A possible structure for calf satellite DNA I

Nucleotide sequence and genomic organization of a tandem satellite array from the rock vole Microtus chrotorrhinus (Rodentia)

A tandem satellite array (herein named MSAT-160) has been isolated and characterized from the rodent Microtus chrotorrhinus. Sequence data from 15 partial or complete monomers revealed a repeat unit length of 160 bp. This unit length was apparently derived from two shorter sub-motifs, one a tetramer (GAAA), the other a hexamer (CTTTCT), through polymerase slippage and mutation. Collectively, perfect or imperfect variants of these two motifs comprise nearly 60% of the component. Southern blot analyses of genomic DNA digested with 14 different restriction endonucleases indicated that most enzymes yielded either classical type A or type B restriction patterns, while RsaI yielded a pattern that combined features of both the A and B types, and BamHI appeared to lack sites altogether in MSAT-160. An examination of restriction patterns from 16 individuals with three enzymes failed to identify intraspecific variation, while a related study compared 11 species and documented interspecific distinctiveness (Modi, submitted). Fluorescence in situ hybridization indicated that the satellite DNA was located at the centromeres of several autosomes and at sex chromosome heterochromatin.

Structure and properties of a highly repetitive DNA sequence in sheep

Cleavage of sheep DNA with the restriction endonuclease EcoR I yields three discrete size classes (370, 435 and 800bp) of highly repetitive DNA. The 435bp long fragment was cloned and its nucleotide sequence determined. All three classes of repetitive DNA are related to each other as seen by cross-hybridisation. They are tandemly arranged in the genome and in situ hybridisation to sheep lymphocyte chromosomes show their location mainly in the centromere region of all chromosomes. The primary sequence of the repetitive DNA shows a close structural similarity to the bovine 1.715 satellite DNA, however only poor cross-hybridisation between the sheep and cattle repetitive DNA could be shown.

Nature and organization of the sequence variations in the long-range periodicity calf satellite DNA I

The nucleotide sequences of a series of cloned repeats of the bovine satellite DNA I have been established and compared to the average sequence already determined by the other workers. Variations, which are essentially single base changes, deletions or additions, are found within clustered copies and, thus, define subfractions and domains of the satellite DNA. These results are confirmed by restriction enzyme analysis of the cloned repeats or of the total purified satellite DNA. These subfractions are essentially overlapping. Certain short regions of the DNA repeat do not appear to be involved in the changes, which are spread in a concerted way through the whole bovine karyotype. The significance of these results is discussed in the light of the recent suggestion made that gene conversion-like events are susceptible to introduce homogeneity of polymorphism within the elements of repeated families of DNA sequences.

Sequence analysis of bovine satellite I DNA (1.715 gm/cm3)

The 1402 bp Eco RI repeating unit of bovine satellite I DNA (rho CsCl = 1.715 gm/cm3) has been cloned in pBR322. The sequence of this cloned repeat has been determined and is greater than 97% homologous to the sequence reported for another clone of satellite I (48) and for uncloned satellite I DNA (49). The internal sequence structure of the Eco RI repeat contains imperfect direct and inverted repeats of a variety of lengths and frequencies. The most outstanding repeat structures center on the hexanucleotide CTCGAG which, at a stringency of greater than 80% sequence homology, occurs at 26 locations within the RI repeat. Two of these 6 bp units are found within the 31 bp consensus sequence of a repeating structure which spans the entire length of the 1402 bp repeat (49). The 31 bp consensus sequence contains an internal dodecanucleotide repeat, as do the consensus sequences of the repeat units determined for 3 other bovine satellite DNAs (rho CsCl = 1.706, 1.711a, 1.720 gm/cm3). Based on this evidence, we present a model for the evolutionary relationship between satellite I and the other bovine satellites.

The primary structure of bovine satellite 1.715

The primary structure of the 1402 bp repeat unit of bovine satellite 1.715 has been determined using a dimer inserted at the SalI site of plasmid pBR322 and cloned in E. coli. In contrast with bovine satellites 1.706, 1.720b and 1.711a, the 1.715 satellite has a complex sequence with no obvious internal short prototype repeat. The sequence consists however of repeats ranging in length from 6 to 13 nucleotides. In addition, the hexanucleotide, AGATGA, present in the prototype sequences of satellites 1.706, 1.720b and 1.711a, is found in satellite 1.715 in repeats as long as, or longer than, 8 nucleotides, establishing a homology link among those satellites on one hand and satellite 1.715 (and the related satellite 1.711b) on the other. In turn, this suggests a common evolutionary origin. A comparison of the maps for 15 restriction enzymes of cloned and uncloned satellite indicates very little sequence divergence among the repeat units of the latter, most of the differences being due to methylation.

