RNA m6A modification facilitates DNA methylation during maize kernel development.

N6-methyladenosine (m6A) in mRNA and 5-methylcytosine (5mC) in DNA have critical functions for regulating gene expression and modulating plant growth and development. However, the interplay between m6A and 5mC is an elusive territory and remains unclear mechanistically in plants. We reported an occurrence of crosstalk between m6A and 5mC in maize (Zea mays) via the interaction between mRNA adenosine methylase (ZmMTA), the core component of the m6A methyltransferase complex, and decrease in DNA methylation 1 (ZmDDM1), a key chromatin-remodeling factor that regulates DNA methylation. Genes with m6A modification were coordinated with a much higher level of DNA methylation than genes without m6A modification. Dysfunction of ZmMTA caused severe arrest during maize embryogenesis and endosperm development, leading to a significant decrease in CHH methylation in the 5' region of m6A-modified genes. Instead, loss of function of ZmDDM1 had no noteworthy effects on ZmMTA-related activity. This study establishes a direct link between m6A and 5mC during maize kernel development and provides insights into the interplay between RNA modification and DNA methylation.

ZmRPN1 confers quantitative variation in pollen number and boosts hybrid seed production in maize.

The number of pollen grains is a critical determinant of reproductive success in seed plants and varies among species and individuals. However, in contrast with many mutant-screening studies relevant to anther and pollen development, the natural genetic basis for variations in pollen number remains largely unexplored. To address this issue, we carried out a genome-wide association study in maize, ultimately revealing that a large presence/absence variation in the promoter region of ZmRPN1 alters its expression level and thereby contributes to pollen number variation. Molecular analyses showed that ZmRPN1 interacts with ZmMSP1, which is known as a germline cell number regulator, and facilitates ZmMSP1 localization to the plasma membrane. Importantly, ZmRPN1 dysfunction resulted in a substantial increase in pollen number, consequently boosting seed production by increasing female-male planting ratio. Together, our findings uncover a key gene controlling pollen number, and therefore, modulation of ZmRPN1 expression could be efficiently used to develop elite pollinators for modern hybrid maize breeding.

ZmCCT10-relayed photoperiod sensitivity regulates natural variation in the arithmetical formation of male germinal cells in maize.

Extensive mutational screening studies have documented genes regulating anther and pollen development. Knowledge concerning how formation of male germinal cell is arithmetically controlled in natural populations, under different environmental conditions, is lacking. We counted pollen number within a single anther and a maize-teosinte BC2 S3 recombinant inbred line population to identify ZmCCT10 as a major determinant of pollen number variation. ZmCCT10 was originally identified as a photoperiod-sensitive negative regulator of flowering. ZmCCT10 inactivation, after transposon insertion within its promoter, is proposed to have accelerated maize spread toward higher latitudes, thus allowing temperate maize to flower under long-day conditions. We showed that the active ZmCCT10 allele decreased pollen formation. As different active and inactive ZmCCT10 alleles have been found in natural maize populations, this represents the first report of a gene controlling pollen number in a crop natural population. These findings suggest that higher pollen number, which provides a competitive advantage in open-pollinated populations, may have been one of the major driving forces for the selection of an inactive ZmCCT10 allele during tropical maize domestication. We provide evidence that ZmCCT10 has opposite effects on cell proliferation of archesporial and tapetum cells and it modulates expression of key regulators during early anther development.

Genome-wide association study reveals the genetic architecture of root hair length in maize.

BACKGROUND: Root hair, a special type of tubular-shaped cell, outgrows from root epidermal cell and plays important roles in the acquisition of nutrients and water, as well as interactions with biotic and abiotic stress. Although many genes involved in root hair development have been identified, genetic basis of natural variation in root hair growth has never been explored. RESULTS: Here, we utilized a maize association panel including 281 inbred lines with tropical, subtropical, and temperate origins to decipher the phenotypic diversity and genetic basis of root hair length. We demonstrated significant associations of root hair length with many metabolic pathways and other agronomic traits. Combining root hair phenotypes with 1.25 million single nucleotide polymorphisms (SNPs) via genome-wide association study (GWAS) revealed several candidate genes implicated in cellular signaling, polar growth, disease resistance and various metabolic pathways. CONCLUSIONS: These results illustrate the genetic basis of root hair length in maize, offering a list of candidate genes predictably contributing to root hair growth, which are invaluable resource for the future functional investigation.

