YTH Domain: A Family of N6-methyladenosine (m6A) Readers

Like protein and DNA, different types of RNA molecules undergo various modifications. Accumulating evidence suggests that these RNA modifications serve as sophisticated codes to mediate RNA behaviors and many important biological functions. N⁶-methyladenosine (m⁶A) is the most abundant internal RNA modification found in a variety of eukaryotic RNAs, including but not limited to mRNAs, tRNAs, rRNAs, and long non-coding RNAs (lncRNAs). In mammalian cells, m⁶A can be incorporated by a methyltransferase complex and removed by demethylases, which ensures that the m⁶A modification is reversible and dynamic. Moreover, m⁶A is recognized by the YT521-B homology (YTH) domain-containing proteins, which subsequently direct different complexes to regulate RNA signaling pathways, such as RNA metabolism, RNA splicing, RNA folding, and protein translation. Herein, we summarize the recent progresses made in understanding the molecular mechanisms underlying the m⁶A recognition by YTH domain-containing proteins, which would shed new light on m⁶A-specific recognition and provide clues to the future identification of reader proteins of many other RNA modifications.     

Single‐Crystalline Ultrathin Co3O4 Nanosheets with Massive Vacancy Defects for Enhanced Electrocatalysis

The role of vacancy defects is demonstrated to be positive in various energy‐related processes. However, introducing vacancy defects into single‐crystalline nanostructures with given facets and studying their defect effect on electrocatalytic properties remains a great challenge. Here this study deliberately introduces oxygen defects into single‐crystalline ultrathin Co₃O₄ nanosheets with O‐terminated {111} facets by mild solvothermal reduction using ethylene glycol under alkaline condition. As‐prepared defect‐rich Co₃O₄ nanosheets show a low overpotential of 220 mV with a small Tafel slope of 49.1 mV dec^?1 for the oxygen evolution reaction (OER), which is among the best Co‐based OER catalysts to date and even more active than the state‐of‐the‐art IrO₂ catalyst. Such vacancy defects are formed by balancing with reducing environments under solvothermal conditions, but are surprisingly stable even after 1000 cycles of scanning under OER working conditions. Density functional theory plus U calculation attributes the enhanced performance to the oxygen vacancies and consequently exposed second‐layered Co metal sites, which leads to the lowered OER activation energy of 2.26 eV and improved electrical conductivity. This mild solvothermal reduction concept opens a new door for the understanding and future designing of advanced defect‐based electrocatalysts.     

Rapid improvement of rice eating and cooking quality through gene editing toward glutelin as target

Rice eating and cooking quality(ECQ) is a major concern of breeders and consumers, determining market competitiveness worldwide. Rice grain protein content(GPC) is negatively related to ECQ,making it possible to improve ECQ by manipulating GPC. However, GPC is genetically complex and sensitive to environmental conditions; therefore, little progress has been made in traditional breeding for ECQ. Here, we report that CRISPR/Cas9-mediated knockout of genes encoding the grain storage protein gluteli...     

细胞分裂素生物合成基因在调节一组烟草病理相关蛋白基因表达中的作用

对一组病理相关蛋白基因在烟草 ( N icotiana tabacum cv. Wisconsin 38)中的表达情况进行了研究 ,包括 :碱性几丁质酶、β- 1 ,3-葡萄糖苷酶、渗透蛋白及伸展蛋白。RNA杂交实验表明在正常烟草植株中上述 4个基因具有发育和器官专一性的表达。在含有细胞分裂素生物合成基因的转基因烟草丛生芽中 ,这 4个基因的表达受过量合成的内源细胞分裂素和载体效应的共同调节 ,细胞分裂素降低这些基因的表达 ,而载体效应则促进它们的表达。热激处理也明显降低这 4种基因的表达水平。上述结果表明这些病理相关蛋白基因具有复杂的调控系统     

Stimulation of Na+-K+-2Cl- cotransporter in neuronal cells by excitatory neurotransmitter glutamate

