An RRM domain protein SOE suppresses transgene silencing in rice.

Gene expression is regulated at multiple levels, including RNA processing and DNA methylation/demethylation. How these regulations are controlled remains unclear. Here, through analysis of a suppressor for the OsEIN2 over-expressor, we identified an RNA recognition motif protein SUPPRESSOR OF EIN2 (SOE). SOE is localized in nuclear speckles and interacts with several components of the spliceosome. We find SOE associates with hundreds of targets and directly binds to a DNA glycosylase gene DNG701 pre-mRNA for efficient splicing and stabilization, allowing for subsequent DNG701-mediated DNA demethylation of the transgene promoter for proper gene expression. The V81M substitution in the suppressor mutant protein mSOE impaired its protein stability and binding activity to DNG701 pre-mRNA, leading to transgene silencing. SOE mutation enhances grain size and yield. Haplotype analysis in c. 3000 rice accessions reveals that the haplotype 1 (Hap 1) promoter is associated with high 1000-grain weight, and most of the japonica accessions, but not indica ones, have the Hap 1 elite allele. Our study discovers a novel mechanism for the regulation of gene expression and provides an elite allele for the promotion of yield potentials in rice.

Therapeutic effects and mechanisms of isoxanthohumol on DSS-induced colitis: regulating T cell development, restoring gut microbiota, and improving metabolic disorders.

Ulcerative colitis (UC) is a severe hazard to human health. Since pathogenesis of UC is still unclear, current therapy for UC treatment is far from optimal. Isoxanthohumol (IXN), a prenylflavonoid from hops and beer, possesses anti-microbial, anti-oxidant, anti-inflammatory, and anti-angiogenic properties. However, the potential effects of IXN on the alleviation of colitis and the action of the mechanism is rarely studied. Here, we found that administration of IXN (60 mg/kg/day, gavage) significantly attenuated dextran sodium sulfate (DSS)-induced colitis, evidenced by reduced DAI scores and histological improvements, as well as suppressed the pro-inflammatory Th17/Th1 cells but promoted the anti-inflammatory Treg cells. Mechanically, oral IXN regulated T cell development, including inhibiting CD4+ T cell proliferation, promoting apoptosis, and regulating Treg/Th17 balance. Furthermore, IXN relieved colitis by restoring gut microbiota disorder and increasing gut microbiota diversity, which was manifested by maintaining the ratio of Firmicutes/Bacteroidetes balance, promoting abundance of Bacteroidetes and Ruminococcus, and suppressing abundance of proteobacteria. At the same time, the untargeted metabolic analysis of serum samples showed that IXN promoted the upregulation of D-( +)-mannose and L-threonine and regulated pyruvate metabolic pathway. Collectively, our findings revealed that IXN could be applied as a functional food component and served as a therapeutic agent for the treatment of UC.

Selection for a Zinc-Finger Protein Contributes to Seed Oil Increase during Soybean Domestication.

Seed oil is a momentous agronomical trait of soybean (Glycine max) targeted by domestication in breeding. Although multiple oil-related genes have been uncovered, knowledge of the regulatory mechanism of seed oil biosynthesis is currently limited. We demonstrate that the seed-preferred gene GmZF351, encoding a tandem CCCH zinc finger protein, is selected during domestication. Further analysis shows that GmZF351 facilitates oil accumulation by directly activating WRINKLED1, BIOTIN CARBOXYL CARRIER PROTEIN2, 3-KETOACYL-ACYL CARRIER PROTEIN SYNTHASE III, DIACYLGLYCEROL O-ACYLTRANSFERASE1, and OLEOSIN2 in transgenic Arabidopsis (Arabidopsis thaliana) seeds. Overexpression of GmZF351 in transgenic soybean also activates lipid biosynthesis genes, thereby accelerating seed oil accumulation. The ZF351 haplotype from the cultivated soybean group and the wild soybean (Glycine soja) subgroup III correlates well with high gene expression level, seed oil contents and promoter activity, suggesting that selection of GmZF351 expression leads to increased seed oil content in cultivated soybean. Our study provides novel insights into the regulatory mechanism for seed oil accumulation, and the manipulation of GmZF351 may have great potential in the improvement of oil production in soybean and other related crops.

