Changes in DNA methylation assessed by genomic bisulfite sequencing suggest a role for DNA methylation in cotton fruiting branch development

Transcriptional response of cultivated peanut (Arachis hypogaea L.) roots to salt stress and the role of DNA methylation

KEY MESSAGE

Our study unravels a complex multi-layered molecular response of peanut roots to salinity, where reprograming of gene-expression is partly executed by changes in methylome via RdDM pathway and exerted through transcription factors. Peanut (Arachis hypogaea L.) is a major oilseed crop of global importance, whose production is severely impacted by salinity. Here, we have explored the transcriptional response of peanut roots to salinity stress using deep sequencing. Further, we have unravelled the salinity-induced changes in peanut root methylome. When peanut seedlings were grown under high-salt conditions for 7 days, their root and shoot growth was significantly impaired. A large-scale transcriptional reprogramming was recorded where 1926 genes were down- and 3260 genes were up-regulated due to salt stress in peanut roots. The molecular response of peanut root comprised several layers of regulators, which included the genes related to ion transport, osmolyte accumulation, signal transduction, and salt stress-responsive genes. Several negative regulators are also differentially expressed in peanut roots, which may contribute to its susceptibility. This response is regulated by a large number of transcription factors (TFs) and epigenetically by changes in DNA methylation. The DNA methylation changes in roots were highly complex and context dependent when exposed to salt stress. An inverse relationship between the changes in gene expression and methylation status was partially observed for several important gene sets and TFs. A treatment with 5'-azacytidine recovered the inhibitory impact of salt stress in peanut roots. Thus, a complex multilayered molecular response to salinity in peanut roots was observed. A part of this response may be modulated by the reprogramming of RNA-directed DNA methylation pathway. This investigation also serves as a resource for future gene-mining and methylation studies for improving peanut resistance to salt stress.

SlSAMS1 enhances salt tolerance through regulation DNA methylation of SlGI in tomato

S-adenosylmethionine (SAM), which is synthesized from methionine and ATP catalyzed by S-adenosylmethionine synthetase (SAMS), is an important methyl donor in plants. SAMS and DNA methylation play an important role in the plant response to abiotic stresses. Previous studies have shown that SAMS improves salt tolerance in tomato plants, but it is not clear whether the DNA methylation pathway mediates SAMS-induced salt tolerance. This study confirmed that SlSAMS1-overexpressing plants exhibited improved salt tolerance. Through whole-genome bisulfite sequencing (WGBS) and transcriptome sequencing (RNA-seq) analysis, the study screened the circadian rhythm pathway and identified the gene SlGI in this pathway, which was regulated by SlSAMS1. The gene body region of SlGI, the core gene of the circadian rhythm pathway, was hypermethylated in SlSAMS1-overexpressing plants, and its expression level was significantly increased. Furthermore, the SlGI-overexpressing plants showed higher salt tolerance, less reduction in plant height and fresh weight, lower electrolyte leakage, malondialdehyde and H2O2 content, and higher antioxidant enzyme activity compared to wild type plants. Therefore, SlSAMS1-overexpressing plants regulated significant changes in CHG-type methylation sites of the SlGI gene body and its expression levels, leading to an enhanced salt tolerance of tomato plants.

Methylome and transcriptome analysis of flowering branches building of Citrus plants induced by drought stress

Citrus plants exhibit positive floral response under water stress conditions, however, the mechanistic understanding of floral induction remains largely unexplored in water deficit. In this study, DNA methylomic and transcriptomic analyses were integrated to explore the flowering bud formation as well as branches building after light drought stress. While comparing with the conventional watering group (CK), the light drought group treated with five months (LD) showed a significant increase in the flowering branches, whereas an apparent decrease in vegetative branches. Global DNA methylation analysis showed that the LD Group acquired DNA methylation in more than 70090 genomic regions and lost DNA methylation in about 18421 genomic regions compared with normal watering group, this indicates that water deficiency leads to a global increase in the expression of DNA methylation in citrus. In the same time, we verified that the increase of DNA methylation level in LD group was correlated with the decrease of DNA demethylase related gene expression. Interestingly, in transcription analysis, it was found that the promoting flower genes of the LD group did not increase but decreased similarly with repressing genes, which is contrary to the intended result. Thus, we thought the lower expression of suppressors FLC and BFT were the key influencing factor to stimulate the flowering branches formation after LD treatment. Moreover, there was a strong negative correlation between the genes expression level and methylation level of the flowering induction/flower development genes. In general, we thought high global DNA methylation level induced by water deficit regulate the flowering branches building by reducing FLC and BFT genes expression.

