Crossovers Research Articles

Интеграция традиций в музыкальном стиле «кроссовер» как способ минимизации межпоколенческого ценностного раскола

Интеграция традиций в музыкальном стиле «кроссовер» как способ минимизации межпоколенческого ценностного раскола

High-resolution insight into recombination events at the SD1 locus in rice.

Recombination during meiosis plays an important role in genome evolution by reshuffling existing genetic variations into fresh combinations with the possibility of recovery of lost ancestral genotypes. While crossover (CO) events have been well studied, gene conversion events (GCs), which represent non-reciprocal information transfer between chromosomes, are poorly documented and difficult to detect due to their relatively small converted tract size. Here, we document these GC events and their phenotypic effects at an important locus in rice containing the SD1 gene, where multiple defective alleles contributed to the semi-dwarf phenotype of rice in the 'Green Revolution' of the 1960s. Here, physical separation of two defects allows recombination to generate the wild-type SD1 gene, for which plant height can then be used as a reporter. By screening 18000 F2 progeny from a cross between two semi-dwarf cultivars that carry these different defective alleles, we detected 24 GC events, indicating a conversion rate of ~3.3×10-4 per marker per generation in a single meiotic cycle in rice. Furthermore, our data show that indels and single-nucleotide polymorphisms (SNPs) do not differ significantly in GC rates, at least at the SD1 locus. Our results provide strong evidence that GC by itself can regain an ancestral phenotype that was lost through mutation. This GC detection approach is likely to be broadly applicable to natural or artificial alleles of other phenotype-related functional genes, which are abundant in other plant genomes.

Manipulation of crossover frequency and distribution for plant breeding

The crossovers (COs) that occur during meiotic recombination lead to genetic diversity upon which natural and artificial selection can act. The potential of tinkering with the mechanisms of meiotic recombination to increase the amount of genetic diversity accessible for breeders has been under the research spotlight for years. A wide variety of approaches have been proposed to increase CO frequency, alter CO distribution and induce COs between non-homologous chromosomal regions. For most of these approaches, translational biology will be crucial for demonstrating how these strategies can be of practical use in plant breeding. In this review, we describe how tinkering with meiotic recombination could benefit plant breeding and give concrete examples of how these strategies could be implemented into breeding programs.

Marketing analytics: delineating the field while welcoming crossover

Marketing analytics: delineating the field while welcoming crossover

The Largest Subunit of DNA Polymerase Delta Is Required for Normal Formation of Meiotic Type I Crossovers.

Meiotic recombination contributes to the maintenance of the association between homologous chromosomes (homologs) and ensures the accurate segregation of homologs during anaphase I, thus facilitating the redistribution of alleles among progeny. Meiotic recombination is initiated by the programmed formation of DNA double strand breaks, the repair of which requires DNA synthesis, but the role of DNA synthesis proteins during meiosis is largely unknown. Here, we hypothesized that the lagging strand-specific DNA Polymerase δ (POL δ) might be required for meiotic recombination, based on a previous analysis of DNA Replication Factor1 that suggested a role for lagging strand synthesis in meiotic recombination. In Arabidopsis (Arabidopsis thaliana), complete mutation of the catalytic subunit of POL δ, encoded by AtPOLD1, leads to embryo lethality. Therefore, we used a meiocyte-specific knockdown strategy to test this hypothesis. Reduced expression of AtPOLD1 in meiocytes caused decreased fertility and meiotic defects, including incomplete synapsis, the formation of multivalents, chromosome fragmentation, and improper segregation. Analysis of meiotic crossover (CO) frequencies showed that AtPOLD1RNAi plants had significantly fewer interference-sensitive COs than the wild type, indicating that AtPOL δ participates in type I CO formation. AtPOLD1RNAi atpol2a double mutant meiocytes displayed more severe meiotic phenotypes than those of either single mutant, suggesting that the function of AtPOLD1 and AtPOL2A is not identical in meiotic recombination. Given that POL δ is highly conserved among eukaryotes, we hypothesize that the described role of POL δ here in meiotic recombination likely exists widely in eukaryotes.

