A Kinesin-14 Motor Activates Neocentromeres to Promote Meiotic Drive in Maize.

Maize abnormal chromosome 10 (Ab10) encodes a classic example of true meiotic drive that converts heterochromatic regions called knobs into motile neocentromeres that are preferentially transmitted to egg cells. Here, we identify a cluster of eight genes on Ab10, called the Kinesin driver (Kindr) complex, that are required for both neocentromere motility and preferential transmission. Two meiotic drive mutants that lack neocentromere activity proved to be kindr epimutants with increased DNA methylation across the entire gene cluster. RNAi of Kindr induced a third epimutant and corresponding loss of meiotic drive. Kinesin gliding assays and immunolocalization revealed that KINDR is a functional minus-end-directed kinesin that localizes specifically to knobs containing 180 bp repeats. Sequence comparisons suggest that Kindr diverged from a Kinesin-14A ancestor ∼12 mya and has driven the accumulation of > 500 Mb of knob repeats and affected the segregation of thousands of genes linked to knobs on all 10 chromosomes.

Distinct kinesin motors drive two types of maize neocentromeres.

A maize chromosome variant called abnormal chromosome 10 (Ab10) converts knobs on chromosome arms into neocentromeres, causing their preferential segregation to egg cells in a process known as meiotic drive. We previously demonstrated that the gene Kinesin driver (Kindr) on Ab10 encodes a kinesin-14 required to mobilize neocentromeres made up of the major tandem repeat knob180. Here we describe a second kinesin-14 gene, TR-1 kinesin (Trkin), that is required to mobilize neocentromeres made up of the minor tandem repeat TR-1. Trkin lies in a 4-Mb region of Ab10 that is not syntenic with any other region of the maize genome and shows extraordinary sequence divergence from Kindr and other kinesins in plants. Despite its unusual structure, Trkin encodes a functional minus end-directed kinesin that specifically colocalizes with TR-1 in meiosis, forming long drawn out neocentromeres. TRKIN contains a nuclear localization signal and localizes to knobs earlier in prophase than KINDR. The fact that TR-1 repeats often co-occur with knob180 repeats suggests that the current role of the TRKIN/TR-1 system is to facilitate the meiotic drive of the KINDR/knob180 system.

Large haplotypes highlight a complex age structure within the maize pan-genome.

The genomes of maize and other eukaryotes contain stable haplotypes in regions of low recombination. These regions, including centromeres, long heterochromatic blocks, and rDNA arrays, have been difficult to analyze with respect to their diversity and origin. Greatly improved genome assemblies are now available that enable comparative genomics over these and other nongenic spaces. Using 26 complete maize genomes, we developed methods to align intergenic sequences while excluding genes and regulatory regions. The centromere haplotypes (cenhaps) extend for megabases on either side of the functional centromere regions and appear as evolutionary strata, with haplotype divergence/coalescence times dating as far back as 450 thousand years ago (kya). Application of the same methods to other low recombination regions (heterochromatic knobs and rDNA) and all intergenic spaces revealed that deep coalescence times are ubiquitous across the maize pan-genome. Divergence estimates vary over a broad timescale with peaks at ∼16 and 300 kya, reflecting a complex history of gene flow among diverging populations and changes in population size associated with domestication. Cenhaps and other long haplotypes provide vivid displays of this ancient diversity.

The maize gene maternal derepression of r1 encodes a DNA glycosylase that demethylates DNA and reduces siRNA expression in the endosperm.

Demethylation of transposons can activate the expression of nearby genes and cause imprinted gene expression in the endosperm; this demethylation is hypothesized to lead to expression of transposon small interfering RNAs (siRNAs) that reinforce silencing in the next generation through transfer either into egg or embryo. Here we describe maize (Zea mays) maternal derepression of r1 (mdr1), which encodes a DNA glycosylase with homology to Arabidopsis thaliana DEMETER and which is partially responsible for demethylation of thousands of regions in endosperm. Instead of promoting siRNA expression in endosperm, MDR1 activity inhibits it. Methylation of most repetitive DNA elements in endosperm is not significantly affected by MDR1, with an exception of Helitrons. While maternally-expressed imprinted genes preferentially overlap with MDR1 demethylated regions, the majority of genes that overlap demethylated regions are not imprinted. Double mutant megagametophytes lacking both MDR1 and its close homolog DNG102 result in early seed failure, and double mutant microgametophytes fail pre-fertilization. These data establish DNA demethylation by glycosylases as essential in maize endosperm and pollen and suggest that neither transposon repression nor genomic imprinting is its main function in endosperm.

