A hypothesis for the initiation of genetic recombination in eukaryotes

Mitotic intragenic recombination in the yeast Saccharomyces: marker-effects on conversion and reciprocity of recombination

We have made a large scale analysis of prototrophic products of spontaneous and induced mitotic recombination within LYS2 gene of the yeast Saccharomyces. The mutant alleles staying in heterozygote with the wild type allele were uncovered and analysed.Among thirteen lys2 mutations used in the study three had reduced frequencies of mitotic gene conversion. These rarely converting mutations gave a remarkably high proportion of reciprocal events (up to 38%) in pairwise combinations, never seen for any other pair of alleles studied. Two of these mutations are the deletions of large parts of LYS2 gene.The results suggest that mispairing in the region of deletion blocks the hybrid DNA migration and leads to the reduced conversion ability of deletions. Comparison of uncovered alleles ratio in all allele combinations tested lead us to another hypothesis about bidirectional migration of hybrid DNA.

Recombination-stimulating sequences in yeast ribosomal DNA correspond to sequences regulating transcription by RNA polymerase I

A DNA sequence (HOT1) from the repeated ribosomal RNA gene cluster of Saccharomyces cerevisiae can stimulate genetic exchange when inserted at novel locations in the yeast genome. Localization of the sequences required for HOT1 activity demonstrates that two noncontiguous fragments of DNA are required for the stimulation of recombination. One of these fragments contains the transcription initiation site for the major 35S ribosomal RNA precursor. The other contains an enhancer of RNA polymerase I transcription. We suggest that transcription by RNA polymerase I initiating in the inserted rDNA and proceeding through the adjacent sequences is responsible for the stimulation of exchange. Consistent with this interpretation, insertion of the putative termination site for RNA polymerase I transcription between HOT1 and the adjacent recombining DNA abolishes the recombination stimulation. Transcription through both copies of the homologous recombining sequences appears to be necessary for enhanced exchange.

A restriction and modification model for the initiation and control of recombination in Neurospora

It is hypothesized that the products of Neurosporarec+genes mask recombinators such ascogby modifying DNA and that unmodified recombinators act as recognition sites for an endonuclease with scission properties like those of the type I restriction enzymes found inE. coli. These cut the DNA in both strands at some variable distance from a recognition site. Repair of a two strand gap initiated in this way would require DNA synthesis using the information contained in the homologous DNA duplex, leading to gene conversion. Crossing over could follow from resolution of two Holliday structures formed during gap repair. The hypothesis explains the polarity in the frequency of conversion events across genetic loci, the observation that chromosomes carrying recombinators are more often converted than is the homologue, and how recombinators can initiate conversion at a distance, as suggested by the pattern of conversion events in thehis-3locus in crosses heterozygous for the translocation TM429.

DNA synthesis at selective sites during pachytene in mouse spermatocytes

DNA repair replication has been previously demonstrated to occur in mouse spermatocytes during the pachytene stage. The results reported in this study provide a more detailed characterization of pachytene repair by focusing upon specific properties of the sites of replication. Our data demonstrate that single-strand breaks persist within replicated sequences throughout a period which corresponds to a defined interval of the pachytene stage. A large fraction of the sites may be nicked more than once within the same DNA strand, allowing the selective release of replicated DNA sequences from gently denatured spermatocyte DNA. DNA fragments thus prepared from pachytene spermatocytes are not of random sequence composition, but are derived from a specific subset of the mouse genome. Sites of replication are also associated with chromatin of distinctive structure in pachytene spermatocytes, as evidenced by the sensitivity of replicated chromatin to DNase II, and its solubility in the presence of Mg2+. In each of these respects, sequences replicated in pachytene spermatocytes closely resemble their counterparts in the Lilium genome.