C. elegans ZHP-4 is required at multiple distinct steps in the formation of crossovers and their transition to segregation competent chiasmata.

Correct segregation of meiotic chromosomes depends on DNA crossovers (COs) between homologs that culminate into visible physical linkages called chiasmata. COs emerge from a larger population of joint molecules (JM), the remainder of which are repaired as noncrossovers (NCOs) to restore genomic integrity. We present evidence that the RNF212-like C. elegans protein ZHP-4 cooperates with its paralog ZHP-3 to enforce crossover formation at distinct steps during meiotic prophase: in the formation of early JMs and in transition of late CO intermediates into chiasmata. ZHP-3/4 localize to the synaptonemal complex (SC) co-dependently followed by their restriction to sites of designated COs. RING domain mutants revealed a critical function for ZHP-4 in localization of both proteins to the SC and for CO formation. While recombination initiates in zhp-4 mutants, they fail to appropriately acquire pro-crossover factors at abundant early JMs, indicating a function for ZHP-4 in an early step of the CO/NCO decision. At late pachytene stages, hypomorphic mutants exhibit significant levels of crossing over that are accompanied by defects in localization of pro-crossover RMH-1, MSH-5 and COSA-1 to designated crossover sites, and by the appearance of bivalents defective in chromosome remodelling required for segregation. These results reveal a ZHP-4 function at designated CO sites where it is required to stabilize pro-crossover factors at the late crossover intermediate, which in turn are required for the transition to a chiasma that is required for bivalent remodelling. Our study reveals an essential requirement for ZHP-4 in negotiating both the formation of COs and their ability to transition to structures capable of directing accurate chromosome segregation. We propose that ZHP-4 acts in concert with ZHP-3 to propel interhomolog JMs along the crossover pathway by stabilizing pro-CO factors that associate with early and late intermediates, thereby protecting designated crossovers as they transition into the chiasmata required for disjunction.

Meiotic Recombination Differences in Rams from Three Breeds of Sheep in the US

Meiotic recombination is an important contributor to genetic variation and ensures proper chromosome segregation during gametogenesis. Previous studies suggest that at least 1 crossover (CO) per chromosome arm is important to avoid mis-segregation. While the total number of COs per spermatocyte is known to differ in mice, this is only beginning to be evaluated in sheep. This study used a cytogenetic approach to quantify and compare the number of COs per spermatocyte in rams from 3 breeds of sheep: Suffolk, Icelandic, and Targhee. In total, 2,758 spermatocytes and over 170,000 COs were examined. Suffolk rams exhibited the lowest mean number of COs (61.1 ± 0.15) compared to Icelandic (63.5 ± 0.27) and Targhee (65.9 ± 0.26) rams. Significant differences in the number of COs per spermatocyte were observed between Suffolk, Icelandic, and Targhee breeds as well as within each breed. Additionally, the number and location of COs were characterized for homologous chromosomes in a subset of spermatocytes for each ram. A positive correlation was identified between the number of COs and the length of the homologous chromosome pair. Suffolk and Icelandic rams exhibited up to 7 COs per chromosome, while Targhee rams exhibited up to 9. Further, distinct CO location preferences on homologous chromosome pairs with 1, 2, 3, and 4 COs were observed in all 3 breeds. These data in sheep will aid in elucidating the mechanism of mammalian meiotic recombination, an important contributor to genetic diversity.

The Number of Meiotic Double-Strand Breaks Influences Crossover Distribution in Arabidopsis.

Meiotic recombination generates genetic diversity and ensures proper chromosome segregation. Recombination is initiated by the programmed formation of double-strand breaks (DSBs) in chromosomal DNA by DNA Topoisomerase VI-A Subunit (SPO11), a topoisomerase-like enzyme. Repair of some DSBs leads to the formation of crossovers (COs). In most organisms, including plants, the number of DSBs greatly exceeds the number of COs and which DSBs become CO sites is tightly controlled. The CO landscape is affected by DNA sequence and epigenome features of chromosomes as well as by global mechanisms controlling recombination dynamics. The latter are poorly understood and their effects on CO distribution are not well elucidated. To study how recombination dynamics affects CO distribution, we engineered Arabidopsis thaliana plants to carry hypomorphic alleles of SPO11-1 Two independent transgenic lines showed ∼30% and 40% reductions in DSB numbers, which were commensurate with the dosage of the SPO11-1 transcript. The reduction in DSB number resulted in proportional, although smaller, reductions of the number of COs. Most interestingly, CO distribution along the chromosomes was dramatically altered, with substantially fewer COs forming in pericentromeric chromosome regions. These results indicate that SPO11 activity, and the resulting DSB numbers are major factors shaping the CO landscape.

