Nucleotide sequence analysis of the spacer regions flanking the rat rRNA transcription unit and identification of repetitive elements.

We investigated the organization of the rat rDNA non-transcribed spacer (NTS) by determining the sequence of large NTS segments located upstream (2501 bp) and downstream (4025 bp) from the rRNA transcription unit. We identified four B2-like and two ID mobile elements. They may be grouped in three pairs with the members of each pair located in the upstream and downstream NTS. The ID sequences are identical to the consensus sequence, while the pairs of B2-like elements show 85% and 50/65% homology to the consensus B2 sequence. The proximal part of the downstream NTS contains a region of widely diverged SalI tandem repeats. A considerable part of the analyzed upstream and downstream NTS sequences is constituted by different types of simple sequences and long poly(purine) X poly(pyrimidine) tracts. These data show that the rat rDNA NTS regions flanking the rRNA transcription unit are characterized by a combination of short interspersed (B2-superfamily) and various simple sequences.

[Structural organization of the non-transcribed spacer of the rat ribosomal repeated sequence]. / Strukturnaia organizatsiia netranskribiruemogo speisera ribosomnogo povtora krysy.

Three types of repetitive sequences were found in the non-transcribed spacer of the rat ribosomal genes. Two internal repeats (100-150 bp long) flank the transcribed region encoding pre-rRNA. A number of internal repeats localized at approximately 300 bp upstream the transcription initiation site ranges from 1 to 9. This leads to heterogeneity in this region of the non-transcribed spacer. The non-transcribed spacer comprises of four regions with highly repetitive sequences. Two of these regions are localized 2.0-5.0 kb downstream the 3'-end of the 28S rRNA gene and the other two are localized 3.0-5.0 kb upstream the transcription initiation site. It is shown that these highly repetitive sequences are not only dispersed within the genome, but are found also in the family of extended repeats. One of the dispersed repeats localized upstream the transcribed region is reiterated more than 100 thousand times within the genome and is homologous to the mouse B2 sequence. The dispersed repeats downstream from the transcribed region are repeated 30-40 thousand times within the genome. The nucleotide sequences of the extended region of this sequence (approximately 1.0 kb) has typical blocks of (AC)n, (ACC)n, (GAG)n, (CTGT)n, (TAAC)n, (CCTG)n and (G)n types. Two palindromes and sufficiently long straight repeats were found. The structural-functional organization of the rat ribosomal repeating unit is a convenient model for studying the principles of organization of the genetic material in mammalian cells.

Structural organization of rat ribosomal RNA genes: interspersed sequences and their putative role in the alignment of nucleosomes.

We have observed four regions containing highly repetitive interspersed sequences in the nontranscribed spacer (NTS) of the rat rRNA genes. Two of them (A and B) are located at a distance of 3-5 kb upstream from the transcription start point and two others (C and D) at a distance of 2-5 kb downstream from the 3' end of the 28S rRNA gene. These repetitive sequences are widely dispersed in the genome and are included both in small-copy regions and in the families of extended reiterated sequences. The sequences of three fragments were determined: one from the C2 region, 1100 bp in length and two from A and C1 regions, 110-120 bp long. These regions are characterized by the presence of 'simple' sequences, such as (AC)n, (ACC)n, (GAG)n, (GGGA)n, (TAAG)n, and also of long blocks, (G)n and (A)n. In the C2 region two palindromes, 16 and 14 nt long, were found, one of them including a XhoI site. Mobile element B2 was observed in regions B and C. All four regions, A, B, C and D, contain sets of simple sequences, among which some common elements have been found. Theoretical prediction of the nucleosomal disposition in the C region indicates that the combination of simple sequences existing in the given area secures fixed positions of the nucleosomes, one of the nucleosomes being formed on the B2 element. Moreover, a striking periodicity, with the repeat length close to that of the rat nucleosomal DNA, has been observed. A hypothesis is put forward that the simple sequences can dictate the location of nucleosomes on the adjoining DNA sequences, thereby regulating the gene activity.

