Microsatellite locus amplification using deer antler DNA.
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Animals↗
Biomedical subjects
R M Denome
Publications and source records attributed to R M Denome.
Characterization of a satellite DNA from Antilocapra americana.
The nucleotide sequence of a cloned satellite DNA from Antilocapra americana (American pronghorn antelope) is presented. The 1477-bp satellite is composed of degenerate 31-bp sub-repeats which are very similar in sequence to those of the major satellite DNAs from cattle and sheep. The sub-repeat sequence is more degenerate and variable in pronghorn than it is in cattle or sheep. The sequence is organized in the pronghorn genome in multicopy tandem arrays.
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Spatial constraints on polyadenylation signal function.
Efficient cleavage and polyadenylation of eukaryotic messenger RNAs require at least two signal elements: an AAUAAA or closely related sequence located 7-30 base pairs (bp) upstream of the site of processing, and a G/U- or U-rich sequence located 3' to the cleavage site. The herpes simplex virus type 1 thymidine kinase (tk) gene contains two copies of the AATAAA hexanucleotide and a GT-rich region. We have shown that the first AATAAA and the GT-rich region are essential for efficient processing, both in vivo and in vitro, whereas the second AATAAA does not appear to play any role in the formation of tk mRNA 3' ends. The failure of a signal containing only the second AATAAA and the GT-rich element to signal cleavage and polyadenylation suggested that these two elements might be too close together to constitute a functional polyadenylation signal. The experiments described in this report were directed at determining the effects on mRNA 3' end formation of alterations in spacing between signal elements. Wild-type tk contains 19 bp between these two elements. Constructs were made in which an AATAAA and the GT-rich region were separated by various distances ranging from 7 to 43 bp. The quantity and location of 3' ends of the tk mRNA produced by these constructs in Cos-1 cells were measured by S1 nuclease protection analysis. Signal efficiency was gradually reduced as the separation between the two signal elements was increased; with a separation of 43 bp, the signal functioned at approximately one-eighth the efficiency of the parental construction. Bringing the two signals closer together resulted in decreased signal efficiency; with a separation of 7 or 9 bp, no tk mRNA polyadenylated within the normal region was produced. Altering the sequences between these two elements without changing the distance had small effects on processing efficiency.
Base Sequence↗
RNA metabolism in nuclei: adenovirus and heat shock alter intranuclear RNA compartmentalization.
Nuclear RNA compartmentalization has received little attention as an area where regulation of gene expression could occur. RNA transcription and processing occur in association with the nuclear matrix, a salt-insoluble proteinaceous network that fills the nuclear space and is contiguous with the peripheral lamina and pore complexes. Described here are experiments that determine the fate of nuclear RNA after it has completed these matrix-associated maturation steps. Continuous label experiments indicate that after nuclear RNA is processed it changes its state of attachment in the nucleus so that it is now removed from the nucleus in the high salt extraction step of matrix isolation. It is this salt-extractable RNA that will be transported to the cytoplasm. Late in adenovirus infection and following heat shock, when transport of cellular RNA is decreased, cellular transcripts do not make the transition from the matrix-associated to the salt-extractable nuclear pool. The implication of these data for the regulation of gene expression is discussed.
Adenoviruses, Human↗
Patterns of polyadenylation site selection in gene constructs containing multiple polyadenylation signals.
We have constructed a series of plasmids containing multiple polyadenylation signals downstream of the herpes simplex virus type 1 (HSV) thymidine kinase (tk)-coding region. The signals used were from the simian virus 40 (SV40) late gene, the HSV tk gene, and an AATAAA-containing segment of the SV40 early region. This last fragment signals polyadenylation poorly in our constructs and not at all during SV40 infection. All plasmids contained the SV40 origin of replication. Plasmids were transfected into Cos-1 cells; after 48 h, cytoplasmic RNA was isolated and the quantity and 3'-end structure of tk mRNAs was analyzed by using S1 nuclease protection assays. In all constructs, all polyadenylation signals were used. Increasing the number of poly(A) signals 3' to the tk-coding region did not affect the total amount of polyadenylated RNA produced, even with the weakest signal. Increasing the distance between two signals caused an increase in the use of the 5' signal and a decrease in the use of the 3' signal. Changing the distance between the 5' cap and first signal did not affect signal use. Analyses of cytoplasmic mRNA stability, nuclear RNA distribution, and transcription in the polyadenylation signal region indicated that the distribution of tk RNAs ending at different poly(A) sites was the result of poly(A) signal choice, not other aspects of RNA metabolism. Four possible mechanisms of polyadenylation signal recognition are discussed.
Base Sequence↗
Fine-structure analysis of the processing and polyadenylation region of the herpes simplex virus type 1 thymidine kinase gene by using linker scanning, internal deletion, and insertion mutations.
