Mismatch-specific post-meiotic segregation frequency in yeast suggests a heteroduplex recombination intermediate

Post-meiotic segregation of alleles, which is seen, for example, in the 5:3 distribution of alleles in the products of a single meiosis in fungi, has been thought to be due to the non-repair of heteroduplex regions formed during genetic recombination. In current models of genetic recombination, heteroduplex DNA is formed either as the primary intermediate generated by two interacting non-sister chromatids or as a short region flanking a double-stranded gap. The frequency of post-meiotic segregation differs for different alleles, and this is presumed to reflect the varying efficiencies with which different types of mismatches in the heteroduplex are repaired. To gain some insight into this process, we have now determined the nucleotide sequences of various yeast alleles with different post-meiotic segregation frequencies and compared the mismatches predicted to occur in heteroduplexes of these alleles with wild-type DNA with those repaired with varying efficiency in bacterial systems. A striking correlation is observed, with the mismatches predicted for high post-meiotic segregation frequency alleles being similar to mismatches repaired with low efficiency in bacteria. These results support the view that postmeiotic segregation frequency reflects heteroduplex repair efficiency and the contention that meiotic gene conversion is the result of the successful repair of heteroduplex mismatches.     

The role of heteroduplex correction in gene conversion in Saccharomyces cerevisiae

Two different models have been proposed to explain the relative frequencies of the non-mendelian allelic segregations which are detected by tetrad analysis after meiosis in fungi. The first model maintains that 6:2 type tetrads result from correction of heteroduplexes containing mismatched sites and 5:3 type tetrads result from failure to correct mismatched sites. The second model suggests that 6:2 segregations result from the filling-in of double-strand gaps using information obtained from both strands of a homologous duplex. In this model 5:3 type tetrads result if the allele is included in the heteroduplex regions flanking the gap and the resulting mismatched nucleotides are not corrected. We have studied the correction of heteroduplex plasmid DNA in pms1 mutant strains of Saccharomyces cerevisiae, which are known to exhibit higher frequencies of 5:3 type tetrads and lower frequencies of 6:2 tetrads than wild-type strains. Our results suggest that the pms1 mutation causes a defect in mismatch correction, supporting the hypothesis that meiotic gene conversion in wild-type yeast cells often results from the correction of heteroduplex DNA.     

Preferential DNA secondary structure mutagenesis in the lagging strand of replication in E. coli

When present in single-stranded DNA, palindromic or quasi-palindromic sequences have the potential to form complex secondary structures, including hairpins, which may facilitate interstrand misalignment of direct repeats and be responsible for diverse types of replication-based mutations, including deletions, additions, frameshifts and duplications. In regions of palindromic symmetry, specific deletion events may involve the formation of a hairpin or other DNA secondary structures which can stabilize the misalignment of direct repeats. One model suggests that these deletions occur during DNA replication by slippage of the template strand and misalignment with the progeny strand. The concurrent DNA replication model, involving an asymmetric dimeric DNA polymerase III complex which replicates the leading and lagging strands, has significant implications for mutagenesis. The intermittent looping of the lagging strand template, and the fact that the lagging strand template may contain a region of single-stranded DNA the length of an Okazaki fragment, provides an opportunity for DNA secondary-structure formation and misalignment. Here we report our design of a palindromic fragment to create an 'asymmetric palindromic insert' in the chloramphenicol acetyltransferase gene of plasmid pBR325. The frequency with which the insert was deleted in Escherichia coli depends on the orientation of the gene in the plasmid. Our results suggest that replication-dependent deletion between direct repeats may occur preferentially in the lagging strand.     

