Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

The PA-X host shutoff site 100 V exerts a contrary effect on viral fitness of the highly pathogenic H7N9 influenza A virus in mice and chickens

Several viruses, including influenza A virus (IAV), encode viral factors to hijack cellular RNA biogenesis processes to direct the degradation of host mRNAs, termed "host shutoff." Host shutoff enables viruses to simultaneously reduce antiviral responses and provides preferential access for viral mRNAs to cellular translation machinery. IAV PA-X is one of these factors that selectively shuts off the global host genes. However, the specific role of PA-X host shutoff activity in viral fitness of IAV remains poorly understood. Herein, we successfully mapped PA-X 100 V as a novel site important for host shutoff of the H7N9 and H5N1 viruses. By analysing the polymorphism of this residue in various subtype viruses, we found that PA-X 100 was highly variable in H7N9 viruses. Structural analysis revealed that 100 V was generally close to the PA-X endonuclease active site, which may account for its host shutoff activity. By generating the corresponding mutant viruses derived from the parental H7N9 virus and the PA-X-deficient H7N9 virus, we determined that PA-X 100 V significantly enhanced viral fitness in mice while diminishing viral virulence in chickens. Mechanistically, PA-X 100 V significantly increased viral polymerase activity and viral replication in mammalian cells. Furthermore, PA-X 100 V highly blunted the global host response in 293T cells, particularly restraining genes involved in energy metabolism and inflammatory response. Collectively, our data provided information about the intricate role of the PA-X host shutoff site in regulating the viral fitness of the H7N9 influenza virus, which furthers our understanding of the complicated pathogenesis of the influenza A virus.

Gill and brain transcriptomic analysis of mandarin fish(Siniperca chuatsi)reveals hypoxia-induced mitochondrial dysfunction and modulation of metabolism

The oxygen content in the fish ponds is facing greater challenges than before in the aquaculture of mandarin fish (Siniperca chuatsi) due to the change of climate and eutrophication. Until now, little is known about the molecular mechanisms underlying the harmful effects of hypoxia on this species. In this work, we built transcriptomes for the mandarin fish that were exposed to decreased oxygen concentration at two times points (24 h and 96 h). The respiratory metabolism activities of pyruvate kinase (PK), hexokinase (HK), lactate dehydrogenase (LDH), succinate dehydrogenase (SDH) and malate dehydrogenase (MDH) had different significantly changes during hypoxic treatment. Histological observation of the gill and brain also revealed some damages by hypoxia. A total of 196,355 transcripts were involved in the Gene Ontology analysis, and the numbers of differentially expressed genes (DEGs) in the brain and the gill between the control and experiment groups are 141 and 552 respectively involved in the different hypoxic stress time. The DEGs were then analyzed using KEGG enrichment analysis. The results showed significant differences in the expression of some genes involved in ribosome pathways,biosynthesis of amino acids, hippo signaling pathway, and pentose phosphate pathway,glycolysis/gluconeogenesis pathway and the TCA cycle. The huge number of transcriptome sequences collected in this study has enhanced the mandarin fish gene resources, and the identified DEGs and related pathway analysis give essential information for understanding biological responses to hypoxia.

Effects of hypoxia on survival, apoptosis, and the transcriptome of the Chinese yellow pond turtle (Mauremys mutica)

Mauremys mutica is a widely cultured pond turtle in China that can hold its breath underwater for up to 7 h. However, the adaptive mechanism of this hypoxia-resistant phenotype remains unknown. In the present study, no M. mutica died until 6 h of hypoxic stress. Inflammation was observed in the lungs of dead individuals along with a lung cell apoptosis rate of 12.3% in the death group, which was about six times that of the survival group. Transcriptome sequencing produced 379,659,748 clean reads, and 38,981 genes were obtained. A total of 1566, 1555 and 756 differentially expressed genes (DEGs) were detected between the survival group and the death group, the survival group and the control group, and the death group and the control group, respectively. And the DEGs were enriched in the inflammation, apoptosis, sugar transport, antioxidant, fructose, and mannose metabolism, arginine and proline metabolism, glycosaminoglycan biosynthesis, P53, and MAPK signaling pathways. This study offers new insight into the molecular mechanisms occurring in the lungs of M. mutica during acute hypoxia, which may facilitate genetic selection for hypoxia-resistant lines inM. mutica.