Transcriptome-wide analysis of epitranscriptome and translational efficiency associated with heterosis in maize.

Heterosis has been extensively utilized to increase productivity in crops, yet the underlying molecular mechanisms remain largely elusive. Here, we generated transcriptome-wide profiles of mRNA abundance, m6A methylation, and translational efficiency from the maize F1 hybrid B73×Mo17 and its two parental lines to ascertain the contribution of each regulatory layer to heterosis at the seedling stage. We documented that although the global abundance and distribution of m6A remained unchanged, a greater number of genes had gained an m6A modification in the hybrid. Superior variations were observed at the m6A modification and translational efficiency levels when compared with mRNA abundance between the hybrid and parents. In the hybrid, the vast majority of genes with m6A modification exhibited a non-additive expression pattern, the percentage of which was much higher than that at levels of mRNA abundance and translational efficiency. Non-additive genes involved in different biological processes were hierarchically coordinated by discrete combinations of three regulatory layers. These findings suggest that transcriptional and post-transcriptional regulation of gene expression make distinct contributions to heterosis in hybrid maize. Overall, this integrated multi-omics analysis provides a valuable portfolio for interpreting transcriptional and post-transcriptional regulation of gene expression in hybrid maize, and paves the way for exploring molecular mechanisms underlying hybrid vigor.

Physiological Analysis and Transcriptome Analysis of Asian Honey Bee (Apis cerana cerana) in Response to Sublethal Neonicotinoid Imidacloprid.

Asian honey bee (Apis cerana) is the most important Chinese indigenous species, while its toxicological characteristic against neonicotinoids is poorly known. Here, we combined physiological experiments with a genome-wide transcriptome analysis to understand the molecular basis of genetic variation that responds to sublethal imidacloprid at different exposure durations in A. cerana. We found that LC5 dose of imidacloprid had a negative impact on climbing ability and sucrose responsiveness in A. cerana. When bees were fed with LC5 dose of imidacloprid, the enzyme activities of P450 and CarE were decreased, while the GSTs activity was not influenced by the pesticide exposure. The dynamic transcriptomic profiles of A. cerana workers exposed to LC5 dose of imidacloprid for 1 h, 8 h, and 16 h were obtained by high-throughput RNA-sequencing. We performed the expression patterns of differentially expressed genes (DEGs) through trend analysis, and conducted the gene ontology analysis and KEGG pathway enrichment analysis with DEGs in up- and down-regulated pattern profiles. We observed that more genes involved in metabolism, catalytic activity, and structural molecule activity are down-regulated; while more up-regulated genes were enriched in terms associated with response to stimulus, transporter activity, and signal transducer activity. Additionally, genes related to the phenylalanine metabolism pathway, FoxO signaling pathway, and mTOR signaling pathway as indicated in the KEGG analysis were significantly up-related in the exposed bees. Our findings provide a comprehensive understanding of Asian honey bee in response to neonicotinoids sublethal toxicity, and could be used to further investigate the complex molecular mechanisms in Asian honey bee under pesticide stress.

Natural Variation in RNA m6A Methylation and Its Relationship with Translational Status.

N 6 -methyladenosine (m6A) is the most abundant modification of eukaryotic mRNA. Although m6A has been demonstrated to affect almost all aspects of RNA metabolism, its global contribution to the post-transcriptional balancing of translational efficiency remains elusive in plants. In this study, we performed a parallel analysis of the transcriptome-wide mRNA m6A distribution and polysome profiling in two maize (Zea mays) inbred lines to assess the global correlation of m6A modification with translational status. m6A sites are widely distributed in thousands of protein-coding genes, confined to a consensus motif and primarily enriched in the 3' untranslated regions, and highly coordinated with alternative polyadenylation usage, suggesting a role of m6A modification in regulating alternative polyadenylation site choice. More importantly, we identified that the m6A modification shows multifaceted correlations with the translational status depending on its strength and genic location. Moreover, we observed a substantial intraspecies variation in m6A modification, and this natural variation was shown to be partly driven by gene-specific expression and alternative splicing. Together, these findings provide an invaluable resource for ascertaining transcripts that are subject to m6A modification in maize and pave the way to a better understanding of natural m6A variation in mediating gene expression regulation.