Soybean GmMYB73 promotes lipid accumulation in transgenic plants.

BACKGROUND: Soybean is one of the most important oil crops. The regulatory genes involved in oil accumulation are largely unclear. We initiated studies to identify genes that regulate this process. RESULTS: One MYB-type gene GmMYB73 was found to display differential expression in soybean seeds of different developing stages by microarray analysis and was further investigated for its functions in lipid accumulation. GmMYB73 is a small protein with single MYB repeat and has similarity to CPC-like MYB proteins from Arabidopsis. GmMYB73 interacted with GL3 and EGL3, and then suppressed GL2, a negative regulator of oil accumulation. GmMYB73 overexpression enhanced lipid contents in both seeds and leaves of transgenic Arabidopsis plants. Seed length and thousand-seed weight were also promoted. GmMYB73 introduction into the Arabidopsis try cpc double mutant rescued the total lipids, seed size and thousand-seed weight. GmMYB73 also elevated lipid levels in seeds and leaves of transgenic Lotus, and in transgenic hairy roots of soybean plants. GmMYB73 promoted PLDα1 expression, whose promoter can be bound and inhibited by GL2. PLDα1 mutation reduced triacylglycerol levels mildly in seeds but significantly in leaves of Arabidopsis plants. CONCLUSIONS: GmMYB73 may reduce GL2, and then release GL2-inhibited PLDα1 expression for lipid accumulation. Manipulation of GmMYB73 may potentially improve oil production in legume crop plants.

The transcription factor AtDOF4.2 regulates shoot branching and seed coat formation in Arabidopsis.

Plant-specific DOF (DNA-binding with one finger)-type transcription factors regulate various biological processes. In the present study we characterized a silique-abundant gene AtDOF (Arabidopsis thaliana DOF) 4.2 for its functions in Arabidopsis. AtDOF4.2 is localized in the nuclear region and has transcriptional activation activity in both yeast and plant protoplast assays. The T-M-D motif in AtDOF4.2 is essential for its activation. AtDOF4.2-overexpressing plants exhibit an increased branching phenotype and mutation of the T-M-D motif in AtDOF4.2 significantly reduces branching in transgenic plants. AtDOF4.2 may achieve this function through the up-regulation of three branching-related genes, AtSTM (A. thaliana SHOOT MERISTEMLESS), AtTFL1 (A. thaliana TERMINAL FLOWER1) and AtCYP83B1 (A. thaliana CYTOCHROME P450 83B1). The seeds of an AtDOF4.2-overexpressing plant show a collapse-like morphology in the epidermal cells of the seed coat. The mucilage contents and the concentration and composition of mucilage monosaccharides are significantly changed in the seed coat of transgenic plants. AtDOF4.2 may exert its effects on the seed epidermis through the direct binding and activation of the cell wall loosening-related gene AtEXPA9 (A. thaliana EXPANSIN-A9). The dof4.2 mutant did not exhibit changes in branching or its seed coat; however, the silique length and seed yield were increased. AtDOF4.4, which is a close homologue of AtDOF4.2, also promotes shoot branching and affects silique size and seed yield. Manipulation of these genes should have a practical use in the improvement of agronomic traits in important crops.

Effectiveness of tranexamic acid in reducing blood loss in spinal surgery: a meta-analysis.