Identification of lncRNA in circulating exosomes as potential biomarkers for MCI among the elderly

BACKGROUND

The abnormal expression of lncRNA in elderly patients with mild cognitive impairment (MCI), and the ability of exosomes to stably carry non-coding RNAs provide a reliable physiological basis for exosomal lncRNA in plasma as a biomarker of MCI.

METHODS

This case-control study enrolled 155 patients with MCI and 155 healthy controls from a community-based population aged≥60 years. The expression profiles of lncRNA and mRNA in plasma exosomes were analyzed and validated using high-throughput RNA sequencing and qRT-PCR. Pathway enrichment analysis were performed on differentially expressed transcripts to screen for target lncRNAs and genes. Multivariate logistic regression models were used to construct clinical predictive models. The receiver operating characteristic curve was used to analyze the predictive value, with an 184-sample external database validated.

RESULTS

132 lncRNAs and 459 mRNAs were significantly changed in plasma exosomes of MCI patients compared to healthy controls. LINC001380, ENST00000484033, and ENST00000531087 were screened as candidate exo-lncRNAs for predicting MCI. In logistic regression models, odds ratios and 95%CI for target exo-IncRNAs in MCI patients compared to healthy controls were 1.15(1.03-1.28) for LINC001380, 1.21(1.10-1.34) for ENST00000484033, and 1.23(1.08-1.40) for ENST00000531087, respectively. ROC curve analysis showed that the AUC of the combined predicted probability of target lncRNAs was 70.0 %(64.1 %-76.0 %). In the external database, the AUC for the target genes ATP2A2 and PSEN1 was 69.5 %(61.8 %-77.15 %).

CONCLUSION

This study provided evidence for the specific expression of plasma exosomal lncRNAs in MCI and its possible biological mechanism. The combined detection of the expression levels of lncRNA-LINC001380, lncRNA-ENST00000484033, and lncRNA-ENST00000531087 in plasma exosomes may provide early diagnosis and prevention of cognitive impairment.

Differentiation of long Non-Coding RNA expression profiles in three Fruiting stages of grape

Grapes are considered a crucial fruit crop with extensive uses globally. Cluster compactness is an undesirable trait for the productivity of Yaghooti grape, and it reduces its desirability among consumers. The RNA-Seq data were analyzed in three stages of cluster development using the FEELnc software, leading to the identification of 849 lncRNAs. 183 lncRNAs were differentially expressed during cluster development stages. The GO and KEGG enrichment analyses of these lncRNAs revealed that they target 1,814 genes, including CKX, PG, PME, NPC2, and UGT. The analysis demonstrated a relationship between these lncRNAs and key processes such as grape growth and development, secondary metabolite synthesis, and resistance to both biotic and abiotic stresses. These findings, combined with molecular experiments on lncRNA interactions with other regulatory factors, could enhance Yaghooti grape quality and decrease cluster compactness.

IGF2BP2 orchestrates global expression and alternative splicing profiles associated with glioblastoma development in U251 cells