Genome-wide non-mendelian inheritance of extra-genomic information in Arabidopsis

A fundamental tenet of classical mendelian genetics is that allelic information is stably inherited from one generation to the next, resulting in predictable segregation patterns of differing alleles. Although several exceptions to this principle are known, all represent specialized cases that are mechanistically restricted to either a limited set of specific genes (for example mating type conversion in yeast) or specific types of alleles (for example alleles containing transposons or repeated sequences). Here we show that Arabidopsis plants homozygous for recessive mutant alleles of the organ fusion gene HOTHEAD (HTH) can inherit allele-specific DNA sequence information that was not present in the chromosomal genome of their parents but was present in previous generations. This previously undescribed process is shown to occur at all DNA sequence polymorphisms examined and therefore seems to be a general mechanism for extra-genomic inheritance of DNA sequence information. We postulate that these genetic restoration events are the result of a template-directed process that makes use of an ancestral RNA-sequence cache.     

Introduction of homologous DNA sequences into mammalian cells induces mutations in the cognate gene

Injection of homologous DNA sequences into nuclei of cultured mammalian cells induces mutations in the cognate chromosomal gene. It appears that these mutations result from incorrect repair of a heteroduplex formed between the introduced and the chromosomal sequence. This phenomenon is termed 'heteroduplex induced mutagenesis'. The high frequency of these events suggests that this method may prove useful for introducing mutations into specific mammalian genes.     

Mitochondrial DNA repairs double-strand breaks in yeast chromosomes

The endosymbiotic theory for the origin of eukaryotic cells proposes that genetic information can be transferred from mitochondria to the nucleus of a cell, and genes that are probably of mitochondrial origin have been found in nuclear chromosomes. Occasionally, short or rearranged sequences homologous to mitochondrial DNA are seen in the chromosomes of different organisms including yeast, plants and humans. Here we report a mechanism by which fragments of mitochondrial DNA, in single or tandem array, are transferred to yeast chromosomes under natural conditions during the repair of double-strand breaks in haploid mitotic cells. These repair insertions originate from noncontiguous regions of the mitochondrial genome. Our analysis of the Saccharomyces cerevisiae mitochondrial genome indicates that the yeast nuclear genome does indeed contain several short sequences of mitochondrial origin which are similar in size and composition to those that repair double-strand breaks. These sequences are located predominantly in non-coding regions of the chromosomes, frequently in the vicinity of retrotransposon long terminal repeats, and appear as recent integration events. Thus, colonization of the yeast genome by mitochondrial DNA is an ongoing process.     

Rad54 protein promotes branch migration of Holliday junctions

Homologous recombination has a crucial function in the repair of DNA double-strand breaks and in faithful chromosome segregation. The mechanism of homologous recombination involves the search for homology and invasion of the ends of a broken DNA molecule into homologous duplex DNA to form a cross-stranded structure, a Holliday junction (HJ). A HJ is able to undergo branch migration along DNA, generating increasing or decreasing lengths of heteroduplex. In both prokaryotes and eukaryotes, the physical evidence for HJs, the key intermediate in homologous recombination, was provided by electron microscopy. In bacteria there are specialized enzymes that promote branch migration of HJs. However, in eukaryotes the identity of homologous recombination branch-migration protein(s) has remained elusive. Here we show that Rad54, a Swi2/Snf2 protein, binds HJ-like structures with high specificity and promotes their bidirectional branch migration in an ATPase-dependent manner. The activity seemed to be conserved in human and yeast Rad54 orthologues. In vitro, Rad54 has been shown to stimulate DNA pairing of Rad51, a key homologous recombination protein. However, genetic data indicate that Rad54 protein might also act at later stages of homologous recombination, after Rad51 (ref. 13). Novel DNA branch-migration activity is fully consistent with this late homologous recombination function of Rad54 protein.     

Need for DNA topoisomerase activity as a swivel for DNA replication for transcription of ribosomal RNA

