Variation in copy number of a 24-base pair tandem repeat in the chloroplast DNA of Oenothera hookeri strain Johansen

1988 ◽  
Vol 14 (3) ◽  
pp. 287-292 ◽  
Author(s):  
Kimberly Blasko ◽  
Sara A. Kaplan ◽  
Kelly G. Higgins ◽  
Ruth Wolfson ◽  
Barbara B. Sears
Keyword(s):  
Chloroplast Dna ◽  
Tandem Repeat ◽  
Base Pair ◽  
Copy Number ◽  
Oenothera Hookeri

Replication from a proximal simian virus 40 origin is severely inhibited by multiple reiterations of the 72-base-pair repeat enhancer sequence

1988 ◽  
Vol 8 (4) ◽  
pp. 1509-1517
Author(s):  
R Kumar ◽  
K P Yoon ◽  
K N Subramanian
Keyword(s):  
Transcriptional Activation ◽  
Base Pair ◽  
Copy Number ◽  
Simian Virus 40 ◽  
Simian Virus ◽  
Origin Of Replication ◽  
Replication Efficiency ◽  
Sv40 Origin ◽  
Multiple Copies ◽  
In Cis

In a previous study in our laboratory, the effect of the reiteration frequency of the simian virus 40 (SV40) 72-base-pair (bp) repeat enhancer on transcription from the proximal SV40 early promoter was investigated (R. Kumar, T. A. Firak, C. T. Schroll, and K. N. Subramanian, Proc. Natl. Acad. Sci. USA 83:3199-3203, 1986). Increasing the enhancer copy number to four increased transcription proportionately; further increments in enhancer copy number reversed this effect, resulting in a decrease in the transcriptional activation. In the present study, the effect of enhancer reiteration on the replication efficiency of plasmids containing the SV40 origin of replication was investigated in transient replication assays in vivo in COS-1 monkey kidney cells producing the SV40 large tumor antigen required for replication. A plasmid containing the SV40 core origin and three copies of the replication-activating, G+C-rich 21-bp repeat promoter element replicated efficiently. Plasmids containing multiple copies of the 72-bp repeat enhancer cloned in head-to-tail linkage adjacent to the 21-bp repeat and the core origin replicated less efficiently; the decrease in replication efficiency could be correlated with the number of copies of the 72-bp repeat; replication was severely curtailed when 10 or more copies of the 72-bp repeat were present. Replication was not significantly inhibited by an increase in the number of copies of the 21-bp repeat to 15 or by the presence of three copies of a 360-bp pBR322 sequence in the immediate vicinity. Multiple copies of the 72-bp enhancer in cis were unable to inhibit replication from a second SV40 origin of replication situated 2 kilobase pairs away from the enhancer reiteration. Replication of four different test plasmids was not inhibited in trans by cotransfection of an excess of a potential competitor plasmid containing a 24-copy reiteration of the 72-bp enhancer. These results indicate that multiple tandem reiterations of the 72-bp enhancer inhibit replication only when they are present in cis adjacent to the origin of replication. Possible explanations for this inhibitory effect, such as an unfavorable local chromatin structure induced by the multimeric enhancer region or reduced or improper communications between factors bound to the multimeric region and the adjacent replication origin, are discussed.

Variation in primary sequence and tandem repeat copy number among i-antigens of Ichthyophthirius multifiliis☆

2002 ◽  
Vol 120 (1) ◽  
pp. 93-106 ◽  
Author(s):  
Yuankai Lin ◽  
Tian Long Lin ◽  
Chia-Cheng Wang ◽  
Xuting Wang ◽  
Knut Stieger ◽  
...  
Keyword(s):  
Tandem Repeat ◽  
Copy Number ◽  
Ichthyophthirius Multifiliis ◽  
Primary Sequence ◽  
Repeat Copy Number ◽  
Repeat Copy

scholarly journals Kinetic Complexity, Homogeneity, and Copy Number of Chloroplast DNA from the Marine Alga Olisthodiscus luteus

1981 ◽  
Vol 68 (6) ◽  
pp. 1468-1473 ◽  
Author(s):  
Duncan R. Ersland ◽  
Jane Aldrich ◽  
Rose Ann Cattolico
Keyword(s):  
Chloroplast Dna ◽  
Copy Number ◽  
Marine Alga ◽  
Olisthodiscus Luteus

scholarly journals Replication from a proximal simian virus 40 origin is severely inhibited by multiple reiterations of the 72-base-pair repeat enhancer sequence.

1988 ◽  
Vol 8 (4) ◽  
pp. 1509-1517 ◽  
Author(s):  
R Kumar ◽  
K P Yoon ◽  
K N Subramanian
Keyword(s):  
Transcriptional Activation ◽  
Base Pair ◽  
Copy Number ◽  
Simian Virus 40 ◽  
Simian Virus ◽  
Origin Of Replication ◽  
Replication Efficiency ◽  
Sv40 Origin ◽  
Multiple Copies ◽  
In Cis

