DNA sequence organization in the starfish Dermasterias imbricata

1980 ◽  
Vol 58 (4) ◽  
pp. 352-360 ◽  
Author(s):  
Michael J. Smith ◽  
A. Lui ◽  
K. K. Gibson ◽  
J. K. Etzkorn
Keyword(s):  
Genomic Dna ◽  
Repetitive Sequences ◽  
Single Copy ◽  
Base Pairs ◽  
S1 Nuclease ◽  
Sequence Organization ◽  
A Genome ◽  
Short Period ◽  
Nuclease Digestion ◽  
Kinetics Of

The sequence arrangement in the genomic DNA of the starfish Dermasterias imbricata has been examined. Analyses of kinetics of reassociation in solution at DNA lengths of 400, 3100, and 6200 base pairs (bp) demonstrate the interspersion of repetitive and unique DNA. At a fragment length of 400 bp, 45% of the DNA reacts at a rate appropriate for single-copy sequences in a genome of this size (0.54 pg). Interspersion of repetitive sequences is also demonstrated by the reduced hyperchromicity of 3100- or 6200-bp fragments reacted to Cot 10, where only repetitive sequences have formed duplex. S1 nuclease digestion of 3100-bp fragments reassociated to Cot 10 shows that both short (~ 230 bp) and long (≥ 2600 bp) repetitive sequences are present in this DNA. These data demonstrate a short period interspersion pattern in Dermasterias.

DNA sequence organization in the common Pacific starfish Pisaster ochraceous

1978 ◽  
Vol 56 (11) ◽  
pp. 1048-1054 ◽  
Author(s):  
Michael J. Smith ◽  
Robin Boal
Keyword(s):  
Dna Sequences ◽  
Repetitive Sequences ◽  
Single Copy ◽  
Sea Star ◽  
Base Pairs ◽  
S1 Nuclease ◽  
Reassociation Kinetics ◽  
Short Period ◽  
The Common ◽  
Copy Dna

The sequence arrangement of the genomic DNA from the common sea star Pisaster ochraceous has been examined. Reassociation kinetics at DNA fragment lengths of 300 base pairs (bp) indicate the presence of at least three repetitive components in this DNA. The majority of these repetitive sequences are reiterated over the range from 10 to 100's. Approximately one-third of the nucleotides are found in repetitive sequences. Analysis of the reassociation kinetics of 3000-bp DNA fragments demonstrates the interspersion of repetitive and unique DNA sequences. The hyperchromicity of 3000-bp fragments reassociated to low Cot values (the product of moles of nucleotide per litre and time in seconds), and the size distribution of S1 nuclease resistant DNA duplex in these reassociation products, indicate a short-period interspersion pattern in the starfish genome. Repetitive segments (400 ± 100 bp) are interspersed with longer unique DNA sequences. At a fragment length of 3000 bp the major fraction of the single-copy DNA is found in such an arrangement. In addition to short repetitive segments a substantial portion of the repetitive DNA nucleotides are found in segments excluded by Sepharose CL-2B (≥ 2000 bp). As much as one-quarter of the repetitive sequence nucleotides can be assigned to long segments.

scholarly journals Microdissection of and microcloning from the short arm of human chromosome 2.

1986 ◽  
Vol 6 (11) ◽  
pp. 3826-3830 ◽  
Author(s):  
G P Bates ◽  
B J Wainwright ◽  
R Williamson ◽  
S D Brown
Keyword(s):  
Human Chromosome ◽  
Dna Sequences ◽  
Chromosomal Location ◽  
Genetic Diseases ◽  
Repetitive Sequences ◽  
Single Copy ◽  
Chromosome 2 ◽  
Insert Size ◽  
Base Pairs ◽  
The Mean

A bank of cloned DNA sequences from the distal half of the short arm of human chromosome 2 was generated by using microdissection and microcloning techniques. DNA was purified from 106 chromosomal fragments, manually dissected from peripheral lymphocytes in metaphase, and cloned into the EcoRI site of lambda gt10. A total of 257 putative recombinants were recovered, of which 41% were found to contain human inserts. The mean insert size was 380 base pairs (median size, 83 base pairs), and fewer than 10% of the clones contained highly repetitive sequences. All single-copy sequences examined were shown to map to the short arm of chromosome 2 by using hybrid panels. This technique provides a rapid method of isolating probes specific to a human subchromosomal region to generate linked markers to genetic diseases for which the chromosomal location is known.