HEIP1 regulates crossover formation during meiosis in rice

During meiosis, the number of double-strand breaks (DSBs) far exceeds the final number of crossovers (COs). Therefore, to identify proteins involved in determining which of these DSBs repaired into COs is critical in understanding the mechanism of CO control. Across species, HEI10-related proteins play important roles in CO formation. Here, through screening for HEI10-interacting proteins via a yeast two-hybrid system, we identify a CO protein HEI10 Interaction Protein 1 (HEIP1) in rice. HEIP1 colocalizes with HEI10 in a dynamic fashion along the meiotic chromosomes and specially localizes onto crossover sites from late pachytene to diplotene. Between these two proteins, HEI10 is required for the loading of HEIP1, but not vice versa. Moreover, mutations of the HEIP1 gene cause the severe reduction of chiasma frequency, whereas early homologous recombination processes are not disturbed and synapsis proceeds normally. HEIP1 interacts directly with ZIP4 and MSH5. In addition, the loading of HEIP1 depends on ZIP4, but not on MER3, MSH4, or MSH5. Together, our results suggest that HEIP1 may be a member of the ZMM group and acts as a key element regulating CO formation.

Call for Papers: Crossover

Call for Papers: Crossover

740P - Final results of a phase II quality of life (QOL) randomized, cross-over (CO) study with gemcitabine (Gem) and nab-paclitaxel (n-P) in locally advanced or metastatic pancreatic ductal adenocarcinoma (PDAC): QOLINPAC

740P - Final results of a phase II quality of life (QOL) randomized, cross-over (CO) study with gemcitabine (Gem) and nab-paclitaxel (n-P) in locally advanced or metastatic pancreatic ductal adenocarcinoma (PDAC): QOLINPAC

Local Inversion Heterozygosity Alters Recombination throughout the Genome

Crossovers (COs) are formed during meiosis by the repair of programmed DNA double-strand breaks (DSBs) and are required for the proper segregation of chromosomes. More DSBs are made than COs, and the remaining DSBs are repaired as noncrossovers (NCOs). The distribution of recombination events along a chromosome occurs in a stereotyped pattern that is shaped by CO-promoting and CO-suppressing forces, collectively referred to as crossover patterning mechanisms. Chromosome inversions are structural aberrations that, when heterozygous, disrupt the recombination landscape by suppressing crossing over. In Drosophila species, the local suppression of COs by heterozygous inversions triggers an increase in crossing over on freely recombining chromosomes termed the interchromosomal (IC) effect [1, 2]. The molecular mechanism(s) by which heterozygous inversions suppress COs, whether noncrossover gene conversions (NCOGCs) are similarly affected, and what mediates the increase in COs in the rest of the genome remain open questions. By sequencing whole genomes ofindividual offspring from mothers containing heterozygous inversions, we show that, although COs are suppressed by inversions, NCOGCs occur throughout inversions at higher than wild-type frequencies. We confirm that CO frequency increases on the freely recombining chromosomes, yet CO interference remains intact. Intriguingly, NCOGCs do not increase in frequency on the freely recombining chromosomes and the total number of DSBs is approximately the same per genome. Together, our data show that heterozygous inversions change the recombination landscape by altering the relative proportions of COs and NCOGCs and suggest that DSB fate may be plastic until a CO assurance checkpoint has been satisfied.

The genetic architecture of genome-wide recombination rate variation in allopolyploid wheat revealed by nested association mapping.