Haplotype-resolved genome assembly of Populus tremula × P. alba reveals aspen-specific megabase satellite DNA.

Populus species play a foundational role in diverse ecosystems and are important renewable feedstocks for bioenergy and bioproducts. Hybrid aspen Populus tremula × P. alba INRA 717-1B4 is a widely used transformation model in tree functional genomics and biotechnology research. As an outcrossing interspecific hybrid, its genome is riddled with sequence polymorphisms which present a challenge for sequence-sensitive analyses. Here we report a telomere-to-telomere genome for this hybrid aspen with two chromosome-scale, haplotype-resolved assemblies. We performed a comprehensive analysis of the repetitive landscape and identified both tandem repeat array-based and array-less centromeres. Unexpectedly, the most abundant satellite repeats in both haplotypes lie outside of the centromeres, consist of a 147 bp monomer PtaM147, frequently span >1 megabases, and form heterochromatic knobs. PtaM147 repeats are detected exclusively in aspens (section Populus) but PtaM147-like sequences occur in LTR-retrotransposons of closely related species, suggesting their origin from the retrotransposons. The genomic resource generated for this transformation model genotype has greatly improved the design and analysis of genome editing experiments that are highly sensitive to sequence polymorphisms. The work should motivate future hypothesis-driven research to probe into the function of the abundant and aspen-specific PtaM147 satellite DNA.

Sequence of the supernumerary B chromosome of maize provides insight into its drive mechanism and evolution.

B chromosomes are enigmatic elements in thousands of plant and animal genomes that persist in populations despite being nonessential. They circumvent the laws of Mendelian inheritance but the molecular mechanisms underlying this behavior remain unknown. Here we present the sequence, annotation, and analysis of the maize B chromosome providing insight into its drive mechanism. The sequence assembly reveals detailed locations of the elements involved with the cis and trans functions of its drive mechanism, consisting of nondisjunction at the second pollen mitosis and preferential fertilization of the egg by the B-containing sperm. We identified 758 protein-coding genes in 125.9 Mb of B chromosome sequence, of which at least 88 are expressed. Our results demonstrate that transposable elements in the B chromosome are shared with the standard A chromosome set but multiple lines of evidence fail to detect a syntenic genic region in the A chromosomes, suggesting a distant origin. The current gene content is a result of continuous transfer from the A chromosomal complement over an extended evolutionary time with subsequent degradation but with selection for maintenance of this nonvital chromosome.

The maize abnormal chromosome 10 meiotic drive haplotype: a review.

The maize abnormal chromosome 10 (Ab10) haplotype encodes a meiotic drive system that converts heterochromatic knobs into centromere-like bodies that are preferentially segregated through female meiosis. Ab10 was first described in the 1940s and has been intensively studied. Here I provide a comprehensive review of the literature, starting from the discovery of knobs and Ab10, preceding through the classic literature, and finishing with molecular structure and mechanisms. The defining features of the Ab10 haplotype are its two specialized kinesins, Kinesin driver and TR-1 kinesin, that activate neocentromeres at knobs containing different classes of the tandem repeat. In most Ab10 haplotypes, the two kinesin/knob systems cooperate to promote maximum meiotic drive. However, recent interpretations suggest that each kinesin/knob system can function as an independent meiotic driver and that in some cases they compete with each other. Ab10 is present at low frequencies throughout the genus Zea and has significantly expanded genome size by promoting the formation of knobs throughout the genome.

Improved maize reference genome with single-molecule technologies.