Molecular organization of the human Raf-1 promoter region

1990 ◽  
Vol 10 (7) ◽  
pp. 3325-3333
Author(s):  
T W Beck ◽  
U Brennscheidt ◽  
G Sithanandam ◽  
J Cleveland ◽  
U R Rapp
Keyword(s):  
Promoter Region ◽  
Genomic Dna ◽  
Housekeeping Gene ◽  
Molecular Organization ◽  
Nucleotide Sequencing ◽  
Base Pairs ◽  
S1 Nuclease ◽  
Octamer Motif ◽  
Potential Binding ◽  
Potential Binding Site

A genomic DNA fragment containing the Raf-1 promoter region was isolated by using a cDNA extension clone. Nucleotide sequencing of genomic DNA clones, primer extension, and S1 nuclease assays have been used to identify the 5' ends of Raf-1 RNAs. Consistent with its ubiquitous expression, the Raf-1 promoter region had features of a housekeeping gene in that it was GC-rich (HTF-like), lacked TATA and CAAT boxes, and contained heterogeneous RNA start sites and four potential binding sites for the transcription factor SP1. In addition, an octamer motif (ATTTCAT), a potential binding site for the octamer family of transcription factors, was located at -734 base pairs. The Raf-1 promoter region drove reporter gene expression 30-fold over the promoterless reporter in Cos 7 cells.

DNA REASSOCIATION KINETICS OF FOUR CONIFERS

1980 ◽  
Vol 22 (1) ◽  
pp. 69-79 ◽  
Author(s):  
Adrian V. Rake ◽  
Jerome P. Miksche ◽  
Richard B. Hall ◽  
Kenneth M. Hansen
Keyword(s):  
Genome Size ◽  
Picea Glauca ◽  
Pinus Banksiana ◽  
Pinus Resinosa ◽  
Single Copy ◽  
Rrna Gene ◽  
Pinus Lambertiana ◽  
A Genome ◽  
Copy Dna ◽  
Kinetics Of

The DNA genome size of four conifers was determined cytophotometrically and the diploid amounts of DNA per cell of Picea glauca (Moench)Voss, Pinus banksiana Lamb., Pinus lambertiana Dougl., and Pinus resinosa Ait. were 19.3, 29.8, 87.7 and 43.1 pg., respectively. These DNA values yield rRNA gene numbers considerably lower than previously published (Hotta and Miksche, 1974). The DNA was further characterized by studying the kinetics of reassociation. The results indicated that in all four conifers there are four repeated nucleotide sequence fractions and one unique fraction. The genome size as determined by reassociation of the single copy DNA approximated the genome size determined by cytophotometry for Picea glauca and Pinus banksiana. Pinus lambertiana and Pinus resinosa appeared to have a genome size, as determined by cytophotometry, larger than the genome sizes determined by reassociation, indicating possible ploidy of their respective genomes.

scholarly journals Molecular organization of the human Raf-1 promoter region.

