Potential Regulatory Genes Research Articles

The PHD transcription factor ThPHD5 regulates antioxidant enzyme activity to increase salt tolerance in Tamarix hispida.

PHD proteins are an important class of transcription factors (TFs) that are widely distributed in eukaryotes and play crucial roles in many aspects of plant growth, development and response to stress. We identified a transcription factor, ThPHD5, from the PHD family in Tamarix hispida based on its potential involvement in abiotic stress response processes. In this study, the salt tolerance function of ThPHD5 from T. hispida was further characterized. The qRTPCR results showed ThPHD5 was expressed in response to NaCl, PEG and ABA treatments. Transient transformation analysis revealed that ThPHD5 improved salt tolerance in T. hispida by increasing POD and SOD activity and decreasing the MDA, total ROS content and electrolyte leakage. To explore the salt tolerance mechanism of the ThPHD5 TF, its binding DNA motifs and potential downstream regulatory genes were analyzed. The results showed that ThPHD5 affect the expression of 7 antioxidant enzyme-related genes. The Yeast one-hybrid (Y1H) and Electrophoretic Mobility Shift Assay (EMSA) results indicated ThPHD5 could bind to ABRE, MYB and Dof cis-acting elements. ChIP-PCR further confirmed ThPHD5 exercise its regulatory function by directly binding motifs on the ThPOD16, ThSOD and ThSOD1 promoters. Taken together, these findings indicate the ThPHD5 TF improves salt tolerance in T. hispida by regulating the expression of antioxidant enzyme-related genes to increase antioxidant enzyme activity, enhance the ROS scavenge ability, reduce ROS accumulation and cellular damage.

Transcriptome analysis of liver and ileum reveals potential regulation of long non-coding RNA in pigs with divergent feed efficiency.

LncRNA plays a significant role in regulating feed efficiency. This study aims to explore the key long non-coding RNAs, associated genes, and pathways in pigs with extreme feed efficiencies. We screened pigs with extremely high and low RFI through a 12-week animal growth trial and then conducted transcriptome analysis on their liver and ileum tissues. We analyzed the differential expressed lncRNAs, miRNAs, and mRNAs through target gene prediction and functional analysis. And we identified key lncRNAs and their potential regulatory genes associated with feed efficiency through the construction of competitive endogenous RNA network. Differentially expressed lncRNAs were pinpointed in the liver, revealing 23 crucial target genes primarily associated with GTP metabolism and glycolipid biosynthesis. In the ileum, a screening identified 92 pivotal target genes, mainly linked to lipid and small molecule metabolism. Moreover, LOC106504303 and LOC102160805 emerged as potentially significant lncRNAs respectively, playing roles in mitochondrial oxidative phosphorylation in the liver, and lipid and cholesterol metabolism in the ileum. The lncRNAs regulate energy metabolism and biosynthesis in the liver, and the digestive absorption capacity in the small intestine, affecting the feed efficiency of pigs.

Insights into terpenes profiling and transcriptional analyses during flowering of different Cannabis sativa L. chemotypes

Terpenes, volatile compounds known for their aromatic and therapeutic properties, play a pivotal role in shaping the overall chemical profile of Cannabis sativa L. Their biosynthesis in planta occurs in trichomes and involves the 2-C-methyl-D-erythritol 4-phosphate (MEP) and the mevalonic acid (MVA) pathways, responsible for producing the substrates utilized by a family of enzymes, the terpene synthases (TPS), for terpene production. In this work, a comprehensive approach combining chemical analyses of the volatile compounds characterizing the aroma of the inflorescences three C. sativa genotypes collected at three stages of maturity and the transcriptional analyses of key genes involved in the terpene biosynthesis was adopted to study this pathway. The results revealed different terpene profiles among genotypes, which were characterized by peculiar compounds belonging to the sesqui- (CINBOL and Fibrante) or monoterpene (Ermo) categories. Both structural and putative regulatory genes were analysed by RT-qPCR, revealing distinct transcriptional profiles of Terpene Synthases, contributing to the diversity of mono and sesquiterpenes synthesized. Furthermore, the research delved into potential regulatory genes associated with trichome formation, a crucial factor influencing terpene accumulation. This integrated approach highlighted complex mechanisms governing terpene accumulation in cannabis, while also offering potential regulators putatively involved in this pathway.

