scholarly journals Sequence structures of two developmentally regulated, alternative DNA deletion junctions in Tetrahymena thermophila.

1988 ◽  
Vol 8 (9) ◽  
pp. 3947-3950 ◽  
Author(s):  
C F Austerberry ◽  
M C Yao
Keyword(s):  
Dna Sequences ◽  
Base Pair ◽  
Tetrahymena Thermophila ◽  
Developmental Regulation ◽  
Direct Repeat ◽  
Similar Sequence ◽  
Developmentally Regulated ◽  
Dna Deletion ◽  
Inverted Orientation ◽  
The Right

Deletions of specific DNA sequences are known to occur in Tetrahymena thermophila as a developmentally regulated process. Deletions of a particular region (region M) were previously shown to be of two alternative sizes, 0.6 or 0.9 kilobases (kb) (C.F. Austerberry, C.D. Allis, and M.-C. Yao, Proc. Natl. Acad. Sci. USA 81: 7383-7387). In this study, the nucleotide sequences for both deletions were determined. These two deletions share the same right junction, but their left junctions are 0.3 kb apart. An 8-base-pair (bp) sequence is present at both junctions of the 0.6-kb deletion, but only 5 bp of this direct repeat are present at the left junction of the 0.9-kb deletion. Further comparison revealed a common 10-bp sequence near each of the two left junctions and a similar sequence in inverted orientation near the right junction. These sequences may play a role in the developmental regulation of the deletion process.

Sequence structures of two developmentally regulated, alternative DNA deletion junctions in Tetrahymena thermophila

1988 ◽  
Vol 8 (9) ◽  
pp. 3947-3950
Author(s):  
C F Austerberry ◽  
M C Yao
Keyword(s):  
Dna Sequences ◽  
Base Pair ◽  
Tetrahymena Thermophila ◽  
Developmental Regulation ◽  
Direct Repeat ◽  
Similar Sequence ◽  
Developmentally Regulated ◽  
Dna Deletion ◽  
Inverted Orientation ◽  
The Right

Deletions of specific DNA sequences are known to occur in Tetrahymena thermophila as a developmentally regulated process. Deletions of a particular region (region M) were previously shown to be of two alternative sizes, 0.6 or 0.9 kilobases (kb) (C.F. Austerberry, C.D. Allis, and M.-C. Yao, Proc. Natl. Acad. Sci. USA 81: 7383-7387). In this study, the nucleotide sequences for both deletions were determined. These two deletions share the same right junction, but their left junctions are 0.3 kb apart. An 8-base-pair (bp) sequence is present at both junctions of the 0.6-kb deletion, but only 5 bp of this direct repeat are present at the left junction of the 0.9-kb deletion. Further comparison revealed a common 10-bp sequence near each of the two left junctions and a similar sequence in inverted orientation near the right junction. These sequences may play a role in the developmental regulation of the deletion process.

Nucleotide sequence structure and consistency of a developmentally regulated DNA deletion in Tetrahymena thermophila

1987 ◽  
Vol 7 (1) ◽  
pp. 435-443 ◽  
Author(s):  
C F Austerberry ◽  
M C Yao
Keyword(s):  
Tetrahymena Thermophila ◽  
Germ Line ◽  
Dna Recombination ◽  
Chromosome Breakage ◽  
Base Pairs ◽  
Developmentally Regulated ◽  
Junction Sequence ◽  
Macronuclear Development ◽  
Dna Deletion ◽  
Minor Degree

DNA deletion by site-specific chromosome breakage and rejoining occurs extensively during macronuclear development in the ciliate Tetrahymena thermophila. We have sequenced both the micronuclear (germ line) and rearranged macronuclear (somatic) forms of one region from which 1.1 kilobases of micronuclear DNA are reproducibly deleted during macronuclear development. The deletion junctions lie within a pair of 6-base-pair direct repeats. The termini of the deleted sequence are not inverted repeats. The precision of deletion at the nucleotide level was also characterized by hybridization with a synthetic oligonucleotide matching the determined macronuclear (rejoined) junction sequence. This deletion occurs in a remarkably sequence-specific manner. However, a very minor degree of variability in the macronuclear junction sequences was detected and was shown to be inherent in the mechanism of deletion itself. These results suggest that DNA deletion during macronuclear development in T. thermophila may constitute a novel type of DNA recombination and that it can create sequence heterogeneity on the order of a few base pairs at rejoining junctions.