SummaryRecombination affects the fate of alleles in populations by imposing constraints on the reshuffling of genetic information. Understanding the genetic basis of these constraints is critical for manipulating the recombination process to improve the resolution of genetic mapping, and reducing the negative effects of linkage drag and deleterious genetic load in breeding. Using sequence‐based genotyping of a wheat nested association mapping (NAM) population of 2,100 recombinant inbred lines created by crossing 29 diverse lines, we mapped QTL affecting the distribution and frequency of 102 000 crossovers (CO). Genome‐wide recombination rate variation was mostly defined by rare alleles with small effects together explaining up to 48.6% of variation. Most QTL were additive and showed predominantly trans‐acting effects. The QTL affecting the proximal COs also acted additively without increasing the frequency of distal COs. We showed that the regions with decreased recombination carry more single nucleotide polymorphisms (SNPs) with possible deleterious effects than the regions with a high recombination rate. Therefore, our study offers insights into the genetic basis of recombination rate variation in wheat and its effect on the distribution of deleterious SNPs across the genome. The identified trans‐acting additive QTL can be utilized to manipulate CO frequency and distribution in the large polyploid wheat genome opening the possibility to improve the efficiency of gene pyramiding and reducing the deleterious genetic load in the low‐recombining pericentromeric regions of chromosomes.

Abstract 1644: Progression-free survival (PFS) as a surrogate for overall survival (OS)

Abstract Background: PFS is criticized as being not reliably predictive of OS, and statistically significant gains may be clinically insignificant. However, PFS has the advantage as an endpoint of needing shorter follow up/fewer patients and is not rendered falsely negative by crossover (CO) and long post progression survival (PPS). Absolute PFS gain may be a surrogate for absolute OS gain (Ann Oncol 2016;27:373). Method: We extracted PFS/OS data from randomized drug comparisons with >200 incurable solid tumor patients published 01/2007-06/12/2017 in J Clinical Oncology and New England J Medicine. For comparisons with CO unspecified or in <20% of patients, and p<0.05 for PFS or OS, we used nonlinear regression analysis (NLRA) of PFS/OS curves (omitting curve sections with <~10 residual patients) to determine PFS/OS half-lives (t1/2s: time to progression/death in half the remaining patients). We calculated ΔmPFS and ΔmOS (experimental minus control arm medians) and ΔPFSt1/2 and ΔOSt1/2 (experimental minus control arm t1/2s). Results: 249 trials and 287 across-arm comparisons were evaluable. The table presents ΔPFS/ΔOS associations for studies with PFS p<0.05 and CO<20% or unspecified. PFS changenNo. (%) of comparisons with associated change in OS (ΔmOS for ΔmPFS or ΔOSt1/2 for ΔPFSt1/2)ΔOS <2 monthsΔOS > 2 monthsΔmPFS: <1.5 months3224 (75%)8 (25%)>1.5 months4722 (47%)25 (53%)ΔPFSt1/2: <1.5 months3531 (89%)4 (11%)>1.5 months6210 (16%)52 (84%)>2 months414 (10%)37 (90%)ΔOS <3 monthsΔOS >3 monthsΔPFSt1/2: >3 months263 (12%)23 (88%)ΔOS <4 monthsΔOS >4 monthsΔPFSt1/2: >4 months131 (8%)12 (92%)Concordance of ΔOS with ΔPFS for ΔPFS < vs >1.5 months better for t1/2s than medians, Fisher's exact test p=0.0004, and correlation of ΔOS with ΔPFS was also better for t1/2s (R2=0.60, p<0.0001, slope = 1.51) than for medians (R2=0.37, p<0.0001, slope = 0.88) To assess the risk of ΔPFS under-predicting ΔOS, we then assessed all comparisons, irrespective of CO and PFS significance. Of 287 comparisons, 13 (5%) had ΔOS >2m with p<0.05 but ΔPFS <1.5m or ΔPFS p>0.05. In 7/13, PFS curves fit NLRA 2-phase decay models (suggesting 2 distinct subpopulations), vs 25/100 with PFS 2-phase decay in other comparisons (Fisher's exact test p=0.047). Conclusions: Demonstrating ΔPFSt1/2 >1.5-2.0 months with p<.05 indicates an 84-90% probability of a ΔOSt1/2 gain >2 months, and could be a useful ΔOSt1/2 surrogate. This endpoint could mitigate impact of CO and PPS while making trials faster/cheaper. T1/2s are superior to medians. If PFS curves fit NLRA 2 phase models in phase II trials one should collect full phase III OS data (censored at CO) to reduce risk of a false negative. Citation Format: David J. Stewart, Dominick Bosse, John Hilton, Glenwood Goss, Michael Fung-Kee-Fung, Derek Jonker. Progression-free survival (PFS) as a surrogate for overall survival (OS) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1644.

