Meiotic crossover patterns: Obligatory crossover,interference and homeostasis in a single process

During meiosis, crossover recombination is tightly regulated. A spatial patterning phenomenon known as interference ensures that crossovers are well-spaced along the chromosomes. Additionally, every pair of homologs acquires at least one crossover. A third feature, crossover homeostasis, buffers the system such that the number of crossovers remains steady despite decreases or increases in the number of earlier recombinational interactions. Here we summarize recent work from our laboratory supporting the idea that all 3 of these aspects are intrinsic consequences of a single basic process and suggesting that the underlying logic of this process corresponds to that embodied in a particular (beam-film) model.     

Meiotic crossover patterns: Obligatory crossover,interference and homeostasis in a single process

During meiosis, crossover recombination is tightly regulated. A spatial patterning phenomenon known as interference ensures that crossovers are well-spaced along the chromosomes. Additionally, every pair of homologs acquires at least one crossover. A third feature, crossover homeostasis, buffers the system such that the number of crossovers remains steady despite decreases or increases in the number of earlier recombinational interactions. Here we summarize recent work from our laboratory supporting the idea that all 3 of these aspects are intrinsic consequences of a single basic process and suggesting that the underlying logic of this process corresponds to that embodied in a particular (beam-film) model.     

Spin crossover behaviour in the iron(II)-2,2-dipyridilamine system: Synthesis, X-ray structure and magnetic studies

The monomeric compounds [Fe(dpa)₂(X)₂] · solv [X = NCS⁻(solv = 0.5H₂O) (1), (2) and dpa = 2,2-dipyridilamine] have been synthesised and characterised. They crystallise in the P2₁/n and in the Cc monoclinic systems, respectively. Four of six nitrogen atoms coordinated to the Fe(II) ions belong to two dpa ligands which lie in cis conformation. The remaining positions are occupied by two nitrogen atoms of the pseudo-halide ligands. The magnetic susceptibility measurements at ambient pressure have revealed that compound 1 exhibits an incomplete spin crossover behaviour (T_1/2 ≈ 88 K), whereas compound 2 remains in the high-spin configuration. Pressure studies performed on compound 1 have shown virtually complete spin crossover behaviour as pressure attains 6.5 kbar.     

The crystal structure of lambda-Gam protein suggests a model for RecBCD inhibition

In Escherichia coli, RecBCD processes double-stranded DNA breaks during the initial stages of homologous recombination. RecBCD contains helicase and nuclease activities, and unwinds and digests the blunt-ended DNA until a specific eight-nucleotide sequence, Chi, is encountered. Chi modulates the nuclease activity of RecBCD and results in a resected DNA end, which is a substrate for RecA during subsequent steps in recombination. RecBCD also acts as a defence mechanism against bacteriophage infection by digesting linear viral DNA present during virus replication or resulting from the action of restriction endonucleases. To avoid this fate, bacteriophage lambda encodes the gene Gam whose product is an inhibitor of RecBCD. Gam has been shown to bind to RecBCD and inhibit its helicase and nuclease activities. We show that Gam inhibits RecBCD by preventing it from binding DNA. We have solved the crystal structure of Gam from two different crystal forms. Using the published crystal structure of RecBCD in complex with DNA we suggest models for the molecular mechanism of Gam-mediated inhibition of RecBCD. We also propose that Gam could be a mimetic of single-stranded, and perhaps also double-stranded, DNA.     

Synthesis and characterization of [Fe(III)(qsal)2][M(III)(pds)2] (M = Cu, Au)

Salts of the Fe(III) spin crossover cation [Fe^III(qsal)₂]⁺ (qsalH = N-(8-quinolyl)salicylaldimine) and monoanions [M^III(pds)₂]⁻ (M = Cu, Au; pds = pirazine-2,3-diselenolate) with formula [Fe^III(qsal)₂][M^III(pds)₂] were prepared and characterized by single crystal X-ray diffraction and magnetic measurements. These two salts present magnetic properties essentially due to the Fe^III centres in the high-spin state (S = 5/2), and do not have any spin transition.     

