Pc Genes Research Articles

Virulence of Puccinia coronata var avenae f. sp. avenae (oat crown rust) in Canada during 2016 to 2020 and comparison of extensive vs intensive sampling methods

Puccinia coronata var avenae f. sp. avenae (Pca), the causal fungus of crown rust of oats, is a significant threat to oat production in the eastern prairie region (Manitoba and eastern Saskatchewan; EPR), Ontario and Quebec (eastern Canada; EC), in Canada. Development of oat lines with effective resistance to Pca has been a priority for oat breeding programmes in Canada, and helped mitigate reductions in oat yield and quality. This requires knowledge of the virulence characteristics of the Pca population in Canada. Our objectives were to determine the incidence and severity of Pca in Canada, the presence and frequency of virulence and races in Pca populations and compare the traditional extensive sampling method (few isolates per field from many fields) to an intensive sampling method (many isolates per field from a few fields) for obtaining genetically diverse collections. The incidence and severity of crown rust of oat in Canada was lower in 2016 to 2020 than has been reported in previous years. Virulence to all the 24 Pc genes studied was observed over the 5 years in EC and the EPR. The most effective genes were Pc94, Pc98 and Pc101 in EC and Pc50, Pc96, Pc97 and Pc98 in the EPR. Approximately 81% of 424 races identified were of unique virulence phenotypes over the 5 years, indicating a highly variable Pca population in Canada. Races JTQG-91 and GTQG-91 were the most common races identified. Collections of Pca obtained using the extensive sampling method were observed to be more genetically diverse than collections obtained using the intensive sampling method in 2018 and 2020, but not in 2019.

Virulence Patterns of Oat Crown Rust in Australia - Season 2022.

Puccinia coronata f. sp. avenae (Pca) is an important foliar pathogen of oat which causes crown rust disease. The virulence profile of 48 Pca isolates derived from different locations in Australia was characterized using a collection of oat lines often utilized in rust surveys in the United States and Australia. This analysis indicates that Pca populations in Eastern Australia are broadly virulent, which contrasts with the population in Western Australia (WA). Several oat lines/Pc genes are effective against all rust samples collected from WA, suggesting they may provide useful resistance in this region if deployed in combination. We identified 19 lines from the United States oat differential set that display disease resistance to Pca in WA, with some in agreement with previous rust survey reports. We adopted the 10-letter nomenclature system to define oat crown rust races in Australia and compare the frequency of those virulence traits to published data from the United States. Based on this nomenclature, 42 unique races were detected among the 48 isolates, reflecting the high diversity of virulence phenotypes for Pca in Australia. Nevertheless, the Pca population in the United States is substantially more broadly virulent than that of Australia. Close examination of resistance profiles for the oat differential set lines after infection with Pca supports hypotheses of allelism or redundancy among Pc genes or the presence of several resistance genes in some oat differential lines. These findings illustrate the need to deconvolute the oat differential set using molecular tools.[Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Three Decades of Rust Surveys in the United States Reveal Drastic Virulence Changes in Oat Crown Rust.

To better understand how the pathogenicity of the oat crown rust pathogen Puccinia coronata f. sp. avenae (Pca) has changed in the United States, 30 years of United States Department of Agriculture (USDA) survey isolates (n = 5,456) tested on 30 to 40 differential lines were analyzed for overall and Pc-resistance-gene-specific virulence trends and correlations. Pca is incredibly pathologically diverse, with 88% of races represented by a single isolate. There are a slightly higher proportion of unique races from the Northern region of the United States, and for one fourth of the years, Northern region isolates were significantly more virulent than Southern isolates, which supports the idea that sexual recombination in this region is mediated by the alternate host as a major factor in creating new races. However, there is also support for regular isolate movement between North and South regions as isolates in the United States are steadily accumulating virulences at a rate of 0.35 virulences per year. Virulence significantly increased for 23 and decreased for four of the 40 differential lines. In the past few years, virulence has reached 90% or greater for 16 differential lines. There were also strong correlations in virulence for certain Pc genes that are likely identical, allelic, or target the same or closely linked pathogen effectors (e.g., Pc39, Pc55, and Pc71), and the results were largely in concordance with recent genome-wide association study (GWAS) effector studies using USDA isolate subsets. Understanding changes in Pca pathogenicity is essential for the responsible deployment and management of Pc resistance genes for sustainable and profitable oat production.

