Structure and unusual characteristics of a new family of transposable elements in the sea urchin Strongylocentrotus purpuratus

1985 ◽  
Vol 5 (10) ◽  
pp. 2804-2813
Author(s):  
J B Cohen ◽  
B Hoffman-Liebermann ◽  
L Kedes
Keyword(s):  
Transposable Elements ◽  
Transposable Element ◽  
Sea Urchin ◽  
Strongylocentrotus Purpuratus ◽  
Repetitive Sequences ◽  
Inverted Repeats ◽  
Genomic Locus ◽  
Unusual Structure ◽  
New Family ◽  
Flanking Regions

The transposable element family TU of the sea urchin Strongylocentrotus purpuratus, a higher eucaryote, has recently been described (D. Liebermann, B. Hoffman-Liebermann, J. Weinthal, G. Childs, R. Maxson, A. Mauron, S.N. Cohen, and L. Kedes, Nature [London] 306:342-347, 1983). A member of this family, TU4, has an insertion, called ISTU4, of non-TU DNA. ISTU4 is a member of a family of repetitive sequences, which are present in some 1,000 copies per haploid S. purpuratus genome (B. Hoffman-Liebermann, D. Liebermann, L.H. Kedes, and S.N. Cohen, Mol. Cell. Biol. 5:991-1001, 1985). We analyzed this insertion to determine whether it is itself a transposable element. The nucleotide sequence of ISTU4 was determined and showed an unusual structure. There are four, approximately 150 nucleotides long, imperfect direct repeats followed by a single truncated version of these repeats. This region is bounded at either side by approximately 100-nucleotide-long sequences that are not related to each other or to the repeats. Nucleotide sequences at the boundaries of ISTU4-homologous and flanking regions in five genomic clones show that ISTU4 represents a family of sequences with discrete ends, which we call Tsp elements. We showed that the genomic locus that carries a Tsp element in one individual was empty in other individuals and conclude that Tsp elements are a new and different type of transposable element. Tsp elements lack two features common to most other transposable elements: Tsp integration does not result in the duplication of host DNA, and there are no inverted repeats at their termini, although short inverted repeats are present at a distance from the termini.

scholarly journals Structure and unusual characteristics of a new family of transposable elements in the sea urchin Strongylocentrotus purpuratus.

1985 ◽  
Vol 5 (10) ◽  
pp. 2804-2813 ◽  
Author(s):  
J B Cohen ◽  
B Hoffman-Liebermann ◽  
L Kedes
Keyword(s):  
Transposable Elements ◽  
Transposable Element ◽  
Sea Urchin ◽  
Strongylocentrotus Purpuratus ◽  
Repetitive Sequences ◽  
Inverted Repeats ◽  
Genomic Locus ◽  
Unusual Structure ◽  
New Family ◽  
Flanking Regions

The transposable element family TU of the sea urchin Strongylocentrotus purpuratus, a higher eucaryote, has recently been described (D. Liebermann, B. Hoffman-Liebermann, J. Weinthal, G. Childs, R. Maxson, A. Mauron, S.N. Cohen, and L. Kedes, Nature [London] 306:342-347, 1983). A member of this family, TU4, has an insertion, called ISTU4, of non-TU DNA. ISTU4 is a member of a family of repetitive sequences, which are present in some 1,000 copies per haploid S. purpuratus genome (B. Hoffman-Liebermann, D. Liebermann, L.H. Kedes, and S.N. Cohen, Mol. Cell. Biol. 5:991-1001, 1985). We analyzed this insertion to determine whether it is itself a transposable element. The nucleotide sequence of ISTU4 was determined and showed an unusual structure. There are four, approximately 150 nucleotides long, imperfect direct repeats followed by a single truncated version of these repeats. This region is bounded at either side by approximately 100-nucleotide-long sequences that are not related to each other or to the repeats. Nucleotide sequences at the boundaries of ISTU4-homologous and flanking regions in five genomic clones show that ISTU4 represents a family of sequences with discrete ends, which we call Tsp elements. We showed that the genomic locus that carries a Tsp element in one individual was empty in other individuals and conclude that Tsp elements are a new and different type of transposable element. Tsp elements lack two features common to most other transposable elements: Tsp integration does not result in the duplication of host DNA, and there are no inverted repeats at their termini, although short inverted repeats are present at a distance from the termini.

scholarly journals Tsp transposons: a heterogeneous family of mobile sequences in the genome of the sea urchin Strongylocentrotus purpuratus.