Variation in Crossover Frequencies Perturb Crossover Assurance Without Affecting Meiotic Chromosome Segregation in Saccharomyces cerevisiae

The segregation of homologous chromosomes during the Meiosis I division requires an obligate crossover per homolog pair (crossover assurance). In Saccharomyces cerevisiae and mammals, Msh4 and Msh5 proteins stabilize Holliday junctions and its progenitors to facilitate crossing over. S. cerevisiae msh4/5 hypomorphs that reduce crossover levels up to twofold at specific loci on chromosomes VII, VIII, and XV without affecting homolog segregation were identified recently. We use the msh4–R676W hypomorph to ask if the obligate crossover is insulated from variation in crossover frequencies, using a S. cerevisiae S288c/YJM789 hybrid to map recombination genome-wide. The msh4–R676W hypomorph made on average 64 crossovers per meiosis compared to 94 made in wild type and 49 in the msh4Δ mutant confirming the defect seen at individual loci on a genome-wide scale. Crossover reductions in msh4–R676W and msh4Δ were significant across chromosomes regardless of size, unlike previous observations made at specific loci. The msh4–R676W hypomorph showed reduced crossover interference. Although crossover reduction in msh4–R676W is modest, 42% of the four viable spore tetrads showed nonexchange chromosomes. These results, along with modeling of crossover distribution, suggest the significant reduction in crossovers across chromosomes and the loss of interference compromises the obligate crossover in the msh4 hypomorph. The high spore viability of the msh4 hypomorph is maintained by efficient segregation of the natural nonexchange chromosomes. Our results suggest that variation in crossover frequencies can compromise the obligate crossover and also support a mechanistic role for interference in obligate crossover formation.     

Crossover Formation During Rice Meiosis Relies on Interaction of OsMSH4 and OsMSH5

MSH4 encodes a MutS protein that plays a specialized role in meiosis. In eukaryotic species, such as budding yeast, mice, Caenorhabditis elegans, and Arabidopsis, msh4 mutants display meiotic defects with a reduced number of chiasmata. Here, we characterized rice MSH4 by map-based cloning. In Osmsh4 mutants, the chiasma frequency was dramatically decreased to ∼10% of the wild type, but the synaptonemal complex was normally installed. The double mutant analysis showed that in the Osmsh4 Osmsh5 mutant, the reduction of chiasmata was greater than other zmm mutants. This was consistent with the absence of localization for OsZIP4 and OsMER3 in Osmsh4 and suggests an earlier role for OsMSH4 and OsMSH5 than other ZMM proteins where they may be required to stabilize progenitor Holliday junctions. Using yeast two-hybrid and pull-down assays, we verified the direct physical association between OsMSH4 and OsMSH5 and OsMSH5 and HEI10 in plants for the first time. The MSH4–MSH5 heterodimer has been demonstrated in mammals to stabilize the formation of progenitor and double Holliday junctions that may be resolved as crossovers (COs). We propose that OsMSH4 interacts with OsMSH5 to promote formation of the majority of COs in rice.     

A linkage map of the porcine genome from a large-scale White Duroc × Erhualian resource population and evaluation of factors affecting recombination rates

A porcine genome linkage map composed of 194 microsatellite markers was constructed with a large-scale White Duroc × Erhualian resource population. The marker order on this linkage map was consistent with the USDA-MARC reference map except for two markers on SSC3, two markers on SSC13 and two markers on SSCX. The length of the sex-averaged map (2344.9 cM) was nearly the same as that of the USDA-MARC and NIAI map. Highly significant heterogeneity in recombination rates between sexes was observed. Except for SSC1 and SSC13, the female autosomes had higher average recombination rates than the male autosomes. Moreover, recombination rates in the pseudoautosomal region were greater in males than in females. These observations are consistent with those of previous reports. The recombination rates on each paternal and maternal chromosome of F₂ animals were calculated. Recombination rates were not significantly affected by the age (in days) or parity of the F₁ animals. However, recombination rates on paternal chromosomes were affected by the mating season of the F₁ animals. This could represent an effect of environmental temperature on spermatogenesis.     