SNHG22 overexpression indicates poor prognosis and induces chemotherapy resistance via the miR-2467/Gal-1 signaling pathway in epithelial ovarian carcinoma.

Recently, an increasing number of studies have reported that dysregulation of long noncoding RNAs (lncRNAs) plays an important role in cancer initiation and progression, including in epithelial ovarian carcinoma (EOC). However, little is known about the detailed biological functions of the lncRNA small nucleolar RNA host gene 22 (SNHG22) during the progression of EOC. Here, we found that SNHG22 was significantly increased in EOC tissues and was significantly associated with a low level of differentiation. Forced SNHG22 expression promoted chemotherapy resistance in EOC cells. Knockdown of SNHG22 expression increased the sensitivity of EOC cells to cisplatin and paclitaxel. Importantly, we found that SNHG22 could directly interact with miR-2467 and lead to the release of miR-2467-targeted Gal-1 mRNA. Moreover, SNHG22 overexpression induced EOC cell resistance to chemotherapy agents via PI3K/AKT and ERK cascade activation. In summary, our findings demonstrate that SNHG22 plays a critical role in the chemotherapy resistance of EOC by mediating the miR-2467/Gal-1 regulatory axis.

Characterization of LRL5 as a key regulator of root hair growth in maize.

Root hair, a special type of tubular-shaped cell, outgrows from the root epidermal cell and plays important roles in the acquisition of nutrients and water, as well as interactions with biotic and abiotic stresses. Studies in the model plant Arabidopsis have revealed that root-hair initiation and elongation are hierarchically regulated by a group of basic helix-loop-helix (bHLH) transcription factors (TFs). However, knowledge regarding the regulatory pathways of these bHLH TFs in controlling root hair growth remains limited. In this study, RNA-seq analysis was conducted to profile the transcriptome in the elongating maize root hair and >1000 genes with preferential expression in root hair were identified. A consensus cis-element previously featured as the potential bHLH-TF binding sites was present in the regulatory regions for the majority of the root hair-preferentially expressed genes. In addition, an individual change in ZmLRL5, the highest-expressed bHLH-TF in maize root hair resulted in a dramatic reduction in the elongation of root hair, and rendered the growth of root hair hypersensitive to translational inhibition. Moreover, RNA-seq, yeast-one-hybrid and ribosome profile analysis suggested that ZmLRL5 may function as a key player in orchestrating the translational process by directly regulating the expression of translational processes/ribosomal genes during maize root hair growth.

ATX3, ATX4, and ATX5 Encode Putative H3K4 Methyltransferases and Are Critical for Plant Development.

Methylation of Lys residues in the tail of the H3 histone is a key regulator of chromatin state and gene expression, conferred by a large family of enzymes containing an evolutionarily conserved SET domain. One of the main types of SET domain proteins are those controlling H3K4 di- and trimethylation. The genome of Arabidopsis (Arabidopsis thaliana) encodes 12 such proteins, including five ARABIDOPSIS TRITHORAX (ATX) proteins and seven ATX-Related proteins. Here, we examined three until-now-unexplored ATX proteins, ATX3, ATX4, and ATX5. We found that they exhibit similar domain structures and expression patterns and are redundantly required for vegetative and reproductive development. Concurrent disruption of the ATX3, ATX4, and ATX5 genes caused marked reduction in H3K4me2 and H3K4me3 levels genome-wide and resulted in thousands of genes expressed ectopically. Furthermore, atx3/atx4/atx5 triple mutants resulted in exaggerated phenotypes when combined with the atx2 mutant but not with atx1 Together, we conclude that ATX3, ATX4, and ATX5 are redundantly required for H3K4 di- and trimethylation at thousands of sites located across the genome, and genomic features associated with targeted regions are different from the ATXR3/SDG2-controlled sites in Arabidopsis.

