A symmetrical six-base-pair target site sequence determines Tn10 insertion specificity

Cell ◽  
1982 ◽  
Vol 28 (1) ◽  
pp. 155-163 ◽  
Author(s):  
Shirley M. Halling ◽  
Nancy Kleckner
Keyword(s):  
Base Pair ◽  
Target Site ◽  
Tn10 Insertion

scholarly journals Evidence that chicken CR1 elements represent a novel family of retroposons.

1989 ◽  
Vol 9 (8) ◽  
pp. 3563-3566 ◽  
Author(s):  
R Silva ◽  
J B Burch
Keyword(s):  
Base Pair ◽  
Repetitive Element ◽  
Direct Repeat ◽  
Target Site ◽  
Target Site Duplication ◽  
Target Sites

We report the first precise delineation of a chicken CR1 element and show that it is flanked by a 6-base-pair target site duplication that occurred when this repetitive element transposed. The 3' end of this CR1 element is defined by an 8-base-pair imperfect direct repeat, and we infer that this sequence represents the 3' end of all intact CR1 elements. In contrast, the 5' ends are not unique, and we argue that this variation existed at the time each element transposed. We also provide evidence that CR1 elements transposed into preferred target sites. CR1 elements therefore appear to represent a novel class of passive retroposons.

scholarly journals IS481 and IS1002 ofBordetella pertussis Create a 6-Base-Pair Duplication upon Insertion at a Consensus Target Site

1998 ◽  
Vol 180 (18) ◽  
pp. 4963-4966 ◽  
Author(s):  
Scott Stibitz
Keyword(s):  
Dna Sequence ◽  
Bordetella Pertussis ◽  
Base Pair ◽  
Insertion Sequence ◽  
Target Site ◽  
Inverted Repeats ◽  
Recognition Sequence ◽  
Base Pairs ◽  
Terminal Inverted Repeats ◽  
Ofbordetella Pertussis

ABSTRACT The insertion sequence IS481 and its isoform IS1002 have been observed to transpose into thebvgAS locus of Bordetella pertussis, for which the DNA sequence has previously been determined. Upon insertion of IS481 at three different sites and IS1002 at one site, a 6-bp sequence originally present was found at the junction of bvg and insertion sequence DNA. This indicates that, contrary to prior reports, IS481 and IS1002 do create a duplication upon insertion. In this light, examination of these and other examples of IS481 and IS1002reported in the literature leads to the observation that the 6-bp recognition sequence usually fits the consensus NCTAGN. The near-palindromic nature of this sequence, when directly repeated at the ends of IS481 or IS1002, apparently led to the interpretation that 5 of these base pairs were part of the terminal inverted repeats flanking these elements.

A rapidly rearranging retrotransposon within the miniexon gene locus of Crithidia fasciculata

1990 ◽  
Vol 10 (2) ◽  
pp. 615-624
Author(s):  
A Gabriel ◽  
T J Yen ◽  
D C Schwartz ◽  
C L Smith ◽  
J D Boeke ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
Base Pair ◽  
Gene Locus ◽  
Target Site ◽  
Crithidia Fasciculata ◽  
Reading Frame ◽  
Retrotransposable Element ◽  
Multiple Copies ◽  
Codon Reading ◽  
Terminal Poly

The tandemly arrayed miniexon genes of the trypanosomatid Crithidia fasciculata are interrupted at specific sites by multiple copies of an inserted element. The element, termed Crithidia retrotransposable element 1 (CRE1), is flanked by 29-base-pair target site duplications and contains a long 3'-terminal poly(dA) stretch. A single 1,140-codon reading frame is similar in sequence to the integrase and reverse transcriptase regions of retroviral pol polyproteins. Cloned lines derived from a stock of C. fasciculata have unique arrangements of CRE1s. In different cloned lines, CRE1s, in association with miniexon genes, are located on multiple chromosomes. By examining the arrangement of CRE1s in subclones, we estimate that the element rearranges at a rate of ca. 1% per generation. These results indicate that the C. fasciculata miniexon locus is the target for a novel retrotransposon.