DNA Methyltransferases: From Evolution to Clinical Applications

DNA methylation is an epigenetic mark that living beings have used in different environments. The MTases family catalyzes DNA methylation. This process is conserved from archaea to eukaryotes, from fertilization to every stage of development, and from the early stages of cancer to metastasis. The family of DNMTs has been classified into DNMT1, DNMT2, and DNMT3. Each DNMT has been duplicated or deleted, having consequences on DNMT structure and cellular function, resulting in a conserved evolutionary reaction of DNA methylation. DNMTs are conserved in the five kingdoms of life: bacteria, protists, fungi, plants, and animals. The importance of DNMTs in whether methylate or not has a historical adaptation that in mammals has been discovered in complex regulatory mechanisms to develop another padlock to genomic insurance stability. The regulatory mechanisms that control DNMTs expression are involved in a diversity of cell phenotypes and are associated with pathologies transcription deregulation. This work focused on DNA methyltransferases, their biology, functions, and new inhibitory mechanisms reported. We also discuss different approaches to inhibit DNMTs, the use of non-coding RNAs and nucleoside chemical compounds in recent studies, and their importance in biological, clinical, and industry research.

Insight Between the Epigenetics and Transcription Responding of Cotton Hypocotyl Cellular Elongation Under Salt-Alkaline Stress

Gossypium barbadense is a cultivated cotton not only known for producing superior fiber but also for its salt and alkaline resistance. Here, we used Whole Genome Bisulfite Sequencing (WGBS) technology to map the cytosine methylation of the whole genome of the G. barbadense hypocotyl at single base resolution. The methylation sequencing results showed that the mapping rates of the three samples were 75.32, 77.54, and 77.94%, respectively. In addition, the Bisulfite Sequence (BS) conversion rate was 99.78%. Approximately 71.03, 53.87, and 6.26% of the cytosine were methylated at CG, CHG, and CHH sequence contexts, respectively. A comprehensive analysis of DNA methylation and transcriptome data showed that the methylation level of the promoter region was a positive correlation in the CHH context. Saline-alkaline stress was related to the methylation changes of many genes, transcription factors (TFs) and transposable elements (TEs), respectively. We explored the regulatory mechanism of DNA methylation in response to salt and alkaline stress during cotton hypocotyl elongation. Our data shed light into the relationship of methylation regulation at the germination stage of G. barbadense hypocotyl cell elongation and salt-alkali treatment. The results of this research help understand the early growth regulation mechanism of G. barbadense in response to abiotic stress.

Understanding In Vitro Tissue Culture-Induced Variation Phenomenon in Microspore System

In vitro tissue culture plant regeneration is a complicated process that requires stressful conditions affecting the cell functioning at multiple levels, including signaling pathways, transcriptome functioning, the interaction between cellular organelles (retro-, anterograde), compounds methylation, biochemical cycles, and DNA mutations. Unfortunately, the network linking all these aspects is not well understood, and the available knowledge is not systemized. Moreover, some aspects of the phenomenon are poorly studied. The present review attempts to present a broad range of aspects involved in the tissue culture-induced variation and hopefully would stimulate further investigations allowing a better understanding of the phenomenon and the cell functioning.

Whole Genome Re-sequencing of Soybean Accession EC241780 Providing Genomic Landscape of Candidate Genes Involved in Rust Resistance

BACKGROUND

In this study, whole genome re-sequencing of rust resistant soybean genotype EC241780 was performed to understand the genomic landscape involved in the resistance mechanism.

METHODS

A total of 374 million raw reads were obtained with paired-end sequencing performed with Illumina HiSeq 2500 instrument, out of which 287.3 million high quality reads were mapped to Williams 82 reference genome. Comparative sequence analysis of EC241780 with rust susceptible cultivars Williams 82 and JS 335 was performed to identify sequence variation and to prioritise the candidate genes.