Complete and accurate reference genomes and annotations provide fundamental tools for characterization of genetic and functional variation. These resources facilitate the determination of biological processes and support translation of research findings into improved and sustainable agricultural technologies. Many reference genomes for crop plants have been generated over the past decade, but these genomes are often fragmented and missing complex repeat regions. Here we report the assembly and annotation of a reference genome of maize, a genetic and agricultural model species, using single-molecule real-time sequencing and high-resolution optical mapping. Relative to the previous reference genome, our assembly features a 52-fold increase in contig length and notable improvements in the assembly of intergenic spaces and centromeres. Characterization of the repetitive portion of the genome revealed more than 130,000 intact transposable elements, allowing us to identify transposable element lineage expansions that are unique to maize. Gene annotations were updated using 111,000 full-length transcripts obtained by single-molecule real-time sequencing. In addition, comparative optical mapping of two other inbred maize lines revealed a prevalence of deletions in regions of low gene density and maize lineage-specific genes.

Genome-Scale Sequence Disruption Following Biolistic Transformation in Rice and Maize.

Biolistic transformation delivers nucleic acids into plant cells by bombarding the cells with microprojectiles, which are micron-scale, typically gold particles. Despite the wide use of this technique, little is known about its effect on the cell's genome. We biolistically transformed linear 48-kb phage lambda and two different circular plasmids into rice (Oryza sativa) and maize (Zea mays) and analyzed the results by whole genome sequencing and optical mapping. Although some transgenic events showed simple insertions, others showed extreme genome damage in the form of chromosome truncations, large deletions, partial trisomy, and evidence of chromothripsis and breakage-fusion bridge cycling. Several transgenic events contained megabase-scale arrays of introduced DNA mixed with genomic fragments assembled by nonhomologous or microhomology-mediated joining. Damaged regions of the genome, assayed by the presence of small fragments displaced elsewhere, were often repaired without a trace, presumably by homology-dependent repair (HDR). The results suggest a model whereby successful biolistic transformation relies on a combination of end joining to insert foreign DNA and HDR to repair collateral damage caused by the microprojectiles. The differing levels of genome damage observed among transgenic events may reflect the stage of the cell cycle and the availability of templates for HDR.

Frequent Spindle Assembly Errors Require Structural Rearrangement to Complete Meiosis in Zea mays.

The success of an organism is contingent upon its ability to faithfully pass on its genetic material. In the meiosis of many species, the process of chromosome segregation requires that bipolar spindles be formed without the aid of dedicated microtubule organizing centers, such as centrosomes. Here, we describe detailed analyses of acentrosomal spindle assembly and disassembly in time-lapse images, from live meiotic cells of Zea mays. Microtubules organized on the nuclear envelope with a perinuclear ring structure until nuclear envelope breakdown, at which point microtubules began bundling into a bipolar form. However, the process and timing of spindle assembly was highly variable, with frequent assembly errors in both meiosis I and II. Approximately 61% of cells formed incorrect spindle morphologies, with the most prevalent being tripolar spindles. The erroneous spindles were actively rearranged to bipolar through a coalescence of poles before proceeding to anaphase. Spindle disassembly occurred as a two-state process with a slow depolymerization, followed by a quick collapse. The results demonstrate that maize meiosis I and II spindle assembly is remarkably fluid in the early assembly stages, but otherwise proceeds through a predictable series of events.

Is It Ordered Correctly? Validating Genome Assemblies by Optical Mapping.

Long-read single-molecule sequencing, Hi-C sequencing, and improved bioinformatic tools are ushering in an era where complete genome assembly will become common for species with few or no classical genetic resources. There are no guidelines for how to proceed in such cases. Ideally, such genomes would be sequenced by two different methods so that one assembly serves as confirmation of the other; however, cost constraints make this approach unlikely. Overreliance on synteny as a means of confirming and ordering contigs will lead to compounded errors. Optical mapping is an accessible and relatively mature technology that can be used for genome assembly validation. We discuss how optical mapping can be used as a validation tool for genome assemblies and how to interpret the results. In addition, we discuss methods for using optical map data to enhance genome assemblies derived from both traditional sequence contigs and Hi-C pseudomolecules.

