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

Residual recombination in Neurospora crassa spo11 deletion homozygotes occurs during meiosis

Spo11 is considered responsible for initiation of meiotic recombination in higher organisms, but previous analysis using spo11 (RIP) mutants suggests that the his-3 region of Neurospora crassa experiences spo11-independent recombination. However, despite possessing several stop codons, it is conceivable that the mutants are not completely null. Also, since lack of spo11 interferes with chromosomal pairing and proper segregation at Meiosis I, spores can be partially diploid for a period after meiosis. Thus, it is possible that the recombination observed could be an abnormal event, occurring during the period of aneuploidy rather than during meiosis. To test the former hypothesis, we generated spo11 deletion homozygotes. Using crosses heteroallelic for his-3 mutations, we showed that His(+) progeny are generated in spo11 deletion homozygotes at a frequency at least as high as in wild type and, as in the spo11 (RIP) mutants, local crossing over is not reduced. To test the latter hypothesis, we utilised mutations in either end of a histone H1-GFP fusion gene, inserted between the recombination hotspot cog and his-3, in which GFP(+) spores arise as a result of recombination in a cross between the two GFP alleles. In a control cross homozygous for spo11 (+), the frequency at which GFP(+) spores arise is comparable to the frequency of His(+) spores and glowing nuclei first appear during prophase, prior to metaphase I, as expected for a product of meiotic recombination. Similarly in spo11 deletion homozygotes, GFP(+) spores arise at high frequency and glowing nuclei are first seen before metaphase, indicating that allelic recombination occurs during meiosis in the absence of spo11. We have therefore shown that spo11 is not essential for either his-3 allelic recombination or crossing over in the vicinity of his-3, and that spo11-independent allelic recombination is meiotic, indicating that there is a spo11-independent mechanism for initiation of recombination in Neurospora.

Use of fluorescent protein to analyse recombination at three loci in Neurospora crassa

We have inserted a histone H1-GFP fusion gene adjacent to three loci on different chromosomes of Neurospora crassa and made mating pairs in which a wild type version of GFP is crossed to one with a mutation in the 5' end of GFP. The loci are his-3, am and his-5, chosen because recombination mechanisms appear to differ between his-3 and am, and because crossing over adjacent to his-5, like his-3, is regulated by rec-2. At his-3, the frequencies of crossing over between GFP and the centromere and of conversion of 5'GFP to GFP(+) are comparable to those obtained by classical recombination assays, as is the effect of rec-2 on these frequencies, suggesting that our system does not alter the process of recombination. At each locus we have obtained sufficient data, on both gene conversion and crossing over, to be able to assess the effect of deletion of any gene involved in recombination. In addition, crosses between a GFP(+) strain and one with normal sequence at all three loci have been used to measure the interval to the centromere and to show that GFP experiences gene conversion with this system. Since any gene expressed in meiosis is silenced in Neurospora if hemizygous, any of our GFP(+) strains can be used as a quick screen to determine if a gene deleted by the Neurospora Genome Project is involved in crossing over or gene conversion.

High density analysis of randomly selected Neurospora octads reveals conversion associated with crossovers located between cog and his-3

We analysed 148 octads from a Neurospora cross maximised for sequence heterology in the his-3 region and detected non-Mendelian segregation at his-3, cot-1 and lys-4 loci. This was in all cases 6:2 or 2:6, with no evidence of post-meiotic segregation (PMS) in these genes. High density snp analysis was used to place crossovers between his-3 and the centromere-distal marker ad-3, and sequencing to refine the location of crossovers between his-3 and the recombination hotspot cog. Crossovers appeared to have a non-random distribution, falling close to his-3 or more than 40 kb distal, and all those in which the location was determined were flanked by sequences showing gene conversion and/or PMS amongst the polymorphisms. This octad study confirms the validity of assumptions made during random spore analyses and suggests that recombination hotspots at cot-1 and lys-4 may, unlike the relatively cold recombination initiator at the am locus, be high frequency recombinators similar to cog.