Adaptation of Chinese perch (Siniperca chuatsi) to different levels of dietary carbohydrates

The objective of the study was to investigate the effects of dietary carbohydrate on growth performance, feed utilization, proximate compositions, and hepatic glucolipid metabolism in Chinese perch. Triplicate groups of Chinese perch (29.51 ± 0.24 g) were fed five isonitrogenous and isolipidic diets containing graded levels of carbohydrate (2.4%, 9.7%, 16.5%, 23.9%, and 30.1%) for 8 weeks. The results based on second-order polynomial regression analysis of specific growth rate (SGR) proved that Chinese perch obtained the best growth performance at the 10.93% dietary carbohydrate level. Compared to 2.4%-carbohydrate group, 9.7%-carbohydrate group exhibited the increase in daily weight gain (DWG) and protein retention ratio (PER) and the decrease in feed conversion efficiency (FCR). Moreover, 9.7%-carbohydrate group showed the increase in the mRNA levels of pfk and cs involved in aerobic oxidation pathway, the content of liver glycogen increased significantly, and no change in glucose level. Above results suggested that a part of carbohydrates may be converted into energy for growth by aerobic oxidation pathway, or converted into glycogen for storage to maintain glucose homeostasis in Chinese perch fed with moderate-carbohydrate diet. Differently, 23.9%-carbohydrate and 30.1%-carbohydrate groups showed the decrease in DWG and PER, and the increase in FCR, compared to 2.4%-carbohydrate group. Additionally, 23.9%-carbohydrate and 30.1%-carbohydrate group presented the increase in the mRNA levels of g6pca and pc involved in gluconeogenesis, which caused the increase in plasma glucose level. However, other plasma indices related to TG-metabolite and its transport (total cholesterol, and low-density lipoprotein) did not show difference, which combined with elevated fatty acid synthesis-related gene accα mRNA level resulted in excessive liver lipid deposition. Above results indicated that unregulated gluconeogenesis and invalid outward transportation of liver TG-rich metabolites may account for the glucose intolerance of Chinese perch fed with carbohydrate-rich diet. Furthermore, compared to the results from the 4th week, the expression of gk, pfk, pc, cs, and accα genes significantly increased in the 30.1%-carbohydrate group at the 8th week. Both liver and muscle exhibited a significant elevation in crude fat content, while Daily DWG experienced a noticeable decrease. These results indicated that the glucose metabolism and growth of Chinese perch in the high-carbohydrate group are influenced by the interaction of feeding duration and carbohydrate levels. And within a certain time frame, Chinese perch can tolerate a diet rich in carbohydrates.

Hub genes, key miRNAs and interaction analyses in type 2 diabetes mellitus: an integrative in silico approach.

Diabetes is a rising global metabolic disorder and leads to long-term consequences. As a multifactorial disease, the gene-associated mechanisms are important to know. This study applied a bioinformatics approach to explore the molecular underpinning of type 2 diabetes mellitus through differential gene expression analysis. We used microarray datasets GSE16415 and GSE29226 to identify differentially expressed genes between type 2 diabetes and normal samples using R software. Following that, using the STRING database, the protein-protein interaction network was constructed and further analyzed by Cytoscape software. The EnrichR database was used for Gene Ontology and pathway enrichment analysis to explore key pathways and functional annotations of hub genes. We also used miRTarBase and TargetScan databases to predict miRNAs targeting hub genes. We identified 21 hub genes in type 2 diabetes, some showing more significant changes in the PPI network. Our results revealed that GLUL, SLC32A1, PC, MAPK10, MAPT, and POSTN genes are more important in the PPI network and can be experimentally investigated as therapeutic targets. Hsa-miR-492 and hsa-miR-16-5p are suggested for diagnosis and prognosis by targeting GLUL, SLC32A1, PC, MAPK10, and MAPT genes involved in the insulin signaling pathway. Insight: Type 2 diabetes, as a rising global and multifactorial disorder, is important to know the gene-associated mechanisms. In an integrative bioinformatics analysis, we integrated different finding datasets to put together and find valuable diagnostic and prognostic hub genes and miRNAs. In contrast, genes, RNAs, and enzymes interact systematically in pathways. Using multiple databases and software, we identified differential expression between hub genes of diabetes and normal samples. We explored different protein-protein interaction networks, gene ontology, key pathway analysis, and predicted miRNAs that target hub genes. This study reported 21 significant hub genes and some miRNAs in the insulin signaling pathway for innovative and potential diagnostic and therapeutic purposes.