BACKGROUND: The aim of present meta-analysis was to evaluate the effectiveness of tranexamic acid (TXA) use in reducing blood loss and the related thrombotic complications in spinal surgery. METHODS: Three databases (MEDLINE, EMBASE, and the Cochrane Library) were searched through October 2012 to identify the relevant randomized controlled trials (RCTs) regarding the TXA effective in spinal surgery. Mean differences (MDs) of blood loss, blood transfusions, and postoperative partial thromboplastic time (PTT), odds ratios (ORs) of blood transfusion and thrombotic complication in TXA-treated group compared to placebo group were extracted and combined using random-effect meta-analysis. RESULTS: A total of 6 RCTs comprising 411 patients were included in the meta-analysis according to the pre-defined selection criteria. TXA-treated group had significantly less amount of blood loss and blood transfusions per patient, and had smaller proportion of patients who required a blood transfusion compared with the placebo group. The use of TXA can significantly reduce the postoperative PTT with weighted MD of -1.59 [(95% confidence interval (CI):-3.07, -0.10] There is a null association between thrombosis complications and the use of TXA. CONCLUSION: We conclude that the use of TXA in patients undergoing spinal surgery appears to be effective in reducing the amount of blood loss, the volume of blood transfusion, the transfusion rate, and the postoperative PTT. However, data were too limited for any conclusions regarding safety. More high-quality RCTs are required before recommending the administered of TXA in spinal surgery.

Soybean GmbZIP123 gene enhances lipid content in the seeds of transgenic Arabidopsis plants.

Soybean is one of most important oil crops and a significant increase in lipid content in soybean seeds would facilitate vegetable oil production in the world. Although the pathways for lipid biosynthesis in higher plants have been uncovered, our understanding of regulatory mechanism controlling lipid accumulation is still limited. In this study, we identified 87 transcription factor genes with a higher abundance at the stage of lipid accumulation in soybean seeds. One of these genes, GmbZIP123, was selected to further study its function in regulation of lipid accumulation. Overexpression of GmbZIP123 enhanced lipid content in the seeds of transgenic Arabidopsis thaliana plants. The GmbZIP123 transgene promoted expression of two sucrose transporter genes (SUC1 and SUC5) and three cell-wall invertase genes (cwINV1, cwINV3, and cwINV6) by binding directly to the promoters of these genes. Consistently, the cell-wall invertase activity and sugar translocation were all enhanced in siliques of GmbZIP123 transgenic plants. Higher levels of glucose, fructose, and sucrose were also found in seeds of GmbZIP123 transgenic plants. These results suggest that GmbZIP123 may participate in regulation of lipid accumulation in soybean seeds by controlling sugar transport into seeds from photoautotrophic tissues. This study provides novel insights into the regulatory mechanism for lipid accumulation in seeds and may facilitate improvements in oil production in soybean and other oil crops through genetic manipulation of the GmbZIP123 gene.

[A modified goat model of acute spinal cord compression injury from a percutaneous balloon catheter: method feasibility and preliminary observation].

OBJECTIVE: To establish a goat model of acute spinal cord compression injury through a modified percutaneous technique with a Foley double-lumen urine catheter and explore the method feasibility and preliminary observation. METHODS: Twelve adult male Chongming goats were randomly divided into 3 groups:control (A, n = 4), 0.5 ml compression (B, n = 4) and 1 ml compression (C, n = 4). After local anesthesia, all animals received epidural balloon catheter (5Fr) insertion via a percutaneous trans-lumbosacral interlaminar space technique that mimicked the method used in vascular access for angiography. The balloon catheter was advanced under fluoroscopic guidance until its distal tip reached the middle of T6 level.One week later, for groups B and C, the balloon was inflated by half-strength contrast material, 0.5 ml and 1 ml, respectively. The balloon was left inflated for 30 min and then deflated. The images of computed tomography (CT) and magnetic resonance (MR) were taken before and after surgical procedures.Quantitative assessment of spine canal occupying rate was accomplished by an off-line software program based on CT results. Motor function was assessed by the modified Tarlov scale. Two animals of each group were sacrificed after a total observation period of 48 h and 72 h respectively.Spinal cords from the injured level were then obtained for pathologic examinations. RESULTS: All animals underwent successful catheterization occupying 6.8%±0.7% (Group A), 6.7%±0.7% (Group B) and 6.6%±0.6% (Group C) of spine canal respectively. After inflation, the occupying rate of groups B and C achieved 43.4%±2.5% and 88.1%±2.3% respectively.Ventral compression of spinal cord was noted on MR images.Hindlimb movement remained normal after catheter insertion in all groups. All animals in group B and C became paraplegic after inflation. And a positive correlation existed between injection volume and Tarlov score. Pathological findings confirmed neuron atrophy, increased gap around neurons, mild demyelination and vacuolar degeneration both in groups B and C at 48 h after injury. Pathological changes deteriorated at 72 h after injury. CONCLUSION: The results of behavioral evaluation, radiographic images and pathological examination reveal an evidence of acute spinal cord injury. Percutaneous epidural balloon catheter insertion differs from previous techniques by avoiding surgical exposure and associated artifacts, yet it offers injury mechanisms similar to those of human spinal cord injury. As a new means of modeling spinal cord injury in animals, this technique has many potential applications.

