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Chapter 50 : Site-specific non-LTR retrotransposons

Author: Haruhiko Fujiwara1
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Affiliations: 1: Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277-8562, Japan
Content Type: Monograph
Publication Year: 2015

Category: Clinical Microbiology

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Abstract:

DNA transposons are the mobile elements that move by a “cut and paste” mechanism ( ). In contrast, retrotransposons encode reverse transcriptase, and move by a “copy and paste” mechanism. The process of retrotransposon insertion into genomic locations involves an RNA intermediate. Retrotransposons can be classified into long terminal repeat (LTR) and non-LTR retrotransposons. LTR retrotransposons have LTRs at both ends and resemble retroviruses in both structure and integration mechanisms. Non-LTR retrotransposons comprise two subtypes, long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs). Non-LTR retrotransposons are in general 4 to 7 kb long and do not carry LTRs, and their retrotransposition mechanism is different from that of LTR retrotransposons. SINEs are nonautonomous retrotransposons of 100 to 500 bp that do not encode proteins. It has been proposed that the proteins encoded by LINEs are the source of the enzymatic retrotransposition machinery of SINEs ( ).

Citation: Fujiwara H. 2015. Site-specific non-LTR retrotransposons, p 1147-1163. In Craig N, Chandler M, Gellert M, Lambowitz A, Rice P, Sandmeyer S (ed), Mobile DNA III. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MDNA3-0001-2014
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Site-specific non-LTR retrotransposons
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Citation: Fujiwara H. 2015. Site-specific non-LTR retrotransposons, p 1147-1163. In Craig N, Chandler M, Gellert M, Lambowitz A, Rice P, Sandmeyer S (ed), Mobile DNA III. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MDNA3-0001-2014
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Figure 1
Two types of genomic insertion of non-LTR elements.
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Figure 1

Two types of genomic insertion of non-LTR elements.

Citation: Fujiwara H. 2015. Site-specific non-LTR retrotransposons, p 1147-1163. In Craig N, Chandler M, Gellert M, Lambowitz A, Rice P, Sandmeyer S (ed), Mobile DNA III. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MDNA3-0001-2014
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Figure 2
Schematic structure of each clade of site-specific non-LTR retrotransposons. The ORF1 in APE-encoding elements is shown as a short rectangle. An ORF2 in APE-encoding elements or ORF in RLE-encoding elements is shown as a long rectangle. A ZF-like structure is shown as a vertical bold line. A ZF-like structure in ORF1 of APE-encoding elements is shown as a zinc knuckle: Cx2Cx4Hx4Cx5-8Cx2Cx3Hx4C. In R2 clade elements, some elements have an additional ZF-like structure shown as a dotted vertical line. Myb-like (Myb) domains are found in R2 clade-elements and in TRAS families in the R1-clade.
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Figure 2

Schematic structure of each clade of site-specific non-LTR retrotransposons. The ORF1 in APE-encoding elements is shown as a short rectangle. An ORF2 in APE-encoding elements or ORF in RLE-encoding elements is shown as a long rectangle. A ZF-like structure is shown as a vertical bold line. A ZF-like structure in ORF1 of APE-encoding elements is shown as a zinc knuckle: Cx2Cx4Hx4Cx5-8Cx2Cx3Hx4C. In R2 clade elements, some elements have an additional ZF-like structure shown as a dotted vertical line. Myb-like (Myb) domains are found in R2 clade-elements and in TRAS families in the R1-clade.

Citation: Fujiwara H. 2015. Site-specific non-LTR retrotransposons, p 1147-1163. In Craig N, Chandler M, Gellert M, Lambowitz A, Rice P, Sandmeyer S (ed), Mobile DNA III. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MDNA3-0001-2014
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Figure 3
rDNA-specific-elements (R-elements) and telomere-specific-elements. Locations and insertion sites of rDNA-specific non-LTR elements (A) and telomere-specific non-LTR elements (B) are shown schematically. Arrows indicate the 5′ to 3′ orientation of non-LTR element insertion. Three telomere-specific elements, TART, HeT-A, and TAHRE, in are located at extreme ends of chromosome (their locations are in random order).
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Figure 3

rDNA-specific-elements (R-elements) and telomere-specific-elements. Locations and insertion sites of rDNA-specific non-LTR elements (A) and telomere-specific non-LTR elements (B) are shown schematically. Arrows indicate the 5′ to 3′ orientation of non-LTR element insertion. Three telomere-specific elements, TART, HeT-A, and TAHRE, in are located at extreme ends of chromosome (their locations are in random order).