The Potential Related Genes and Mechanisms Involved in Improving the Treadmill Exercise Ability of APP/PS1 Mice.

Alzheimer's disease (AD) causes a decline in skeletal muscle function, which can further exacerbate the cognitive dysfunction of patients with AD. It has been widely established that exercise improves AD brain pathology, but the role of skeletal muscle in AD is still poorly understood. In this study, we investigated the effects of treadmill exercise on the exercise ability of APP/PS1 transgenic AD mice and explored potential gene expression changes in their skeletal muscle. The APP/PS1 mice were subjected to a treadmill exercise for 12 weeks, followed by the Morris water maze and the open field test. After behavioral experiments, the changes in morphology, area, collagen fiber deposition, and ultrastructure of the skeletal muscle were determined; the balance of skeletal muscle protein synthesis and decomposition was analyzed; and changes in gene expression were investigated using RNA-Seq. We found that this exercise strategy can promote the learning and memory abilities of AD mice, reduce their anxiety-like behavior, improve their exercise ability, alleviate skeletal muscle atrophy, and optimize the microstructure. It can also enhance skeletal muscle protein synthesis and decomposition and improve several signaling pathways, such as the JAK-STAT, Wnt, and NOD-like receptors while decreasing calcium, cAMP, cGMP-PKG, and other signaling pathways. Six KEGG enrichment signaling pathways were downregulated and five signaling pathways were upregulated in the AD mice compared with wild-type mice, and these pathways were precisely reversed after the treadmill exercise. The expression of transcription factors such as Fosb and Egr1 in the skeletal muscle of AD mice decreased, followed by a decrease in the regulated target genes Socs1, Srrm4, and Il1b, a trend that was reversed following the exercise intervention. After exercise, AD mice exhibited a similar gene expression to that of wild-type mice, indicating enhanced exercise ability. The potential regulatory pathways and related genes identified in this study provide valuable insights for the clinical management and treatment of AD.

Transcriptomic profiling reveals potential regulatory genes and molecular mechanisms of residual feed intake in Jian carp (Cyprinus carpio var. Jian)

Feed efficiency is one of the most important economic traits in animal production. Improving feed efficiency through genetic selection or other approaches will reduce production costs and mitigate environmental impacts. Residual feed intake (RFI) has some advantages over traditional feed efficiency metrics as a selection criterion for improving feed efficiency, because it is not a ratio and unrelated to growth. In this study, high RFI (HRFI) and low RFI (LRFI) Jian carp (Cyprinus carpio var. Jian) were tested for feed efficiency traits and serum biochemical indices. No significant differences were observed in the growth rates between HRFI and LRFI group, but daily feed intake of LRFI was significantly lower than that of the HRFI group. The results indicated that significantly higher content of triglyceride (TG) and total cholesterol (T-CHO) in the LRFI group was significantly correlated with RFI. We also selected HRFI and LRFI carp for transcriptomic analysis to determine differentially expressed genes (DEGs) in the liver tissues of 12 individuals. A total of 830 DEGs were identified between HRFI and LRFI group, of which 486 genes were up-regulated and 344 genes were down-regulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that DEGs were mainly enriched in fatty acid metabolism, ErbB signaling pathway, phosphatidylinositol signaling system, and autophagy. Lipid metabolism and autophagy-related genes, were considered candidate genes that played a crucial role in regulating feed efficiency. Taken together, these results indicated that differences in RFI affect Jian carp metabolism and cell fate, and that alterations in fatty acid metabolism and autophagy are key physiological modes of regulation in low RFI Jian carp. Our data provide valuable candidate genes and candidate pathways, which will help to study the molecular mechanisms of feed efficiency in carp.