RESULTS

Comparative analysis indicates that genotype EC241780 has high sequence similarity with rust resistant genotype PI 200492 and the resistance in EC241780 is conferred by the Rpp1 locus. Based on the sequence variations and functional annotations, three genes Glyma18G51715, Glyma18G51741 and Glyma18G51765 encoding for NBS-LRR family protein were identified as the most prominent candidate for Rpp1 locus.

CONCLUSION

The study provides insights of genome-wide sequence variation more particularly at Rpp1 loci which will help to develop rust resistant soybean cultivars through efficient exploration of the genomic resource.

Screening of abiotic stress-responsive cotton genes using a cotton full-length cDNA overexpressing Arabidopsis library

Cotton (Gossypium hirsutum L.) is a major crop and the main source of natural fiber worldwide. Because various abiotic and biotic stresses strongly influence cotton fiber yield and quality, improved stress resistance of this crop plant is urgently needed. In this study, we used Gateway technology to construct a normalized full-length cDNA overexpressing (FOX) library from upland cotton cultivar ZM12 under various stress conditions. The library was transformed into Arabidopsis to produce a cotton-FOX-Arabidopsis library. Screening of this library yielded 6,830 transgenic Arabidopsis lines, of which 757 were selected for sequencing to ultimately obtain 659 cotton ESTs. GO and KEGG analyses mapped most of the cotton ESTs to plant biological process, cellular component, and molecular function categories. Next, 156 potential stress-responsive cotton genes were identified from the cotton-FOX-Arabidopsis library under drought, salt, ABA, and other stress conditions. Four stress-related genes identified from the library, designated as GhCAS, GhAPX, GhSDH, and GhPOD, were cloned from cotton complementary DNA, and their expression patterns under stress were analyzed. Phenotypic experiments indicated that overexpression of these cotton genes in Arabidopsis affected the response to abiotic stress. The method developed in this study lays a foundation for high-throughput cloning and rapid identification of cotton functional genes.

Four-microRNA signature for detection of type 2 diabetes

BACKGROUND

Sensitive, novel, and accurate biomarkers for the detection of physiological changes in type 2 diabetes (T2DM) at an early stage are urgently needed.

AIM

To build a multi-parameter diagnostic model for the early detection of T2DM.

METHODS

MiR-148b, miR-223, miR-130a, and miR-19a levels were detected by real-time polymerase chain reaction in serum of healthy controls, individuals with impaired glucose regulation, and T2DM patients. The diagnostic value of miR-148b, miR-223, miR-130a, and miR-19a, alone or in combination, was analyzed.

RESULTS

The area under the curve (AUC) of miR-223, which had the best diagnostic value for discriminating the impaired glucose regulation and T2DM groups, was 0.84, and the sensitivity and specificity were 73.37% and 81.37%, respectively. The AUC of the four-miRNA signature was 0.90, and the sensitivity and specificity were 78.82% and 88.23%, respectively. In the validation set, the AUC was 0.88, and the sensitivity and specificity were 78.36% and 87.63%, respectively.

CONCLUSION

In summary, we have built a multi-parameter diagnostic model consisting of miR-148b, miR-223, miR-130a, and miR-19a for the detection of T2DM. It may be a potential tool for the early detection of T2DM.

Potential microRNA panel for the diagnosis and prediction of overall survival of hepatocellular carcinoma with hepatitis B virus infection

BACKGROUND

In hepatocellular carcinoma (HCC), abnormal expression of multiple microRNAs (miRNAs) has been shown to be involved in the malignant biological behavior of liver cancer. The vast majority of liver cancer cases in China are closely related to hepatitis B virus (HBV) infection, but there are few studies on the changes of miRNA expression in the progression from HBV infection to hepatoma.

AIM

To explore the role of miRNAs in the progression of HBV infection to cirrhosis and even to liver cancer.