[Preliminary investigation on emission of PCDD/Fs and DL-PCBs through flue gas from coke plants in China].

According to the Stockholm Convention, polychlorinated dibenzo-p-dioxins/dibenzofurans (PCDD/Fs) and dioxin-like polychlorinated biphenyls (DL-PCBs) are classified into unintentionally produced persistent organic pollutants (UP-POPs), and named dioxins. Coke production as a thermal process contains organic matters, metal and chlorine, is considered to be a potential source of dioxins. Intensive studies on the emission of dioxins from coking industry are still very scarce. In order to estimate the emission properties of dioxins through coke production, isotope dilution HRGC/HRMS technique was used to determine the concentration of dioxins through flue gas during heating of coal. Three results were obtained. First, total toxic equivalents at each stationary emission source were in the range of 3.9-30.0 pg x m(-3) (at WHO-TEQ) for dioxins which was lower than other thermal processes such as municipal solid waste incineration. Second, higher chlorinated PCDD/Fs were the dominant congeners. Third, emissions of dioxins were dependent on coking pattern. Stamping coking and higher coking chamber may lead to lower emission.

Correlation between periostin and SNCG and esophageal cancer invasion, infiltration and apoptosis.

OBJECTIVE: To investigate the correlation between periostin and SNCG and esophageal cancer invasion, infiltration and apoptosis. METHODS: A total of 78 cases esophageal surgical resection specimens were collected, expression of periostin and SNCG in esophageal cancer were detected. Effect of periostin and SNCG in esophageal carcinoma invasion and infiltration was analyzed. RESULTS: The upregulated rate of periostin had significant difference in esophageal cancer tissues (39.74%), adjacent tissues (17.86%) and normal tissues (0.00%); The positive expression rates of SNCG had significant difference in esophageal cancer tissues (61.54%), adjacent tissues (32.14%) and normal tissues (1.96%); The upregulated rate of periostin had a significant correlation with lymph node metastasis, adventitia invasion, TNM stage; The positive expression rates of SNCG had a significant correlation with differentiation degree, lymph node metastasis, adventitia invasion, TNM stage; Apoptosis index of the positive of expression of SNCG of esophageal cancer tissue (4.541±2.267) was significantly lower than that of the negative expression (7.316±2.582) (P<0.05). CONCLUSIONS: SNCG may play an important role in invasion, infiltration and apoptosis of esophageal cancer and serve as target spots in the targeted therapy of esophageal cancer.

[Safety concentration of genotoxic carcinogens in water pollution accident based on human health risk].

It was an urgent problem to determine short-term exposure safety concentration of genetic carcinogens in water pollution accident in China. Based on the hypothesis that the relationship between exposure dosage and carcinogenic risk was linear, the calculation process of genetic carcinogens safety concentration was put forwarded, and the method using life-time exposed safety concentration to calculate short-term exposure safety concentration was set up. Based on the statistical result of water pollution accident occurred in china during 2000-2010, arsenic was a major characteristic contaminate in water pollution accident. According to the method of short-term exposure safety concentration of genotoxic carcinogens, the safety concentration of arsenic was 0.5 mg x L(-1), it showed that the method was feasible in emergence management of water pollution accident.

[Safety value of contaminant in water pollution accident based on human health risk].

The acute human health risk assessment of contaminant in water pollution accident is a new study field of environmental sciences. This study established a model for calculating acute safety value of contaminant in water pollutant. The acute safety value of contaminant in mainly water pollution during 2000-2010 was calculated by this model. The safety value of sodium cyanide, cadmium, formaldehyde, ammonia, toluene, nitrobenzene, microcystin-LR were 0.1, 0.6, 8, 20, 6, 0.07, 0.004 mg x L(-1), respectively. The differences of safety value calculate methods between acute and chronic exposure were compared from the following aspects, the toxicology exposure end-point, allocation of intake, exposure sensitive subpopulation.