Loss of RNA-Directed DNA Methylation in Maize Chromomethylase and DDM1-Type Nucleosome Remodeler Mutants.

Plants make use of distinct types of DNA methylation characterized by their DNA methyltransferases and modes of regulation. One type, RNA-directed DNA methylation (RdDM), is guided by small interfering RNAs (siRNAs) to the edges of transposons that are close to genes, areas called mCHH islands in maize (Zea mays). Another type, chromomethylation, is guided by histone H3 lysine 9 methylation to heterochromatin across the genome. We examined DNA methylation and small RNA expression in plant tissues that were mutant for both copies of the genes encoding chromomethylases as well as mutants for both copies of the genes encoding DECREASED DNA METHYLATION1 (DDM1)-type nucleosome remodelers, which facilitate chromomethylation. Both sets of double mutants were nonviable but produced embryos and endosperm. RdDM was severely compromised in the double mutant embryos, both in terms of DNA methylation and siRNAs. Loss of 24-nucleotide siRNA from mCHH islands was coupled with a gain of 21-, 22-, and 24-nucleotide siRNAs in heterochromatin. These results reveal a requirement for both chromomethylation and DDM1-type nucleosome remodeling for RdDM in mCHH islands, which we hypothesize is due to dilution of RdDM components across the genome when heterochromatin is compromised.

Charting the path to fully synthetic plant chromosomes.

The concepts of synthetic biology have the potential to transform plant genetics, both in how we analyze genetic pathways and how we transfer that knowledge into useful applications. While synthetic biology can be applied at the level of the single gene or small groups of genes, this commentary focuses on the ultimate challenge of designing fully synthetic plant chromosomes. Engineering at this scale will allow us to manipulate whole genome architecture and to modify multiple pathways and traits simultaneously. Advances in genome synthesis make it likely that the initial phases of plant chromosome construction will occur in bacteria and yeast. Here I discuss the next steps, including specific ways of overcoming technical barriers associated with plant transformation, functional centromere design, and ensuring accurate meiotic transmission.

A new approach to actinic folliculitis: prophylactic narrowband ultraviolet B phototherapy.

BACKGROUND: We have observed an increasing number of patients referred to the Scottish Photobiology Service (SPS), who were later diagnosed with actinic folliculitis (AF) and had positive phototesting results. Treatment options for AF are limited, with only a few reports in the literature. The use of prophylactic narrowband ultraviolet B (NB-UVB) phototherapy for AF has not previously been described, and we report on this for the first time. AIM: To analyse the clinical characteristics, phototesting results and responses to treatment for patients with AF diagnosed by the SPS. METHODS: We undertook a retrospective review over 10 years of all case notes of patients who were assessed and diagnosed with AF through the SPS, based at the Photobiology Unit, Dundee, UK. RESULTS: All 10 patients were women. Mean age of onset was 25 years and mean time to referral for investigation was 7 years. The commonest site involved was the face, with the main clinical feature being monomorphic pustules appearing after sunlight exposure. The eruption could be provoked with iterative doses of broadband UVA irradiation in five patients. All patients were offered photoprotective advice and prophylactic NB-UVB phototherapy. Five patients proceeded with phototherapy; four of these completed the desensitization course and all four reported either a delay in symptom onset or total prevention of rash induction, with complete efficacy of desensitization maintained for 3 years in one patient. CONCLUSION: We demonstrate the successful use of UVA provocation testing as a diagnostic tool in AF. Additionally, we recommend the use of prophylactic NB-UVB phototherapy in AF as an effective and well-tolerated approach.

Narrowband ultraviolet B phototherapy is associated with a reduction in topical corticosteroid and clinical improvement in atopic dermatitis: a historical inception cohort study.