Toxicological effects, absorption and biodegradation of bisphenols with different functional groups in Chromochloris zofingiensis

Bisphenols (BPs) are recognized as endocrine disrupting compounds and have garnered increasing attention due to their widespread utilization. However, the varying biological toxicities and underlying mechanisms of BPs with different functional groups remain unknown. In the present study, the toxic effects of four BPs (BPA, BPS, BPAF, and TBBPA) on a photosynthetic microalgae Chromochloris zofingiensis were compared. Results showed that halogen-containing BPs exhibited higher cellular uptake, leading to more severe oxidative stress, lower photosynthetic efficiency, and greater accumulation of starch and lipids. Specifically, TBBPA with bromine groups showed a greater toxicity than BPAF with fluorine groups, possibly due to the incomplete debromination in C. zofingiensis. Transcriptomic analysis revealed that halogen-containing BPs triggered greater number of differentially expressed genes (DEGs), and only 64 common DEGs were found among different BPs, indicating that the effects of BPs with different functional groups varied greatly. Genes involved in endocytosis, peroxisomes, and endoplasmic reticulum protein processing pathways were mostly upregulated across different BPs, while photosynthesis-related genes showed varied expression, possibly due to their distinct functional groups. Additionally, SIN3A, ZFP36L, CHMP, and ATF2 emerged as potential key regulatory genes. Overall, this study thoroughly explained how functional groups impact the toxicity and biodegradation of BPs in C. zofingiensis.

Genome-Wide Transcriptome Analysis of a Virulent sRNA, Trans217, in Xanthomonas oryzae pv. oryzae (Xoo), the Causative Agent of Rice Bacterial Blight.

Small non-coding RNAs (sRNAs) act as post-transcriptional regulators to participate in many cellular processes. Among these, sRNA trans217 has been identified as a key virulent factor associated with pathogenicity in rice, triggering hypersensitive reactions in non-host tobacco and facilitating the secretion of the PthXo1 effector in Xanthomonas oryzae pv. oryzae (Xoo) strain PXO99A. Elucidating potential targets and downstream regulatory genes is crucial for understanding cellular networks governing pathogenicity and plant resistance. To explore the targets regulated by sRNA trans217, transcriptome sequencing was carried out to assess differential expression genes (DEGs) between the wild-type strain PXO99A and a mutant lacking the sRNA fragment under both virulence-inducing or normal growth conditions. DEG analysis revealed that sRNA trans217 was responsible for diverse functions, such as type III secretion system (T3SS), glutamate synthase activity, and oxidative stress response. Three genes were selected for further investigation due to their significant differential expression and biological relevance. Deletion of PXO_RS08490 attenuated the pathogenicity of Xoo in rice and reduced the tolerance level of PXO99A to hydrogen peroxide. These findings suggest a regulatory role of sRNA trans217 in modulating bacterial virulence through multiple gene targets, either directly or indirectly.

Hepatopancreas Transcriptome Analysis of Spinibarbus sinensis to Reveal Different Growth-Related Genes.

Spinibarbus sinensis, also known as Qingbo, is an important economic fish in China. However, the detailed mechanisms underlying its growth are still unknown. To excavate the genes and signaling pathways related to its growth, we compared the transcriptome profiles of the hepatopancreas tissues of S. sinensis, with two groups of growth rate for evaluation. An average of 66,304,909 and 68,739,585 clean reads were obtained in the fast growth (FG) and slow growth (SG) group, respectively. The differential gene expression analysis results showed that 272 differentially expressed genes (DEGs) were screened between the FG and SG groups, including 101 up-regulated genes and 171 down-regulated genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis results showed that GO terms related to metabolic process, organic substance metabolic process, and catalytic activity were enriched, pathway signals related to steroid biosynthesis and protein digestion and absorption were also detected. Meanwhile, the potential key regulatory genes sst2, fndc4, and cckra related to the growth of S. sinensis were screened. Reverse transcript fluorescence quantitative PCR (RT-qPCR) validation of 18 DEGs associated with growth differences showed that the RT-qPCR results were consistent with RNA-seq analysis, and nine genes, stk31, gpr149, angptl1, fstl1, sik1, ror2, nlrc3, pdlim2, and nav2 were significantly expressed in the FG group. bmp1, stc1, gpatch8, sstrt2, s100a1, ktf6, cckar6, sync1, bhlha15, a total of nine genes were significantly expressed in the SG group. This study provides basic information for improving the growth characteristics of S. sinensis and the functional research of candidate genes.