Mutation of msh-2 in Neurospora crassa does not reduce the incidence of recombinants with multiple patches of donor chromosome sequence

The Neurospora homologue msh-2 of the Escherichia coli mismatch repair gene mutS was mutated by repeat-induced point mutation (RIP) of a 1.9-kb duplication covering 1661bp of the coding sequence and 302 bp 5' of the gene. msh-2(RIP-LK1) exhibited a mutator phenotype conferring a 17-fold increase in the frequency of spontaneous mitotic reversion of his-3 allele K458. In msh-2(RIP-LK1) homozygotes, recombination frequency at the his-3 locus increased up to 2.9-fold over that in msh-2(+) diploids. Progeny of crosses homozygous msh-2(RIP-LK1), like those from crosses homozygous msh-2(+) frequently had multiple patches of donor chromosome sequence, suggesting that patchiness in msh-2(+) crosses is not explained by incomplete repair of heteroduplex DNA by MSH-2. These findings are consistent with data from the analysis of events in a Neurospora translocation heterozygote that suggested multiple patches of donor chromosome sequence arising during recombination reflect multiple template switches during DNA repair synthesis.

Lessons from the genome sequence of Neurospora crassa: tracing the path from genomic blueprint to multicellular organism

We present an analysis of over 1,100 of the approximately 10,000 predicted proteins encoded by the genome sequence of the filamentous fungus Neurospora crassa. Seven major areas of Neurospora genomics and biology are covered. First, the basic features of the genome, including the automated assembly, gene calls, and global gene analyses are summarized. The second section covers components of the centromere and kinetochore complexes, chromatin assembly and modification, and transcription and translation initiation factors. The third area discusses genome defense mechanisms, including repeat induced point mutation, quelling and meiotic silencing, and DNA repair and recombination. In the fourth section, topics relevant to metabolism and transport include extracellular digestion; membrane transporters; aspects of carbon, sulfur, nitrogen, and lipid metabolism; the mitochondrion and energy metabolism; the proteasome; and protein glycosylation, secretion, and endocytosis. Environmental sensing is the focus of the fifth section with a treatment of two-component systems; GTP-binding proteins; mitogen-activated protein, p21-activated, and germinal center kinases; calcium signaling; protein phosphatases; photobiology; circadian rhythms; and heat shock and stress responses. The sixth area of analysis is growth and development; it encompasses cell wall synthesis, proteins important for hyphal polarity, cytoskeletal components, the cyclin/cyclin-dependent kinase machinery, macroconidiation, meiosis, and the sexual cycle. The seventh section covers topics relevant to animal and plant pathogenesis and human disease. The results demonstrate that a large proportion of Neurospora genes do not have homologues in the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe. The group of unshared genes includes potential new targets for antifungals as well as loci implicated in human and plant physiology and disease.

Targeting vectors for gene diversification by meiotic recombination in Neurospora crassa

We have constructed a pair of vectors, pDV2 and pDV3, that enable targeted insertion of exogenous DNA into Linkage Group I of Neurospora crassa at the his-3 locus. Transplaced sequences are inserted between his-3 and the cog(L) recombination hot spot and include his-3 mutations that allow meiotic recombination initiated by cog(L) to be monitored. Selection of correctly placed transforming DNA is based on complementation between different his-3 alleles borne by the plasmids and transformation hosts. The system allows investigation of the effect of any given sequence on recombination as well as diversification of sets of related sequences in vivo for directed evolution of genes.

Recombination events in Neurospora crassa may cross a translocation breakpoint by a template-switching mechanism

To assist investigation of the effect of sequence heterology on recombination in Neurospora crassa, we inserted the Herpes simplex thymidine kinase gene (TK) as an unselected marker on linkage group I, giving a gene order of Cen-his-3-TK-cog-lpl. We show here that in crosses heterozygous for TK, conversion of a his-3 allele on one homolog is accompanied by transfer of the heterologous sequence between cog and his-3 from the other homolog, indicating that recombination is initiated centromere-distal of TK. We have identified a 10-nucleotide motif in the cog region that, although unlikely to be sufficient for hotspot activity, is required for high-frequency recombination and, because conversion of silent sequence markers declines on either side, may be the recombination initiation site. Additionally, we have mapped conversion tracts in His(+) progeny of a translocation heterozygote, in which the translocation breakpoint separates cog from the 5' end of his-3. We present molecular evidence of recombination on both sides of the breakpoint. Because recombination is initiated close to cog and the event must therefore cross the translocation breakpoint, we suggest that template switching occurs in some recombination events, with repair synthesis alternating between use of the homolog and the initiating chromatid as template.