Distinct histone modifications define initiation and repair of meiotic recombination in the mouse

Little is known about the factors determining the location and activity of the rapidly evolving meiotic crossover hotspots that shape genome diversity. Here, we show that several histone modifications are enriched at the active mouse Psmb9 hotspot, and we distinguish those marks that precede from those that follow hotspot recombinational activity. H3K4Me3, H3K4Me2 and H3K9Ac are specifically enriched in the chromatids that carry an active initiation site, and in the absence of DNA double-strand breaks (DSBs) in Spo11^−/− mice. We thus propose that these marks are part of the substrate for recombination initiation at the Psmb9 hotspot. In contrast, hyperacetylation of H4 is increased as a consequence of DSB formation, as shown by its dependency on Spo11 and by the enrichment detected on both recombining chromatids. In addition, the comparison with another hotspot, Hlx1, strongly suggests that H3K4Me3 and H4 hyperacetylation are common features of DSB formation and repair, respectively. Altogether, the chromatin signatures of the Psmb9 and Hlx1 hotspots provide a basis for understanding the distribution of meiotic recombination.     

Pairwise fitting of piecewise mixed models for the joint modeling of multivariate longitudinal outcomes,in a randomized crossover trial

Many statistical models have been proposed in the literature for the analysis of longitudinal data. One may propose to model two or more correlated longitudinal processes simultaneously, with a goal of understanding their association over time. Joint modeling is then required to carefully study the association structure among the outcomes as well as drawing joint inferences about the different outcomes. In this study, we sought to model the associations among six nutrition outcomes while circumventing the computational challenge posed by their clustered and high-dimensional nature. We analyzed data from a 2 $$ 2 randomized crossover trial conducted in Kenya, to compare the effect of high-dose and low-dose iodine in household salt on systolic blood pressure (SBP) and diastolic blood pressure (DBP) in women of reproductive age and their household matching pair of school-aged children. Two additional outcomes, namely, urinary iodine concentration (UIC) in women and children were measured repeatedly to monitor the amount of iodine excreted through urine. We extended the model proposed by Mwangi et al. (2021, Communications in Statistics: Case Studies, Data Analysis and Applications, 7(3), 413–431) allowing flexible piecewise joint models for six outcomes to depend on separate random effects, which are themselves correlated. This entailed fitting 15 bivariate general linear mixed models and deriving inference for the joint model using pseudo-likelihood theory. We analyzed the outcomes separately and jointly using piecewise linear mixed-effects (PLME) model and further validated the results using current state-of-the-art Jones and Kenward methodology (JKME model) used for analyzing randomized crossover trials. The results indicate that high-dose iodine in salt significantly reduced blood pressure (BP) compared to low-dose iodine in salt. Estimates for the random effects and residual error components showed that SBP and DBP had strong positive correlation, with effect of the random slope indicating that significantly related outcomes are strongly associated in their evolution. There was a moderately strong inverse relationship between evolutions of UIC and BP both in women and children. These findings confirmed the original hypothesis that high-dose iodine salt has significant lowering effect on BP. We further sought to evaluate the performance of our proposed PLME model against the widely used JKME model, within the multivariate joint modeling framework through a simulation study mimicking a $$ crossover design. From our findings, the multivariate joint PLME model performed exceptionally well both in estimation of random-effects matrix (G) and Hessian matrix (H), allowing satisfactory model convergence during estimation. It allowed a more complex fit to the data with both random intercepts and slopes effects compared to the multivariate joint JKME model that allowed for random intercepts only. When a hierarchical viewpoint is adopted, in the sense that outcomes are specified conditionally upon random effects, the variance–covariance matrix of the random effects must be positive definite. In some cases, additional random effects could explain much variability in the data, thus improving precision in estimation of the estimands (effect size) parameters. The key highlight in this evaluation shows that multivariate joint JKME model is a powerful tool especially while fitting mixed models with random intercepts only, in crossover design settings. Addition of random slopes may lead to model complexities in most cases, resulting in unsatisfactory model convergence during estimation. To circumvent convergence pitfalls, extention of JKME model to PLME model allows a more flexible fit to the data (generated from crossover design settings), especially in the multivariate joint modeling framework.     