BACKGROUND: Despite decades of use, the magnitude of efficacy of narrowband ultraviolet B (NB-UVB) phototherapy for atopic dermatitis (AD) beyond industry-sponsored trials remains unclear. AIM: To evaluate the clinical efficacy of NB-UVB in AD under real-world conditions. METHODS: We conducted a historical inception cohort study using automated recording of dispensed drugs to provide an objective treatment outcome in a large population catchment of 420 000 people over 15 years. We analysed clinical treatment outcomes, recorded multicentre and prospectively over 15 years, of a large AD treatment cohort (n = 844), along with the drugs dispensed to this cohort. RESULTS: The majority (70%) of patients with AD received significantly fewer topical corticosteroids (TCS) during the 12-month window after finishing NB-UVB compared with the 12-month window before starting the treatment (median reduction from 37.5 to 19.7 g/month). The number of patients dispensed with oral corticosteroids and antihistamines also dropped significantly (from 20% to 10% and from 69% to 31%, respectively), while all AD-unrelated drugs dispensed remained unchanged. Clinically, NB-UVB treatment achieved a 'clear' or 'almost clear' status in 48.7% of patients, while 20.4% achieved 'moderate clearance'. Treatment outcomes scores were validated by a strong correlation with reduction in AD-specific drug treatment. CONCLUSION: Our data confirm the significant efficacy of NB-UVB for AD under conditions of routine care.

Photodiagnostic services in the UK and Republic of Ireland: a British Photodermatology Group Workshop Report.

BACKGROUND: Photodiagnostic investigations are essential for the accurate diagnosis of abnormal cutaneous photosensitivity and provide important information for the management of patients with photodermatoses (cutaneous photosensitivity disorders). Although photodiagnosis has been undertaken since the early 1970s, specialist services in the United Kingdom (UK) and Republic of Ireland are limited and there is no formal guidance on diagnostic approach. Indeed, there is a limited literature in this area of methodology and diagnostic practice. OBJECTIVES: The primary objective was to undertake a British Photodermatology Group Workshop to review the role and activities of specialist centres in the UK and Republic of Ireland in order to ascertain whether there were consensus practices. Secondary objectives were to identify key priorities for service, training and research. METHODS: An initial detailed survey review of current activities was undertaken prior to the Workshop and data from this survey were used to inform discussion at the Workshop, which was attended by key photodermatology experts from the UK and Republic of Ireland. RESULTS/CONCLUSIONS: We have undertaken a detailed review of current Photodiagnostic Services in the UK and Republic of Ireland and report on our findings from the 12 centres and we have identified key areas of consensus practice. This is an important step in the process of standardising and optimising procedures and protocols and defining minimum clinical standards for photodiagnostic investigations, which are of such diagnostic importance in Dermatology.

RNA as a structural and regulatory component of the centromere.

Despite many challenges, great progress has been made in identifying kinetochore proteins and understanding their overall functions relative to spindles and centromeric DNA. In contrast, less is known about the specialized centromeric chromatin environment and how it may be involved in regulating the assembly of kinetochore proteins. Multiple independent lines of evidence have implicated transcription and the resulting RNA as an important part of this process. Here, we summarize recent literature demonstrating the roles of centromeric RNA in regulating kinetochore assembly and maintenance. We also review literature suggesting that the process of centromeric transcription may be as important as the resulting RNA and that such transcription may be involved in recruiting the centromeric histone variant CENH3.

Quantitative analysis of topical treatments in atopic dermatitis: unexpectedly low use of emollients and strong correlation of topical corticosteroid use both with depression and concurrent asthma.

