Limits...
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.

Show MeSH
Structures of SINEU families/subfamilies. (A) Schematic structures of SINEU families/subfamilies. The regions similar to U1 snRNA gene are colored in red, while those similar to U2 gene are in yellow. The 3′ regions shared among all SINEU-1 subfamilies are in blue. Average identity of each copy to the respective consensus is shown in parentheses. Numbers in parentheses are shown to distinguish multiple U1- or U2-derived sequences and correspond to those shown in (B). (B) Alignment of U1- and U2-derived sequences of SINEU subfamilies and Tx1 families. 5′ sequences of each SINEU subfamily are aligned with U1 and U2 snRNA genes. Nucleotides identical to either U1 or U2 gene are shaded. Double slashes indicate that the following sequences are shown in the next line.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4494074&req=5

evv100-F1: Structures of SINEU families/subfamilies. (A) Schematic structures of SINEU families/subfamilies. The regions similar to U1 snRNA gene are colored in red, while those similar to U2 gene are in yellow. The 3′ regions shared among all SINEU-1 subfamilies are in blue. Average identity of each copy to the respective consensus is shown in parentheses. Numbers in parentheses are shown to distinguish multiple U1- or U2-derived sequences and correspond to those shown in (B). (B) Alignment of U1- and U2-derived sequences of SINEU subfamilies and Tx1 families. 5′ sequences of each SINEU subfamily are aligned with U1 and U2 snRNA genes. Nucleotides identical to either U1 or U2 gene are shaded. Double slashes indicate that the following sequences are shown in the next line.

Mentions: From the characterization of transposable elements from the genomes of three species of crocodilians, A. mississippiensis, C. porosus, and G. gangeticus (Green et al. 2014), SINE families whose 5′ regions originated from either U1 or U2 snRNA genes were characterized. They are designated as SINEU and classified into three families (SINEU-1, SINEU-2, and SINEU-3) based on their structures (fig. 1). No SINEU families were detected outside of crocodilians. SINEU-1 was further classified into 11 subfamilies based on their structures and sequences. The 5′ ends of SINEU elements do not always correspond to the 5′ end of a U1 or U2 snRNA sequence; however, this might be an artifact from constructing consensus sequences from divergent copies. All groups of SINEU have 3′ polyA tail.Fig. 1.—


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

Kojima KK - Genome Biol Evol (2015)

Structures of SINEU families/subfamilies. (A) Schematic structures of SINEU families/subfamilies. The regions similar to U1 snRNA gene are colored in red, while those similar to U2 gene are in yellow. The 3′ regions shared among all SINEU-1 subfamilies are in blue. Average identity of each copy to the respective consensus is shown in parentheses. Numbers in parentheses are shown to distinguish multiple U1- or U2-derived sequences and correspond to those shown in (B). (B) Alignment of U1- and U2-derived sequences of SINEU subfamilies and Tx1 families. 5′ sequences of each SINEU subfamily are aligned with U1 and U2 snRNA genes. Nucleotides identical to either U1 or U2 gene are shaded. Double slashes indicate that the following sequences are shown in the next line.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

evv100-F1: Structures of SINEU families/subfamilies. (A) Schematic structures of SINEU families/subfamilies. The regions similar to U1 snRNA gene are colored in red, while those similar to U2 gene are in yellow. The 3′ regions shared among all SINEU-1 subfamilies are in blue. Average identity of each copy to the respective consensus is shown in parentheses. Numbers in parentheses are shown to distinguish multiple U1- or U2-derived sequences and correspond to those shown in (B). (B) Alignment of U1- and U2-derived sequences of SINEU subfamilies and Tx1 families. 5′ sequences of each SINEU subfamily are aligned with U1 and U2 snRNA genes. Nucleotides identical to either U1 or U2 gene are shaded. Double slashes indicate that the following sequences are shown in the next line.
Mentions: From the characterization of transposable elements from the genomes of three species of crocodilians, A. mississippiensis, C. porosus, and G. gangeticus (Green et al. 2014), SINE families whose 5′ regions originated from either U1 or U2 snRNA genes were characterized. They are designated as SINEU and classified into three families (SINEU-1, SINEU-2, and SINEU-3) based on their structures (fig. 1). No SINEU families were detected outside of crocodilians. SINEU-1 was further classified into 11 subfamilies based on their structures and sequences. The 5′ ends of SINEU elements do not always correspond to the 5′ end of a U1 or U2 snRNA sequence; however, this might be an artifact from constructing consensus sequences from divergent copies. All groups of SINEU have 3′ polyA tail.Fig. 1.—

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