Is Complete Correction of Cervical Sagittal Malalignment Necessary During 4-Level Anterior Cervical Discectomy and Fusion Surgery in Patients With Kyphosis?

STUDY DESIGN: Retrospective analysis. OBJECTIVE: We investigated whether complete correction of cervical sagittal malalignment is necessary during 4-level anterior cervical discectomy and fusion (ACDF) in patients with kyphosis. METHODS: This retrospective study included 84 patients who underwent 4-level ACDF surgery at a university hospital between January 2010 and December 2015. Based on the degree of cervical lordosis correction, patients were categorized into the following groups: mild (0-10°), moderate (10-20°), and complete correction (>20°). The clinical outcomes, radiological parameters, and functional outcomes were analyzed. RESULTS: We observed no significant intergroup differences in the baseline characteristics. The cervical sagittal vertical axis (CSVA) correction loss at the final follow-up was lesser in the mild- and moderate- than in the complete-correction group. The spinocranial angle (SCA) and T1 slope (T1 S) were significantly higher in the moderate- and complete-correction groups than in the mild-correction group, 3 days postoperatively. The cervical proximal junctional kyphosis (CPJK), adjacent segment degeneration (ASD), and ASD following CPJK rates were higher in the complete-correction group. We observed no significant intergroup differences in postoperative complications; however, 5 patients showed internal fixation failure in the complete-correction group; 4 of these patients required reoperation. No significant intergroup difference was observed in the Japanese Orthopedic Association and neck disability index scores at any time point. CONCLUSIONS: A mild-to-moderate correction of cervical lordosis is superior to complete correction in patients with kyphosis who undergo 4-level ACDF because this approach is associated with lesser axial stress and CSVA correction loss.

Hybrid fixation versus conventional cage-plate construct in 3-level ACDF: Introduce the "seesaw theory" of stand-alone cage.

STUDY DESIGN: A retrospective study. BACKGROUND: Conventional cage-plate construct (CCP) was widely used in anterior cervical discectomy and fusion (ACDF), but the rigid fixation limits the motion of fused segments. Self-locking stand-alone cage (SSC) was an alternative for ACDF procedures and showed several superiorities. However, the effect of hybrid fixation in 3-level ACDF remains unknown. OBJECTIVE: To assess the clinical and radiological outcomes of hybrid fixation with SSC and CCP against conventional CCP in 3-level ACDF. METHOD: A retrospective review of patients who underwent 3-level ACDF at Renji Hospital between January 2018 and December 2019 was performed. Eighty-three patients met the inclusion and exclusion criteria and were stratified into 2 groups based on the fixation methods. The clinical outcomes, functional outcomes, and radiological parameters were collected and analyzed. RESULTS: No significant difference was observed between the two groups in the mean age, sex, body mass index, hospital stay, and duration of follow-up. The postoperative C2-7 Cobb angle in the CCP group was significantly greater than that in the hybrid group. The rate of cervical proximal junctional kyphosis (CPJK) in the hybrid group was significantly lower than that in the CCP group. The CCP group suffered significantly higher rates of adjacent segment degeneration (ASD) than the hybrid group at 2 years postoperatively. Moreover, the incidence of postoperative dysphagia was lower in the hybrid group. No significant differences were observed in JOA and NDI scores between the two groups. CONCLUSION: The hybrid fixation achieved comparable clinical outcomes against CCP fixation, indicating that hybrid fixation is an alternative procedure in 3-level ACDF.

