Deoxyadenylate-rich sequences in mammalian DNA

Long poly(A) tracts in the human genome are associated with the Alu family of repeated elements

Long poly(dA).poly(dT) tracts (poly(A) tracts), regions of DNA containing at least 20 contiguous dA residues on one strand and dT residues on the complementary strand, are found in about 2 X 10(4) copies interspersed throughout the human genome. Using poly(dA).poly(dA) as a hybridization probe, we identified recombinant lambda phage that contained inserts of human DNA with poly(A) tracts. Three such tracts have been characterized by restriction mapping and sequence analysis. One major poly(A) tract is present within each insert and is composed of from 28 to 35 A residues. In each case, the poly(A) tract directly abuts the 3' end of the human Alu element, indicating that the major class of poly(A) tracts in the human genome is associated with this family of repeats. The poly(A) tracts are also adjacent to A-rich sequences and, in one case, to a polypurine tract, having the structure GA3-GA3-GA4-GA6-GA5-GA4. We suggest that repetitive cycles of unequal crossing over may give rise to both the long poly(A) and polypurine tracts observed in this study.

Simple sequences are ubiquitous repetitive components of eukaryotic genomes

Simple sequences are stretches of DNA which consist of only one, or a few tandemly repeated nucleotides, for example poly (dA) X poly (dT) or poly (dG-dT) X poly (dC-dA). These two types of simple sequence have been shown to be repetitive and interspersed in many eukaryotic genomes. Several other types have been found by sequencing eukaryotic DNA. In this report we have undertaken a systematical survey for simple sequences. We hybridized synthetical simple sequence DNA to genome blots of phylogenetically different organisms. We found that many, probably even all possible types of simple sequence are repetitive components of eukaryotic genomes. We propose therefore that they arise by common mechanisms namely slippage replication and unequal crossover and that they might have no general function with regards to gene expression. This latter inference is supported by the fact that we have detected simple sequences only in the metabolically inactive micronucleus of the protozoan Stylonychia, but not in the metabolically active macronucleus which is derived from the micronucleus by chromosome diminution.

Simple DNA sequences of Drosophila virilis isolated by screening with RNA

We isolated clones from different types of genomic Drosophila virilis libraries by screening with mRNA labelled in vitro. The DNA regions of the clones showing cross-hybridization with the RNA were sequenced. All of them contained different types of simple sequences, which most probably were solely responsible for the hybridization. We show that simple sequences and their transcription are not a phenomenon that is restricted to Drosophila. Simple sequences can be detected in all eucaryotes and at least three types (poly[d(G--T)] X poly[d(C--A)], poly[d(G--A)] X poly-[d(C--T)] and poly(dA) X poly(dT] are also widely transcribed.

Detection, sizing, and quantitation of polyadenylated ribonucleic acid in the nanogram-picogram range

A method is described for using very high specific activity [3H]poly(deoxythymidylate) [[3H]poly(dT)] to detect, size, and quantiate subnanogram amounts of nonradioactive polyadenylated RNA. Short (approximately 100 nucleotides long) [3H]poly(dT) is hybridized to the poly(adenylate) [poly(A)] tracts in polyadenylated RNAs. The RNA may then be sized and quantitated by sucrose gradient analysis. The addition of the small [3H]poly(dT) molecules does not significantly alter the s values of RNAs. The amount of [3H]poly(dT) hybridized to polyadenylated RNA increases linearly with the amount of RNA. A room temperature hydroxylapatite (HA) method has also been developed to detect and quantitate poly(A)-containing RNA after hybridization to radioactive poly(dT). S-1 nuclease (S-1) analysis can also be used to measure the poly(A) content of polyadenylated RNA to less than nanogram RNA amounts. For both the S-1 and HA approaches, the amount of [3H]poly(dT) hybridized increases with the amount of RNA and the methods can detect to as little as 10(-12) g of polyadenylated RNA with [3H]poly(dT). Greater sensitivity is possible with higher specific activity poly(dT). The approaches presented here significantly extend the uses of radioactive homopolymers to detect, quantitate, and characterize RNAs containing complementary homopolymer tracts.

Measurement of polyadenylic acid by hybridization with polyuridylic acid: a source of error due to the lability of tritiated polyuridylic acid in trichloroacetic acid

During brief exposure to trichloroacetic acid at 0 degree C, significant amounts of tritiated polyuridylic acid are converted to acid-soluble products. The loss of polymeric radioactivity is dependent on both acid concentration and the time of exposure to acid. When trichloroacetic acid precipitation is used to recover the tritiated polyuridylic acid present in a hybrid with polyadenylic acid, significant underestimates of the hybridized radioactivity can occur because of the lability of tritiated polyuridylic acid. Conditions are given which minimize the lability and permit quantitative recovery of tritiated polyuridylic acid by trichloroacetic acid precipitation.