Cross-species identification of cancer resistance-associated genes that may mediate human cancer risk.

Cancer is a predominant disease across animals. We applied a comparative genomics approach to systematically characterize genes whose conservation levels correlate positively (PC) or negatively (NC) with cancer resistance estimates across 193 vertebrates. Pathway analysis reveals that NC genes are enriched for metabolic functions and PC genes in cell cycle regulation, DNA repair, and immune response, pointing to their corresponding roles in mediating cancer risk. We find that PC genes are less tolerant to loss-of-function (LoF) mutations, are enriched in cancer driver genes, and are associated with germline mutations that increase human cancer risk. Their relevance to cancer risk is further supported via the analysis of mouse functional genomics and cancer mortality of zoo mammals’ data. In sum, our study describes a cross-species genomic analysis pointing to candidate genes that may mediate human cancer risk.

DNA markers in oat breeding for crown rust resistance (a review)

Crown rust is the most harmful disease of oat (Avena sativa L.) around the world. The purpose of this review is to analyze and generalize the available information about DNA markers developed for oat breeding for resistance to crown rust. The review reveals the mechanisms of the A. sativa resistance to the fungus Puccinia coronata Corda f. sp. avenae Erikss. which causes crown rust disease. Special attention is paid to the race-specific resistance caused by the action of Pc genes and the nonspecific resistance controlled mainly by the loci of quantitative traits. Strategies for creating resistant genotypes and the role of molecular markers in oat breeding for crown rust resistance are discussed. Currently, research is focused mainly on the search for and development of molecular markers related to the oat race-specific resistance to P. coronata.The article presents the technological advantages and disadvantages of the existing DNA markers. KASP, TaqMan and HRM markers are currently the most promising technologies for identifying crown rust resistance genes. The validated SCAR and STS markers for the Pc39, Pc68, Pc91, Pc94 genes are recommended as the most available for implementation in practical oat breeding. The results of recent studies on identifying loci of nonspecific resistance to P. coronata are also presented. In general, the use of DNA markers has significant potential for creating oat genotypes resistant to crown rust under present-day conditions. DNA markers of various types are recommended for practical use, in particular for pyramiding genes and increasing the resistance period of new cultivars. Introduction of DNA markers into oat breeding will increase with the growth of molecular genetic data and the improvement of technologies for identifying genes and loci associated with both race-specific and nonspecific resistance of oat to P. coronata.

New Insights into the Evolution of the Electron Transfer from Cytochrome f to Photosystem I in the Green and Red Branches of Photosynthetic Eukaryotes

In cyanobacteria and most green algae of the eukaryotic green lineage, the copper-protein plastocyanin (Pc) alternatively replaces the heme-protein cytochrome c6 (Cc6) as the soluble electron carrier from cytochrome f (Cf) to photosystem I (PSI). The functional and structural equivalence of ‘green’ Pc and Cc6 has been well established, representing an example of convergent evolution of two unrelated proteins. However, plants only produce Pc, despite having evolved from green algae. On the other hand, Cc6 is the only soluble donor available in most species of the red lineage of photosynthetic organisms, which includes, among others, red algae and diatoms. Interestingly, Pc genes have been identified in oceanic diatoms, probably acquired by horizontal gene transfer from green algae. However, the mechanisms that regulate the expression of a functional Pc in diatoms are still unclear. In the green eukaryotic lineage, the transfer of electrons from Cf to PSI has been characterized in depth. The conclusion is that in the green lineage, this process involves strong electrostatic interactions between partners, which ensure a high affinity and an efficient electron transfer (ET) at the cost of limiting the turnover of the process. In the red lineage, recent kinetic and structural modeling data suggest a different strategy, based on weaker electrostatic interactions between partners, with lower affinity and less efficient ET, but favoring instead the protein exchange and the turnover of the process. Finally, in diatoms the interaction of the acquired green-type Pc with both Cf and PSI may not yet be optimized.