METHODS

We screened differentially expressed miRNAs in 40 HBV cirrhosis, 40 normal and 15 HCC tissues by using a TaqMan Low Density Array and real time quantitative polymerase chain reaction. To evaluate the power of the selected miRNAs to predict disease, we calculated the area under the receiver-operating-characteristic curves. The overall survival of HBV cirrhosis patients was analyzed via Kaplan-Meier analysis.

RESULTS

The levels of miR-375, miR-122 and miR-143 were significantly lower in HBV cirrhosis tissues, while miR-224 was significantly higher than in the controls (P < 0.0001). The area under the curves of the receiver-operating-characteristic curve for the 4-miRNA panel was 0.991 (95%CI: 0.974-1). Patients with a lower expression level of miR-224 or higher expression levels of miR-375, miR-122 and miR-143 had longer overall survival.

CONCLUSION

The four miRNAs (miR-375, miR-122, miR-143 and miR-224) may be helpful for early diagnosis of HBV infection, HBV cirrhosis, and prediction of its overall survival.

Evaluation of the value of multiparameter combined analysis of serum markers in the early diagnosis of gastric cancer

BACKGROUND

In early gastric cancer (GC), tumor markers are increased in the blood. The levels of these markers have been used as important indexes for GC screening, early diagnosis and prognostic evaluation. However, specific tumor markers have not yet been discovered. Diagnosis based on a single tumor marker has limited significance. The detection rate of GC is still very low.

AIM

To improve the diagnostic value of blood markers for GC.

METHODS

We used a multiparameter joint analysis of 77 indexes of malignant GC and gastric polyp (GP), 64 indexes of GC and healthy controls (Ctrls).

RESULTS

By analyzing the data, there are 27 indexes in the final Ctrls vs GC with P values < 0.01, the area under the curve (AUC) of albumin is the largest in Ctrls vs GC, and the AUC was 0.907. 30 indexes in GP vs GC have P values < 0.01. Among them, the D-dimer showed an AUC of 0.729. The 27 indexes in Ctrls vs GC and 30 indexes in GP vs GC were used for binary logistic regression, discriminant analysis, classification tree analysis and artificial neural network analysis model. For the ability to distinguish between Ctrls vs GC, GP vs GC, artificial neural networks had better diagnostic value when compared with classification tree, binary logistic regression, and discriminant analysis. When compared Ctrl and GC, the overall prediction accuracy was 92.9%, and the AUC was 0.992 (0.980, 1.000). When compared GP and GC, the overall prediction accuracy was 77.9%, and the AUC was 0.969 (0.948, 0.990).

CONCLUSION

The diagnostic effect of multi-parameter joint artificial neural networks analysis is significantly better than the single-index test diagnosis, and it may provide an assistant method for the detection of GC.

Light- and temperature-entrainable circadian clock in soybean development

In plants, the spatiotemporal expression of circadian oscillators provides adaptive advantages in diverse species. However, the molecular basis of circadian clock in soybean is not known. In this study, we used soybean hairy roots expression system to monitor endogenous circadian rhythms and the sensitivity of circadian clock to environmental stimuli. We discovered in experiments with constant light and temperature conditions that the promoters of clock genes GmLCLb2 and GmPRR9b1 drive a self-sustained, robust oscillation of about 24-h in soybean hairy roots. Moreover, we demonstrate that circadian clock is entrainable by ambient light/dark or temperature cycles. Specifically, we show that light and cold temperature pulses can induce phase shifts of circadian rhythm, and we found that the magnitude and direction of phase responses depends on the specific time of these two zeitgeber stimuli. We obtained a quadruple mutant lacking the soybean gene GmLCLa1, LCLa2, LCLb1, and LCLb2 using CRISPR, and found that loss-of-function of these four GmLCL orthologs leads to an extreme short-period circadian rhythm and late-flowering phenotype in transgenic soybean. Our study establishes that the morning-phased GmLCLs genes act constitutively to maintain circadian rhythmicity and demonstrates that their absence delays the transition from vegetative growth to reproductive development.

Clinical value evaluation of serum markers for early diagnosis of colorectal cancer

BACKGROUND

Early screening for colorectal cancer (CRC) is important in clinical practice. However, the currently methods are inadequate because of high cost and low diagnostic value.