1985 ◽  
Vol 5 (10) ◽  
pp. 2814-2825 ◽  
Author(s):  
J B Cohen ◽  
D Liebermann ◽  
L Kedes
Keyword(s):  
Structural Analysis ◽  
Nucleotide Sequence ◽  
Sea Urchin ◽  
Base Pair ◽  
Strongylocentrotus Purpuratus ◽  
Repetitive Sequences ◽  
Preceding Paper ◽  
Nucleotide Sequence Analysis ◽  
Structural Domain ◽  
Base Pairs

In the preceding paper (J.B. Cohen, B. Hoffman-Liebermann, and L. Kedes, Mol. Cell. Biol., 5:2804-2813, 1985), we described the nucleotide sequence of ISTU4, which is a member of a new family of repetitive sequences, the Tsp family, present in a higher eucaryote, the sea urchin Strongylocentrotus purpuratus. We provided evidence that individual members of this family can act as transposable elements. Here we describe our structural analysis of the Tsp element family, which numbers about 1,000 members per haploid genome. Hybridization and nucleotide sequence analysis of several genomic Tsp clones demonstrate that structurally most Tsp elements resemble ISTU4. Tsp elements range in size up to about 1.3 kilobase pairs, have terminal domains that are conserved between the various examples studied, and contain a central portion of varying size, which may be extensively diverged. Structurally, however, the central portions are very similar and consist of several approximately 150-base-pairs-long, tandemly arranged, imperfect repeats, which are followed by a truncated repeat. The structural analysis is consistent with the possibility that the individual Tsp elements differ by multiples of these 150-base-pair repeats. One variant genomic clone has a solitary repeat and lacks the truncated repeat. The nucleotide sequences of different repeats of a single Tsp element can diverge extensively. The truncated repeat is divergent from most of the repeats, but in one case it is almost identical to a repeat of the same element. Comparison of the sequences from different elements enabled us to determine the boundaries of each structural domain and allows us to propose that each of these domains may be independent units of genetic information. Analysis of the population of Tsp-related sequences in the S. purpuratus genome by genomic blot hybridization suggests that most Tsp family members share the same overall structure. In addition, there is a structural element, about 70 base pairs long, that appears to interrupt the tandem arrangement of the 150-base-pair repeats at regular intervals.

scholarly journals Cloning of the Mutator transposable element MuA2, a putative regulator of somatic mutability of the a1-Mum2 allele in maize.

Genetics ◽  
1991 ◽  
Vol 129 (3) ◽  
pp. 845-854 ◽  
Author(s):  
M M Qin ◽  
D S Robertson ◽  
A H Ellingboe
Keyword(s):  
Transposable Elements ◽  
Transposable Element ◽  
Copy Number ◽  
Inverted Repeats ◽  
Terminal Inverted Repeats ◽  
Somatic Instability ◽  
Mutator Activity ◽  
Element System ◽  
Lines Of Evidence

Abstract The identification of the autonomous or transposase-encoding element of the Mutator (Mu) transposable element system of maize is necessary to the characterization of the system. We reported previously that a transcript homologous to the internal region of the MuA element is associated with activity of the Mutator system. We describe here the cloning of another Mu element, designated MuA2, that cosegregates with Mutator activity as assayed by somatic instability of the a1-Mum2 allele. The MuA2 element has features typical of the transposable elements of the Mutator family, including the 210-bp terminal inverted repeats. Several lines of evidence suggest that MuA2 is an autonomous or transposase-encoding element of the Mu family: (1) MuA2 cosegregates with a genetically defined element that regulates somatic mutability of the a1-Mum2 allele; (2) MuA2 is hypomethylated while most other MuA2-hybridizing sequences in the genome are extensively methylated; (3) the increase of the copy number of MuA2 is concomitant with the increase of regulator elements; (4) MuA2-like elements are found in Mutator lines but not in non-Mutator inbreds. We propose that autonomous or transposase-encoding elements of the Mu family may be structurally conserved and MuA2-like.