Evidence that chicken CR1 elements represent a novel family of retroposons

1989 ◽  
Vol 9 (8) ◽  
pp. 3563-3566
Author(s):  
R Silva ◽  
J B Burch
Keyword(s):  
Base Pair ◽  
Repetitive Element ◽  
Direct Repeat ◽  
Target Site ◽  
Target Site Duplication ◽  
Target Sites

We report the first precise delineation of a chicken CR1 element and show that it is flanked by a 6-base-pair target site duplication that occurred when this repetitive element transposed. The 3' end of this CR1 element is defined by an 8-base-pair imperfect direct repeat, and we infer that this sequence represents the 3' end of all intact CR1 elements. In contrast, the 5' ends are not unique, and we argue that this variation existed at the time each element transposed. We also provide evidence that CR1 elements transposed into preferred target sites. CR1 elements therefore appear to represent a novel class of passive retroposons.

scholarly journals A rapidly rearranging retrotransposon within the miniexon gene locus of Crithidia fasciculata.

1990 ◽  
Vol 10 (2) ◽  
pp. 615-624 ◽  
Author(s):  
A Gabriel ◽  
T J Yen ◽  
D C Schwartz ◽  
C L Smith ◽  
J D Boeke ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
Base Pair ◽  
Gene Locus ◽  
Target Site ◽  
Crithidia Fasciculata ◽  
Reading Frame ◽  
Retrotransposable Element ◽  
Multiple Copies ◽  
Codon Reading ◽  
Terminal Poly

The tandemly arrayed miniexon genes of the trypanosomatid Crithidia fasciculata are interrupted at specific sites by multiple copies of an inserted element. The element, termed Crithidia retrotransposable element 1 (CRE1), is flanked by 29-base-pair target site duplications and contains a long 3'-terminal poly(dA) stretch. A single 1,140-codon reading frame is similar in sequence to the integrase and reverse transcriptase regions of retroviral pol polyproteins. Cloned lines derived from a stock of C. fasciculata have unique arrangements of CRE1s. In different cloned lines, CRE1s, in association with miniexon genes, are located on multiple chromosomes. By examining the arrangement of CRE1s in subclones, we estimate that the element rearranges at a rate of ca. 1% per generation. These results indicate that the C. fasciculata miniexon locus is the target for a novel retrotransposon.

Detection of the Glanzmann's Thrombasthenia Mutations in Arab and Iraqi-Jewish Patients by Polymerase Chain Reaction and Restriction Analysis of Blood or Urine Samples

1991 ◽  
Vol 66 (04) ◽  
pp. 500-504 ◽  
Author(s):  
H Peretz ◽  
U Seligsohn ◽  
E Zwang ◽  
B S Coller ◽  
P J Newman
Keyword(s):  
Polymerase Chain Reaction ◽  
Base Pair ◽  
Restriction Analysis ◽  
Urine Samples ◽  
Chain Reaction ◽  
Base Pairs ◽  
Glanzmann’S Thrombasthenia ◽  
Glanzmann's Thrombasthenia ◽  
Base Pair Deletion ◽  
Polymerase Chain

SummarySevere Glanzmann's thrombasthenia is relatively frequent in Iraqi-Jews and Arabs residing in Israel. We have recently described the mutations responsible for the disease in Iraqi-Jews – an 11 base pair deletion in exon 12 of the glycoprotein IIIa gene, and in Arabs – a 13 base pair deletion at the AG acceptor splice site of exon 4 on the glycoprotein IIb gene. In this communication we show that the Iraqi-Jewish mutation can be identified directly by polymerase chain reaction and gel electrophoresis. With specially designed oligonucleotide primers encompassing the mutation site, an 80 base pair segment amplified in healthy controls was clearly distinguished from the 69 base pair segment produced in patients. Patients from 11 unrelated Iraqi-Jewish families had the same mutation. The Arab mutation was identified by first amplifying a DNA segment consisting of 312 base pairs in controls and of 299 base pairs in patients, and then digestion by a restriction enzyme Stu-1, which recognizes a site that is absent in the mutant gene. In controls the 312 bp segment was digested into 235 and 77 bp fragments, while in patients there was no change in the size of the amplified 299 bp segment. The mutation was found in patients from 3 out of 5 unrelated Arab families. Both Iraqi-Jewish and Arab mutations were detectable in DNA extracted from blood and urine samples. The described simple methods of identifying the mutations should be useful for detection of the numerous potential carriers among the affected kindreds and for prenatal diagnosis using DNA extracted from chorionic villi samples.

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