Chromosome rearrangements in Neurospora and other filamentous fungi

Knowledge of fungal chromosome rearrangements comes primarily from N. crassa, but important information has also been obtained from A. nidulans and S. macrospora. Rearrangements have been identified in other Sordaria species and in Cochliobolus, Coprinus, Magnaporthe, Podospora, and Ustilago. In Neurospora, heterozygosity for most chromosome rearrangements is signaled by the appearance of unpigmented deficiency ascospores, with frequencies and ascus types that are characteristic of the type of rearrangement. Summary information is provided on each of 355 rearrangements analyzed in N. crassa. These include 262 reciprocal translocations, 31 insertional translocations, 27 quasiterminal translocations, 6 pericentric inversions, 1 intrachromosomal transposition, and numerous complex or cryptic rearrangements. Breakpoints are distributed more or less randomly among the seven chromosomes. Sixty of the rearrangements have readily detected mutant phenotypes, of which half are allelic with known genes. Constitutive mutations at certain positively regulated loci involve rearrangements having one breakpoint in an upstream regulatory region. Of 11 rearrangements that have one breakpoint in or near the NOR, most appear genetically to be terminal but are in fact physically reciprocal. Partial diploid strains can be obtained as recombinant progeny from crosses heterozygous for insertional or quasiterminal rearrangements. Duplications produced in this way precisely define segments that cover more than two thirds of the genome. Duplication-producing rearrangements have many uses, including precise genetic mapping by duplication coverage and alignment of physical and genetic maps. Typically, fertility is greatly reduced in crosses parented by a duplication strain. The finding that genes within the duplicated segment have undergone RIP mutation in some of the surviving progeny suggests that RIP may be responsible for the infertility. Meiotically generated recessive-lethal segmental deficiencies can be rescued in heterokaryons. New rearrangements are found in 10% or more of strains in which transforming DNA has been stably integrated. Electrophoretic separation of rearranged chromosomal DNAs has found useful applications. Synaptic adjustment occurs in inversion heterozygotes, leading progressively to nonhomologous association of synaptonemal complex lateral elements, transforming loop pairing into linear pairing. Transvection has been demonstrated in Neurospora. Beginnings have been made in constructing effective balancers. Experience has increased our understanding of several phenomena that may complicate analysis. With some rearrangements, nondisjunction of centromeres from reciprocal translocation quadrivalents results in 3:1 segregation and produces asci with four deficiency ascospores that occupy diagnostic positions in linear asci. Three-to-one segregation is most frequent when breakpoints are near centromeres. With some rearrangements, inviable deficiency ascospores become pigmented. Diagnosis must then depend on ascospore viability. In crosses between highly inbred strains, analysis may be handicapped by random ascospore abortion. This is minimized by using noninbred strains as testers.

Long, interrupted conversion tracts initiated by cog in Neurospora crassa

Multiple polymorphisms distinguish Emerson and Lindegren strains of Neurospora crassa within the histidine-3 gene and in its distal flank. Restriction site and sequence length polymorphism in a set of 14 PCR products covering this 6.9-kb region were used to identify the parental origin of DNA sequence information in prototrophic progeny of crosses heterozygous for auxotrophic mutations in his-3 and the silent sequence differences. Forty-one percent of conversion tracts are interrupted. Where the absence of rec-2+ permits activity of the recombination hotspot cog, conversion appears to originate at cog and conversion tracts are up to 5.9 kb long. The chromosome bearing cog(L), the dominant allele that confers a high frequency of recombination, is almost invariably the recipient of information. In progeny from crosses heterozygous rec-2/rec-2+, conversion tracts are much shorter, most are not initiated at cog and either chromosome seems equally likely to be converted. Although 32% of his-3 prototrophs have a crossover that may be associated with conversion, it is suggested that the apparent association between conversion and crossing over at this locus may be due to confounding of coincidental events rather than to a mechanistic relationship.

The chromosomal region which includes the recombinator cog in Neurospora crassa is highly polymorphic

The St Lawrence ST74-OR23-IVA and Lindegren Y8743 strains of Neurospora crassa have a different provenance from wild collections and dissimilar cog alleles; that in Lindegren, cogLa (previously designated cog+), is a more efficient recombinator than cogS74A and cogEa (previously cog), the alleles in St Lawrence and Emerson a respectively. Restriction fragment length polymorphisms (RFLPs) and sequence polymorphisms (SPs) were used to map the difference between cogLa and cogS74A to a region that extends from 2.3 to 3.2 kb 3' of the his-3 coding sequence. The DNA sequences from 400 bp 3' of his-3 to 120 bp 3' of the cog region in these strains were found to be homologous but to diverge by 3.5%. The differences include single-base pair changes, short insertion/deletions, differences in the length of poly-T tracts, and three longer sequences present only in St Lawrence: a 98-bp inverted repeat transposable element we have previously called Guest, which has generated a 3-bp direct repeat of the target site present in Lindegren, and 15-bp and 20-bp sequences that have no obvious structural features nor similarity to Guest. Southern analysis of other laboratory strains revealed four major and several minor variants of this region. All strains assayed are descendants of Lindegren A, Lindegren a, Abbott 4A and Abbott 12a, and it is clear that each of these progenitors collected from the wild population had a different variant of the cog region. Sequence divergence of this degree seems remarkable, even in an intergenic region, for fully interfertile strains of a single species.