DNA methylation dynamics at transposable elements in mammals

2019 ◽  
Vol 63 (6) ◽  
pp. 677-689
Author(s):  
Natasha Jansz
Keyword(s):  
Dna Methylation ◽  
Transposable Elements ◽  
Transposable Element ◽  
Human Development ◽  
Developmental Regulation ◽  
Repetitive Sequences ◽  
Single Copy ◽  
Regulatory Sequences ◽  
Dynamic Regulation ◽  
Element Activity

Abstract Transposable elements dominate the mammalian genome, but their contribution to genetic and epigenetic regulation has been largely overlooked. This was in part due to technical limitations, which made the study of repetitive sequences at single copy resolution difficult. The advancement of next-generation sequencing assays in the last decade has greatly enhanced our understanding of transposable element function. In some instances, specific transposable elements are thought to have been co-opted into regulatory roles during both mouse and human development, while in disease such regulatory potential can contribute to malignancy. DNA methylation is arguably the best characterised regulator of transposable element activity. DNA methylation is associated with transposable element repression, and acts to limit their genotoxic potential. In specific developmental contexts, erasure of DNA methylation is associated with a burst of transposable element expression. Developmental regulation of DNA methylation enables transposon activation, ensuring their survival and propagation throughout the host genome, and also allows the host access to regulatory sequences encoded within the elements. Here I discuss DNA methylation at transposable elements, describing its function and dynamic regulation throughout murine and human development.

scholarly journals Tools and best practices for retrotransposon analysis using high-throughput sequencing data

Mobile DNA ◽  
2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Aurélie Teissandier ◽  
Nicolas Servant ◽  
Emmanuel Barillot ◽  
Deborah Bourc’his
Keyword(s):  
Transposable Elements ◽  
Transposable Element ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Reference Genome ◽  
Repetitive Sequences ◽  
Simulated Data ◽  
Sequencing Data ◽  
Sequencing Technologies ◽  
Human Genomes

Abstract Background Sequencing technologies give access to a precise picture of the molecular mechanisms acting upon genome regulation. One of the biggest technical challenges with sequencing data is to map millions of reads to a reference genome. This problem is exacerbated when dealing with repetitive sequences such as transposable elements that occupy half of the mammalian genome mass. Sequenced reads coming from these regions introduce ambiguities in the mapping step. Therefore, applying dedicated parameters and algorithms has to be taken into consideration when transposable elements regulation is investigated with sequencing datasets. Results Here, we used simulated reads on the mouse and human genomes to define the best parameters for aligning transposable element-derived reads on a reference genome. The efficiency of the most commonly used aligners was compared and we further evaluated how transposable element representation should be estimated using available methods. The mappability of the different transposon families in the mouse and the human genomes was calculated giving an overview into their evolution. Conclusions Based on simulated data, we provided recommendations on the alignment and the quantification steps to be performed when transposon expression or regulation is studied, and identified the limits in detecting specific young transposon families of the mouse and human genomes. These principles may help the community to adopt standard procedures and raise awareness of the difficulties encountered in the study of transposable elements.

scholarly journals Composite transposable elements in the Xenopus laevis genome.