1990 ◽  
Vol 10 (7) ◽  
pp. 3325-3333 ◽  
Author(s):  
T W Beck ◽  
U Brennscheidt ◽  
G Sithanandam ◽  
J Cleveland ◽  
U R Rapp
Keyword(s):  
Promoter Region ◽  
Genomic Dna ◽  
Housekeeping Gene ◽  
Molecular Organization ◽  
Nucleotide Sequencing ◽  
Base Pairs ◽  
S1 Nuclease ◽  
Octamer Motif ◽  
Potential Binding ◽  
Potential Binding Site

A genomic DNA fragment containing the Raf-1 promoter region was isolated by using a cDNA extension clone. Nucleotide sequencing of genomic DNA clones, primer extension, and S1 nuclease assays have been used to identify the 5' ends of Raf-1 RNAs. Consistent with its ubiquitous expression, the Raf-1 promoter region had features of a housekeeping gene in that it was GC-rich (HTF-like), lacked TATA and CAAT boxes, and contained heterogeneous RNA start sites and four potential binding sites for the transcription factor SP1. In addition, an octamer motif (ATTTCAT), a potential binding site for the octamer family of transcription factors, was located at -734 base pairs. The Raf-1 promoter region drove reporter gene expression 30-fold over the promoterless reporter in Cos 7 cells.

Transcription of a trout protamine gene in vitro: the effects of alteration of promoters

1984 ◽  
Vol 62 (5) ◽  
pp. 291-300 ◽  
Author(s):  
Jacek M. Jankowski ◽  
Gordon H. Dixon
Keyword(s):  
Rna Polymerase Ii ◽  
Dna Sequences ◽  
Tata Box ◽  
Base Pairs ◽  
S1 Nuclease ◽  
Promoter Sequences ◽  
Transcription System ◽  
Nuclease Digestion ◽  
Simplex Virus

An in vitro approach has been used to study trout protamine gene expression using various recombinant plasmids containing trout protamine genes as templates in the HeLa cell lysate transcription system. The specific RNA transcript which is protected against S1 nuclease digestion by hybridization to the protamine gene sequence is α-amanitin sensitive (1 μg/mL), showing that RNA polymerase II is involved. The sizes of transcripts from templates linearized with Bam HI, Rsa I, and Hpa II (all downstream from the putative TATA box) are consistent with those predicted from the known sequence of the protamine gene. Digestion at an Alu I site only 14 base pairs (bp) upstream from TATA box has no effect on the accuracy of transcription in vitro; however, cutting at an Ava II site 9 bp downstream from the TATA box (reading from the first T) abolishes transcription. Chimeric plasmids, in which a herpes simplex virus (HSV-1) thymidine kinase (tk) promoter is tandemly inserted upstream from the trout protamine DNA sequences or as a replacement of the natural protamine promoter, were constructed. Use of these plasmids allowed an examination in a single assay of eight different putative promoter sequences (TATAAAA, TATAAA, TACAAA, TATATA, TATTTAA, CATATTA, TATATTAT, and TATTTAT) that are localized in either the protamine or the tk genes. The canonical TATAAAA promoter (the natural protamine promoter) was the strongest one and, in its presence, none of the others were used significantly for transcription. However, when this promoter was removed the weaker promoters were able to promote transcription.

scholarly journals Genome evolution in mosquitoes: intraspecific and interspecific variation in repetitive DNA amounts and organization

1988 ◽  
Vol 51 (3) ◽  
pp. 185-196 ◽  
Author(s):  
William C. Black ◽  
Karamjit S. Rai
Keyword(s):  
Genome Evolution ◽  
Genome Size ◽  
Intraspecific Variation ◽  
Repetitive Dna ◽  
Mosquito Species ◽  
Repetitive Sequences ◽  
Interspecific Variation ◽  
S1 Nuclease ◽  
Short Period ◽  
Dna Amounts

