The effect of DNA polymorphisms and natural variation on crossover hotspot activity in Arabidopsis hybrids.

In hybrid organisms, genetically divergent homologous chromosomes pair and recombine during meiosis; however, the effect of specific types of polymorphisms on crossover is poorly understood. Here, to analyze this in Arabidopsis, we develop the seed-typing method that enables the massively parallel fine-mapping of crossovers by sequencing. We show that structural variants, observed in one of the generated intervals, do not change crossover frequency unless they are located directly within crossover hotspots. Both natural and Cas9-induced deletions result in lower hotspot activity but are not compensated by increases in immediately adjacent hotspots. To examine the effect of single nucleotide polymorphisms on crossover formation, we analyze hotspot activity in mismatch detection-deficient msh2 mutants. Surprisingly, polymorphic hotspots show reduced activity in msh2. In lines where only the hotspot-containing interval is heterozygous, crossover numbers increase above those in the inbred (homozygous). We conclude that MSH2 shapes crossover distribution by stimulating hotspot activity at polymorphic regions.

MSH2 stimulates interfering and inhibits non-interfering crossovers in response to genetic polymorphism.

Meiotic crossovers can be formed through the interfering pathway, in which one crossover prevents another from forming nearby, or by an independent non-interfering pathway. In Arabidopsis, local sequence polymorphism between homologs can stimulate interfering crossovers in a MSH2-dependent manner. To understand how MSH2 regulates crossovers formed by the two pathways, we combined Arabidopsis mutants that elevate non-interfering crossovers with msh2 mutants. We demonstrate that MSH2 blocks non-interfering crossovers at polymorphic loci, which is the opposite effect to interfering crossovers. We also observe MSH2-independent crossover inhibition at highly polymorphic sites. We measure recombination along the chromosome arms in lines differing in patterns of heterozygosity and observe a MSH2-dependent crossover increase at the boundaries between heterozygous and homozygous regions. Here, we show that MSH2 is a master regulator of meiotic DSB repair in Arabidopsis, with antagonistic effects on interfering and non-interfering crossovers, which shapes the crossover landscape in relation to interhomolog polymorphism.

Efficient Generation of CRISPR/Cas9-Based Mutants Supported by Fluorescent Seed Selection in Different Arabidopsis Accessions.

Investigating the process of gamete formation in plants often requires the use of mutants of selected genes in various genetic backgrounds. For example, analysis of meiotic recombination based on sequencing or genotyping requires the generation of hybrids between two lines. Although T-DNA mutant collections of Arabidopsis thaliana are vast and easily accessible, they are largely confined to Col-0 background. This chapter describes how to efficiently generate knock-out mutants in different Arabidopsis accessions using CRISPR/Cas9 technology. The presented system is based on designing two single-guide RNAs (sgRNAs), which direct the Cas9 endonuclease to generate double-strand breaks at two sites, leading to genomic deletion in targeted gene. The presence of seed-expressed dsRed fluorescence cassette in the CRISPR construct facilitates preselection of genome-edited and transgene-free plants by monitoring the seed fluorescence under the epifluorescent microscope. The protocol provides the detailed information about all steps required to perform genome editing and to obtain loss-of-function mutants in different Arabidopsis accessions within merely two generations.

NuA4 and H2A.Z control environmental responses and autotrophic growth in Arabidopsis.

Nucleosomal acetyltransferase of H4 (NuA4) is an essential transcriptional coactivator in eukaryotes, but remains poorly characterized in plants. Here, we describe Arabidopsis homologs of the NuA4 scaffold proteins Enhancer of Polycomb-Like 1 (AtEPL1) and Esa1-Associated Factor 1 (AtEAF1). Loss of AtEAF1 results in inhibition of growth and chloroplast development. These effects are stronger in the Atepl1 mutant and are further enhanced by loss of Golden2-Like (GLK) transcription factors, suggesting that NuA4 activates nuclear plastid genes alongside GLK. We demonstrate that AtEPL1 is necessary for nucleosomal acetylation of histones H4 and H2A.Z by NuA4 in vitro. These chromatin marks are diminished genome-wide in Atepl1, while another active chromatin mark, H3K9 acetylation (H3K9ac), is locally enhanced. Expression of many chloroplast-related genes depends on NuA4, as they are downregulated with loss of H4ac and H2A.Zac. Finally, we demonstrate that NuA4 promotes H2A.Z deposition and by doing so prevents spurious activation of stress response genes.

License to Regulate: Noncoding RNA Special Agents in Plant Meiosis and Reproduction.