DNA methylase 1 influences temperature responses and development in the invasive pest Tuta absoluta.

DNA methylase 1 (Dnmt1) is an important regulatory factor associated with biochemical signals required for insect development. It responds to changes in the environment and triggers phenotypic plasticity. Meanwhile, Tuta absolutaMeyrick (Lepidoptera: Gelechiidae)-a destructive invasive pest-can rapidly invade and adapt to different habitats; however, the role of Dnmt1 in this organism has not been elucidated. Accordingly, this study investigates the mechanism(s) underlying the rapid adaptation of Tuta absoluta to temperature stress. Potential regulatory genes were screened via RNAi (RNA interference), and the DNA methylase in Tuta absoluta was cloned by RACE (Rapid amplification of cDNA ends). TaDnmt1 was identified as a potential regulatory gene via bioinformatics; its expression was evaluated in response to temperature stress and during different development stages using real-time polymerase chain reaction. Results revealed that TaDnmt1 participates in hot/cold tolerance, temperature preference and larval development. The full-length cDNA sequence of TaDnmt1 is 3765 bp and encodes a 1254 kDa protein with typical Dnmt1 node-conserved structural features and six conserved DNA-binding active motifs. Moreover, TaDnmt1 expression is significantly altered by temperature stress treatments and within different development stages. Hence, TaDnmt1 likely contributes to temperature responses and organismal development. Furthermore, after treating with double-stranded RNA and exposing Tuta absoluta to 35°C heat shock or -12°C cold shock for 1 h, the survival rate significantly decreases; the preferred temperature is 2°C lower than that of the control group. In addition, the epidermal segments become enlarged and irregularly folded while the surface dries up. This results in a significant increase in larval mortality (57%) and a decrease in pupation (49.3%) and eclosion (50.9%) rates. Hence, TaDnmt1 contributes to temperature stress responses and temperature perception, as well as organismal growth and development, via DNA methylation regulation. These findings suggest that the rapid geographic expansion of T absoluta has been closely associated with TaDnmt1-mediated temperature tolerance. This study advances the research on 'thermos Dnmt' and provides a potential target for RNAi-driven regulation of Tuta absoluta.

Integrated analysis of transcriptome and small RNAome reveals regulatory network of rapid and long-term response to heat stress in Rhododendron moulmainense

Main conclusionThe post-transcriptional gene regulatory pathway and small RNA pathway play important roles in regulating the rapid and long-term response of Rhododendron moulmainense to high-temperature stress.The Rhododendron plays an important role in maintaining ecological balance. However, it is difficult to domesticate for use in urban ecosystems due to their strict optimum growth temperature condition, and its evolution and adaptation are little known. Here, we combined transcriptome and small RNAome to reveal the rapid response and long-term adaptability regulation strategies in Rhododendron moulmainense under high-temperature stress. The post-transcriptional gene regulatory pathway plays important roles in stress response, in which the protein folding pathway is rapidly induced at 4 h after heat stress, and alternative splicing plays an important role in regulating gene expression at 7 days after heat stress. The chloroplasts oxidative damage is the main factor inhibiting photosynthesis efficiency. Through WGCNA analysis, we identified gene association patterns and potential key regulatory genes responsible for maintaining the ROS steady-state under heat stress. Finally, we found that the sRNA synthesis pathway is induced under heat stress. Combined with small RNAome, we found that more miRNAs are significantly changed under long-term heat stress. Furthermore, MYBs might play a central role in target gene interaction network of differentially expressed miRNAs in R. moulmainense under heat stress. MYBs are closely related to ABA, consistently, ABA synthesis and signaling pathways are significantly inhibited, and the change in stomatal aperture is not obvious under heat stress. Taken together, we gained valuable insights into the transplantation and long-term conservation domestication of Rhododendron, and provide genetic resources for genetic modification and molecular breeding to improve heat resistance in Rhododendron.

