Biomedical subjects

C M Povinelli

Publications and source records attributed to C M Povinelli.

7 recordsLinked to original sources

PubMed1994

Adaptor-based uracil DNA glycosylase cloning simplifies shotgun library construction for large-scale sequencing.

An improved strategy for the preparation of libraries for the random sequencing of DNA is reported. The protocol is a modification of a previous adaptor-based strategy, and utilizes long (11 base) overhangs, which eliminates the unreliable step of vector-insert ligation. The random inserts are prepared by adaptor ligation, while the M13 vector is prepared as described for uracil DNA glycosylase (UDG) cloning of polymerase chain reaction (PCR) products, using PCR with uracil-containing primers, followed by UDG treatment to produce overhangs. This method has been found to reliably yield large numbers of clones. There is no background due to religation of the vector, and all clones contain inserts. In addition, the method is simple and suitable for export to other investigators. Libraries were constructed from cosmids containing human DNA and from human cDNAs in order to characterize a strategy for shotgun sequencing of multiple shorter fragments.

Base Sequence↗

PubMed1993

Large-scale sequencing library production: an adaptor-based strategy.

A significant bottleneck in large-scale DNA sequencing projects is the creation of high-quality random libraries suitable for sequencing. We have utilized an adaptor-based strategy and developed a simple protocol to reliably generate single-insert random subclone M13 libraries yielding uniform coverage and > 10(3) clones per microgram of DNA. Of the resulting white plaques, 95% contained inserts, < 0.5% were due to adaptors with no insert, and none of the clones were found to contain extraneous DNA (0/600) or multiple inserts (0/300).

Base Sequence↗

PubMed1993

Distribution and characterization of mutations induced by nitrous acid or hydroxylamine in the intron-containing thymidylate synthase gene of bacteriophage T4.

The detailed distribution and characterization of 51 hydroxylamine (HA)-induced and 59 nitrous acid (NA)-induced mutations in the intron-containing bacteriophage T4 thymidylate synthase (td) gene is reported here. Mutations were mapped in 10 regions of the td gene by recombinational marker rescue using plasmid or M13 subclones of the td gene. Phage crosses using deletion mutants with known breakpoints in the 3' end of the td intron subdivided HA and NA mutations which mapped in this region. At least 31 of the mutations map within the 1-kb group I self-splicing intron. Intron mutations mapped only in the 5' and 3' ends of the intron sequence, in accordance with the hypothesis that the 5' and 3' domains of the T4 td intron are essential for correct RNA splicing. RNA sequence analysis of a number of mapped td mutations has identified two intron nucleotides and one exon nucleotide where both HA- and NA-induced mutations commonly occur. These three loci are characterized by a GC dinucleotide, with the mutations occurring at the cytosine residue. Thus, these data indicate at least three potential sites of both HA- and NA-induced mutagenic hotspot activity within the td gene.

Bacteriophage T4↗

PubMed1992

Differential and coordinate responses of the human genes encoding the heat stable alkaline phosphatases to cAMP and sodium butyrate in the choriocarcinoma line JEG-3.

Human heat stable alkaline phosphatases are encoded by two closely related genes: the PLAP-1, which specifies the term placental enzyme, and the PLAP-2, which is expressed primarily in germ cells. In the choriocarcioma line JEG-3, 8-Br-cAMP induced the accumulation of the mRNA of both genes, while sodium butyrate induced the accumulation of PLAP-2 transcripts only. Each agent increased the transcription rate of one or both of the genes, as assayed by run-on transcription. In transfection of JEG-3 cells with PLAP promoters fused to the firefly luciferase gene, the activity of the PLAP-2 promoter (but not PLAP-1) was induced with sodium butyrate, while both promoters were induced by 8-Br-cAMP. Inducibility of the PLAP-2 promoter by 8-Br-cAMP was still observed when the promoter was shortened to -103, leaving intact a sequence resembling a cAMP response element. The extent of transcriptional activation by either agent was not sufficient to explain the accumulation of PLAP mRNA. These studies suggest that both transcriptional and posttranscriptional processes are involved in the induction of the PLAP-1 and PLAP-2 gene in JEG-3 cells.

8-Bromo Cyclic Adenosine Monophosphate↗

PubMed1992

Non-random distribution and co-localization of purine/pyrimidine-encoded information and transcriptional regulatory domains.

In order to detect sequence-based information predictive for the location of eukaryotic transcriptional regulatory domains, the frequencies and distributions of the 36 possible purine/pyrimidine reverse complement hexamer pairs was determined for test sets of real and random sequences. The distribution of one of the hexamer pairs (RRYYRR/YYRRYY, referred to as M1) was further examined in a larger set of sequences (> 32 genes, 230 kb). Predominant clusters of M1 and the locations of eukaryotic transcriptional regulatory domains were found to be associated and non-randomly distributed along the DNA consistent with a periodicity of approximately 1.2 kb. In the context of higher ordered chromatin this would align promoters, enhancers and the predominant clusters of M1 longitudinally along one face of a 30 nm fiber. Using only information about the distribution of the M1 motif, 50-70% of a sequence could be eliminated as being unlikely to contain transcriptional regulatory domains with an 87% recovery of the regulatory domains present.

Animals↗

PubMed1987

Two domains for splicing in the intron of the phage T4 thymidylate synthase (td) gene established by nondirected mutagenesis.

Of 97 nondirected T4 thymidylate synthase-defective (td) mutations, 27 were mapped to the intron of the split td gene. Clustering of these intron mutations defined two domains that are functional in splicing, each within approximately 220 residues of the respective splice sites. Two selected mutations, tdN57 and tdN47, fell within phylogenetically conserved pairings, with tdN57 disrupting the exon I-internal guide pairing (P1) in the 5' domain and tdN47 destabilizing the P9 helix in the 3' domain. A splicing assay with synthetic oligonucleotides complementary to RNA junction sequences revealed processing defects for T4tdN57 and T4tdN47, both of which are impaired in cleavage at the 5' and 3' splice sites. Thus prokaryotic genetics facilitates association of specific residue changes with their consequences to splicing.

Base Sequence↗

PubMedDate not supplied

Trace expression of the germ-cell alkaline phosphatase gene in human placenta.

We have developed hybridization probes that clearly distinguish the RNA transcripts of the two closely related human heat-stable alkaline phosphatase genes. RNA from the PLAP-1 gene, encoding the term placental alkaline phosphatase, is the predominant transcript in placenta from 8 weeks to term. Transcripts from the PLAP-2 gene, encoding the germ-cell or PLAP-like enzyme, are also detectable in the placenta, but at no more than 2 per cent the level of PLAP-1 transcripts.

Alkaline Phosphatase↗