Distribution of 5-methylcytosine in the DNA of somatic and germline cells from bovine tissues

Genomic DNA of calf thymus contains 1.5 times as much 5-methylcytosine as similar sperm DNA, but the major EcoRI repeat fragment from satellite I of thymus contains ten times as much 5-methylcytosine as the corresponding fragment from sperm DNA. Restriction enzyme analyses of the total DNA and the satellite I fragment show that three HpaII sites in the fragment are completely unmethylated in sperm but fully methylated in thymus DNA. Under-methylation of many sites in the satellite DNAs can probably account for the lower level of methylation of sperm DNA rather than hemimethylation as previously suggested. These results are also discussed in relation to maintenance and de novo (initiation-type) methylases.

Inserted sequences in bovine satellite DNA's

The nucleotide sequence of the 1413-base-pair repeat unit of bovine 1.711a satellite DNA (density in cesium chloride, 1.711 grams per cubic centimeter) has been determined. The repeat unit contains two segments consisting of variants of a basic 23-base-pair sequence that is closely related to sequences of bovine 1.706 satellite DNA. A third segment of the repeat unit contains an unrelated 611-base-pair sequence that is not internally repetitive. This segment is flanked by inverted repeats of 8 base pairs and, on one side, by a direct repeat of the terminal sequence. A related segment is present in bovine 1.711b satellite DNA and is inserted into sequences derived from the 1.715 satellite. These nucleotide sequences suggest the timing of some of the stages in the evolution of these complex, closely related satellite DNA's and indicate the mechanisms inherent in their divergence from a common ancestor.

The organisation of the long range periodicity calf satellite DNA I variants as revealed by restriction enzyme analysis

The analysis of a large number of restriction sites within the long range periodicity calf satellite DNA I does not reveal a superimposable shorter repeat. Although some restriction sites are present in almost all the 100,000 tandemly arranged copies of the 1460 bp repetition unit, other sites such as Atu CI occur at much lower frequencies. When present they are distributed randomly along the satellite DNA molecules. The missing sites appear to result from random and presumably single base alterations. Digestion with the enzymes Hha I and Kpn I showed another type of variant to exist within the calf satellite DNA I. Unlike Atu CI the distributions of the variants detected by these enzymes are not random and organised on long stretches of satellite DNA. The possible functional significance and evolutionary implication of these results are discussed.

Analysis of DNA double- and single-strand breaks by two dimensional electrophoresis: action of micrococcal nuclease on chromatin and DNA, and degradation in vivo of lens fiber chromatin

We describe a novel system for two dimensional electrophoresis at neutral and alkaline pH for determining the double-stranded and single-stranded lengths of DNA. With this system we analysed the mode of micrococcal nuclease digestion of DNA in cellular and SV40 viral chromatin and of supercoiled SV40 DNA. The enzyme reaction occurred in two steps : the enzyme first introduced single-strand breaks, then converted these to double-strand breaks by an adjacent cleavage on the opposite strand. Digestion of cellular chromatin DNA occurred by a similar mechanism. Chromatin fragments produced by limited micrococcal nuclease action contained many single-strand breaks, which may be important when this method is used to prepare chromatin fragments for biochemical and biophysical studies. Nucleosome monomer to tetramer produced at later stages of digestion contained few if any single-strand breaks.

Segmental amplification in a satellite DNA: restriction enzyme analysis of the major satellite of Macropus rufogriseus

The 1.708 g/cc satellite DNA of the red necked wallaby is shown to consist of a number of related families of sequences arranged in tandem arrays. Particular families are subpopulations of other families; their distribution supports a model of successive amplification events during the generation of the satellite. In each amplification episode one 2,500 bp unit is multiplied into a tandemly repeated array of that unit (segmental amplification). The 1.708 g/cc sequences can be detected in related kangaroo species in much reduced amount, and with changes to the long order periodicity of the repeat units.

Methylation of DNA in mouse early embryos, teratocarcinoma cells and adult tissues of mouse and rabbit

The distribution and amount of 5-methylcytosine (5-MeCyt) in DNA was measured for early embryos of mouse strain CF1 (2 to 4 cell stage to blastocyst) and mouse teratocarcinoma cells. In each case, the pattern of methylation was examined by use of the restriction enzymes Hha I and HPA II HPA II, which cut DNA at the sites 5'GCGC and 5'CCGG respectively, when the cytosines at these sites are not methylated. Mouse embryo DNA was found to have the same level of methylation as adult mouse tissues, and no changes in methylation were seen during differentiation of the teratocarcinoma cells. The ratio of 5-MeCyt/Cyt in DNA was measured by high performance liquid chromatography for the differentiating teratocarcinoma cells and for several adult mouse and rabbit tissues. The variation between tissues or between teratocarcinoma cells at different stages of differentiation was less than 10 percent. These results are discussed in view of proposals that 5-MeCyt plays a role in differentiation.