AIM

To develop a new examination method based on the serum biomarker panel for the early detection of CRC.

METHODS

Three hundred and fifty cases of CRC, 300 cases of colorectal polyps and 360 cases of normal controls. Combined with the results of area under curve (AUC) and correlation analysis, the binary Logistic regression analysis of the remaining indexes which is in accordance with the requirements was carried out, and discriminant analysis, classification tree and artificial neural network analysis were used to analyze the remaining indexes at the same time.

RESULTS

By comparison of these methods, we obtained the ability to distinguish CRC from healthy control group, malignant disease group and benign disease group. Artificial neural network had the best diagnostic value when compared with binary logistic regression, discriminant analysis, and classification tree. The AUC of CRC and the control group was 0.992 (0.987, 0.997), sensitivity and specificity were 98.9% and 95.6%. The AUC of the malignant disease group and benign group was 0.996 (0.992, 0.999), sensitivity and specificity were 97.4% and 96.7%.

CONCLUSION

Artificial neural network diagnosis method can improve the sensitivity and specificity of the diagnosis of CRC, and a novel assistant diagnostic method was built for the early detection of CRC.

Systematic Analysis of the DNA Methylase and Demethylase Gene Families in Rapeseed (Brassica napus L.) and Their Expression Variations After Salt and Heat stresses

DNA methylation is a process through which methyl groups are added to the DNA molecule, thereby modifying the activity of a DNA segment without changing the sequence. Increasing evidence has shown that DNA methylation is involved in various aspects of plant growth and development via a number of key processes including genomic imprinting and repression of transposable elements. DNA methylase and demethylase are two crucial enzymes that play significant roles in dynamically maintaining genome DNA methylation status in plants. In this work, 22 DNA methylase genes and six DNA demethylase genes were identified in rapeseed (Brassica napus L.) genome. These DNA methylase and DNA demethylase genes can be classified into four (BnaCMTs, BnaMET1s, BnaDRMs and BnaDNMT2s) and three (BnaDMEs, BnaDML3s and BnaROS1s) subfamilies, respectively. Further analysis of gene structure and conserved domains showed that each sub-class is highly conserved between rapeseed and Arabidopsis. Expression analysis conducted by RNA-seq as well as qRT-PCR suggested that these DNA methylation/demethylation-related genes may be involved in the heat/salt stress responses in rapeseed. Taken together, our findings may provide valuable information for future functional characterization of these two types of epigenetic regulatory enzymes in polyploid species such as rapeseed, as well as for analyzing their evolutionary relationships within the plant kingdom.

Functional analysis of the GbDWARF14 gene associated with branching development in cotton

Plant architecture, including branching pattern, is an important agronomic trait of cotton crops. In recent years, strigolactones (SLs) have been considered important plant hormones that regulate branch development. In some species such as Arabidopsis, DWARF14 is an unconventional receptor that plays an important role in the SL signaling pathway. However, studies on SL receptors in cotton are still lacking. Here, we cloned and analysed the structure of the GbD14 gene in Gossypium barbadense and found that it contains the domains necessary for a SL receptor. The GbD14 gene was expressed primarily in the roots, leaves and vascular bundles, and the GbD14 protein was determined via GFP to localize to the cytoplasm and nucleus. Gene expression analysis revealed that the GbD14 gene not only responded to SL signals but also was differentially expressed between cotton plants whose types of branching differed. In particular, GbD14 was expressed mainly in the axillary buds of normal-branching cotton, while it was expressed the most in the leaves of nulliplex-branch cotton. In cotton, the GbD14 gene can be induced by SL and other plant hormones, such as indoleacetic acid, abscisic acid, and jasmonic acid. Compared with wild-type Arabidopsis, GbD14-overexpressing Arabidopsis responded more rapidly to SL signals. Moreover, we also found that GbD14 can rescue the multi-branched phenotype of Arabidopsis Atd14 mutants. Our results indicate that the function of GbD14 is similar to that of AtD14, and GbD14 may be a receptor for SL in cotton and involved in regulating branch development. This research provides a theoretical basis for a profound understanding of the molecular mechanism of branch development and ideal plant architecture for cotton breeding improvements.