny of Tx1 non-LTR retrotransposons. Only Tx1 families whose targets are known were analyzed with crocodilian Tx1 families. Bootstrap values of 1,000 replicates are shown at nodes if they are over 500. Names of crocodilian families are in bold. Three lineages of crocodilian Tx1 families are indicated by asterisks. Target sequences are shown in parentheses after names. The transposon superfamilies are shown when the targets are transposon, while the repeat units are shown when the targets are microsatellites. U2, U2 snRNA; Sat, satellites; U5, U5 snRNA; 5S, 5S rRNA.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

evv100-F3: Phylogeny of Tx1 non-LTR retrotransposons. Only Tx1 families whose targets are known were analyzed with crocodilian Tx1 families. Bootstrap values of 1,000 replicates are shown at nodes if they are over 500. Names of crocodilian families are in bold. Three lineages of crocodilian Tx1 families are indicated by asterisks. Target sequences are shown in parentheses after names. The transposon superfamilies are shown when the targets are transposon, while the repeat units are shown when the targets are microsatellites. U2, U2 snRNA; Sat, satellites; U5, U5 snRNA; 5S, 5S rRNA.
Mentions: Some families of Tx1 non-LTR retrotransposons from crocodilians are also preferentially inserted into Mariner-N4_AMi. On the basis of the phylogeny of RT sequences, crocodilian Tx1 families are classified into three groups (fig. 3, asterisks). One group is coclustered with Keno. Most crocodilian Tx1 families in this group are preferentially inserted into Mariner-N4_AMi and its related transposons (supplementary figs. S3 and S4, Supplementary Material online). This Tx1 group was designated “Tx1-Mar.” Exceptions are Tx1-8_Crp and Tx1-4_AMi, preferentially inserted into specific groups of LTR retrotransposons.Fig. 3.—

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
Related in: MedlinePlus