Yeast strains with mutations in the genes for DNA topoisomerases I and II have been identified previously in both Saccharomyces cerevisiae and Schizosaccharomyces pombe. The topoisomerase II mutants (top2) are conditional-lethal temperature-sensitive (ts) mutants. They are defective in the termination of DNA replication and the segregation of daughter chromosomes, but otherwise appear to replicate and transcribe DNA normally. Topoisomerase I mutants (top1), including strains with null mutations are viable and exhibit no obvious growth defects, demonstrating that DNA topoisomerase I is not essential for viability in yeast. In contrast to the single mutants, top1 top2 ts double mutants from both Schizosaccharomyces pombe and Saccharomyces cerevisiae grow poorly at the permissive temperature and stop growth rapidly at the non-permissive temperature. Here we report that DNA and ribosomal RNA synthesis are drastically inhibited in an S. cerevisiae top1 top2 ts double mutant at the restrictive temperature, but that the rate of poly(A)+ RNA synthesis is reduced only about threefold and transfer DNA synthesis remains relatively normal. The results suggest that DNA replication and at least ribosomal RNA synthesis require an active topoisomerase, presumably to act as a swivel to relieve torsional stress, and that either topoisomerase can perform the required function (except in termination of DNA replication where topoisomerase II is required).     

川渝盆地主汛期短时强降水事件日变化特征研究

利用四川盆地和重庆地区1980-2012年主汛期（5-9月）基本站小时降水观测资料,分析了短时强降水事件降水量、频次和强度的日变化特征,研究了短时强降水事件日峰值位相和空间分布特征,事件极值降水日变化和持续时间等分布特征,得出以下主要结论：1）川渝盆地短时强降水事件开始时间的日变化上（01：00-24：00时,北京时间,下同）,表现为“V”型结构下典型夜间峰值位相特征;结束时间的日变化上,表现为多个峰值型结构分布.强降水事件持续时间的日变化上,频次和降水量均呈双峰型结构,频次极大峰值出现在3 h,而强度上随着持续时间的延长,呈现逐渐增加的趋势;2）短时强降水事件极值开始时间空间分布上,极大频次和极大降水量出现在20：00-01：00时内,主要分布在盆地南部和西部大部分地区;日峰值频次结束时间主要发生在20：00-01：00时和08：00-13：00时两个时段内,主要分布于盆地南部、中部和西部大部分地区;3）短时强降水事件极值降水的日变化上,降水量和频次呈现单峰型结构,白天多为短时间（2~4 h）强降水事件出现极值,而傍晚开始至第二天清晨,持续2~10 h强降水事件出现极值均有发生;强降水事件极值降水持续时间日变化,1~24 h内呈单峰型结构,峰值出现在2 h.     

酿酒酵母孢子萌发的激光镊子拉曼光谱研究

【目的】在生理状态下利用激光镊子拉曼光谱系统对单个酿酒酵母孢子萌发过程进行实时监测,探讨掩盖在群体平均信息下的个体生命信息。【方法】将葡萄糖溶液加入酿酒酵母孢子悬液中诱导孢子萌发,在孢子萌发过程中每隔30min取样并利用激光镊子拉曼光谱系统测定单个酵母孢子的拉曼光谱。【结果】单细胞实时平均拉曼光谱可显示孢子萌发过程中细胞内生物分子的变化:萌发期内分别归属于DNA、蛋白质的722cm-1,1006cm-1峰的峰高基本不变,随后在生长期上升明显,说明生长期胞内开始大量复制DNA,并合成蛋白质;归属脂类的1751cm-1峰的减弱趋势明显,可能是胞内脂类物质消耗造成的。整个萌发生长过程中,源自葡糖糖和海藻糖的858cm-1,908cm-1,1084cm-1,1118cm-1等峰强度先下降后上升,表明在适宜的生长条件下,海藻糖可能转化为单糖被细胞吸收利用,当营养物质逐渐被消耗时,细胞会再次累积海藻糖以抵抗外界不利条件。【结论】激光镊子拉曼光谱技术可反映胞内生物大分子的活动规律,获知单个酵母孢子萌发过程中物质变化的丰富信息,是探索单个活细胞实时生化变化的有效工具。     

Expression of recessive alleles by chromosomal mechanisms in retinoblastoma

Inheritance of a mutation at the Rb-1 locus, which has been mapped to band q14 of human chromosome 13, results in predisposition to retinoblastoma. Cloned DNA segments homologous to arbitrary loci of human chromosome 13 and which reveal polymorphic restriction endonuclease recognition sequences, have been used to look for somatic genetic events that might occur during tumorigenesis. A comparison of constitutional and tumour genotypes from several cases indicates that tumorigenesis may result from the development of homozygosity for the mutant allele at the Rb-1 locus. The homozygosity in these cases results from mitotic nondisjunction, resulting in loss of the homologous wild-type chromosome, or from a mitotic recombination event.     