Chitosan modulates Pochonia chlamydosporia gene expression during nematode egg parasitism.

SummaryClimate change makes plant‐parasitic nematodes (PPN) an increasing threat to commercial crops. PPN can be managed sustainably by the biocontrol fungus Pochonia chlamydosporia (Pc). Chitosan generated from chitin deacetylation enhances PPN parasitism by Pc. In this work, we investigate the molecular mechanisms of Pc for chitosan resistance and root‐knot nematode (RKN) parasitism, using transcriptomics. Chitosan and RKN modify the expression of Pc genes, mainly those involved in oxidation–reduction processes. Both agents significantly modify the expression of genes associated to 113 GO terms and 180 Pc genes. Genes encoding putative glycoproteins (Pc adhesives) to nematode eggshell, as well as genes involved in redox, carbohydrate and lipid metabolism trigger the response to chitosan. We identify genes expressed in both the parasitic and endophytic phases of the Pc lifecycle; these include proteases, chitosanases and transcription factors. Using the Pathogen—Host Interaction database (PHI‐base), our previous RNA‐seq data and RT‐PCR of Pc colonizing banana we have investigated genes expressed both in the parasitic and endophytic phases of Pc lifecycle.

The multiple effects of hydrogen sulfide on cadmium toxicity in tobacco may be interacted with CaM signal transduction

Soilless culture experiments with tobacco were conducted to explore how the signal molecule H2S (0.3, 0.6, 0.9, and 1.2 μM) alleviated the toxicity of Cd2+ (50 mg/L). The results suggested that photosynthesis was enhanced as H2S improved the tobacco ΦPSII, ETR, Photo, Cond, and Tr, and that by increasing the NPQ, it consumed considerable amount of energy to enhance plant resistances during Cd2+ exposure. Furthermore, H2S increased the gene transcription of NtSOD3, NtPOD1, and CAT1, to enhance antioxidant enzyme activity, which reduces the generation of the reactive oxygen protective membrane integrity. Additionally, H2S increased the gene expression of the tobacco PC genes, Pr2 and Pr8 promoted the formation of the Cd2+ complexes and transportation to the vacuole, resulting in improved Cd-ATPase gene expression, away from organelles, to alleviate the Cd2+ poison. Furthermore, H2S regulated the relative absorption of K+ and Ca2+, which antagonized the Cd2+, and reduced its transportation to the aboveground plant material. Finally, the expression level of CaM increased with the application of H2S, and was highly correlated with the fitted results of a variety of resistance indicators, thereby indicating that H2S regulatory resistance mechanisms might be associated with Ca2+ signal transduction.

The RNA exosome shapes the expression of key protein-coding genes.

The ribonucleolytic exosome complex is central for nuclear RNA degradation, primarily targeting non-coding RNAs. Still, the nuclear exosome could have protein-coding (pc) gene-specific regulatory activities. By depleting an exosome core component, or components of exosome adaptor complexes, we identify ∼2900 transcription start sites (TSSs) from within pc genes that produce exosome-sensitive transcripts. At least 1000 of these overlap with annotated mRNA TSSs and a considerable portion of their transcripts share the annotated mRNA 3′ end. We identify two types of pc-genes, both employing a single, annotated TSS across cells, but the first type primarily produces full-length, exosome-sensitive transcripts, whereas the second primarily produces prematurely terminated transcripts. Genes within the former type often belong to immediate early response transcription factors, while genes within the latter are likely transcribed as a consequence of their proximity to upstream TSSs on the opposite strand. Conversely, when genes have multiple active TSSs, alternative TSSs that produce exosome-sensitive transcripts typically do not contribute substantially to overall gene expression, and most such transcripts are prematurely terminated. Our results display a complex landscape of sense transcription within pc-genes and imply a direct role for nuclear RNA turnover in the regulation of a subset of pc-genes.