Glioblastoma (GBM) is a highly invasive and malignant central nervous system tumor with a median survival duration of 15 months despite multimodal therapy. The insulin-like growth factor 2 mRNA binding protein 2 (IGF2BP2) has been implicated in various cancers and is known to regulate RNA metabolism and alternative splicing (AS). However, its role in GBM remains unclear. Overexpression of IGF2BP2 led to significant alterations in gene expression, with 472 genes upregulated and 99 downregulated. Gene ontology (GO) analysis indicated enrichment in immune-related biological processes. Notably, IGF2BP2 was found to regulate AS events, with 1372 regulated AS genes (RASGs) and 2096 significantly distinct ASEs identified. Furthermore, IGF2BP2 selectively bound to 3' and 5' untranslated regions (UTRs) via GG[AU]C motifs, and IFIH1 was identified as a direct binding partner and upregulated gene upon IGF2BP2 overexpression. Functional enrichment analysis suggested that IGF2BP2 influences pathways related to RNA splicing and immune responses. Our findings demonstrate that IGF2BP2 plays a crucial role in GBM by modulating the transcriptome and AS events. The upregulation of immune-related genes and the regulation of AS by IGF2BP2 highlight its potential as a therapeutic target in GBM, particularly for immunotherapy. The study provides a foundation for further investigation into the molecular mechanisms of IGF2BP2 in GBM and its implications for cancer treatment.

Sex specific gene expression is present prior to metamorphosis in the sea urchin

A profound collaboration between the germline and somatic cells of an organism is the creation of a functional gonad. Here we establish a foundation for studying molecular gonadogenesis in the sea urchin by use of RNA-seq, quantitative mRNA measurements, and in-situ hybridizations throughout the life cycle of the variegated sea urchin, Lytechinus variegatus (Lv). We found through three distinct analyses that the ovary and testis of this echinoderm expresses unique transcripts involved in gametogenesis, and also discovered uncharacterized gene products unique to each gonad. We further developed a pipeline integrating timepoint RNA-seq data throughout development to identify hallmark gene expression in gonads. We found that meiotic and candidate genes involved in sex determination are first expressed surprisingly early during larval growth, and well before metamorphosis. We further discovered that individual larvae express varying amounts of male- or female-hallmarks before metamorphosis, including germline, oocyte, sperm, and meiotic related genes. These distinct male- or female-gonad gene profiles may indicate the onset of, and commitment to, development of a bipotential gonad primordium, and may include metabolic differences, supported by the observation that transcripts involved in glycolysis are highly enriched in the ovary compared to the testis. Together these data support a hypothesis that sex determination is initiated prior to metamorphosis in the sea urchin and that the many uncharacterized genes unique to each gonad type characterized herein may reveal unique pathways and mechanisms in echinoderm reproduction.

A gain-of-function mutation at the C-terminus of FT-D1 promotes heading by interacting with 14-3-3A and FDL6 in wheat

Vernalization and photoperiod pathways converging at FT1 control the transition to flowering in wheat. Here, we identified a gain-of-function mutation in FT-D1 that results in earlier heading date (HD), and shorter plant height and spike length in the gamma ray-induced eh1 wheat mutant. Knockout of the wild-type and overexpression of the mutated FT-D1 indicate that both alleles are functional to affect HD and plant height. Protein interaction assays demonstrated that the frameshift mutation in FT-D1eh1 exon 3 led to gain-of-function interactions with 14-3-3A and FDL6, thereby enabling the formation of florigen activation complex (FAC) and consequently activating a flowering-related transcriptomic programme. This mutation did not affect FT-D1eh1 interactions with TaNaKR5 or TaFTIP7, both of which could modulate HD, potentially via mediating FT-D1 translocation to the shoot apical meristem. Furthermore, the 'Segment B' external loop is essential for FT-D1 interaction with FDL6, while residue Y85 is required for interactions with TaNaKR5 and TaFTIP7. Finally, the flowering regulatory hub gene, ELF5, was identified as the FT-D1 regulatory target. This study illustrates FT-D1 function in determining wheat HD with a suite of interaction partners and provides genetic resources for tuning HD in elite wheat lines.