Oocyte-specific expression of mouse Zp-2: developmental regulation of the zona pellucida genes

1990 ◽  
Vol 10 (4) ◽  
pp. 1507-1515
Author(s):  
L F Liang ◽  
S M Chamow ◽  
J Dean
Keyword(s):  
Dna Sequences ◽  
Zona Pellucida ◽  
Developmental Regulation ◽  
Genetic Locus ◽  
Single Copy ◽  
Specific Gene ◽  
Gene Transcript ◽  
Developmentally Regulated ◽  
Specific Expression ◽  
Oocyte Growth

The zona pellucida surrounds all mammalian oocytes and plays a vital role at fertilization and in early development. The genes that code for two of the mouse zona proteins (ZP2 and ZP3) represent a developmentally regulated set of genes whose expression serves as markers of mouse oocyte growth and differentiation. We previously characterized the single-copy Zp-3 gene and showed that its expression is oocyte specific and restricted to a narrow window of oocyte development. We now define the Zp-2 gene transcript and show that it is coordinately expressed with Zp-3 only during the 2-week growth phase of oogenesis that occurs prior to ovulation. Like Zp-3, the expression of Zp-2 is restricted to oocytes, and, although not detectable in resting oocytes, both ZP2 and ZP3 transcripts accumulate to become very abundant messengers in 50-microns-diameter oocytes. Ovulated eggs contain ZP2 and ZP3 transcripts which are 200 nucleotides shorter than those found in growing oocytes and have an abundance of less than 5% of the peak levels. In an attempt to understand the molecular details associated with the developmentally regulated, tissue-specific gene expression of the zona genes, the Zp-2 genetic locus has been characterized and its 5' flanking sequences have been compared with those of Zp-3. Both genes contain three short (8- to 12-base-pair) DNA sequences of 80 to 88% identity located within 250 base pairs of their transcription start sites.

scholarly journals The 2.1-kb Inverted Repeat DNA Sequences Flank themat2,3Silent Region in Two Species of Schizosaccharomyces and Are Involved in Epigenetic Silencing inSchizosaccharomyces pombe

Genetics ◽  
2002 ◽  
Vol 162 (2) ◽  
pp. 591-602 ◽  
Author(s):  
Gurjeet Singh ◽  
Amar J S Klar
Keyword(s):  
Dna Sequences ◽  
Inverted Repeat ◽  
Transcriptional Silencing ◽  
Epigenetic Silencing ◽  
Inverted Orientation ◽  
Repeat Dna ◽  
Sequence Elements ◽  
Left And Right ◽  
The Right ◽  
Silent Region

AbstractThe mat2,3 region of the fission yeast Schizosaccharomyces pombe exhibits a phenomenon of transcriptional silencing. This region is flanked by two identical DNA sequence elements, 2.1 kb in length, present in inverted orientation: IRL on the left and IRR on the right of the silent region. The repeats do not encode any ORF. The inverted repeat DNA region is also present in a newly identified related species, which we named S. kambucha. Interestingly, the left and right repeats share perfect identity within a species, but show ∼2% bases interspecies variation. Deletion of IRL results in variegated expression of markers inserted in the silent region, while deletion of the IRR causes their derepression. When deletions of these repeats were genetically combined with mutations in different trans-acting genes previously shown to cause a partial defect in silencing, only mutations in clr1 and clr3 showed additive defects in silencing with the deletion of IRL. The rate of mat1 switching is also affected by deletion of repeats. The IRL or IRR deletion did not cause significant derepression of the mat2 or mat3 loci. These results implicate repeats for maintaining full repression of the mat2,3 region, for efficient mat1 switching, and further support the notion that multiple pathways cooperate to silence the mat2,3 domain.

scholarly journals A small family of elements with long inverted repeats is located near sites of developmentally regulated DNA rearrangement in Tetrahymena thermophila.

1994 ◽  
Vol 14 (9) ◽  
pp. 5939-5949 ◽  
Author(s):  
J M Wells ◽  
J L Ellingson ◽  
D M Catt ◽  
P J Berger ◽  
K M Karrer
Keyword(s):  
Dna Sequences ◽  
Inverted Repeat ◽  
Tandem Repeats ◽  
Tetrahymena Thermophila ◽  
Germ Line ◽  
Inverted Repeats ◽  
Dna Rearrangement ◽  
Dna Rearrangements ◽  
Developmentally Regulated ◽  
Small Family