DNA sequence and shape are predictive for meiotic crossovers throughout the plant kingdom.

A better understanding of genomic features influencing the location of meiotic crossovers (COs) in plant species is both of fundamental importance and of practical relevance for plant breeding. Using CO positions with sufficiently high resolution from four plant species [Arabidopsis thaliana, Solanum lycopersicum (tomato), Zea mays (maize) and Oryza sativa (rice)] we have trained machine-learning models to predict the susceptibility to CO formation. Our results show that CO occurrence within various plant genomes can be predicted by DNA sequence and shape features. Several features related to genome content and to genomic accessibility were consistently either positively or negatively related to COs in all four species. Other features were found as predictive only in specific species. Gene annotation-related features were especially predictive for maize, whereas in tomato and Arabidopsis propeller twist and helical twist (DNA shape features) and AT/TA dinucleotides were found to be the most important. In rice, high roll (another DNA shape feature) and low CA dinucleotide frequency in particular were found to be associated with CO occurrence. The accuracy of our models was sufficient for Arabidopsis and rice (area under receiver operating characteristic curve, AUROC>0.5), and was high for tomato and maize (AUROC≫0.5), demonstrating that DNA sequence and shape are predictive for meiotic COs throughout the plant kingdom.

High-resolution crossover mapping reveals similarities and differences of male and female recombination in maize

Meiotic crossovers (COs) are not uniformly distributed across the genome. Factors affecting this phenomenon are not well understood. Although many species exhibit large differences in CO numbers between sexes, sex-specific aspects of CO landscape are particularly poorly elucidated. Here, we conduct high-resolution CO mapping in maize. Our results show that CO numbers as well as their overall distribution are similar in male and female meioses. There are, nevertheless, dissimilarities at local scale. Male and female COs differ in their locations relative to transcription start sites in gene promoters and chromatin marks, including nucleosome occupancy and tri-methylation of lysine 4 of histone H3 (H3K4me3). Our data suggest that sex-specific factors not only affect male–female CO number disparities but also cause fine differences in CO positions. Differences between male and female CO landscapes indicate that recombination has distinct implications for population structure and gene evolution in male and in female meioses.

The conserved LEM-3/Ankle1 nuclease is involved in the combinatorial regulation of meiotic recombination repair and chromosome segregation in Caenorhabditis elegans.

Homologous recombination is essential for crossover (CO) formation and accurate chromosome segregation during meiosis. It is of considerable importance to work out how recombination intermediates are processed, leading to CO and non-crossover (NCO) outcome. Genetic analysis in budding yeast and Caenorhabditis elegans indicates that the processing of meiotic recombination intermediates involves a combination of nucleases and DNA repair enzymes. We previously reported that in C. elegans meiotic joint molecule resolution is mediated by two redundant pathways, conferred by the SLX-1 and MUS-81 nucleases, and by the HIM-6 Bloom helicase in conjunction with the XPF-1 endonuclease, respectively. Both pathways require the scaffold protein SLX-4. However, in the absence of all these enzymes, residual processing of meiotic recombination intermediates still occurs and CO formation is reduced but not abolished. Here we show that the LEM-3 nuclease, mutation of which by itself does not have an overt meiotic phenotype, genetically interacts with slx-1 and mus-81 mutants, the respective double mutants displaying 100% embryonic lethality. The combined loss of LEM-3 and MUS-81 leads to altered processing of recombination intermediates, a delayed disassembly of foci associated with CO designated sites, and the formation of univalents linked by SPO-11 dependent chromatin bridges (dissociated bivalents). However, LEM-3 foci do not colocalize with ZHP-3, a marker that congresses into CO designated sites. In addition, neither CO frequency nor distribution is altered in lem-3 single mutants or in combination with mus-81 or slx-4 mutations. Finally, we found persistent chromatin bridges during meiotic divisions in lem-3; slx-4 double mutants. Supported by the localization of LEM-3 between dividing meiotic nuclei, this data suggest that LEM-3 is able to process erroneous recombination intermediates that persist into the second meiotic division.