Sex-specific transcriptomic effects of low-dose inorganic arsenic exposure on bone marrow-derived macrophages

Both tissue-resident macrophages and monocytes recruited from the bone marrow that transform into tissue-resident cells play critical roles in mediating homeostasis as well as in the pathology of inflammatory diseases. Inorganic arsenic (iAs) is the most common drinking water contaminant worldwide and represents a major public health concern. There are numerous diseases caused by iAs exposure in which macrophages are involved, including cardiovascular disease, cancer, and increased risk of (respiratory) infectious diseases. Notably, prenatal iAs exposure is also associated with negative birth outcomes and developmental immunotoxicity (DIT) contributing to long-term adverse outcomes of these immune-related diseases. Therefore, understanding the effects of iAs exposure on macrophages, particularly during immune development or tissue injury and inflammation, can help us better grasp the full range of arsenic immunotoxicity and better design therapeutic targets for iAs-induced diseases particularly in exposed populations. In contrast to prior published studies which often only focused on the effect of iAs on mature macrophages after development, in this study, we analyzed the transcriptome of M0-, M1- and M2-polarized male and female murine bone marrow-derived macrophages (BMDMs) which were exposed to iAs during the differentiation phase, as a model to study iAs (developmental) immunotoxicity. We identified differentially expressed genes by iAs in a sex- and stimulation-dependent manner and used bioinformatics tools to predict protein-protein interactions, transcriptional regulatory networks, and associated biological processes. Overall, our data suggest that M1-stimulated, especially female-derived, BMDMs are most susceptible to iAs exposure during differentiation. Most notably, we observed significant downregulation of major proinflammatory transcription factors, like IRF8, and its downstream targets, as well as genes encoding proteins involved in pattern recognition and antigen presentation, such as TLR7, TLR8, and H2-D1, potentially providing causal insight regarding the role of (early-life) arsenic exposure in perturbing immune responses to infectious diseases. We also observed significant downregulation of genes involved in processes crucial to coordinating a proinflammatory response including leukocyte migration, differentiation, and cytokine and chemokine production and response. Finally, we discovered that 24 X-linked genes were dysregulated in iAs-exposed female stimulation groups compared to only 3 across the iAs-exposed male stimulation groups. These findings elucidate the potential mechanisms underlying the sex-differential iAs-associated immune-related disease risk.

Warm temperature perceived at the vegetative stage affects progeny seed germination in natural accessions of Arabidopsis thaliana

Temperatures perceived early in the life cycle of mother plants can affect the germination of the offspring seeds. In Arabidopsis thaliana, vernalisation-insensitive mutants showed altered germination response to elevated maternal temperature, hence revealing a strong genetic determinism. However, the genetic control of this maternal effect and its prevalence across natural populations remain unclear. Here, we exposed a collection of European accessions of A. thaliana to increased temperature during the vegetative phase and assessed germination in their progeny to identify the genetic basis of transgenerational germination response. We found that genotypes with rapidly germinating progeny after early maternal exposure to elevated temperature originated from regions with low-light radiation. Combining genome-wide association, expression analysis and functional assays across multiple genetic backgrounds, we show a central role for PHYB in mediating the response to maternally perceived temperature at the vegetative stage. Differential gene expression analysis in leaves identified a similar genetic network as previously found in seed endosperm under elevated temperature, supporting the pleiotropic involvement of PHYB signalling across different tissues and stages. This provides evidence that complex environmental responses modulated by the maternal genotype can rely on a consistent set of genes yet produce different effects at the different stages of exposure.

IGF2BP1 promotes multiple myeloma with chromosome 1q gain via increasing CDC5L expression in an m6A-dependent manner