Inhibin A contributes to the tumorigenesis of oral squamous cell carcinoma by KIAA1429-mediated m6A modification.

Inhibin A and N6-methyladenosine methylation modifications participate in oral squamous cell carcinoma development. However, the N6-methyladenosine modification of Inhibin A in oral squamous cell carcinoma has not been revealed. This study reveals a key gene "Inhibin A" that may affect the tumorigenesis of oral squamous cell carcinoma and its molecular mechanisms on N6-methyladenosine methyltransferase KIAA1429-mediated N6-methyladenosine methylation modification. Bioinformatics analysis and quantitative real-time polymerase chain reaction identified the potential regulatory genes in oral squamous cell carcinoma. We examined the changes in the proliferation (Cell Counting Kit-8 assay), migration (transwell migration assay), and invasion (transwell invasion assays) of oral squamous cell carcinoma cells. We performed a xenograft tumor experiment to validate the role of Inhibin A in oral squamous cell carcinoma in vivo. The interactions between Inhibin A and KIAA1429 were analyzed using bioinformatics, methylated RNA immunoprecipitation-qPCR, quantitative real-time polymerase chain reaction, and Western blotting experiments. Inhibin A had the highest expression in patients with oral squamous cell carcinoma. Inhibin A silencing impaired the ability of oral squamous cell carcinoma cells to proliferate, migrate, and invade, as well as limited the tumorous growth of oral squamous cell carcinoma cells in vivo. Bioinformatics analysis showed that Inhibin A expression positively interacted with KIAA1429 expression in The Cancer Genome Atlas database. The levels were also upregulated in our clinical samples. Furthermore, KIAA1429 silencing repressed the N6-methyladenosine level of Inhibin A in oral squamous cell carcinoma. Inhibin A promotes the tumorigenesis of oral squamous cell carcinoma by KIAA1429-mediated N6-methyladenosine modification. This study adds to our current knowledge of the molecular mechanisms underlying oral squamous cell carcinoma malignancy.

Depletion of CPNE7 sensitizes colorectal cancer to 5-fluorouracil by downregulating ATG9B expression.

We aimed to explore the biological function of CPNE7 and determine the impact of CPNE7 on chemotherapy resistance in colorectal cancer (CRC) patients. According to the Gene Expression Profiling Interactive Analysis database and previously published data, CPNE7 was identified as a potential oncogene in CRC. RT-qPCR and Western blotting were performed to verify the expression of CPNE7. Chi-square test was used to evaluate the associations between CPNE7 and clinical features. Cell proliferation, colony formation, cell migration and invasion, cell cycle and apoptosis were assessed to determine the effects of CPNE7. Transcriptome sequencing was used to identify potential downstream regulatory genes, and gene set enrichment analysis was performed to investigate downstream pathways. The effect of CPNE7 on 5-fluorouracil chemosensitivity was verified by half maximal inhibitory concentration (IC50). Subcutaneous tumorigenesis assay was used to examine the role of CPNE7 in sensitivity of CRC to chemotherapy invivo. Transmission electron microscopy was used to detect autophagosomes. CPNE7 was highly expressed in CRC tissues, and its expression was correlated with T stage and tumour site. Knockdown of CPNE7 inhibited the proliferation and colony formation of CRC cells and promoted apoptosis. Knockdown of CPNE7 suppressed the expression of ATG9B and enhanced the sensitivity of CRC cells to 5-fluorouracil invitro and invivo. Knockdown of CPNE7 reversed the induction of the autophagy pathway by rapamycin and reduced the number of autophagosomes. Depletion of CPNE7 attenuated the malignant proliferation of CRC cells and enhanced the chemosensitivity of CRC cells to 5-fluorouracil.