In a previous study in our laboratory, the effect of the reiteration frequency of the simian virus 40 (SV40) 72-base-pair (bp) repeat enhancer on transcription from the proximal SV40 early promoter was investigated (R. Kumar, T. A. Firak, C. T. Schroll, and K. N. Subramanian, Proc. Natl. Acad. Sci. USA 83:3199-3203, 1986). Increasing the enhancer copy number to four increased transcription proportionately; further increments in enhancer copy number reversed this effect, resulting in a decrease in the transcriptional activation. In the present study, the effect of enhancer reiteration on the replication efficiency of plasmids containing the SV40 origin of replication was investigated in transient replication assays in vivo in COS-1 monkey kidney cells producing the SV40 large tumor antigen required for replication. A plasmid containing the SV40 core origin and three copies of the replication-activating, G+C-rich 21-bp repeat promoter element replicated efficiently. Plasmids containing multiple copies of the 72-bp repeat enhancer cloned in head-to-tail linkage adjacent to the 21-bp repeat and the core origin replicated less efficiently; the decrease in replication efficiency could be correlated with the number of copies of the 72-bp repeat; replication was severely curtailed when 10 or more copies of the 72-bp repeat were present. Replication was not significantly inhibited by an increase in the number of copies of the 21-bp repeat to 15 or by the presence of three copies of a 360-bp pBR322 sequence in the immediate vicinity. Multiple copies of the 72-bp enhancer in cis were unable to inhibit replication from a second SV40 origin of replication situated 2 kilobase pairs away from the enhancer reiteration. Replication of four different test plasmids was not inhibited in trans by cotransfection of an excess of a potential competitor plasmid containing a 24-copy reiteration of the 72-bp enhancer. These results indicate that multiple tandem reiterations of the 72-bp enhancer inhibit replication only when they are present in cis adjacent to the origin of replication. Possible explanations for this inhibitory effect, such as an unfavorable local chromatin structure induced by the multimeric enhancer region or reduced or improper communications between factors bound to the multimeric region and the adjacent replication origin, are discussed.

Structure and expression of a tandem gene pair in Leishmania donovani that encodes a protein structurally homologous to eucaryotic cation-transporting ATPases

1987 ◽  
Vol 7 (11) ◽  
pp. 3937-3946
Author(s):  
J C Meade ◽  
J Shaw ◽  
S Lemaster ◽  
G Gallagher ◽  
J R Stringer
Keyword(s):  
Amino Acids ◽  
Nucleotide Sequence ◽  
Tandem Repeat ◽  
Base Pair ◽  
Leishmania Donovani ◽  
Oligonucleotide Probe ◽  
Open Reading Frame ◽  
Reading Frame ◽  
Atpase Gene ◽  
Sequence Encoding

An oligonucleotide probe was used to clone a cation-transporting ATPase gene from the genome of Leishmania donovani. The nucleotide sequence of the gene contained a 2,922-base-pair open reading frame that was predicted to encode a 107,406-dalton protein composed of 974 amino acids. The predicted L. donovani protein contained all the structural and functional domains expected to be present in a cation-transporting ATPase of the aspartyl phosphate class. The nucleotide sequence encoding the ATPase gene was duplicated in tandem in the parasite genome. Partial sequenation of the second member of the tandem repeat, which lay 2 kilobase pairs downstream of the ATPase gene, indicated that it was either identical to the first gene or very closely related to it. RNA homologous to either the ATPase gene or its adjacent relative was 5 kilobases in size and was approximately equally abundant in both promastigote and amastigote forms of the organism.

A 15 base-pair AT-Rich Variable Number Tandem Repeat in the Type III Procollagen Gene (COL3A1) as an Informative Marker for 2q31-2q32.3

Matrix ◽  
1992 ◽  
Vol 12 (1) ◽  
pp. 44-49 ◽  
Author(s):  
Peter K. Mays ◽  
Gerard Tromp ◽  
Helena Kuivaniemi ◽  
Markku Ryynänen ◽  
Darwin J. Prockop
Keyword(s):  
Tandem Repeat ◽  
Base Pair ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Informative Marker ◽  
Type Iii ◽  
Type Iii Procollagen

Band shift analysis of three base-pair repeat alleles in the short tandem repeat locus D12S391

1998 ◽  
Vol 93 (2-3) ◽  
pp. 79-88 ◽  
Author(s):  
C.P Phillips ◽  
D Syndercombe Court ◽  
M.V Lareu ◽  
J Hasskamp ◽  
A Carracedo
Keyword(s):  
Tandem Repeat ◽  
Base Pair ◽  
Short Tandem Repeat ◽  
Short Tandem Repeat Locus ◽  
Band Shift ◽  
Tandem Repeat Locus ◽  
Shift Analysis ◽  
Repeat Locus ◽  
Short Tandem

scholarly journals Degenerate 87-base-pair tandem repeats create hydrophilic/hydrophobic alternating domains in human mucin peptides mapped to 11p15

1993 ◽  
Vol 293 (2) ◽  
pp. 329-337 ◽  
Author(s):  
J Dufosse ◽  
N Porchet ◽  
J P Audie ◽  
V Guyonnet Duperat ◽  
A Laine ◽  
...  
Keyword(s):  
Cdna Library ◽  
Tandem Repeat ◽  
Base Pair ◽  
Tandem Repeats ◽  
Inflammatory Diseases ◽  
Peptide Structure ◽  
Cdna Clones ◽  
Protein Backbone ◽  
Chromosome 11P15 ◽  
Reading Frame

A human tracheobronchial lambda gt 11 cDNA library was screened using antiserum prepared against the deglycosylated protein backbone of human tracheobronchial mucins. Two cDNAs, designated JER 28 and 57, obtained from this immunoscreening, were used to isolate two other cDNA clones, JUL 7 and JUL 10, from a human tracheobronchial lambda gt 10 cDNA library. These four clones (561, 1830, 1631 and 991 bp), which mapped to chromosome 11p15, were all found to contain degenerate 87-base-pair tandem repeats which encode non-repetitive peptides. Numerous deletions or insertions in an otherwise virtually perfect 87-base-pair tandem repeat create many shifts in reading frame which completely destroy the repetitive peptide structure. The peptide is composed of alternate hydrophobic and hydrophilic domains which probably differ in the extent to which they are glycosylated. The mRNAs are expressed both in the respiratory and in the digestive tracts. These human mucin probes may be important in assessing the abnormal mucins associated with inflammatory diseases or carcinoma from human mucosae.

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