Multiple myeloma (MM) patients with chromosome 1q gain (1q+) are clinically and biologically heterogeneous. The underlying molecular mechanisms are still under investigation, while the identification of targets for effective therapy of this subgroup of MM patients is urgently needed. We aimed to investigate the clinical significance and the regulatory mechanisms of insulin-like growth factor 2 messenger RNA (mRNA) binding protein 1 (IGF2BP1), a N6-methyladenosine (m6A) reader, in MM patients with 1q+. We found that MM patients with 1q+ exhibit a significantly higher level of IGF2BP1 mRNA than controls, while higher IGF2BP1 expression predicted a worse prognosis in MM patients with 1q+. IGF2BP1 overexpression promoted cell proliferation and G1-to-S phase transition of the cell cycle in NCI-H929 cells. Through comprehensive in silico analyses of existing public datasets and in-house generated high-throughput sequencing datasets, along with in vitro experiments, we identified CDC5L as a target of IGFBP1, which can bind to the m6A sites of CDC5L mRNA to up-regulate its protein abundance. Higher CDC5L expression also predicted a worse prognosis of MM patients with 1q+. Moreover, both knockdown and mutation of CDC5L attenuated the pro-proliferative effect of IGF2BP1. Furthermore, IGF2BP1 inhibitor BTYNB effectively inhibited CDC5L expression in MM cells with 1q+ and suppressed the proliferation of these cells in vitro and in vivo. Therefore, IGF2BP1 acts as a post-transcriptional enhancer of CDC5L in an m6A-dependent manner to promote the proliferation of MM cells with 1q+. Our work identified a novel IGF2BP1-CDC5L axis and provided new insight into developing targeted therapeutics for MM patients with 1q+.

Effects of high-temperature stress on gene expression related to photosynthesis in two jujube (Ziziphus jujuba Mill.) varieties

Elevated temperatures critically impact crop growth, development, and yield, with photosynthesis being the most temperature-sensitive physiological process in plants. This study focused on assessing the photosynthetic response and genetic adaptation of two different heat-resistant jujube varieties 'Junzao' (J) and 'Fucuimi' (F), to high-temperature stress (42°C Day/30°C Night). Comparative analyses of leaf photosynthetic indices, microstructural changes, and transcriptome sequencing were conducted. Results indicated superior high-temperature adaptability in F, evidenced by alterations in leaf stomatal behavior - particularly in J, where defense cells exhibited significant water loss, shrinkage, and reduced stomatal opening, alongside a marked increase in stomatal density. Through transcriptome sequencing 13,884 differentially expressed genes (DEGs) were identified, significantly enriched in pathways related to plant-pathogen interactions, amino acid biosynthesis, starch and sucrose metabolism, and carbohydrate metabolism. Key findings include the identification of photosynthetic pathway related DEGs and HSFA1s as central regulators of thermal morphogenesis and heat stress response. Revealing their upregulation in F and downregulation in J. The results indicate that these genes play a crucial role in improving heat tolerance in F. This study unveils critical photosynthetic genes involved in heat stress, providing a theoretical foundation for comprehending the molecular mechanisms underlying jujube heat tolerance.

Cov-trans: an efficient algorithm for discontinuous transcript assembly in coronaviruses

BACKGROUND

Discontinuous transcription allows coronaviruses to efficiently replicate and transmit within host cells, enhancing their adaptability and survival. Assembling viral transcripts is crucial for virology research and the development of antiviral strategies. However, traditional transcript assembly methods primarily designed for variable alternative splicing events in eukaryotes are not suitable for the viral transcript assembly problem. The current algorithms designed for assembling viral transcripts often struggle with low accuracy in determining the transcript boundaries. There is an urgent need to develop a highly accurate viral transcript assembly algorithm.

RESULTS

In this work, we propose Cov-trans, a reference-based transcript assembler specifically tailored for the discontinuous transcription of coronaviruses. Cov-trans first identifies canonical transcripts based on discontinuous transcription mechanisms, start and stop codons, as well as reads alignment information. Subsequently, it formulates the assembly of non-canonical transcripts as a path extraction problem, and introduces a mixed integer linear programming to recover these non-canonical transcripts.

CONCLUSION

Experimental results show that Cov-trans outperforms other assemblers in both accuracy and recall, with a notable strength in accurately identifying the boundaries of transcripts. Cov-trans is freely available at https://github.com/computer-Bioinfo/Cov-trans.git .