Induction of gut in Caenorhabditis elegans embryos.

Two types of developmental events can cause an embryonic cell to adopt a fate different from that of its neighbours: during a cell division particular contents may be segregated to only one daughter cell and cells may experience different external cues, commonly in the form of inductive cell interactions. Work on development in the nematode Caenorhabditis elegans suggests that most cell fates are specified without a need for cell interactions. In particular, the gut cell lineage of C. elegans has been used as a primary example of specification by differential segregation of determinants. Here I re-examine the role of induction in gut specification by isolating early blastomeres. In C. elegans, the gut derives from all the progeny of a single blastomere (E) of the eight-cell stage. When a gut precursor cell (EMS) is isolated during the first half of the four-cell stage, gut does not differentiate. Gut differentiation is rescued by recombining EMS with its posterior neighbour (P2), but not by recombining EMS with one or both of the other two cells of the four-cell stage. These results demonstrate that P2 induces EMS to form gut in C. elegans.     

Construction of heteroduplex DNA and<Emphasis Type="Italic">in vitro</Emphasis> model for functional analysis of mismatch repair

Functional deficiency of mismatch repair (MMR) system is one of the mechanisms of tumorigenesis. With the development of the investigation and the requirement from the clinical diagnosis and treatment it is necessary to build up a method to evaluate the functional status of the whole MMR system in the concerned tumors. The original ssDNA and dsDNA from wild type (wt) bacteriophage M13mp2 and its three derivates with mutation points in the lacZα gene have been used to construct two kinds of hetero-duplex DNA molecules. One named del(2) has two bases deleted in the negative strand, the other has a G·G mismatch base pair in the negative strand too. Introducing this heteroduplex DNA into E. coli NR9162 (mutS-) without the MMR ability on the indicator plate with x-gal and IPTG, there are three kinds of plaques, mixture plaque as the characteristic phenotype of heteroduplex DNA, blue and clear plaques. If the cell extract is mismatch repair competent the percentage of the mixture plaque will decrease after incubation with these heteroduplex DNA, the repair efficiency is expressed in percentage as 100× (1 minus the ratio of percentages of mixture plaque obtained from the extract-treated sample and untreated samples), which can imply the functional status of MMR system of certain samples. After large T-antigen-dependent SV-40 DNA replication assay cell extract from TK6, a human lymphoblastoid B-cell lymphoma cell line with MMR ability, and Lovo, a human colonic carcinoma cell line with MMR deficiency have incubated with these heteroduplex DNA. The repair efficiency of TK6 to del(2) is more than 60%, to G-G is more than 50%. The Lovo efficiency to del(2) is less than 10%, to G-G is less than 20%. Therefore, in this in vitro model used for functional analysis of mismatch repair of heteroduplex DNA as the repair target, TK6 can serve as the control for MMR proficiency and Lovo as the control for MMR deficiency. Using this model the tumor tissue from a case of hereditary nonpolyposis colorectal cancer (microsatellite instability high, MSI-H) was measured and lack of MMR ability was shown. And a case of sporadic rectal cancer (SRC) (microsatellite stability, MSS) maintains MMR proficiency. The results indicate that the model is sensitive and dependable. It could be used to measure the func- tion status of MMR system in tumor cell and/or tissues. This is a reliable method to investigate the mechanic of tumori-genesis. It is meaningful in the observation of the role of MMR in the initiation and progression of concerned tumors.     