Mapping of the Oat Crown Rust Resistance Gene Pc39 Relative to Single Nucleotide Polymorphism Markers.

Crown rust, caused by Puccinia coronata f. sp. avenae Eriks. (Pca), is among the most important oat diseases resulting in significant yield losses in many growing regions. A gene-for-gene interaction is well established in this pathosystem and has been exploited by oat breeders to control crown rust. Pc39 is a seedling crown rust resistance gene that has been widely deployed in North American oat breeding. DNA markers are desired to accurately predict the specific Pc genes present in breeding germplasm. The objectives of the study were as follows: (i) to map Pc39 in two recombinant inbred line (RIL) populations (AC Assiniboia/MN841801 and AC Medallion/MN841801) and (ii) to identify single nucleotide polymorphism (SNP) markers for postulation of Pc39 in oat germplasm. Pc39 was mapped to a linkage group consisting of 16 SNP markers, which placed the gene on linkage group Mrg11 (chromosome 1C) of the oat consensus map. Pc39 cosegregated with SNP marker GMI_ES01_c12570_390 in the AC Assiniboia/MN841801 RIL population and was flanked by the SNP markers avgbs_126086.1.41 and GMI_ES15_c276_702, with genetic distances of 1.7 and 0.3 cM, respectively. In the AC Medallion/MN841801 RIL population, similar results were obtained but the genetic distances of the flanking markers were 0.4 and 0.4 cM, respectively. Kompetitive Allele-Specific PCR assays were successfully designed for Pc39-linked SNP loci. Two SNP loci defined a haplotype that accurately predicted Pc39 status in a diverse panel of oat germplasm and will be useful for marker-assisted selection in oat breeding.

Virulence Structure and Diversity of Puccinia coronata f. sp. avenae P. Syd. & Syd. in Poland During 2013 to 2015.

The crown rust fungus Puccinia coronata f. sp. avenae P. Syd. & Syd. (Pca) attacks cultivated oat and its wild relatives, causing significant losses to the crop worldwide. Although understanding the origin and dynamics of the pathogen's diversity is critical to developing methods for its control, there are little relevant data on Pca virulence diversity in Europe, the global center of oat production. The goal of this study was to analyze the diversity of Pca populations in Poland in 2013 to 2015 based on their ability to overcome currently available host resistance Pc genes. Pca isolate virulence was evaluated on a panel of lines containing 26 major resistance genes of oat. The isolates were able to overcome from 1 to 16 resistance genes each, with most isolates being virulent on five to seven lines. In all years, a very high level of crown rust pathotype diversity was observed, with Simpson and Evenness indices of 0.99. In total, 156 different pathotypes were detected, with no prevalent pathotype in any of the 3 years analyzed. The results showed that the virulence level of P. coronata isolates was relatively low for each year studied (21% on average), most likely owing to the low take up of Pc genes in Polish oat cultivars, meaning that many sources of resistance are still effective against Pca races occurring in Poland. The long-range dispersal of Puccinia spores supported by the availability of wild, weedy, and cultivated Avena species makes it likely that the virulence profile seen in Poland is representative of much of central Europe and beyond.

Virulence of Puccinia coronata var avenae f. sp. avenae (oat crown rust) in Canada during 2010 to 2015