Soybean NAC transcription factors promote abiotic stress tolerance and lateral root formation in transgenic plants.

NAC transcription factors play important roles in plant growth, development and stress responses. Previously, we identified multiple NAC genes in soybean (Glycine max). Here, we identify the roles of two genes, GmNAC11 and GmNAC20, in stress responses and other processes. The two genes were differentially induced by multiple abiotic stresses and plant hormones, and their transcripts were abundant in roots and cotyledons. Both genes encoded proteins that localized to the nucleus and bound to the core DNA sequence CGT[G/A]. In the protoplast assay system, GmNAC11 acts as a transcriptional activator, whereas GmNAC20 functions as a mild repressor; however, the C-terminal end of GmANC20 has transcriptional activation activity. Over-expression of GmNAC20 enhances salt and freezing tolerance in transgenic Arabidopsis plants; however, GmNAC11 over-expression only improves salt tolerance. Over-expression of GmNAC20 also promotes lateral root formation. GmNAC20 may regulate stress tolerance through activation of the DREB/CBF-COR pathway, and may control lateral root development by altering auxin signaling-related genes. GmNAC11 probably regulates DREB1A and other stress-related genes. The roles of the two GmNAC genes in stress tolerance were further analyzed in soybean transgenic hairy roots. These results provide a basis for genetic manipulation to improve the agronomic traits of important crops.

Roles of the Neuron-Restrictive Silencer Factor in the Pathophysiological Process of the Central Nervous System.

The neuron-restrictive silencer factor (NRSF), also known as repressor element 1 (RE-1) silencing transcription factor (REST) or X2 box repressor (XBR), is a zinc finger transcription factor that is widely expressed in neuronal and non-neuronal cells. It is a master regulator of the nervous system, and the function of NRSF is the basis of neuronal differentiation, diversity, plasticity, and survival. NRSF can bind to the neuron-restrictive silencer element (NRSE), recruit some co-repressors, and then inhibit transcription of NRSE downstream genes through epigenetic mechanisms. In neurogenesis, NRSF functions not only as a transcriptional silencer that can mediate the transcriptional inhibition of neuron-specific genes in non-neuronal cells and thus give neuron cells specificity, but also as a transcriptional activator to induce neuronal differentiation. Many studies have confirmed the association between NRSF and brain disorders, such as brain injury and neurodegenerative diseases. Overexpression, underexpression, or mutation may lead to neurological disorders. In tumorigenesis, NRSF functions as an oncogene in neuronal tumors, such as neuroblastomas, medulloblastomas, and pheochromocytomas, stimulating their proliferation, which results in poor prognosis. Additionally, NRSF-mediated selective targets gene repression plays an important role in the development and maintenance of neuropathic pain caused by nerve injury, cancer, and diabetes. At present, several compounds that target NRSF or its co-repressors, such as REST-VP16 and X5050, have been shown to be clinically effective against many brain diseases, such as seizures, implying that NRSF and its co-repressors may be potential and promising therapeutic targets for neural disorders. In the present review, we introduced the biological characteristics of NRSF; reviewed the progress to date in understanding the roles of NRSF in the pathophysiological processes of the nervous system, such as neurogenesis, brain disorders, neural tumorigenesis, and neuropathic pain; and suggested new therapeutic approaches to such brain diseases.

Comparison of Accuracy and Clinical Outcomes of Robot-Assisted Versus Fluoroscopy-Guided Pedicle Screw Placement in Posterior Cervical Surgery.