Na⁺-K⁺-2Clcotransporters are important in renal salt reabsorption and in saltsecretion by epithelia. They are also essential in maintenance andregulation of ion gradients and cell volume in both epithelial andnonepithelial cells. Expression ofNa⁺-K⁺-2Clcotransporters in brain tissues is high; however, little is known abouttheir function and regulation in neurons. In this study, we examinedregulation of theNa⁺-K⁺-2Clcotransporter by the excitatory neurotransmitter glutamate. The cotransporter activity in human neuroblastoma SH-SY5Y cells was assessed by bumetanide-sensitiveK⁺ influx, and protein expressionwas evaluated by Western blot analysis. Glutamate was found to induce adose- and time-dependent stimulation ofNa⁺-K⁺-2Clcotransporter activity in SH-SY5Y cells. Moreover, both the glutamate ionotropic receptor agonistN-methyl-D-asparticacid (NMDA) and the metabotropic receptor agonist(±)-1-aminocyclopentane-trans-1,3-dicarboxylic acid (trans-ACPD) significantlystimulated the cotransport activity in these cells.NMDA-mediated stimulation of theNa⁺-K⁺-2Clcotransporter was abolished by the selective NMDA-receptor antagonist (+)-MK-801 hydrogen maleate.trans-ACPD-mediated effect on the cotransporter was blocked by the metabotropic receptor antagonist (+)--methyl-(4-carboxyphenyl)glycine. The results demonstrate thatNa⁺-K⁺-2Clcotransporters in neurons are regulated by activation of both ionotropic and metabotropic glutamate receptors.

     

Genetic diversity in three colonizing orchids with contrasting mating systems

Comparative studies on the genetic attributes of colonizing orchids with diverse mating systems are lacking in the literature. Eulophia sinensis, Spiranthes hongkongensis, and Zeuxine strateumatica are colonizing orchids that frequently occupy newly created habitats in Hong Kong. Mating system studies showed that E. sinensis is a self-compatible but pollinator-dependent outcrossing species, S. hongkongensis is a self-pollinating taxon, and Z srateumatica is apomictic. Population genetic attributes of these orchid species were investigated. Despite their contrasting mating systems, electrophoretic surveys revealed a striking lack of allozyme variation, both within and among populations, in all three species. However, gene duplications were evident in these species, due to their likely polyploid origins, The percentage of duplicate loci exhibiting "fixed heterozygosity" was 10, 21.4, and 20% in E. sinensis, S. hongkongensis, and Z. strateumatica, respectively. The genetic attributes of these orchids are compared to those found in other colonizing plant species.     

Association analysis for udder health based on SNP-panel and sequence data in Danish Holsteins

Background

The sensitivity of genome-wide association studies for the detection of quantitative trait loci (QTL) depends on the density of markers examined and the statistical models used. This study compares the performance of three marker densities to refine six previously detected QTL regions for mastitis traits: 54 k markers of a medium-density SNP (single nucleotide polymorphism) chip (MD), imputed 777 k markers of a high-density SNP chip (HD), and imputed whole-genome sequencing data (SEQ). Each dataset contained data for 4496 Danish Holstein cattle. Comparisons were performed using a linear mixed model (LM) and a Bayesian variable selection model (BVS).

Results

After quality control, 587, 7825, and 78 856 SNPs in the six targeted regions remained for MD, HD, and SEQ data, respectively. In general, the association patterns between SNPs and traits were similar for the three marker densities when tested using the same statistical model. With the LM model, 120 (MD), 967 (HD), and 7209 (SEQ) SNPs were significantly associated with mastitis, whereas with the BVS model, 43 (MD), 131 (HD), and 1052 (SEQ) significant SNPs (Bayes factor > 3.2) were observed. A total of 26 (MD), 75 (HD), and 465 (SEQ) significant SNPs were identified by both models. In addition, one, 16, and 33 QTL peaks for MD, HD, and SEQ data were detected according to the QTL intensity profile of SNP bins by post-analysis of the BVS model.

Conclusions

The power to detect significant associations increased with increasing marker density. The BVS model resulted in clearer boundaries between linked QTL than the LM model. Using SEQ data, the six targeted regions were refined to 33 candidate QTL regions for udder health. The comparison between these candidate QTL regions and known genes suggested that NPFFR2, SLC4A4, DCK, LIFR, and EDN3 may be considered as candidate genes for mastitis susceptibility.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-015-0129-1) contains supplementary material, which is available to authorized users.