The complexity of the subcellular processes that take place during meiosis requires a significant remodeling of cellular metabolism and dynamic changes in the organization of chromosomes and the cytoskeleton. Recently, investigations of meiotic transcriptomes have revealed additional noncoding RNA factors (ncRNAs) that directly or indirectly influence the course of meiosis. Plant meiosis is the point at which almost all known noncoding RNA-dependent regulatory pathways meet to influence diverse processes related to cell functioning and division. ncRNAs have been shown to prevent transposon reactivation, create germline-specific DNA methylation patterns, and affect the expression of meiosis-specific genes. They can also influence chromosome-level processes, including the stimulation of chromosome condensation, the definition of centromeric chromatin, and perhaps even the regulation of meiotic recombination. In many cases, our understanding of the mechanisms underlying these processes remains limited. In this review, we will examine how the different functions of each type of ncRNA have been adopted in plants, devoting attention to both well-studied examples and other possible functions about which we can only speculate for now. We will also briefly discuss the most important challenges in the investigation of ncRNAs in plant meiosis.

Tribochemical Interactions between Graphene and ZDDP in Friction Tests for Uncoated and W-DLC-Coated HS6-5-2C Steel.

If a lubricant contains structures capable of conducting energy, reactions involving zinc dialkyldithiophosphate (ZDDP) may take place both very close to and away from the solid surfaces, with this indicating that ZDDP can be a highly effective anti-wear (AW) additive. The central thesis of this article is that the tribocatalytic effect is observed only when the energy emitted by the solids is transmitted by ordered molecular structures present in the lubricant, e.g., graphene. The friction tests were carried out for 100Cr6 steel balls in a sliding contact with uncoated or W-DLC-coated HS6-5-2C steel discs in the presence of polyalphaolefin 8 (PAO 8) as the lubricant, which was enhanced with graphene and/or ZDDP. There is sufficient evidence of the interactions occurring between ZDDP and graphene and their effects on the tribological performance of the system. It was also found that the higher the concentration of zinc in the wear area, the lower the wear. This was probably due to the energy transfer resulting from the catalytic decomposition of ZDDP molecules. Graphene, playing the role of the catalyst, contributed to that energy transfer.

Tribochemical Interactions between Carbon Nanotubes and ZDDP Antiwear Additive during Tribofilm Formation on Uncoated and DLC-Coated Steel.

The data from the authors' earlier investigations show that molecules of zinc dithiophosphate (ZDDP) added to a lubricant can absorb energy emitted by a solid surface, which is where triboreactions occur. If the lubricant contains structures able to conduct energy, the ZDDP reactions can occur even at a relatively large distance from the solid surface, which should increase the effectiveness of ZDDP as an antiwear additive. The purpose of this paper was to verify the thesis that the tribocatalytic effect depends on the ability of the solid surface to emit electrons/energy and the ability of ordered molecular structures, such as carbon nanotubes (CNTs), to conduct energy and, most likely, to enhance the energy transfer. The tribological tests were performed using a TRB3 tribotester for 100Cr6 steel balls and uncoated or a-C:H coated HS6-5-2C steel discs. Polyalphaolefin 8 (PAO8) and PAO8 mixed with ZDDP and CNTs were used as lubricants. The results of the tribological tests suggested that: (a) the effect of the interactions between ZDDP and CNTs was clearly visible; (b) the structure and properties of the solid surface layer had a significant influence on the antiwear action of the ZDDP additive.

The Indirect Tribological Role of Carbon Nanotubes Stimulating Zinc Dithiophosphate Anti-Wear Film Formation.

Experimental studies reveal that the simultaneous addition of zinc dialkyl dithiophosphates (ZDDPs) and multi-wall carbon nanotubes (MWCNTs) to a poly-alpha-olefin base oil strongly reduces wear. In this paper, it is shown that MWCNTs promote the formation of an anti-wear (AW) layer on the metal surface that is much thicker than what ZDDPs can create as a sole additive. More importantly, the nanotubes' action is indirect, i.e., MWCNTs neither mechanically nor structurally strengthen the AW film. A new mechanism for this effect is also proposed, which is supported by detailed tribometer results, friction track 3D-topography measurements, electron diffraction spectroscopy (EDS), and Raman spectroscopy. In this mechanism, MWCNTs mediate the transfer of both thermal and electric energy released on the metal surface in the friction process. As a result, this energy penetrates more deeply into the oil volume, thus extending the spatial range of tribochemical reactions involving ZDDPs.