Extensive DNA rearrangement occurs during the development of the somatic macronucleus from the germ line micronucleus in ciliated protozoans. The micronuclear junctions and the macronuclear product of a developmentally regulated DNA rearrangement in Tetrahymena thermophila, Tlr1, have been cloned. The intrachromosomal rearrangement joins sequences that are separated by more than 13 kb in the micronucleus with the elimination of moderately repeated micronucleus-specific DNA sequences. There is a long, 825-bp, inverted repeat near the micronuclear junctions. The inverted repeat contains two different 19-bp tandem repeats. The 19-bp repeats are associated with each other and with DNA rearrangements at seven locations in the micronuclear genome. Southern blot analysis is consistent with the occurrence of the 19-bp repeats within pairs of larger repeated sequences. Another family member was isolated. The 19-mers in that clone are also in close proximity to a rearrangement junction. We propose that the 19-mers define a small family of developmentally regulated DNA rearrangements having elements with long inverted repeats near the junction sites. We discuss the possibility that transposable elements evolve by capture of molecular machinery required for essential cellular functions.

scholarly journals Oocyte-specific expression of mouse Zp-2: developmental regulation of the zona pellucida genes.

1990 ◽  
Vol 10 (4) ◽  
pp. 1507-1515 ◽  
Author(s):  
L F Liang ◽  
S M Chamow ◽  
J Dean
Keyword(s):  
Dna Sequences ◽  
Zona Pellucida ◽  
Developmental Regulation ◽  
Genetic Locus ◽  
Single Copy ◽  
Specific Gene ◽  
Gene Transcript ◽  
Developmentally Regulated ◽  
Specific Expression ◽  
Oocyte Growth

The zona pellucida surrounds all mammalian oocytes and plays a vital role at fertilization and in early development. The genes that code for two of the mouse zona proteins (ZP2 and ZP3) represent a developmentally regulated set of genes whose expression serves as markers of mouse oocyte growth and differentiation. We previously characterized the single-copy Zp-3 gene and showed that its expression is oocyte specific and restricted to a narrow window of oocyte development. We now define the Zp-2 gene transcript and show that it is coordinately expressed with Zp-3 only during the 2-week growth phase of oogenesis that occurs prior to ovulation. Like Zp-3, the expression of Zp-2 is restricted to oocytes, and, although not detectable in resting oocytes, both ZP2 and ZP3 transcripts accumulate to become very abundant messengers in 50-microns-diameter oocytes. Ovulated eggs contain ZP2 and ZP3 transcripts which are 200 nucleotides shorter than those found in growing oocytes and have an abundance of less than 5% of the peak levels. In an attempt to understand the molecular details associated with the developmentally regulated, tissue-specific gene expression of the zona genes, the Zp-2 genetic locus has been characterized and its 5' flanking sequences have been compared with those of Zp-3. Both genes contain three short (8- to 12-base-pair) DNA sequences of 80 to 88% identity located within 250 base pairs of their transcription start sites.

scholarly journals A small family of elements with long inverted repeats is located near sites of developmentally regulated DNA rearrangement in Tetrahymena thermophila

1994 ◽  
Vol 14 (9) ◽  
pp. 5939-5949
Author(s):  
J M Wells ◽  
J L Ellingson ◽  
D M Catt ◽  
P J Berger ◽  
K M Karrer
Keyword(s):  
Dna Sequences ◽  
Inverted Repeat ◽  
Tandem Repeats ◽  
Tetrahymena Thermophila ◽  
Germ Line ◽  
Inverted Repeats ◽  
Dna Rearrangement ◽  
Dna Rearrangements ◽  
Developmentally Regulated ◽  
Small Family

Extensive DNA rearrangement occurs during the development of the somatic macronucleus from the germ line micronucleus in ciliated protozoans. The micronuclear junctions and the macronuclear product of a developmentally regulated DNA rearrangement in Tetrahymena thermophila, Tlr1, have been cloned. The intrachromosomal rearrangement joins sequences that are separated by more than 13 kb in the micronucleus with the elimination of moderately repeated micronucleus-specific DNA sequences. There is a long, 825-bp, inverted repeat near the micronuclear junctions. The inverted repeat contains two different 19-bp tandem repeats. The 19-bp repeats are associated with each other and with DNA rearrangements at seven locations in the micronuclear genome. Southern blot analysis is consistent with the occurrence of the 19-bp repeats within pairs of larger repeated sequences. Another family member was isolated. The 19-mers in that clone are also in close proximity to a rearrangement junction. We propose that the 19-mers define a small family of developmentally regulated DNA rearrangements having elements with long inverted repeats near the junction sites. We discuss the possibility that transposable elements evolve by capture of molecular machinery required for essential cellular functions.

scholarly journals Nucleotide sequence structure and consistency of a developmentally regulated DNA deletion in Tetrahymena thermophila.