1989 ◽  
Vol 9 (7) ◽  
pp. 3018-3027 ◽  
Author(s):  
J E Garrett ◽  
D S Knutzon ◽  
D Carroll
Keyword(s):  
Xenopus Laevis ◽  
Transposable Elements ◽  
Repetitive Sequences ◽  
Open Reading Frames ◽  
The Other ◽  
Inverted Repeats ◽  
Terminal Inverted Repeats ◽  
Gag Proteins ◽  
High Degree ◽  
Reading Frames

Members of two related families of transposable elements, Tx1 and Tx2, were isolated from the genome of Xenopus laevis and characterized. In both families, two versions of the elements were found. The smaller version in each family (Tx1d and Tx2d) consisted largely of two types of 400-base-pair tandem internal repeats. These elements had discrete ends and short inverted terminal repeats characteristic of mobile DNAs that are presumed to move via DNA intermediates, e.g., Drosophila P and maize Ac elements. The longer versions (Tx1c and Tx2c) differed from Tx1d and Tx2d by the presence of a 6.9-kilobase-pair internal segment that included two long open reading frames (ORFs). ORF1 had one cysteine-plus-histidine-rich sequence of the type found in retroviral gag proteins. ORF2 showed more substantial homology to retroviral pol genes and particularly to the analogs of pol found in a subclass of mobile DNAs that are supposed retrotransposons, such as mammalian long interspersed repetitive sequences, Drosophila I factors, silkworm R1 elements, and trypanosome Ingi elements. Thus, the Tx1 elements present a paradox by exhibiting features of two classes of mobile DNAs that are thought to have very different modes of transposition. Two possible resolutions are considered: (i) the composite versions are actually made up of two independent elements, one of the retrotransposon class, which has a high degree of specificity for insertion into a target within the other, P-like element; and (ii) the composite elements are intact, autonomous mobile DNAs, in which the pol-like gene product collaborates with the terminal inverted repeats to cause transposition of the entire unit.

scholarly journals An unusual transposon with long terminal inverted repeats in the sea urchin Strongylocentrotus purpuratus

Nature ◽  
1983 ◽  
Vol 306 (5941) ◽  
pp. 342-347 ◽  
Author(s):  
Dan Liebermann ◽  
Barbara Hoffman-Liebermann ◽  
Joel Weinthal ◽  
Geoffrey Childs ◽  
Robert Maxson ◽  
...  
Keyword(s):  
Sea Urchin ◽  
Strongylocentrotus Purpuratus ◽  
Inverted Repeats ◽  
Terminal Inverted Repeats

scholarly journals Identification of a regulatory transposon that controls the Mutator transposable element system in maize.

Genetics ◽  
1991 ◽  
Vol 129 (1) ◽  
pp. 261-270 ◽  
Author(s):  
P Chomet ◽  
D Lisch ◽  
K J Hardeman ◽  
V L Chandler ◽  
M Freeling
Keyword(s):  
Transposable Elements ◽  
Transposable Element ◽  
Restriction Fragment ◽  
Distinct Element ◽  
Single Locus ◽  
Inverted Repeats ◽  
Terminal Inverted Repeats ◽  
Mutator Activity ◽  
Element System ◽  
Multiple Copies

Abstract The Mutator system of maize consists of more than eight different classes of transposable elements each of which can be found in multiple copies. All Mu elements share the approximately 220-bp terminal inverted repeats, whereas each distinct element class is defined by its unique internal sequences. The regulation of instability of this system has been difficult to elucidate due to its multigenic inheritance. Here we present genetic experiments which demonstrate that there is a single locus, MuR1, which can regulate the transposition of Mu1 elements. We describe the cloning of members of a novel class of Mu elements, MuR, and demonstrate that a member of the class is the regulator of Mutator activity, MuR1. This conclusion is based on several criteria: MuR1 activity and a MuR-homologous restriction fragment cosegregate; when MuR1 undergoes a duplicative transposition, an additional MuR restriction fragment is observed, and MuR1 activity and the cosegregating MuR fragment are simultaneously lost within clonal somatic sectors. In addition, the MuR element hybridizes to transcripts in plants with Mutator activity. Our genetic experiments demonstrate that the MuR1 transposon is necessary to specify Mutator activity in our lines.