Comparing Acceleration and Change of Direction Ability Between Backpedal and Cross-over Run Techniques for Use in American Football.

Angelino, D, McCabe, TJG, and Earp, JE. Comparing acceleration and change of direction ability between backpedal and cross-over run techniques for use in American football. J Strength Cond Res 35(1): 47-55, 2021-In American football, defensive backs guard receivers using either cross-over (CO) run or backpedal (BP) techniques, but the efficacy of these techniques is unknown. The purpose of this study was to compare linear acceleration (LA) and change of direction (CoD) ability when using CO and BP. Collegiate football defensive backs participated in LA (n = 13) and CoD (n = 7) testing. During LA, subjects performed CO, BP, and forward sprints with split times taken between 0-3 and 3-5 yd and ground reaction forces recorded 0 and 3 yd from the start. During CoD testing, subjects performed the CO or BP for 3 yd and then were given a cue to sprint to a gate 5 yd away in 1 of 4 directions (downfield, midfield, sideline, or upfield). In LA, CO was faster than BP between 0-3 yd (Δ -0.20 ± 0.02 seconds, p = 0.000) and 3-5 yd (Δ -0.12 ± 0.02 seconds, p = 0.000). At the start of the movement, CO demonstrated greater propulsive forces (p = 0.017). However, 3 yd from the start, CO demonstrated greater propulsive forces and reduced braking forces (p = 0.000 & 0.003). In CoD, CO was faster than BP when running in the downfield (Δ 0.21 ± 0.05 seconds, p = 0.044) and lateral directions (Δ 0.21 ± 0.08 seconds, p = 0.035), but similar in the upfield direction (Δ 0.01 ± 0.08, p = 0.986). Our results indicate that CO is superior to BP in LA, CoD ability, and movement efficiency and support the use of CO for defensive backs.

Intraindividual Variation of Meiotic Recombination Parameters in Pig Spermatocytes: A Preliminary Study

Meiotic recombination parameters like crossover (CO) rate or synaptonemal complex (SC) length are known to vary strongly between individuals and between cells from the same individual. The origins of this variability remain elusive, and little is known about the variations that might occur between different samples and/or over time within the same individual. To document this question, pachytene cells from 3 boars of the Large White breed were analyzed twice, at a 1-year interval, using immunocytological techniques. CO rate, SC length, and MLH1 inter-foci distances varied significantly between the 3 individuals. CO rate and SC length differed significantly between the 2 sampling periods for 1 individual. However, no significant differences were observed between the 2 samples for CO distribution and inter-foci distances in the 3 boars studied.

Elevated temperature increases meiotic crossover frequency via the interfering (Type I) pathway in Arabidopsis thaliana.

For most eukaryotes, sexual reproduction is a fundamental process that requires meiosis. In turn, meiosis typically depends on a reciprocal exchange of DNA between each pair of homologous chromosomes, known as a crossover (CO), to ensure proper chromosome segregation. The frequency and distribution of COs are regulated by intrinsic and extrinsic environmental factors, but much more is known about the molecular mechanisms governing the former compared to the latter. Here we show that elevated temperature induces meiotic hyper-recombination in Arabidopsis thaliana and we use genetic analysis with mutants in different recombination pathways to demonstrate that the extra COs are derived from the major Type I interference sensitive pathway. We also show that heat-induced COs are not the result of an increase in DNA double-strand breaks and that the hyper-recombinant phenotype is likely specific to thermal stress rather than a more generalized stress response. Taken together, these findings provide initial mechanistic insight into how environmental cues modulate plant meiotic recombination and may also offer practical applications.