Citation: Fujiwara H. 2015. Site-specific non-LTR retrotransposons, p 1147-1163. In Craig N, Chandler M, Gellert M, Lambowitz A, Rice P, Sandmeyer S (ed), Mobile DNA III. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MDNA3-0001-2014
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Figure 4
Evolution of target sequences in R1-clade elements. The phylogeny is constructed on the basis of data in K. K. Kojima and H. Fujiwara ( ). Nonsequence-specific elements are shown as dotted lines and asterisks. Target and flanking sequences of each site-specific element are shown on the right. In the TPRT model, the bottom strand is first nicked and then the top strand is cleaved. The SART and TRAS elements target the same (TTAGG/CCATT) telomeric repeats. However, TRAS first cut the TTAGG bottom strand, whereas SART first cut the CCTAA strand. The bottom-to-top strand cleavage in each target sequence is represented by bent lines. Arrows indicate variation of top-strand cleavage. Broken lines between the top and bottom strands, in TRAS, SART, Waldo, and Mino, indicate unidentified exact cleavage sites because they target the tandem repeats TTAGG and ACAY (or AC). Broken boxes indicate homologous sequences near cleavage sites among RT and R7.
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Figure 4

Evolution of target sequences in R1-clade elements. The phylogeny is constructed on the basis of data in K. K. Kojima and H. Fujiwara ( ). Nonsequence-specific elements are shown as dotted lines and asterisks. Target and flanking sequences of each site-specific element are shown on the right. In the TPRT model, the bottom strand is first nicked and then the top strand is cleaved. The SART and TRAS elements target the same (TTAGG/CCATT) telomeric repeats. However, TRAS first cut the TTAGG bottom strand, whereas SART first cut the CCTAA strand. The bottom-to-top strand cleavage in each target sequence is represented by bent lines. Arrows indicate variation of top-strand cleavage. Broken lines between the top and bottom strands, in TRAS, SART, Waldo, and Mino, indicate unidentified exact cleavage sites because they target the tandem repeats TTAGG and ACAY (or AC). Broken boxes indicate homologous sequences near cleavage sites among RT and R7.

Citation: Fujiwara H. 2015. Site-specific non-LTR retrotransposons, p 1147-1163. In Craig N, Chandler M, Gellert M, Lambowitz A, Rice P, Sandmeyer S (ed), Mobile DNA III. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MDNA3-0001-2014
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Figure 5
Evolution of telomere and TERT structure in higher insects. X in indicates the loss of a TERT gene from the genome. In the silkworm () and the flour beetle (), introns and GQ domains are lost from TERT genes (see text). The phylogenetic tree was constructed based on recent reports ( ).
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Figure 5

Evolution of telomere and TERT structure in higher insects. X in indicates the loss of a TERT gene from the genome. In the silkworm () and the flour beetle (), introns and GQ domains are lost from TERT genes (see text). The phylogenetic tree was constructed based on recent reports ( ).

Citation: Fujiwara H. 2015. Site-specific non-LTR retrotransposons, p 1147-1163. In Craig N, Chandler M, Gellert M, Lambowitz A, Rice P, Sandmeyer S (ed), Mobile DNA III. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MDNA3-0001-2014
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Figure 6
Structures of the silkworm TERT gene. (A) The position of upstream ATG in several TERT genes. The numbers of upstream ATG in each 5′ UTR of TERT are shown on the right. (B) Polyadenylation site of TERT. Poly (A) sequences at the 3′ ends of the TERT gene in genomic DNA and cDNA (corresponding to the mRNA sequence) are shown in bold. (C) The schematic model for the generation of a processed TERT gene from the original TERT with introns by reverse transcription. Four exons are shown as Ex-A to Ex-D.
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Figure 6

Structures of the silkworm TERT gene. (A) The position of upstream ATG in several TERT genes. The numbers of upstream ATG in each 5′ UTR of TERT are shown on the right. (B) Polyadenylation site of TERT. Poly (A) sequences at the 3′ ends of the TERT gene in genomic DNA and cDNA (corresponding to the mRNA sequence) are shown in bold. (C) The schematic model for the generation of a processed TERT gene from the original TERT with introns by reverse transcription. Four exons are shown as Ex-A to Ex-D.