Transcriptional mapping of the rat liver mitochondrial genome.

We have identified and mapped nine discrete poly(A)-containing RNAs (RNA-2 to RNA-10) transcribed from rat liver mitochondrial DNA. The 5'-terminal fragments have been sequenced in five of these. The transcriptional map of rat mitochondrial DNA is homologous to those for mitochondrial DNAs of man and mice. The 5'-terminal nucleotide sequences of poly(A)-containing RNAs from rat liver mitochondria are similar in structure to those of HeLa cells studied by other authors; none of them have leader sequences.

Discrete poly(A)- RNA species from rat liver mitochondria are fragments of 16S mitochondrial rRNA carrying its 5'-termini.

During electrophoresis in polyacrylamide gels containing 7M urea the major discrete components of preparations of rat liver mitochondrial poly(A)+ and poly(A)- RNA species have similar mobilities. Poly(A)- RNA components hybridize to the 16S rRNA gene of mtDNA. Analysis of 5'-terminal sequences of these components revealed their identity to the 5'-terminal sequence of 16S rRNA. These results show that poly(A)- RNA components are fragmentation products of 16S rRNA. Fragmentation occurs nonrandomly from the 3'-end of the original rRNA molecules and lead to formation of products with electrophoretic mobilities similar to those of poly(A)+ RNA components.

The primary structure of oocyte and somatic 5S rRNAs from the loach Misgurnus fossilis.

Somatic and oocyte 5S rRNAs from the liver and unfertilized eggs of the loach (Misgurnus fossilis have been sequenced and found to differ in six nucleotides. All the substitutions are confined to the 5'-half of the molecules; 4 of them are pyrimidine-pyrimidine substitutions, and 2 are purine-pyrimidine ones. Considerable differences, both in the position and the character of substitutions, have been established when these 5S rRNAs were compared with somatic and oocyte 5S rRNAs from Xenopus borealis and Xenopus laevis. Among the known primary structures, somatic 5S rRNA of M. fossilis is most similar to trout 5S rRNA.

Isolation of rat liver 5S RNA genes.

A method for the isolation of structural genes, whose transcripts do not contain terminal poly(A) sequences, is presented. Poly(A) tails of predicted length were synthesized at the 3'-OH ends of RNA molecules employing Escherichia coli ATP : RNA adenyltransferase (EC 2.7.7.19). The gene isolation was performed in two steps: (a) enrichment of DNA fragments carrying the genes of interest, (b) subsequent cloning and amplification of these fragments. The enrichment of given gene sequences requires separate purifications of each of two complementary DNA chains, followed by their annealing. Rat liver 5S RNA genes were isolated by this method. DNA (+)chains were obtained by hybridizing EcoRI-digested and denatured rat liver DNA fragments with the 5S RNA-poly(A). The complex was purified on an oligo(dT)-cellulose column. DNA (-)chains were purified by hybridizing DNA fragments with the 5S cDNA which was coupled to oligo(dT)-cellulose. In the isolated and annealed double-stranded DNA preparation the enrichment of 5S DNA was 350--400-fold, when compared with the total genomic DNA. These purified DNA sequences were inserted into the EcoRI site of pBR325. Out of 1200 recombinant-plasmid colonies, analyzed in the colony-hybridization test, 4 hybridized with [125I]5S RNA.

A rapid method for mapping exposed cytosines in polyribonucleotides. Application to tRNATrp (yeast, beef liver).

A rapid method for mapping exposed cytosine residues in 5'-[32P]-labeled RNA molecules is suggested. The exposed cytosines (C's) are converted into uracyls (U's) by bisulphite treatment at pH 5.8 in the presence of Mg2+, followed by complete modification of the residual (non-exposed) C's by a methoxyamine and bisulphite mixture at pH 5.0. The control RNA is modified only by methoxyamine and bisulphite without the preliminary C leads to U conversion. The location of the exposed C's is determined by comparing the products of partial T1, T2, A and U2 ribonuclease digestions of the C leads to U converted and control RNAs after slab gel polyacrylamide electrophoresis and autoradiography. The method has been applied for mapping exposed cytosine bases in tRNATrp (yeast) which have been found in the anti-codon loop and at the 3'-end of the molecule. In tRNATrp (beef liver), in addition to the same exposed bases, C in the diHU-loop is exposed. The data obtained are in full agreement with what is known about exposed C's for other tRNAs.