BACKGROUND: Despite decades of use, the actual amounts of topical corticosteroids (TCS) and emollients used in moderate-to-severe atopic dermatitis (AD) under real-world conditions are unknown. Thus, it remains unclear whether inadequate use is widespread. OBJECTIVES: To quantify the use of TCS and emollients in moderate-to-severe AD. METHODS: Double-blinded drug prescribing was recorded prospectively at the point of drug dispensing within a catchment area of approximately 450 000 people over a 31-year period in a population-based cohort marked by failure of disease control in primary care (n = 844). For each patient, prescribing was recorded over a 12-month period in order to minimize fluctuations. RESULTS: This approach resulted in a near-complete dataset, which was essentially free of reporting bias and recording bias. Atopic comorbidities matched expected frequencies. Median use of TCS was statistically significantly higher in juvenile patients (age < 16 years) compared with adult patients (49·2 vs. 38·1 g per month), in male vs. female patients (46·8 vs. 29·7 g per month) and in patients receiving concurrent asthma treatment (40·4 vs. 26·7 g per month). TCS use was strongly associated with antidepressant treatment. Emollient use was unexpectedly low with a median of 9·6 g per day (range 1·4-30·1). Results were replicated in an independent validation cohort. CONCLUSIONS: Deficient use of emollients may be a factor contributing to AD severity. Our analysis showed that the use of TCS does not exceed current guidelines. Accurate quantification of topical treatments provides a widely accessible strategy to measure the real-world impact of novel AD treatments. What's already known about this topic? Both emollient and topical corticosteroid (TCS) use have been a mainstay of atopic dermatitis (AD) treatment for over 60 years. The actual quantities used by patients under real-world conditions are unknown. What does this study add? The real-world use of emollients is fourfold lower than the amount recommended in current guidelines. Underuse of emollients may be a significant factor in disease exacerbation. The use of TCS is significantly higher in male patients and is higher in patients with AD who also have asthma. The use of TCS is strongly associated with concurrent antidepressant treatment.

Anaphase asymmetry and dynamic repositioning of the division plane during maize meiosis.

The success of an organism is contingent upon its ability to transmit genetic material through meiotic cell division. In plant meiosis I, the process begins in a large spherical cell without physical cues to guide the process. Yet, two microtubule-based structures, the spindle and phragmoplast, divide the chromosomes and the cell with extraordinary accuracy. Using a live-cell system and fluorescently labeled spindles and chromosomes, we found that the process self- corrects as meiosis proceeds. Metaphase spindles frequently initiate division off-center, and in these cases anaphase progression is asymmetric with the two masses of chromosomes traveling unequal distances on the spindle. The asymmetry is compensatory, such that the chromosomes on the side of the spindle that is farthest from the cell cortex travel a longer distance at a faster rate. The phragmoplast forms at an equidistant point between the telophase nuclei rather than at the original spindle mid-zone. This asymmetry in chromosome movement implies a structural difference between the two halves of a bipolar spindle and could allow meiotic cells to dynamically adapt to errors in metaphase and accurately divide the cell volume.

Narrowband ultraviolet B treatment for psoriasis is highly economical and causes significant savings in cost for topical treatments.

BACKGROUND: Narrowband ultraviolet B (NB-UVB) treatment for psoriasis is considered expensive. However, existing data are based on estimates and do not consider indirect cost savings. OBJECTIVES: To define the actual costs of NB-UVB incurred by the service provider, as well as treatment-associated cost savings. METHODS: We performed data linkage of (i) comprehensive treatment records and (ii) prescribing data for all NB-UVB treatment episodes spanning 6 years in a population of 420 000. We minimized data fluctuation by compiling data from four independent treatment sites, and using drug prescriptions unrelated to psoriasis as a negative control. RESULTS: National Health Service Tayside spent an average of £257 per NB-UVB treatment course (mean 257 ± 63, range 150-286, across four independent treatment sites), contrasting sharply with the estimate of £1882 used by the U.K. National Institute for Health and Care Excellence. The cost of topical treatments averaged £128 per patient in the 12 months prior to NB-UVB, accounting for 42% of the overall drug costs incurred by these patients. This was reduced by 40% to £53 per patient over the 12-month period following NB-UVB treatment, while psoriasis-unrelated drug prescription remained unchanged, suggesting disease-specific effects of NB-UVB. The data were not due to site-specific factors, as confirmed by highly similar results observed between treatment sites operated by distinct staff. Finally, we detail all staff hours directly and indirectly involved in treatment, allowing direct translation of cost into other healthcare systems. CONCLUSIONS: NB-UVB is a low-cost treatment; cost figures currently used in health technology appraisals are an overestimate based on the data presented here. Creating or extending access to NB-UVB is likely to offer additional savings by delaying or avoiding costly third-line treatments for many patients.