Crown rust, caused by Puccinia coronata var. avenae f. sp. avenae (Urban & Marková) (Pca), is an economically significant problem in oat in Canada. The growing of crown rust resistant oat cultivars has been an important management practice. The development of oat cultivars with effective resistance requires knowledge of the virulence genes present in the pathogen population. This study’s objective was to determine the presence and frequency of virulence to 24 oat lines with single Pc genes in isolates of Pca collected in Canada during 2010 to 2015. A total of 692 distinct races were identified, of which 603 were from the eastern Prairie region (EPR) and 89 from eastern Canada. None of the 24 Pc resistance genes studied was effective against all of the Pca isolates from the EPR. The frequency of virulence increased on 15 of the Pc differential lines in the EPR between 2010 and 2015, with the most dramatic increase from 0% to 67% being to Pc91. The most effective resistance genes were Pc94, Pc50, Pc96, Pc97, Pc98 and Pc101. Virulence to Pc58, Pc94, Pc98 and Pc101 was not observed in Pca isolates from eastern Canada. The race structure of the Pca population in Canada was highly variable, with more than 80% of the races identified each year represented by one Pca isolate. The race structure of the Pca populations in eastern Canada and the EPR were distinct, as 80% of the races identified from Pca isolates collected in eastern Canada were not detected in the EPR. The results of this study indicate that the Pca populations in the EPR and eastern Canada continue to evolve in their virulence dynamics, creating a challenge to breed oat lines with effective and stable resistance.

Detached Leaf Assays for Resistance to Crown Rust Reveal Diversity Within Populations of Avena sterilis.

Crown rust is the most widespread and damaging disease of oat (Avena species). Genetic resistance to the pathogen is the preferred method for crop protection but widespread deployment of limited numbers of major effect genes has promoted the rapid emergence and spread of pathogen races that are able to overcome these genes. Combining genes with even partial resistance may help develop durable cultivars that are less vulnerable to changes in pathogen virulence. Partial resistance is expected to be relatively common in populations of wild species where constant pathogen pressure encourages diversity in host resistance mechanisms, but it may be discarded in conventional screens for major gene resistance. Here, we used a detached leaf assay to detect resistance to the crown rust pathogen, Puccinia coronata Cda. f. sp. avenae, in previously uncharacterized collections of the hexaploid wild oat relative A. sterilis made by the Polish National Centre for Plant Genetic Resources. Many of the accessions were collected in Morocco, the center of diversity for the Avena genus. The detached leaf assessment allowed individual plants to be challenged with multiple pathotypes and their responses compared with 34 known differentials. Broad-spectrum resistance was identified within accession PL 51855, which behaved as a single major locus on crossing to three cultivars. The locus provided resistance to over 50 rust pathotypes, a greater range than seen for any of the known host resistance (Pc) genes. Strong resistance was identified in other accessions, and heterogeneity in response within accessions was common. Several accessions show multiple partial resistance responses that may be of value for developing durable resistance in cultivars. Because the sources of resistance in all but two differential lines were collected outside of Morocco, resistance in all accessions tested here are potentially novel. This study demonstrates that diversity within A. sterilis accessions collected in Morocco could be a very valuable source of resistance to crown rust, and it provides new germplasm for use in resistance breeding programs. Detached leaf assessment provides a valuable first step in the identification of promising candidates in complex gene bank accessions.

Mapping of crown rust resistance gene Pc53 in oat (Avena sativa).

Crown rust disease caused by the fungus Puccinia coronata f. sp. avenae (Pca) is a major production constraint of oat in North America, Europe, and Australia. There are over 100 genes effective against one or more Pca races, but only a handful of seedling resistance (Pc) genes have been mapped to a known chromosomal location. The goal of the present study was to use linkage mapping to identify the genomic location of the Pc53 gene, and to produce a list of linked SNPs with potential as molecular markers for marker assisted breeding. The Pc53 gene was placed on the linkage group Mrg08 at 82.4 cM using F5-derived recombinant inbred lines (RILs) from a cross between the Pc53 carrier 6-112-1-15 (PI 311624) and the susceptible cultivar Otana. The map location was validated using RILs from a cross between 6-112-1-15 and the Pc50 differential line. Single nucleotide polymorphism marker GMI_ES02_c14533_567 was the closest to Pc53. A major seedling resistance gene ‘PcKM’ and QTL QcC.Core.08.1, QCr.Core.08.2, QCr.Core.08.3 and QCr.cdl9-12D were previously reported on Mrg08. QPc.Core.08.1 and PcKM were mapped to within 1 cM of Pc53; but previous virulence studies have indicated separate identities. The chromosomal location of Pc53 and SNPs linked with it will facilitate the utilization of Pc53 in oat breeding programs.