Most eucaryotic mRNAs are polyadenylated. In higher eucaryotes, the sequence AATAAA is located 7 to 30 base pairs (bp) upstream from the site of processing and polyadenylation and is a critical part of the signal for processing and polyadenylation. Efficient cleavage and polyadenylation also require sequences downstream of polyadenylation sites. The herpes simplex virus type 1 thymidine kinase (tk) gene contains two copies of the AATAAA hexanucleotide and a GT box (18 of 19 consecutive residues are G or T) previously shown to be required for efficient processing and polyadenylation of tk mRNA (C. N. Cole and T. P. Stacy, Mol. Cell. Biol., 5:2104-2113). To define further the sequence requirements for efficient polyadenylation, we prepared linker scanning, internal deletion, and small insertion mutations in the polyadenylation region of the tk gene. These mutations were analyzed by S1 nuclease protection analysis of cytoplasmic RNA isolated from transfected Cos-1 monkey kidney cells. When the proximal AATAAA was deleted, no tk mRNA polyadenylated in the normal region was detected, whereas replacement of the second AATAAA with an XbaI linker had no effect on polyadenylation. When various portions of the GT box were replaced with linker, the amount of tk mRNA produced was reduced to 23 to 82% of the normal amount, but polyadenylation in the normal region was never abolished. Thus, no single portion of the GT box was absolutely required. In some cases, extended transcripts, polyadenylated at a cryptic site within pBR322, were detected. A spacing of 6 bp between AATAAA and the GT box was too short for efficient processing and polyadenylation. A spacing of 30 bp appeared to work almost as efficiently as did the wild-type spacing of 18 bp. Taken together, these results indicate that efficient polyadenylation requires both AATAAA and downstream GT-rich sequences. In addition, processing and polyadenylation are affected both qualitatively and quantitatively by sequences at polyadenylation sites and at more distant locations.
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Effect of creatine on contents of myosin heavy chain and myosin-heavy-chain mRNA in steady-state chicken muscle-cell cultures.
Embryonic-chick muscle cells reach a steady state with respect to protein metabolism after approx. 1 week in cell culture. To determine if this steady state could be altered by the administration of agents that have been reported to stimulate myosin heavy-chain synthesis, 7-day muscle-cell cultures were treated with 0-1 mM-creatine. Incorporation of [3H]leucine into myosin heavy chain was stimulated by 30-40% at the optimum creatine concentration (0.2 mM), but this stimulation was blocked when actinomycin D (10 micrograms/ml) was also present. However, the quantity of myosin-heavy-chain mRNA as measured by hybridization in vitro was only 15% higher in creatine-treated cultures, and was therefore not entirely responsible for the observed effect. It is important to note that creatine only exerted its action on myosin-heavy-chain synthesis rate in steady-state cultures; creatine was ineffective in altering this rate in rapidly differentiating 3-day muscle cultures. Finally, muscle-cell cultures that had been grown for the entire 7-day culture period in the presence of 0.2 mM-creatine were assayed for quantity of myosin heavy chain. Control and creatine-treated cultures contained 12.7 +/- 1.5 and 20.5 +/- 1.8 micrograms/dish respectively. In conclusion, creatine apparently enhances the quantity of myosin heavy chain in steady-state embryonic muscle-cell cultures, but it probably does not mediate regulation of myosin content in adult skeletal muscle.
Animals↗
Stimulation of myosin heavy chain synthesis in steady-state muscle cultures by the ionophore, A23187, requires transcription of messenger RNA.
After approximately one week in culture, embryonic chick skeletal muscle cells are at a steady state with respect to myosin heavy chain (MHC) concentration and synthesis rate. Muscle cells normally synthesize MHC at a maximum rate of 2.3 X 10 4 MHC/min/nucleus and contain approximately 3 X 10 7 MHC/nucleus. These cells also contain approximately 3500 copies/nucleus of MHC mRNA associated with polysomes and 1600 copies/nucleus of MHC mRNA localized in the nonpolysomal fraction. To determine if nonpolysomal MHC mRNA in mature muscle cultures could be recruited into active translation complexes when MHC synthesis was stimulated, muscle cultures were treated with the Ca 2+ ionophore, A23187 (0-1 micro M). The MHC synthesis rate was stimulated by 25 to 50% relative to stimulation of the rate of total protein synthesis in the presence of A23187, but this stimulation was blocked when 10 microgram/ml actinomycin D was also present. These results suggest that even though 30% of MHC mRNA is not actively engaged in MHC synthesis in mature muscle cultures, stimulation of MHC synthesis by A23187 results from transcription of new MHC mRNA rather than from utilization of pre-existing mRNA.
Animals↗