Citation: Fujiwara H. 2015. Site-specific non-LTR retrotransposons, p 1147-1163. In Craig N, Chandler M, Gellert M, Lambowitz A, Rice P, Sandmeyer S (ed), Mobile DNA III. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MDNA3-0001-2014
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Figure 7
Schematic model for interaction between mRNA of a site-specific non-LTR element and target DNA at the 3′ junction. (A) Interaction between the read-through transcript of a non-LTR element (from copy1) and the target site DNA at the 3′ junction of copy 3. (B) Annealing of R2Ol mRNA with the target DNA (28S rDNA) at the 3′ junction. -transcribed R2Ol with 4 bp of the 28S target sequence at its 3′ end showed the accurate and efficient retrotransposition in the zebrafish embryo. However, the R2Ol mRNA with 3 bp of the 28S target sequence showed insufficient retrotransposition (39%) (H. Mizuno and H. Fujiwara, unpublished data). These observations indicate that annealing of the read-though product of R2Ol to the target DNA at the 3′ junction seems important for its efficient and accurate retrotransposition.
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Figure 7

Schematic model for interaction between mRNA of a site-specific non-LTR element and target DNA at the 3′ junction. (A) Interaction between the read-through transcript of a non-LTR element (from copy1) and the target site DNA at the 3′ junction of copy 3. (B) Annealing of R2Ol mRNA with the target DNA (28S rDNA) at the 3′ junction. -transcribed R2Ol with 4 bp of the 28S target sequence at its 3′ end showed the accurate and efficient retrotransposition in the zebrafish embryo. However, the R2Ol mRNA with 3 bp of the 28S target sequence showed insufficient retrotransposition (39%) (H. Mizuno and H. Fujiwara, unpublished data). These observations indicate that annealing of the read-though product of R2Ol to the target DNA at the 3′ junction seems important for its efficient and accurate retrotransposition.

Citation: Fujiwara H. 2015. Site-specific non-LTR retrotransposons, p 1147-1163. In Craig N, Chandler M, Gellert M, Lambowitz A, Rice P, Sandmeyer S (ed), Mobile DNA III. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MDNA3-0001-2014
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Figure 8
Main factors involved in the target-site selection of site-specific APE-encoding elements. Four main steps of the retrotransposition of non-LTR elements in the cells (transcription, translation, RNP formation, and nuclear import) are shown schematically. Three factors involved in the target-site selection are indicated.
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Figure 8

Main factors involved in the target-site selection of site-specific APE-encoding elements. Four main steps of the retrotransposition of non-LTR elements in the cells (transcription, translation, RNP formation, and nuclear import) are shown schematically. Three factors involved in the target-site selection are indicated.

Citation: Fujiwara H. 2015. Site-specific non-LTR retrotransposons, p 1147-1163. In Craig N, Chandler M, Gellert M, Lambowitz A, Rice P, Sandmeyer S (ed), Mobile DNA III. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MDNA3-0001-2014
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Tables

Site-specific non-LTR retrotransposons
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Citation: Fujiwara H. 2015. Site-specific non-LTR retrotransposons, p 1147-1163. In Craig N, Chandler M, Gellert M, Lambowitz A, Rice P, Sandmeyer S (ed), Mobile DNA III. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MDNA3-0001-2014
/content/10.1128/9781555819217.chap50.tab50-1
TABLE 1
Targets of site-specific non-LTR retrotransposons
Generic image for table
TABLE 1

Targets of site-specific non-LTR retrotransposons

Citation: Fujiwara H. 2015. Site-specific non-LTR retrotransposons, p 1147-1163. In Craig N, Chandler M, Gellert M, Lambowitz A, Rice P, Sandmeyer S (ed), Mobile DNA III. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MDNA3-0001-2014

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