STUDY DESIGN: This was a prospective controlled study. OBJECTIVE: To compare the accuracy and clinical outcomes of robot-assisted (RA) and fluoroscopy-guided (FG) pedicle screw placement in posterior cervical surgery. METHODS: This study included 58 patients. The primary outcome measures were the 1-time success rate and the accuracy of pedicle screw placement according to the Gertzbein-Robbins scales. The secondary outcome measures, including the operative time, intraoperative blood loss, hospital stay, cumulative radiation time, radiation dose, intraoperative advent events, and postoperative complications, were recorded and analyzed. The Japanese Orthopedics Association (JOA) scores and Neck Disability Index (NDI) were used to assess the neurological function of patients before and at 3 and 6 months after surgery. RESULTS: The rate of grade A was significantly higher in the RA group than in the FG group (90.6% and 71.1%; P < .001). The clinically acceptable accuracy was 97.2% in the RA group and 90.7% in the FG group (P = .009). Moreover, the 1-time success rate was significantly higher in the RA group than in the FG group. The RA group had less radiation time (P < .001) and less radiation dose (P = .002) but longer operative time (P = .001). There were no significant differences in terms of intraoperative blood loss, hospital stay, intraoperative adverse events, postoperative complications, JOA scores, and NDI scores at each follow-up time point between the 2 groups. CONCLUSIONS: The RA technique achieved higher accuracy and 1-time success rate of pedicle screw placement in posterior cervical surgery while achieving comparable clinical outcomes.

Identification of miRNAs and their target genes in developing soybean seeds by deep sequencing.

BACKGROUND: MicroRNAs (miRNAs) regulate gene expression by mediating gene silencing at transcriptional and post-transcriptional levels in higher plants. miRNAs and related target genes have been widely studied in model plants such as Arabidopsis and rice; however, the number of identified miRNAs in soybean (Glycine max) is limited, and global identification of the related miRNA targets has not been reported in previous research. RESULTS: In our study, a small RNA library and a degradome library were constructed from developing soybean seeds for deep sequencing. We identified 26 new miRNAs in soybean by bioinformatic analysis and further confirmed their expression by stem-loop RT-PCR. The miRNA star sequences of 38 known miRNAs and 8 new miRNAs were also discovered, providing additional evidence for the existence of miRNAs. Through degradome sequencing, 145 and 25 genes were identified as targets of annotated miRNAs and new miRNAs, respectively. GO analysis indicated that many of the identified miRNA targets may function in soybean seed development. Additionally, a soybean homolog of Arabidopsis suppressor of gene silencing 3 (AtSGS3) was detected as a target of the newly identified miRNA Soy_25, suggesting the presence of feedback control of miRNA biogenesis. CONCLUSIONS: We have identified large numbers of miRNAs and their related target genes through deep sequencing of a small RNA library and a degradome library. Our study provides more information about the regulatory network of miRNAs in soybean and advances our understanding of miRNA functions during seed development.

Plant NAC-type transcription factor proteins contain a NARD domain for repression of transcriptional activation.

Plant-specific transcription factor NAC proteins play essential roles in many biological processes such as development, senescence, morphogenesis, and stress signal transduction pathways. In the NAC family, some members function as transcription activators while others act as repressors. In the present study we found that though the full-length GmNAC20 from soybean did not have transcriptional activation activity, the carboxy-terminal activation domain of GmNAC20 had high transcriptional activation activity in the yeast assay system. Deletion experiments revealed an active repression domain with 35 amino acids, named NARD (NAC Repression Domain), in the d subdomain of NAC DNA-binding domain. NARD can reduce the transcriptional activation ability of diverse transcription factors when fused to either the amino-terminal or the carboxy-terminal of the transcription factors. NARD-like sequences are also present in other NAC family members and they are functional repression domain when fused to VP16 in plant protoplast assay system. Mutation analysis of conserved amino acid residues in NARD showed that the hydrophobic LVFY motif may partially contribute to the repression function. It is hypothesized that the interactions between the repression domain NARD and the carboxy-terminal activation domain may finally determine the ability of NAC family proteins to regulate downstream gene expressions.

Determination of bencycloquidium bromide, a novel anticholinergic compound, in rat tissues by liquid chromatography-electrospray ionization mass spectrometry.