Polycomb/Trithorax group-dependent regulation of the neuronal gene Lim3 involved in Drosophila lifespan control

Molecular mechanisms governing gene expression and defining complex phenotypes are central to understanding the basics of development and aging. Here, we demonstrate that naturally occurring polymorphisms of the Lim3 regulatory region that are associated with variation in gene expression and Drosophila lifespan control are located exclusively in the Polycomb response element (PRE). We find that the Polycomb group (PcG) protein Polycomb (PC) is bound to the PRE only in embryos where Lim3 is present in both repressed and active states. In contrast, the Trithorax group (TrxG) protein absent, small, or homeotic discs 1 (ASH1) is bound downstream of the PRE, to a region adjacent to the Lim3 transcription start site in embryos and adult flies, in which Lim3 is in an active state. Furthermore, mutations in Pc and ash1 genes affect Lim3 expression depending on the structural integrity of the Lim3 PRE, thus confirming functional interactions between these proteins and Lim3 regulatory region. In addition, we demonstrate that the evolutionary conserved Lim3 core promoter provides basic Lim3 expression, whereas structural changes in the Lim3 PRE of distal promoter provide stage-, and tissue-specific Lim3 expression. Therefore, we hypothesize that PcG/TrxG proteins, which are directly involved in Lim3 transcription regulation, participate in lifespan control.

Abstract A11: Gene expression analysis of Polycomb and Trithorax family members reveals putative role of ASXL2 in breast cancer subtypes

Abstract Breast cancer (BC) is one of the largest public health issues in Brazil and worldwide, and it is categorized based on the expression of membrane receptors for estrogen, progesterone, and HER2, giving rise, respectively, to the molecular subtypes Luminal A, Luminal B, HER2, and triple negative (TN). The etiology of BC is related to genetic, epigenetic, and environmental factors. In fact, the new scenario in cancer studies has moved beyond observing genetic changes. In this context, epigenetics arises as a complex factor since its mechanisms, “not involving alterations in DNA sequence,” elevate the complexity of the query object. Among the epigenetic mechanisms, the antagonic protein families Polycomb (Pc) and Trithorax (Trx) have an important role in controlling chromatin conformation and gene expression. These families comprise different members, and alterations in their expression may lead to gene deregulation, since various genes can be activated or inactivated at once. This study aims to evaluate the expression of the main members of both families (Pc and Trx) in in vitro models of the BC molecular subtypes, as well as in a normal breast cell line. In order to achieve this goal, the cell lines HMEC (normal breast), MCF-7 (Luminal A), EVSA-T (Luminal B), HCC-1954 (HER2), and MDA-MB-231 (triple negative) were cultured under specified conditions, and their RNAs were obtained for analysis by real-time quantitative PCR. A total of 18 genes were evaluated: Polycomb Group (PRC2 Complex: EZH1, EZH2, EED, and SIRT1; PRC1 Complex: RING1, PHC3, BMI1, and YY1), Trithorax Group (SWI/SNF Complex: SMARCA2 and SMARCA4; NURF Complex: SMARCA1 and RBBP4; MLL Complex: KMT2A, WDR5, ASH2L, and PRMT6), and the genes ASXL1 and ASXL2 (not categorized into Pc or Trx). The GAPDH gene was used as constitutive control, and gene expression obtained in HMEC was applied in experiment normalization. On a first analysis, the evaluated genes were found overexpressed in the BC cell lines altogether compared to normal breast, suggesting that there is a deregulation in histone modifiers and/or chromatin remodelers in this disease. In relation to the cell lines, MCF-7, EVSA-T, and MDA-MB-231 presented overexpression of Pc and Trx genes in comparison to HMEC. We highlight some genes that were found overexpressed, such as PRMT6 and SMARCA4 (MCF7); EZH1, EZH2, SIRT1, and RBBP4 (EVSA-T), the latter being described as a participant in NURF, but with an expression correlated to the members of PRC2. In the HER2 in vitro model, we observed a heterogenous Pc and Trx expression, which presented itself as reduced, unaltered, or upregulated in a minor level. Furthermore, in the TN model, the genes SMARCA1 and ASXL2 presented a fold change of more than 20x. The ASXL2 gene has been described, in embryonic development, as a potential regulator and/or enhancer for Pc and Trx, a role still not investigated in BC. It has been suggested that the ASXL family can act in activation and repression of Pc and Trx activity, as well as in the transcriptional regulation of Pc and Trx genes and recruitment of Pc and Trx proteins to their targets in chromatin. In silico analysis showed that ASXL2 can interact with members from both families, ratifying its potential role in BC. Our results show that further studies should be undertaken in order to determine the relation between the expression of these genes and their function. Moreover, we observed that there is no antagonism in the expression of Pc and Trx in BC, suggesting that it is possible that both families are acting in the disease, which implies that an investigation of the regulation and location of these complexes in chromatin will allow a better comprehension of its operation and function in BC. Citation Format: Mariana Araujo, Eliana Abdelhay, Stephany Corrêa. Gene expression analysis of Polycomb and Trithorax family members reveals putative role of ASXL2 in breast cancer subtypes [abstract]. In: Proceedings of the AACR International Conference held in cooperation with the Latin American Cooperative Oncology Group (LACOG) on Translational Cancer Medicine; May 4-6, 2017; São Paulo, Brazil. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(1_Suppl):Abstract nr A11.