Discovery of Ureido-Containing Alteropeptilides and Intramolecular Cyclized Alteramides in Pseudoalteromonas flavipulchra S16 by Promoter Engineering of Cryptic Biosynthetic Gene Clusters

Pseudoalteromonas are abundant in the oceans and possess great potential in the synthesis of bioactive natural products. Although many secondary metabolite biosynthetic gene clusters have been identified from Pseudoalteromonas genomes, most of their products have not been characterized. In this study, endogenous constitutive promoters with high transcriptional activity were obtained from Pseudoalteromonas flavipulchra S16 through RNA-seq and a fluorescence assay of luciferase gene expression. Through in situ promoter replacement two silent biosynthetic gene clusters (BGCs) were successfully activated, leading to production of intramolecular cyclized alteramides and two novel ureido-containing linear peptides, alteropeptilides. This study provides a feasible approach for the activation of silent BGCs and the mining of novel compounds from marine bacteria.

Host lipid metabolism influences the variation in resistance of Pekin ducks to duck hepatitis A virus genotype 3

Duck viral hepatitis (DVH) is a common and serious acute infectious disease that has a significantly impact on the duck farming industry. Duck hepatitis A virus type 3 (DHAV-3) is the major causative agent of DVH in East Asia. Host factor indicators of resistance to DHAV-3 in Pekin ducks were investigated using resistant (Z7R) and susceptible (Z7S) duck lines. Before DHAV-3 infection, Z7R had significantly higher HDL-C and LDL-C levels than Z7S. The results of population verification showed that Pekin ducks with HDL-C and/or LDL-C concentrations within their maximum 5 % confidence interval were highly resistant to DHAV-3. RNA-seq identified fifteen differentially expressed genes, primarily involved in lipid metabolism. Additionally, lipidomics identified one hundred distinct metabolites involved in glycerophospholipid metabolism. The ACSL6 gene was found to be significantly associated with OAHFA, PC, and PE. ACSL6, PE, PC, HDLC, and LDL-C co-regulated hepatic lipid metabolism. In conclusion, our results reveal that HDL-C and LDL-C may serve as markers of anti-DHAV-3 infection and lipid metabolism may be related to a potential mechanism of antiviral activity in Pekin ducks, providing a theoretical basis for future studies on the interaction between lipid metabolism and DHAV-3.

Regulation of human interferon signaling by transposon exonization

Innate immune signaling is essential for clearing pathogens and damaged cells and must be tightly regulated to avoid excessive inflammation or autoimmunity. Here, we found that the alternative splicing of exons derived from transposable elements is a key mechanism controlling immune signaling in human cells. By analyzing long-read transcriptome datasets, we identified numerous transposon exonization events predicted to generate functional protein variants of immune genes, including the type I interferon receptor IFNAR2. We demonstrated that the transposon-derived isoform of IFNAR2 is more highly expressed than the canonical isoform in almost all tissues and functions as a decoy receptor that potently inhibits interferon signaling, including in cells infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Our findings uncover a primate-specific axis controlling interferon signaling and show how a transposon exonization event can be co-opted for immune regulation.

Metabolomic and Transcriptomic Analysis Reveals Metabolic-Immune Interactions in Choroid Neovascularization

Choroid neovascularization (CNV) is a distinct type of age-related macular degeneration (AMD) with a poor prognosis and responsible for the majority of vision loss in the elderly population. The laser-induced CNV model is a well-established animal model frequently used to study CNV. In this study, we performed an integrated analysis of metabolomic and transcriptomic data from CNV samples, utilizing multiple approaches including single-sample gene set enrichment analysis (ssGSEA), correlation analysis, and weighted gene co-expression network analysis (WGCNA), alongside various bioinformatics platforms, to identify key metabolic and immune signatures and to investigate their interplay during angiogenesis. Dominant infiltration of macrophages and monocytes was detected and a positive correlation between dysregulated riboflavin metabolism and angiogenesis pathways was characterized. Hub genes such as ectonucleotide pyrophosphatase/phosphodiesterase 1 (Enpp1) and acid phosphatase 5, tartrate resistant (ACP5) emerged as potential central regulators of immune-metabolic crosstalk in CNV. The classification of the immune and metabolic landscape and their critical interactions in CNV models will enhance the understanding of the pathogenesis of neovascular AMD and other neovascular eye diseases, contributing to the development of multi-targeted therapeutic strategies with better efficacy.