The effect of rec-2 on repeat-induced point-mutation (RIP) and recombination events that excise DNA sequence duplications at the his-3 locus in Neurospora crassa

In Neurospora crassa, duplicated DNA suffers both extensive repeat-induced point-mutation (RIP) and also excision by recombination events during the dikaryotic phase of the life cycle that precedes karyogamy and meiosis (reviewed by Selker 1990). This paper describes experiments designed to test the effect of rec-2, a gene known to modulate the local level of meiotic recombination at his-3, on RIP and the excision of tandem duplications. Duplications carrying his-3 sequences and a marker, hygr, that confers hygromycin resistance were constructed by targeted transformation. RIP and excisive recombination were assessed from the progeny of crosses heterozygous for a duplication and having different combinations of rec-2 alleles. In the presence of rec-2+, excision of hygr was reduced to about half of that in crosses homozygous for rec-2. In contrast, rec-2+ had little influence on the frequency of duplications that escaped RIP. Thus, in addition to reducing recombination between his-3 alleles during meiosis, rec-2+ also influences recombination events that lead to the excision of duplications carrying his-3. However, RIP may be independent.

The initiation site for recombination cog is at the 3' end of the his-3 gene in Neurospora crassa

Recombination at his-3 in Neurospora crassa is thought to be initiated through a site designated cog which lies in the his-3 to ad-3 interval of linkage group I. Fragments of the his-3 gene were used to transform various his-3 mutant alleles to prototrophy in order to link the genetic map to the nucleotide sequence. It was established that cog is at the 3' end of his-3 and is therefore not the his-3 promoter. This suggests that cog may be dissimilar to a number of yeast recombinators which are associated with promoters of transcription.

The inheritance of epigenetic defects

Evidence from many sources shows that the control of gene expression in higher organisms is related to the methylation of cytosine in DNA, and that the pattern of methylation is inherited. Loss of methylation, which can result from DNA damage, will lead to heritable abnormalities in gene expression, and these may be important in oncogenesis and aging. Transformed permanent lines often lose gene activity through de novo methylation. It is proposed that epigenetic defects in germline cells due to loss of methylation can be repaired by recombination at meiosis but that some are transmitted to offspring.

Signal for DNA methylation associated with tandem duplication in Neurospora crassa

Most cytosine residues are subject to methylation in the zeta-eta (zeta-eta) region of Neurospora crassa. The region consists of a tandem direct duplication of a 0.8-kilobase-pair element including a 5S rRNA gene. The repeated elements have diverged about 15% by the occurrence of numerous CG to TA mutations, which probably resulted from deamination of methylated cytosines. Most but not all common laboratory strains of N. crassa have methylated duplicated DNA at the zeta-eta locus. However, many strains of N. crassa and strains of N. tetrasperma, N. sitophila, and N. intermedia have one instead of two copies of the homologous DNA and it is not methylated. A cross of strains differing at the zeta-eta locus produced progeny which all had duplicated, methylated, or unique, unmethylated DNA, like the parental strains. We conclude that a signal causing unprecedented heavy DNA methylation is present in the zeta-eta region.

Signal for DNA methylation associated with tandem duplication in Neurospora crassa

Most cytosine residues are subject to methylation in the zeta-eta (zeta-eta) region of Neurospora crassa. The region consists of a tandem direct duplication of a 0.8-kilobase-pair element including a 5S rRNA gene. The repeated elements have diverged about 15% by the occurrence of numerous CG to TA mutations, which probably resulted from deamination of methylated cytosines. Most but not all common laboratory strains of N. crassa have methylated duplicated DNA at the zeta-eta locus. However, many strains of N. crassa and strains of N. tetrasperma, N. sitophila, and N. intermedia have one instead of two copies of the homologous DNA and it is not methylated. A cross of strains differing at the zeta-eta locus produced progeny which all had duplicated, methylated, or unique, unmethylated DNA, like the parental strains. We conclude that a signal causing unprecedented heavy DNA methylation is present in the zeta-eta region.