Transcriptome Analysis of Potential Regulatory Genes under Chemical Doubling in Maize Haploids

Maize is one of the most successful crops with regard to the utilization of heterosis. The haploid induction technique is one of the fastest methods to obtain pure maize material at the present stage. However, the molecular mechanism of haploid doubling is rarely reported. In this study, we treated B73 and ZNC442 haploid young shoots with colchicine for 0 h, 6.2 h, and 10 h, and analyzed the differentially expressed genes (DEGs). We found that colchicine treatment for 6.2 h and 10 h compared to 0 h resulted in a total of 4868 co-DEGs. GO enrichment analysis and KEGG metabolic pathway analysis found significantly enriched 282 GO terms and 31 significantly pathways, respectively. Additionally, The GO term and KEGG pathway genes of spindle, cytoskeleton, microtubules and nuclear division were selected for analysis, and three candidate genes were screened by taking intersections. Zm00001d033112, Zm00001d010525, and Zm00001d043386 were annotated as kinesin-associated protein 13, kinesin-like protein KIN-10C, and kinesin light-chain LC6, respectively. The real-time fluorescence quantification (RT-PCR) results revealed that Zm00001d033112, Zm00001d010525, and Zm00001d043386 had the same trends as RNA-seq. Interestingly, Zm00001d033112 is homologous gene AT3G20150 in Arabidopsis, which was involved in the regulation of chromosome movement and mitotic spindle assembly. Our study suggests that kinesin genes may play an important role in doubling chromosomes, thus providing valuable information for future studies on the molecular mechanisms of chromosome doubling in maize.

Genomic and Comparative Transcriptomic Analyses Reveal Key Genes Associated with the Biosynthesis Regulation of Okaramine B in Penicillium daleae NBP-49626.

Restricted production of fungal secondary metabolites hinders the ability to conduct comprehensive research and development of novel biopesticides. Okaramine B from Penicillium demonstrates remarkable insecticidal efficacy; however, its biosynthetic yield is low, and its regulatory mechanism remains unknown. The present study found that the yield difference was influenced by fermentation modes in okaramine-producing strains and performed genomic and comparative transcriptome analysis of P. daleae strain NBP-49626, which exhibits significant features. The NBP-49626 genome is 37.4 Mb, and it encodes 10,131 protein-encoding genes. Up to 5097 differentially expressed genes (DEGs) were identified during the submerged and semi-solid fermentation processes. The oka gene cluster, lacking regulatory and transport genes, displayed distinct transcriptional patterns in response to the fermentation modes and yield of Okaramine B. Although transcription trends of most known global regulatory genes are inconsistent with those of oka, this study identified five potential regulatory genes, including two novel Zn(II)2Cys6 transcription factors, Reg2 and Reg19. A significant correlation was also observed between tryptophan metabolism and Okaramine B yields. In addition, several transporter genes were identified as DEGs. These results were confirmed using real-time quantitative PCR. This study provides comprehensive information regarding the regulatory mechanism of Okaramine B biosynthesis in Penicillium and is critical to the further yield improvement for the development of insecticides.

CRISPR/Cas9-based genome editing and functional analysis of SlHyPRP1 and SlDEA1 genes of Solanum lycopersicum L. in imparting genetic tolerance to multiple stress factors.