RecBC enzyme nicking at Chi sites during DNA unwinding: location and orientation-dependence of the cutting

Homologous recombination by the E. coli RecBC pathway occurs at elevated frequency near Chi sites. We reported previously that Chi induces RecBC enzyme to cleave one DNA strand--that containing the Chi sequence 5'G-C-T-G-G-T-G-G3'. We report here that the Chi-dependent cleavage occurs four, five, or six nucleotides to the 3' side of the Chi octamer and produces nicks with 3'-OH and 5'-PO4 groups. Chi-dependent cleavage occurs if RecBC enzyme approaches the Chi sequence from the right, but not if it approaches only from the left, during unwinding of the duplex DNA substrate. A single RecBC enzyme molecule appears to cleave the DNA and to release part of it as a single-stranded fragment. These and previous results indicate that Chi-dependent cleavage is concomitant with DNA unwinding by RecBC enzyme and provide an enzymatic basis for the orientation-dependence of Chi recombinational hotspot activity. These observations demonstrate a key step of a proposed model of recombination in which RecBC enzyme produces a potentially invasive single-stranded DNA tail extending from Chi to its left. We discuss the relation between the action of Chi sites and that of special sites enhancing eukaryotic recombination.

In phage lambda, cos is a recombinator in the red pathway

Among lambda particles carrying chromosomes that have failed to replicate during a lytic cycle cross there is a high frequency of Red-mediated recombination near the right-hand end. Earlier work has shown that this recombination is dependent on cos (cohesive end site), the packaging origin of lambda. In contrast to the prediction of the break-copy model proposed earlier, we find a high recombination rate near cos even when only one of the two participating parents has a functional cos at that locus. The exchange is accompanied by loss of the stimulating cos in the recombination product, irrespective of the marker configurations: a+b+cos- rather than a+b+cos+ is produced in the cross a+b-cos- x a-b+cos+ as well as in the cross a+b-cos+ x a-b+cos-. Further analyses of these and earlier data allow the formulation of a detailed model for cos-stimulated, Red-mediated genetic exchange. In this model, cos stimulates exchange by virtue of being a double-strand cut site. The model has several features like that proposed for yeast. This role of cos in the Red pathway contrasts with the role of cos in the RecBC pathway, in which cos serves as an entry site for a recombinase that stimulates exchanges far from cos.

A gradient of sequence divergence in the human adult alpha-globin duplication units

The nucleotide sequences of the two 5'-homology blocks of human alpha-globin gene duplication units were determined. The sequence difference between the two blocks is essentially zero in the 5' portions, and increases gradually toward the 3' ends until it reaches a value of 18 percent. This gradient of sequence divergence is similar to the distribution of the frequencies of gene conversion along several loci in Ascobolus and yeast. Hot spots for initiation of gene correction processes appear to exist near the 5' ends of the human alpha-globin duplication units. The data provide the physical evidence for polar gene correction process in a mammalian genome.

The double-strand-break repair model for recombination

Gene conversion is the nonreciprocal transfer of information from one DNA duplex to another; in meiosis, it is frequently associated with crossing-over. We review the genetic properties of meiotic recombination and previous models of conversion and crossing-over. In these models, recombination is initiated by single-strand nicks, and heteroduplex DNA is generated. Gene conversion is explained by the repair of mismatches present in heteroduplex DNA. We propose a new mechanism for meiotic recombination, in which events are initiated by double-strand breaks that are enlarged to double-strand gaps. Gene conversion can then occur by the repair of a double-strand gap, and postmeiotic segregation can result from heteroduplex DNA formed at the boundaries of the gap-repair region. The repair of double-strand gaps is an efficient process in yeast, and is known to be associated with crossing-over. The genetic implications of the double-strand-break repair model are explored.

Molecular drive: a cohesive mode of species evolution

It is generally accepted that mutations may become fixed in a population by natural selection and genetic drift. In the case of many families of genes and noncoding sequences, however, fixation of mutations within a population may proceed as a consequence of molecular mechanisms of turnover within the genome. These mechanisms can be both random and directional in activity. There are circumstances in which the unusual concerted pattern of fixation permits the establishment of biological novelty and species discontinuities in a manner not predicted by the classical genetics of natural selection and genetic drift.