Tension directly stabilizes reconstituted kinetochore-microtubule attachments

Kinetochores are macromolecular machines that couple chromosomes to dynamic microtubule tips during cell division, thereby generating force to segregate the chromosomes. Accurate segregation depends on selective stabilization of correct 'bi-oriented' kinetochore-microtubule attachments, which come under tension as the result of opposing forces exerted by microtubules. Tension is thought to stabilize these bi-oriented attachments indirectly, by suppressing the destabilizing activity of a kinase, Aurora B. However, a complete mechanistic understanding of the role of tension requires reconstitution of kinetochore-microtubule attachments for biochemical and biophysical analyses in vitro. Here we show that native kinetochore particles retaining the majority of kinetochore proteins can be purified from budding yeast and used to reconstitute dynamic microtubule attachments. Individual kinetochore particles maintain load-bearing associations with assembling and disassembling ends of single microtubules for >30?min, providing a close match to the persistent coupling seen in vivo between budding yeast kinetochores and single microtubules. Moreover, tension increases the lifetimes of the reconstituted attachments directly, through a catch bond-like mechanism that does not require Aurora B. On the basis of these findings, we propose that tension selectively stabilizes proper kinetochore-microtubule attachments in vivo through a combination of direct mechanical stabilization and tension-dependent phosphoregulation.     

Phosphorylation of Sld2 and Sld3 by cyclin-dependent kinases promotes DNA replication in budding yeast

Cyclin-dependent kinases (CDKs) drive major cell cycle events including the initiation of chromosomal DNA replication. We identified two S phase CDK (S-CDK) phosphorylation sites in the budding yeast Sld3 protein that, together, are essential for DNA replication. Here we show that, when phosphorylated, these sites bind to the amino-terminal BRCT repeats of Dpb11. An Sld3-Dpb11 fusion construct bypasses the requirement for both Sld3 phosphorylation and the N-terminal BRCT repeats of Dpb11. Co-expression of this fusion with a phospho-mimicking mutant in a second essential CDK substrate, Sld2, promotes DNA replication in the absence of S-CDK. Therefore, Sld2 and Sld3 are the minimal set of S-CDK targets required for DNA replication. DNA replication in cells lacking G1 phase CDK (G1-CDK) required expression of the Cdc7 kinase regulatory subunit, Dbf4, as well as Sld2 and Sld3 bypass. Our results help to explain how G1- and S-CDKs promote DNA replication in yeast.     

Cryptic simplicity in DNA is a major source of genetic variation

DNA regions which are composed of a single or relatively few short sequence motifs usually in tandem ('pure simple sequences') have been reported in the genomes of diverse species, and have been implicated in a range of functions including gene regulation, signals for gene conversion and recombination, and the replication of telomeres. They are thought to accumulate by DNA slippage and mispairing during replication and recombination or extension of single-strand ends. In order to systematize the range of DNA simplicity and the genetic nature of the regions that are simple, we have undertaken an extensive computer search of the DNA sequence library of the European Molecular Biology Laboratory (EMBL). We show here that nearly all possible simple motifs occur 5-10 times more frequently than equivalent random motifs. Furthermore, a new computer algorithm reveals the widespread occurrence of significantly high levels of a new type of 'cryptic simplicity' in both coding and noncoding DNA. Cryptically simple regions are biased in nucleotide composition and consist of scrambled arrangements of repetitive motifs which differ within and between species. The universal existence of DNA simplicity from monotonous arrays of single motifs to variable permutations of relatively short-lived motifs suggests that ubiquitous slippage-like mechanisms are a major source of genetic variation in all regions of the genome, not predictable by the classical mutation process.     

Genetically haploid spermatids are phenotypically diploid

Because chromosomal homologues segregate from one another during meiosis, spermatids are genetically different. Post-meiotic gene expression could lead to gametic differences, some of which might lead to preferential transmission of certain alleles over others. In both insects and mammals, however, all the cells derived from a single spermatogonial cell develop within a common syncytium formed as a result of incomplete cytokinesis at each of the mitotic and meiotic cell divisions. It has been proposed that the intercellular bridges connecting the cells, which are about 1 micron in diameter, permit the sharing of cytoplasmic constituents, thus ensuring the synchronous development of a clone of cells and gametic equivalence between haploid spermatids. By analysing the product of a transgene which is expressed exclusively in post-meiotic germ cells in hemizygous transgenic mice, we have shown that genetically distinct spermatids share the product of the transgene and hence can be phenotypically equivalent.