CRISPR/Cas is a breakthrough genome editing system because of its precision, target specificity, and efficiency. As a speed breeding system, it is more robust than the conventional breeding and biotechnological approaches for qualitative and quantitative trait improvement. Tomato (Solanum lycopersicum L.) is an economically important crop, but its yield and productivity have been severely impacted due to different abiotic and biotic stresses. The recently identified SlHyPRP1 and SlDEA1 are two potential negative regulatory genes in response to different abiotic (drought and salinity) and biotic stress (bacterial leaf spot and bacterial wilt) conditions in S. lycopersicum L. The present study aimed to evaluate the drought, salinity, bacterial leaf spot, and bacterial wilt tolerance response in S. lycopersicum L. crop through CRISPR/Cas9 genome editing of SlHyPRP1 and SlDEA1 and their functional analysis. The transient single- and dual-gene SlHyPRP1 and SlDEA1 CRISPR-edited plants were phenotypically better responsive to multiple stress factors taken under the study. The CRISPR-edited SlHyPRP1 and SlDEA1 plants showed a higher level of chlorophyll and proline content compared to wild-type (WT) plants under abiotic stress conditions. Reactive oxygen species accumulation and the cell death count per total area of leaves and roots under biotic stress were less in CRISPR-edited SlHyPRP1 and SlDEA1 plants compared to WT plants. The study reveals that the combined loss-of-function of SlHyPRP1 along with SlDEA1 is essential for imparting significant multi-stress tolerance (drought, salinity, bacterial leaf spot, and bacterial wilt) in S. lycopersicum L. The main feature of the study is the detailed genetic characterization of SlDEA1, a poorly studied 8CM family gene in multi-stress tolerance, through the CRISPR/Cas9 gene editing system. The study revealed the key negative regulatory role of SlDEA1 that function together as an anchor gene with SlHyPRP1 in imparting multi-stress tolerance in S. lycopersicum L. It was interesting that the present study also showed that transient CRISPR/Cas9 editing events of SlHyPRP1 and SlDEA1 genes were successfully replicated in stably generated parent-genome-edited line (GEd0) and genome-edited first-generation lines (GEd1) of S. lycopersicum L. With these upshots, the study's key findings demonstrate outstanding value in developing sustainable multi-stress tolerance in S. lycopersicum L. and other crops to cope with climate change.

Transcriptome Profiling Reveals the Gene Network Responding to Low Nitrogen Stress in Wheat

As one of the essential nutrients for plants, nitrogen (N) has a major impact on the yield and quality of wheat worldwide. Due to chemical fertilizer pollution, it has become increasingly important to improve crop yield by increasing N use efficiency (NUE). Therefore, understanding the response mechanisms to low N (LN) stress is essential for the regulation of NUE in wheat. In this study, LN stress significantly accelerated wheat root growth, but inhibited shoot growth. Further transcriptome analysis showed that 8468 differentially expressed genes (DEGs) responded to LN stress. The roots and shoots displayed opposite response patterns, of which the majority of DEGs in roots were up-regulated (66.15%; 2955/4467), but the majority of DEGs in shoots were down-regulated (71.62%; 3274/4565). GO and KEGG analyses showed that nitrate reductase activity, nitrate assimilation, and N metabolism were significantly enriched in both the roots and shoots. Transcription factor (TF) and protein kinase analysis showed that genes such as MYB-related (38/38 genes) may function in a tissue-specific manner to respond to LN stress. Moreover, 20 out of 107 N signaling homologous genes were differentially expressed in wheat. A total of 47 transcriptome datasets were used for weighted gene co-expression network analysis (17,840 genes), and five TFs were identified as the potential hub regulatory genes involved in the response to LN stress in wheat. Our findings provide insight into the functional mechanisms in response to LN stress and five candidate regulatory genes in wheat. These results will provide a basis for further research on promoting NUE in wheat.

Comparison of the transcriptome and metabolome of wheat (Triticum aestivum L.) proteins content during grain formation provides insight.

Wheat is a food crop with a large global cultivation area, and the content and quality of wheat glutenin accumulation are important indicators of the quality of wheat flour. To elucidate the gene expression regulation and metabolic characteristics related to the gluten content during wheat grain formation, transcriptomic and metabolomic analyses were performed for the high gluten content of the Xinchun 26 cultivar and the low proteins content of the Xinchun 34 cultivar at three periods (7 d, 14 d and 21 d) after flowering. Transcriptomic analysis revealed that 5573 unique differentially expressed genes (DEGs) were divided into two categories according to their expression patterns during the three periods. The metabolites detected were mainly divided into 12 classes. Lipid and lipid-like molecule levels and phenylpropanoid and polyketide levels were the highest, and the difference analysis revealed a total of 10 differentially regulated metabolites (DRMs) over the three periods. Joint analysis revealed that the DEGs and DRMs were significantly enriched in starch and sucrose metabolism; the citrate cycle; carbon fixation in photosynthetic organisms; and alanine, aspartate and glutamate metabolism pathways. The genes and contents of the sucrose and gluten synthesis pathways were analysed, and the correlation between gluten content and its related genes was calculated. Based on weighted correlation network analysis (WGCNA), by constructing a coexpression network, a total of 5 specific modules and 8 candidate genes that were strongly correlated with the three developmental stages of wheat grain were identified. This study provides new insights into the role of glutenin content in wheat grain formation and reveals potential regulatory pathways and candidate genes involved in this developmental process.