Tsp transposons: a heterogeneous family of mobile sequences in the genome of the sea urchin Strongylocentrotus purpuratus

1985 ◽  
Vol 5 (10) ◽  
pp. 2814-2825
Author(s):  
J B Cohen ◽  
D Liebermann ◽  
L Kedes
Keyword(s):  
Structural Analysis ◽  
Nucleotide Sequence ◽  
Sea Urchin ◽  
Base Pair ◽  
Strongylocentrotus Purpuratus ◽  
Repetitive Sequences ◽  
Preceding Paper ◽  
Nucleotide Sequence Analysis ◽  
Structural Domain ◽  
Base Pairs

In the preceding paper (J.B. Cohen, B. Hoffman-Liebermann, and L. Kedes, Mol. Cell. Biol., 5:2804-2813, 1985), we described the nucleotide sequence of ISTU4, which is a member of a new family of repetitive sequences, the Tsp family, present in a higher eucaryote, the sea urchin Strongylocentrotus purpuratus. We provided evidence that individual members of this family can act as transposable elements. Here we describe our structural analysis of the Tsp element family, which numbers about 1,000 members per haploid genome. Hybridization and nucleotide sequence analysis of several genomic Tsp clones demonstrate that structurally most Tsp elements resemble ISTU4. Tsp elements range in size up to about 1.3 kilobase pairs, have terminal domains that are conserved between the various examples studied, and contain a central portion of varying size, which may be extensively diverged. Structurally, however, the central portions are very similar and consist of several approximately 150-base-pairs-long, tandemly arranged, imperfect repeats, which are followed by a truncated repeat. The structural analysis is consistent with the possibility that the individual Tsp elements differ by multiples of these 150-base-pair repeats. One variant genomic clone has a solitary repeat and lacks the truncated repeat. The nucleotide sequences of different repeats of a single Tsp element can diverge extensively. The truncated repeat is divergent from most of the repeats, but in one case it is almost identical to a repeat of the same element. Comparison of the sequences from different elements enabled us to determine the boundaries of each structural domain and allows us to propose that each of these domains may be independent units of genetic information. Analysis of the population of Tsp-related sequences in the S. purpuratus genome by genomic blot hybridization suggests that most Tsp family members share the same overall structure. In addition, there is a structural element, about 70 base pairs long, that appears to interrupt the tandem arrangement of the 150-base-pair repeats at regular intervals.

Composite transposable elements in the Xenopus laevis genome

1989 ◽  
Vol 9 (7) ◽  
pp. 3018-3027
Author(s):  
J E Garrett ◽  
D S Knutzon ◽  
D Carroll
Keyword(s):  
Xenopus Laevis ◽  
Transposable Elements ◽  
Repetitive Sequences ◽  
Open Reading Frames ◽  
The Other ◽  
Inverted Repeats ◽  
Terminal Inverted Repeats ◽  
Gag Proteins ◽  
High Degree ◽  
Reading Frames

Members of two related families of transposable elements, Tx1 and Tx2, were isolated from the genome of Xenopus laevis and characterized. In both families, two versions of the elements were found. The smaller version in each family (Tx1d and Tx2d) consisted largely of two types of 400-base-pair tandem internal repeats. These elements had discrete ends and short inverted terminal repeats characteristic of mobile DNAs that are presumed to move via DNA intermediates, e.g., Drosophila P and maize Ac elements. The longer versions (Tx1c and Tx2c) differed from Tx1d and Tx2d by the presence of a 6.9-kilobase-pair internal segment that included two long open reading frames (ORFs). ORF1 had one cysteine-plus-histidine-rich sequence of the type found in retroviral gag proteins. ORF2 showed more substantial homology to retroviral pol genes and particularly to the analogs of pol found in a subclass of mobile DNAs that are supposed retrotransposons, such as mammalian long interspersed repetitive sequences, Drosophila I factors, silkworm R1 elements, and trypanosome Ingi elements. Thus, the Tx1 elements present a paradox by exhibiting features of two classes of mobile DNAs that are thought to have very different modes of transposition. Two possible resolutions are considered: (i) the composite versions are actually made up of two independent elements, one of the retrotransposon class, which has a high degree of specificity for insertion into a target within the other, P-like element; and (ii) the composite elements are intact, autonomous mobile DNAs, in which the pol-like gene product collaborates with the terminal inverted repeats to cause transposition of the entire unit.

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