SummaryDNA reassociation kinetics were used to determine the amounts and organization of repetitive and unique DNA in four mosquito species: Anopheles quadrimaculatus (Say), Culex pipiens (L.), Aedes albopictus (Skuse) and Ae. triseriatus (Say). Intraspecific variation in repetitive DNA amounts was examined in two geographic strains of Ae. albopictus fom Calcutta, India and the island of Mauritius. Repetitive and unique sequences in An. quadrimaculatus were distributed in a pattern of long period interspersion. Repetitive DNA in all other mosquito species exhibited a pattern of short period interspersion. The amounts of fold-back, middle repetitive, and highly repetitive sequences increased with genome size. The amount of foldback DNA increased at a much slower rate than the middle and highly repetitive sequences. Intraspecific variation in genome size in Ae. albopictus was due primarily to the amounts of highly repetitive DNA. S1 nuclease digestion of repetitive DNA in all species revealed a positive correlation between genome size and the proportion of the repetitive DNA consisting of short repeats. The amounts of long and short repeats increased with genome size but short repeats increased at a higher rate. The repetitive DNA of the Mauritius strain contained approximately 15% more short repeats than the Calcutta strain. These findings suggest that genome evolution in mosquitoes has resulted from changes in both the amounts and organization of repetitive elements.

Microdissection of and microcloning from the short arm of human chromosome 2

1986 ◽  
Vol 6 (11) ◽  
pp. 3826-3830
Author(s):  
G P Bates ◽  
B J Wainwright ◽  
R Williamson ◽  
S D Brown
Keyword(s):  
Human Chromosome ◽  
Dna Sequences ◽  
Chromosomal Location ◽  
Genetic Diseases ◽  
Repetitive Sequences ◽  
Single Copy ◽  
Chromosome 2 ◽  
Insert Size ◽  
Base Pairs ◽  
The Mean

A bank of cloned DNA sequences from the distal half of the short arm of human chromosome 2 was generated by using microdissection and microcloning techniques. DNA was purified from 106 chromosomal fragments, manually dissected from peripheral lymphocytes in metaphase, and cloned into the EcoRI site of lambda gt10. A total of 257 putative recombinants were recovered, of which 41% were found to contain human inserts. The mean insert size was 380 base pairs (median size, 83 base pairs), and fewer than 10% of the clones contained highly repetitive sequences. All single-copy sequences examined were shown to map to the short arm of chromosome 2 by using hybrid panels. This technique provides a rapid method of isolating probes specific to a human subchromosomal region to generate linked markers to genetic diseases for which the chromosomal location is known.

scholarly journals DNA damage and heat shock dually regulate genes in Saccharomyces cerevisiae.

1986 ◽  
Vol 6 (1) ◽  
pp. 90-96 ◽  
Author(s):  
T McClanahan ◽  
K McEntee
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Dna Damage ◽  
Heat Shock ◽  
Shock Treatment ◽  
Northern Hybridization ◽  
Heat Shock Treatment ◽  
Base Pairs ◽  
S1 Nuclease ◽  
Hsp70 Family ◽  
Transcriptional Start Sites

Two Saccharomyces cerevisiae genes isolated in a differential hybridization screening for DNA damage regulation (DDR genes) were also transcriptionally regulated by heat shock treatment. A 0.45-kilobase transcript homologous to the DDRA2 gene and a 1.25-kilobase transcript homologous to the DDR48 gene accumulated after exposure of cells to 4-nitroquinoline-1-oxide (NQO; 1 to 1.5 microgram/ml) or brief heat shock (20 min at 37 degrees C). The DDRA2 transcript, which was undetectable in untreated cells, was induced to high levels by these treatments, and the DDR48 transcript increased more than 10-fold as demonstrated by Northern hybridization analysis. Two findings argue that dual regulation of stress-responsive genes is not common in S. cerevisiae. First, two members of the heat shock-inducible hsp70 family of S. cerevisiae, YG100 and YG102, were not induced by exposure to NQO. Second, at least one other DNA-damage-inducible gene, DIN1, was not regulated by heat shock treatment. We examined the structure of the induced RNA homologous to DDRA2 after heat shock and NQO treatments by S1 nuclease protection experiments. Our results demonstrated that the DDRA2 transcript initiates equally frequently at two sites separated by 5 base pairs. Both transcriptional start sites were utilized when cells were exposed to either NQO or heat shock treatment. These results indicate that DDRA2 and DDR48 are members of a unique dually regulated stress-responsive family of genes in S. cerevisiae.

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