Size and distribution of polyadenylic acid sequences in Drosophila polytene DNA and RNA

[3H]Poly(U) hybridizes very rapidly to polytene DNA from Drosophila hydei. When hybridization is performed at 30 degrees C in 2 X SSC to a large excess of DNA, 95% of the poly(U) becomes ribonuclease resistant. Also, complementary RNA transcribed in vitro from polytene DNA hybridizes to poly(U). 023--0.25% of the DNA is composed of (dA)-rich sequences and 0.23--0.31% of cRNA hybridizes to [3H]poly(U). The length of the (dA)-rich sequences on the DNA and cRNA is 40 nucleotides. The Tm values of these hybrids formed between DNA or cRNA-poly(U) is 45 degrees C. The poly(A) fragments from cytoplasmic RNA ranged from 80 to 170 nucleotides in lenght, and migrated in polyacrilamide gels as a broad peak. The average sizes of the poly(A) fragments from the poly(A)-containing RNA transcribed by nuclei isolated from salivary glands in vivo or in vitro were 40, 70, 170 and 70 nucleotides, respectively. Hybridization in situ of [3H]-poly(U) to chromosome squashes indicated that the (dA)-rich sequences are randomly distributed over the whole genome.

Interspersion and transcription of repeated sequences of rat DNA

Repetitive rat DNA reassociated to Cot=0.1 and deprived of "foldback" sequences showed close interspersion with unique sequences. As measured by electron microscopy, the average length of repetitive segments was about 600 +/- 400, and of unique segments 1800-3600 base pairs. Pyrimidine tracts over 80 nucleotides in length were found mainly in foldback and repetitive fractions. Oligo(dT) tracts, 20-30 bases in length prevailed in the DNA fraction reassociated to Cot=0.1. Repetitive and unique DNA fractions were annealed to Millipore filters and hybridized with hnRNA. Up to 1.6% of repetitive DNA reassociated to Cot=0.05 showed base complementarity with hnRNA, whereas the comparative figures for DNA reassociated to Cot=10 and for the unique fraction were 0.8% and 0.3% respectively. When hybridization of hnRNA was carried out in solution in vast DNA excess, no hybrid formation with repetitive sequences reassociated to Cot=0.1 was observed, although hybridization with DNA reassociated to Cot=10 was noticeable.

High molecular weight UMP-rich RNA of germinating wheat embryo

The synthesis of a relatively homogeneous RNA fraction was observed in germinating wheat embryo. The fraction synthesised within the first 3 h of germination had a high molecular weight (approx. 2.10(6)) and a specific nucleotide composition. In particular, the UMP content was unusually high (47 mol%). The high UMP content resulted probably from the presence of UMP-rich regions within the newly-synthesised polynucleotide chain. Neither ribosomal nor transfer DNA sequences were transcribed at the same time. It is suggested that the newly-synthesised RNA fraction represents an mRNA precursor and is transcribed in the immediate response of wheat embryo to the environmental stimuli to germinate.

Template specific inhibitor of mammalian DNA polymerases

A study of the inhibition of mouse cellular DNA polymerases by poly-nucleotides and their vinyl analogs is presented. Poly(dT)-directed poly(dA) synthesis by representatives of all three classes of cellular DNA polymerase could be completely inhibited by poly(9-vinyladenine), although higher concentrations were required in the case of the gamma class enzyme. Studies on the mechanism of the inhibition using the alpha class DNA polymerase and different templates showed that the enzyme activity was inhibited in all cases where base-pairing between the vinyl polymer and the template occurred; poly(9-vinyladenine) did not interfere with the replication of templates to which it does not bind. The inhibition occurred shortly after addition of poly(9-vinyladenine) to ongoing reactions, yet the enzyme was not displaced from the template - primer complex.

Hybridization of polyuridylic acid to human DNA immobilized onto nitrocellulose filters

The level of deoxyadenylate (da) regions in human DNA was estimated from formation of poly(U)-poly(da) triplexes on nitrocellulose filters that were RNAase resistant. The (dA) rich sequences were determined following mild ribonuclease treatment of the poly(U)-DNA hybrids (5 mug/ml at 25 degreesC for 30 min), where as exhaustive ribonuclease treatment (5 mug/ml at 25 degrees C for 6 hr) estimated the more (dA) pure sequences. The level of (dA) rich regions was 0.39% of the DNA and for the more (dA) pure regions it was 0.07%. The (dA) regions were widely distributed throughout human DNA regardless of base composition or sequence repetition. However, a concentration of (dA) regions into main band CsC1 gradient fractions of DNA and into repeated DNA was observed.

Analysis of long pyrimidine polynucleotides in HeLa cell nuclear DNA: absence of polydeoxythymidylate

HeLa cell nuclear DNA contains an unexpectedly large amount of long pyrimidine polynucleotides. These sequences were detected in DNA labeled with [(3)H] thymidine by treatment with formic acid-diphenylamine and subsequent analysis by polyacrylamide gel electrophoresis. About 0.5% of the total thymine residues were found in polynucleotides that migrated more slowly than 4S RNA. No polynucleotides of comparable size were detected in Escherichia coli DNA. The pyrimidine polynucleotides contained no pure poly(dT) sequences (less than 0.0015% of the total residues), as judged by thermal chromatography of a complex formed with poly(A).

Occurrence of uridylate-rich oligonucleotide regions in heterogeneous nuclear RNA of HeLa cells

Heterogeneous nuclear RNA molecules from HeLa cells contain a specific segment of about 30 nucleotides length that is largely (about 80%) uridylic acid. This oligo(U) segment is located predominantly in the larger (70S-90S) heterogeneous nuclear RNA molecules, and is essentially absent in messenger RNA and 45S ribosomal precursor RNA molecules. The oligo(U) hybridizes rapidly to cellular DNA, suggesting that it is transcribed from the repeated regions of the DNA.