Patchwork structure of a bovine satellite DNA

According to a previous restriction nuclease analysis, bovine 1.706 satellite DNA (density 1.706 g/cm3 in CsCl) is organized in an unusual structure of superimposed long- and short-range repeats (Streeck and Zachau, 1978). We have now determined the nucleotide sequence of this satellite DNA in both cloned fragments and fragments from the total satellite DNA. Each long-range repeat unit (about 2350 bp) is divided into four segments. Each segment consists of different variants of a basic 23 bp sequence which is itself composed of a dodecanucleotide and a related undecanucleotide. A total of 2400 nucleotides have been sequenced. Detailed analysis of the sequence divergence reveals that both the overall extent of divergence and the frequency of base changes at individual positions of the 23 bp repeats are characteristically different in the various segments. Preferentially methylated sites and a high incidence of symmetry elements are found. In two of the four segments, 22 of 23 bp of the prototype sequence are included in six overlapping elements of dyad symmetry and in a palindrome. A scheme for the evolution of the satellite DNA from a basic dodecanucleotide is proposed which is based on the different degrees of divergence for the various repeats superimposed in this satellite DNA.

Methylation of mouse liver DNA studied by means of the restriction enzymes msp I and hpa II

The restriction enzymes Hpa II and Msp I both recognize the sequence 5'-CCGG (C, cytosine; G, guanine). However, Hpa II cuts mouse liver DNA to fragments four times larger than does Msp I. The size of DNA cut by Msp I is close to that predicted from base composition and nearest neighbor analysis. The most probable explanation of these results is that in mouse the site 5'-CCGG is highly methylated.

Highly reiterated sequences of SIMIANSIMIANSIMIANSIMIANSIMIAN

A 172-base pair segment of DNA that is repeated several million times in the genome of the African green monkey has been characterized. Sequence analysis revealed that the many repeats of this complex unit are not all identical but represent a set of closely related segments: Sequence divergence occurs at various positions in the segment in a nonrandom manner. The uncloned segment obtained from monkey DNA is compared with a cloned segment of the same DNA which was recombined into the genome of simian virus 40 during permissive infection.

Restriction enzyme analysis of satellite DNA components from the bovine genome

A restriction enzyme analysis was performed on satellite DNA components, isolated, as described in the preceding paper, from the bovine genome by a combination of Cs2SO4/BAMD and Cs2SO4/Ag+ density gradient centrifugation. Such an analysis has led to the unambiguous identification of eight satellite DNA components and to new information on their repeat units; this indicates that identical repeat lengths are shared by them, a fact strongly suggesting a common origin.

Genome analysis of Peromyscus (Rodentia, Cricetidae) VII. Localization of satellite DNA sequences and cytoplasmic poly(A) RNA sequences of P. eremicus on metaphase chromosomes

A satellite DNA fraction from P. eremicus, having a buoyant density of 1.705 g/ml in neutral CsCl density gradients, was isolated. In situ hybridization experiments, using 3H-RNA complementary to this DNA fraction indicated that the short (heterochromatic) arms of most of the autosomes contained this sequence. Conversely, in situ hybridization using 3H-complementary DNA (cDNA) synthesized from the cytoplasmic poly (A) RNA of P. eremicus (comprising a substantial fraction of total messenger RNA) showed that the number of silver grains in the long arms (euchromatin) was significantly higher than that in the short arms. The X chromosomes showed a distinct localization pattern of both sequences.

Analysis of calf-thymus satellite DNA: evidence for specific methylation of cytosine in C-G sequences

Digestion of purified calf tymus satellite I (phi = 1.714 g/cm3) with a series of restriction enzymes shows that modification in this satellite occurs preferentially in the sequence C-G. This was also shown to be the case in the other satellites and in bulk chromosomal calf thymus DNA. Cloning of purified satellite I DNA in Escherichia coli makes sites, previously modified, available for cutting with certain restriction enzymes. All these 'new sites' contain the sequence C-G. High-resolution mass spectros-copy establishes that the satellites contain a low concentration of 5-methylcytosine. This infers that methylation which inhibits retriction enzyme cutting must occur preferentially in the sequence C-G. Hybridization of cRNA of cloned satellite I DNA with the satellites III (phi = 1.706 g/cm3) and IV (phi = 1.710 g/cm3) shows that there is no or little sequence homology between these satellites. Digestion of calf thymus satellite I DNA with endoR. EcoRI and subsequent hybridization studies with the fragments shows two EcoRI fragments in addition to the usual 1400-base-pair EcoRI repeat unit.