X-interface is not the explanation for the slow disassembly of N-cadherin dimers in the apo state

In spite of structural similarities Epithelial- (E-) and Neural- (N-) cadherins are expressed at two types of synapses and differ significantly in dimer disassembly kinetics. Recent studies suggested that the formation of an X-dimer intermediate in E-cadherin is the key requirement for rapid disassembly of the adhesive dimer (Harrison et al., Nat Struct Mol Biol 2010;17:348-357 and Hong et al., J Cell Biol 2011;192:1073-1083). The X-interface in E-cadherin involves three noncovalent interactions, none of which is conserved in N-cadherin. Dimer disassembly is slow at low calcium concentration in N-cadherin, which may be due to the differences in the X-interface residues. To investigate the origin of the slow disassembly kinetics we introduced three point mutations into N-cadherin to provide the opportunity for the formation of X-interface interactions. Spectroscopic studies showed that the triple mutation did not affect the stability or the calcium-binding affinity of the X-enabled N-cadherin mutant. Analytical size exclusion chromatography was used to assay for the effect of the mutation on the rate of dimer disassembly. Contrary to our expectation, the disassembly of dimers of the X-enabled N-cadherin mutant was as slow as seen for wild-type N-cadherin in the apo-state. Thus, the differences in the X-interface residues are not the origin of slow disassembly kinetics of N-cadherin in the apo-state.     

FIGL1 coordinates with dosage-sensitive BRCA2 in modulating meiotic recombination in maize

Meiotic crossover(CO) formation between homologous chromosomes ensures their subsequent proper segregation and generates genetic diversity among offspring. In maize, however, the mechanisms that modulate CO formation remain poorly characterized. Here, we found that both maize BREAST CANCER SUSCEPTIBILITY PROTEIN 2(BRCA2) and AAA-ATPase FIDGETIN-LIKE-1(FIGL1)act as positive factors of CO formation by controlling the assembly or/and stability of two conserved DNA recombinases RAD51 and DMC1 filame...     

Sex determination system of the rosy bitterling, Rhodeus ocellatus ocellatus

The rosy bitterling, Rhodeus ocellatus ocellatus, is the only fish species known in which artificial triploids are always male, regardless of the kind of polyploidization technique used. In order to elucidate the genetic sex determination system of the rosy bitterling, two kinds of gynogenesis were carried out: retention of the second polar body (GRSPB) and suppression of the first cleavage (GSFC). The sex ratio of progeny was nearly 7:1 (:) for both GRSPB and GSFC, while those of control and parental fish were almost 1:1. In backcrosses of female progeny by GRSPB and normal diploid males, male progeny were observed at low frequency (one or two individuals in each experiment), except in one experiment where the appearance rate of males was about 50%. From results of gynogenesis and backcrosses, the following conclusions can be made. The genetic sex determination system of the rosy bitterling is a heterogametic female system (ZW). Survival rate of superfemales (WW), produced by gynogenesis, is much lower than that of males (ZW).There is a possibility that crossovers between sex determining genes and a centromere occur in the first meiosis. With repect to the mechanism of unisexuality (male) of artificial triploids of the rosy bitterling, only males (ZZZ and ZZW) are presumed viable, while females (ZWW) are probably inviable.