ARS2 is a general suppressor of pervasive transcription.

Termination of transcription is important for establishing gene punctuation marks. It is also critical for suppressing many of the pervasive transcription events occurring throughout eukaryotic genomes and coupling their RNA products to efficient decay. In human cells, the ARS2 protein has been implicated in such function as its depletion causes transcriptional read-through of selected gene terminators and because it physically interacts with the ribonucleolytic nuclear RNA exosome. Here, we study the role of ARS2 on transcription and RNA metabolism genome wide. We show that ARS2 depletion negatively impacts levels of promoter-proximal RNA polymerase II at protein-coding (pc) genes. Moreover, our results reveal a general role of ARS2 in transcription termination-coupled RNA turnover at short transcription units like snRNA-, replication-dependent histone-, promoter upstream transcript- and enhancer RNA-loci. Depletion of the ARS2 interaction partner ZC3H18 mimics the ARS2 depletion, although to a milder extent, whereas depletion of the exosome core subunit RRP40 only impacts RNA abundance post-transcriptionally. Interestingly, ARS2 is also involved in transcription termination events within first introns of pc genes. Our work therefore establishes ARS2 as a general suppressor of pervasive transcription with the potential to regulate pc gene expression.

Cold-night responses in grapevine inflorescences

Cold nights impact grapevine flower development and fruit set. Regulation at the female meiosis stepmay be of considerable importance for further understanding on how flower reacts to cold stress. In this study, the impact of chilling temperature (0°C overnight) on carbon metabolism was investigated in the inflorescencesof two cultivars, Pinot noir (Pinot) and Gewurztraminer (Gewurtz.). Fluctuations in photosynthetic activity and carbohydrate metabolism were monitored by analyzing gas exchanges, simultaneous photosystem I and II activities, andcarbohydrate content. Further, the expression of PEPc, PC, FNR, ISO, OXO, AGPase, amylases and invertase genes, activities of various enzymes, as well as metabolomic analysis were attained. Results showed that the chilling night has different impacts depending on cultivars. Thus, in Gewurtz., net photosynthesis (Pn) was transiently increased whereas, in Pinot, the Pn increase was persistent and concomitant with an inhibition of respiration. However, during the days following the cold night, photosynthetic activity was decreased, and the cyclic electron flow was inhibited in Gewurtz., suggesting lower efficient energy dissipation. Likewise, metabolomic analysis revealed that several metabolites contents (namely alanine, GABA, lysine and succinate)were distinctly modulated in the two cultivars. Taking together, these results reflect a photosynthetic metabolism alteration or internal CO2 conductance in Gewurtz. explaining partly why Pinot is less susceptible to cold stress.