An improved rapid enzymatic method of RNA sequencing using chemical modification.

A version of rapid gel sequencing procedure based on the analysis of partial endonuclease hydrolizates of chemically modified 5'-32P-labelled RNA is suggested. Complete and selective modification of cytidilic residues by a methoxyamine-bisulfite mixture leads to the unfolding of the RNA secondary structure and, due to this effect, to the generation of a more uniform set of fragments after partial RNAase hydrolysis. The position of cytidines in an RNA sequence can be determined by restricting the hydrolysis of phosphodiester bonds between the modified CMP residues and their 3'-neighbours with T2 and A RNAases. The method was verified with tRNATrp (yeast) and 5S RNA (rat liver and yeast).

[Conformational heterogeneity of tRNA, detected in the reaction of guanine bases with ketoxal]. / Konformatsionnaia geterogennost' tRNK, vyiavliaemaia pri reaktsii guaninovykh osnovanii s ketoksalem

The study of kinetic characteristics of the reaction of tRNA guanine bases with kethoxal has shown that temperature, ionic strength and Mg2+ ions, i.e. factors directly affecting the spatial structure of tRNA, influence also on its internal modification. The modification degree under stabilized spatial tRNA structure depends also on the concentration of kethoxal and is expressed in fractional values of the number of modified guanosine residues per tRNA molecule, which indicates the heterogeneity of tRNA for the modification degree. Chromatography of tRNA1 Val preparation on BD cellulose after the exhaustive modification with kethoxal under conditions of stabilized spatial structure has revealed a fraction of molecules completely resistant to the modificator, and a fraction containing differently modified tRNA molecules. tRNA heterogeneity after the reaction with kethoxal (the presence of resistant and reactive forms) indicates conformational heterogeneity of tRNA, expressed in the simultaneous presence of at least two conformer families.

Directed cleavage of ribopolynucleotides with nucleases restricted by multiple modification of substrate.

Simultaneous exhaustive modification of cytidine and uridine residues of rRNA with methoxyamine and sodium metabisulfite renders adjacent phosphodiester bonds resistant to pancreatic and T2 ribonucleases. Another method of T2 RNAase restriction is modification of cytidine with methoxyaminebisulfite followed by modification of guanosine residues with beta-ethoxy-alpha-ketobutyraldehyde. Mild alkaline treatment leads to demodification of uridine and guanosine residues leaving intact modified cytidine residues, thus providing a means of stepwise, directed cleavage of the polynucleotide. The series of combined cleavage procedures and methods of isolation of oligo(C), oligo(G) and oligopyrimidine tracts, as well as the procedure of selective cleavage at uridine residues elaborated in the course of the present studies may serve as a basis for more rational procedures of RNA sequencing.

Physical consequences of chemical modification: circular dichroism of the kethoxalated oligoribonucleotides.

Alterations in CD spectra are found in G-containing oligoribonucleotides after modification with kethoxal (beta-ethoxy--alpha-ketobutyraldehyde). Stacking interactions in kethoxalated oligomers are followed by temperature dependence of their CD amplitudes. It is shown that for oligomers with nucleosides in anti-conformation adduct formation destroys the stacking interaction with 3'-neighbour but not with a 5'-neighbour. For nucleosides in non-standard conformation (i.e. syn-conformation of guanine in GpGpCp) the physical alteractions may be seen in those cases, when the substituting group affects the initial conformation or the interplane base contacts via, for instance, blocking NH(2)-group of guanine in GpUp. The results demonstrated that even a single monomer modification in a polymer chain could not be considered as a local event having no influence on the three-dimensional structure. The degree of conformational disorders depends both on the conformation of single nucleotides in the stack and on the nature of the nearest neighbours of the modified base.