Weighted gene co-expression network analysis for hub genes in colorectal cancer.

This study is designed to explore hub genes participating in colorectal cancer (CRC) development through weighted gene co-expression network analysis (WGCNA). Expression profiles of CRC and normal samples were retrieved from the Gene Expression Omnibus (GEO) and the Cancer Genome Atlas (TCGA), and were subjected to WGCNA to filter differentially expressed genes with significant association with CRC. Functional enrichment analysis and protein-protein interaction (PPI) analysis were carried out to filter the candidate genes, further and survival analysis was performed for the candidate genes to obtain potential regulatory hub genes in CRC. Expression analysis was conducted for the candidate genes and a multifactor model was established. After differential analysis and WGCNA, 289 candidate genes were filtered from the GEO and TCGA. Further functional enrichment analysis demonstrated possible regulatory pathways and functions. PPI analysis filtered 15 hub genes and survival analysis indicated a significant correlation of CLCA1, CLCA4, and CPT1A with prognosis of patients with CRC. The multifactor Cox risk model established based on the three genes revealed that if the three genes were a gene set, they had well predictive capacity for the prognosis of patients with CRC. CLCA1, CLCA4, and CPT1A express at low levels in CRC and function as core anti-tumor genes. As a gene set, they can predict prognosis well.

Weighted Gene Co-expression Network Analysis of Glioblastoma Gene Expression Microarray Data

Glioblastoma is a highly aggressive and lethal form of brain cancer characterized by its complex molecular landscape. Understanding the underlying gene expression patterns and their relationships is essential for unraveling the mechanisms driving this disease. In this study, we conducted a Weighted Gene Co-expression Network Analysis (WGCNA) on Glioblastoma gene expression microarray data to identify co-expressed gene modules and potential key regulatory genes associated with the disease. Utilizing a comprehensive dataset of Glioblastoma samples, we performed quality control and preprocessing to ensure the reliability of the data. WGCNA was employed to construct a weighted gene co-expression network, enabling the identification of modules of co-expressed genes. The correlation between these modules and clinical characteristics such as patient survival, tumor grade, and other relevant factors was assessed. Additionally, we conducted functional enrichment analysis to gain insights into the biological processes and pathways associated with the identified gene modules. Our findings revealed distinct gene modules associated with Glioblastoma progression and patient outcomes. Notably, we identified key hub genes within these modules, which may serve as potential biomarkers or therapeutic targets. Furthermore, functional enrichment analysis provided a comprehensive understanding of the biological processes and pathways influenced by these co-expressed gene modules. In conclusion, our Weighted Gene Co-expression Network analysis of Glioblastoma gene expression microarray data has shed light on the complex gene interactions and regulatory networks underlying this aggressive brain cancer. This knowledge may ultimately contribute to the development of novel diagnostic and therapeutic strategies, improving the prognosis for Glioblastoma patients.

Mutation of MYB36 affects isoflavonoid metabolism, growth, and stress responses in Lotus japonicus

AbstractIsoflavonoids are mostly produced by legumes although little is known about why and how legumes are able to regulate the biosynthesis of these particular compounds. Understanding the role of potential regulatory genes of the isoflavonoid biosynthetic pathway constitutes an important topic of research. The LORE1 mutation of the gene encoding the transcription factor MYB36 allowed the identification of this gene as a regulator of isoflavonoid biosynthesis in Lotus japonicus plants. The levels of several isoflavonoid compounds were considerably lower in two lines of Ljmyb36 mutant plants compared to the WT. In addition, we found that Ljmyb36 mutant plants were significantly smaller and showed a substantial decrease in the chlorophyll levels under normal growth conditions. The analysis of plants subjected to different types of abiotic stress conditions further revealed that mutant plants presented a higher sensitivity than WT plants, indicating that the MYB36 transcription factor is also involved in the stress response in L. japonicus plants.