1987 ◽  
Vol 7 (1) ◽  
pp. 435-443 ◽  
Author(s):  
C F Austerberry ◽  
M C Yao
Keyword(s):  
Tetrahymena Thermophila ◽  
Germ Line ◽  
Dna Recombination ◽  
Chromosome Breakage ◽  
Base Pairs ◽  
Developmentally Regulated ◽  
Junction Sequence ◽  
Macronuclear Development ◽  
Dna Deletion ◽  
Minor Degree

DNA deletion by site-specific chromosome breakage and rejoining occurs extensively during macronuclear development in the ciliate Tetrahymena thermophila. We have sequenced both the micronuclear (germ line) and rearranged macronuclear (somatic) forms of one region from which 1.1 kilobases of micronuclear DNA are reproducibly deleted during macronuclear development. The deletion junctions lie within a pair of 6-base-pair direct repeats. The termini of the deleted sequence are not inverted repeats. The precision of deletion at the nucleotide level was also characterized by hybridization with a synthetic oligonucleotide matching the determined macronuclear (rejoined) junction sequence. This deletion occurs in a remarkably sequence-specific manner. However, a very minor degree of variability in the macronuclear junction sequences was detected and was shown to be inherent in the mechanism of deletion itself. These results suggest that DNA deletion during macronuclear development in T. thermophila may constitute a novel type of DNA recombination and that it can create sequence heterogeneity on the order of a few base pairs at rejoining junctions.

kangaroo, a Mobile Element From Volvox carteri, Is a Member of a Newly Recognized Third Class of Retrotransposons

Genetics ◽  
2002 ◽  
Vol 162 (4) ◽  
pp. 1617-1630
Author(s):  
Leonard Duncan ◽  
Kristine Bouckaert ◽  
Fay Yeh ◽  
David L Kirk
Keyword(s):  
Genomic Structure ◽  
Mobile Element ◽  
Direct Repeat ◽  
Structural Features ◽  
Volvox Carteri ◽  
Developmentally Regulated ◽  
Closed Circle ◽  
Integration Mechanisms ◽  
And Function

Abstract Retrotransposons play an important role in the evolution of genomic structure and function. Here we report on the characterization of a novel retrotransposon called kangaroo from the multicellular green alga, Volvox carteri. kangaroo elements are highly mobile and their expression is developmentally regulated. They probably integrate via double-stranded, closed-circle DNA intermediates through the action of an encoded recombinase related to the λ-site-specific integrase. Phylogenetic analysis indicates that kangaroo elements are closely related to other unorthodox retrotransposons including PAT (from a nematode), DIRS-1 (from Dictyostelium), and DrDIRS1 (from zebrafish). PAT and kangaroo both contain split direct repeat (SDR) termini, and here we show that DIRS-1 and DrDIRS1 elements contain terminal features structurally related to SDRs. Thus, these mobile elements appear to define a third class of retrotransposons (the DIRS1 group) that are unified by common structural features, genes, and integration mechanisms, all of which differ from those of LTR and conventional non-LTR retrotransposons.

Micronuclear DNA sequences from Tetrahymena do not confer mitotic stability on ARS plasmids in Saccharomyces

Genome ◽  
1988 ◽  
Vol 30 (5) ◽  
pp. 690-696 ◽  
Author(s):  
Wendy H. Horsfall ◽  
Ronald E. Pearlman
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Dna Sequences ◽  
Copy Number ◽  
Tetrahymena Thermophila ◽  
Assay System ◽  
Mitotic Stability ◽  
Yeast Saccharomyces Cerevisiae ◽  
Genomic Libraries ◽  
Ade2 Gene

Genomic libraries containing micronuclear DNA sequences from Tetrahymena thermophila have been constructed in a vector containing ARS1, SUP11, and ura3 sequences from the yeast Saccharomyces cerevisiae. When transformed into a strain of S. cerevisiae carrying a suppressible ochre mutation in the ade2 gene, viable transformants are obtained only if the transforming plasmid is maintained at a copy number of one or two per cell. Mitotic segregation of the plasmid is easily assessed in a colour assay of transformants. Using this assay system, we showed that micronuclear DNA from Tetrahymena does not contain sequences that confer mitotic stability on yeast ARS-containing plasmids; i.e., sequences that function analogously to yeast centromere sequences. One transformant was analyzed that carries Tetrahymena sequences that maintain the copy number of the ARS plasmid at one or two per cell. However, these sequences do not confer mitotic stability on the transformants and they confer a phenotype in this assay similar to that of the REP3 gene of the yeast 2 μm plasmid.Key words: mitotic stability, centromere, Tetrahymena, Saccharomyces.

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