First, a liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS) method for quantification of bencycloquidium bromide (BCQB) in rat tissue homogenates was developed and validated, which would support investigation on drug distribution into tissues in animal models. 1-ethyl-bencycloquidium bromide was used as the internal standard (IS). Sample preparation in tissue homogenates was achieved by using solid phase extraction on a 3 mL C(18)-cartridge column. Chromatographic separation was analyzed on a Hanbon Lichrospher 5-C(18) column. The mobile phase consisted of methanol-40 mM ammonium acetate buffer-formic acid (75:25:0.25, v/v/v) which was pumped at 1.0 mL min(-1). BCQB was determined using electrospray ionization in a single quadrupole mass spectrometer. LC-ESI-MS was performed in the selected ion monitoring (SIM) mode using target ions at m/z 330.2 for BCQB and m/z 344.2 for the IS. The assay was linear from 3.015 ng mL(-1) to 301.5 ng mL(-1) of BCQB in rat tissue (liver, kidney, lung, trachea, heart, spleen, stomach, intestines, brain, muscle, testicle, ovary and fat) homogenates. The lower limit of quantification (LLOQ) was 3.015 ng mL(-1) of BCQB in all tissue homogenates. Acceptable precision and accuracy were obtained for concentrations over the entire standard curve ranges for tissue homogenates. The method was used to successfully quantify BCQB in rat tissue homogenates for a tissue distribution study of BCQB in rats after intranasal administration.

Genome-wide analysis of DNA methylation in soybean.

Cytosine methylation is an important mechanism for dynamical regulation of gene expression and transposable element (TE) mobility during plant developmental processes. Here, we identified the transcription start sites of genes using high-throughput sequencing and then analyzed the DNA methylation status in soybean roots, stems, leaves, and cotyledons of developing seeds at single-base resolution. Profiling of DNA methylation in different organs revealed 2162 differentially methylated regions among organs, and a portion of hypomethylated regions were correlated with high expression of neighboring genes. Because of the different distribution of class I TEs (retrotransposons) and class II TEs (DNA transposons), the promoters of the lowest-expressed genes showed higher levels of CG and CHG methylation but a lower level of CHH methylation. We further found that the CHH methylation level of class II TEs was higher than class I TEs, possibly due to the presence of more smRNAs in class II TEs. In cotyledons of developing seeds, smRNA abundance was roughly positively correlated with hypermethylated regions but negatively related to hypomethylated regions. These studies provide significant insights into the complicated interplays among DNA methylation, smRNA abundance, TE distribution, and gene expression in soybean.

Identification of rice ethylene-response mutants and characterization of MHZ7/OsEIN2 in distinct ethylene response and yield trait regulation.

Ethylene plays essential roles in adaptive growth of rice plants in water-saturating environment; however, ethylene signaling pathway in rice is largely unclear. In this study, we report identification and characterization of ethylene-response mutants based on the specific ethylene-response phenotypes of etiolated rice seedlings, including ethylene-inhibited root growth and ethylene-promoted coleoptile elongation, which is different from the ethylene triple-response phenotype in Arabidopsis. We establish an efficient system for screening and a set of rice mutants have been identified. Genetic analysis reveals that these mutants form eight complementation groups. All the mutants show insensitivity or reduced sensitivity to ethylene in root growth but exhibit differential responses in coleoptile growth. One mutant group mhz7 has insensitivity to ethylene in both root and coleoptile growth. We identified the corresponding gene by a map-based cloning method. MHZ7 encodes a membrane protein homologous to EIN2, a central component of ethylene signaling in Arabidopsis. Upon ethylene treatment, etiolated MHZ7-overexpressing seedlings exhibit enhanced coleoptile elongation, increased mesocotyl growth and extremely twisted short roots, featuring enhanced ethylene-response phenotypes in rice. Grain length was promoted in MHZ7-transgenic plants and 1000-grain weight was reduced in mhz7 mutants. Leaf senescent process was also affected by MHZ7 expression. Manipulation of ethylene signaling may improve adaptive growth and yield-related traits in rice.