Alternative Splicing Landscape in Mouse Skeletal Muscle and Adipose Tissue: Effects of Intermittent Fasting and Exercise

Alternative splicing contributes to diversify the cellular protein landscape, but aberrant splicing is implicated in many diseases. To which extent mis-splicing contributes to insulin resistance as the causal defect of type 2 diabetes and whether this can be reversed by lifestyle interventions is largely unknown. Therefore, RNA sequencing data from skeletal muscle and adipose tissue of diabetes-susceptible NZO mice treated with or without intermittent fasting and of healthy C57BL/6J mice subjected to exercise were analyzed for alternative splicing differences using Whippet and rMATS. Diet and exercise interventions triggered comparable levels of splicing changes, although the splicing profile of skeletal muscle appeared to be more flexible than that of adipose tissue, with 72-114 differential splicing events in muscle and less than 25 in adipose tissue. Splicing changes induced by time-restricted feeding, alternate-day fasting and exercise were generally mild, with a maximal percent spliced in (PSI) difference of 67%, indicating that alternative splicing plays a rather minor role in lifestyle-induced adaptations of muscle and adipose tissue in mice. However, intron retention contributed to the regulation of gene expression, influencing genes whose expression was directly linked to phenotypic parameters (e.g. Eno2 and Pan2). Alternate-day fasting promoted skipping of exon 7 in Mlxipl (coding for ChREBP), thereby affecting the glucose sensing module of this carbohydrate-responsive transcription factor. Both intermittent fasting and exercise training led to alternative splicing of known diabetes-related GWAS genes (e.g. Abcc8, Ifnar2, Smarcad1), highlighting the potential metabolic relevance of these changes.

Yield increment and transcriptome response caused by blue light treatment in Hericium coralloides

BACKGROUND

Hericium coralloides is a traditional edible and medicinal mushroom. Light is a key factor in forming fruiting bodies of fungi; however, the effects of different light on the yield and morphogenesis of H. coralloides are still unknown. Therefore, the morphology, yield, and transcriptome of H. coralloides under blue, red, and white light conditions were investigated.

RESULT

Fruiting bodies under blue light exhibited superior morphological traits, such as milky white color, larger size, elongated stalks, and higher spine count, leading to higher yields. Different light treatments led to dramatic transcriptome changes ranging from 10,827 differentially expressed genes (DEGs) induced by blue light in Blue-4d to 11,375 DEGs induced by red light in Red-4d and accounted for 64.56% to 67.81% of all expressed genes. This massive amount of light-responsive genes has never been reported in fungi. Gene Ontology analysis showed that light affected nearly all aspects of life in H. coralloides; suggesting that the influence of light on fungi may have been underestimated. Blue light-induced yield increment may be achieved by specifically upregulating the growth-related processes such as DNA replication, chromosomes, and cell division.

CONCLUSIONS

This study offers preliminary insights into the potential role of blue light in modulating gene expression and yield stimulation in H. coralloides, potentially improving cultivation practice.

DCP1A, a MEK substrate, regulates the self-renewal and differentiation of mouse embryonic stem cells

Mitogen-activated extracellular signal-regulated kinase (MEK) inhibitors are widely applied to maintain pluripotency, while prolonged MEK inhibition compromises the developmental potential of mouse embryonic stem cells (ESCs). To understand the mechanism of MEK in pluripotency maintenance, we first demonstrated that MEK regulates gene expression at post-transcriptional steps. Consistently, many of the 66 MEK substrates identified by quantitative phosphoproteomics analysis are involved in RNA processing. We further confirmed that MEK1 phosphorylates S563 of DCP1A, an mRNA decapping cofactor and processing body (P body) component. DCP1A, as well as two other P body components, EDC4 and DCP2, are required for the self-renewal and differentiation of ESCs, indicating the role of P bodies in ESCs. Dephosphorylation of DCP1A S563 facilitates both self-renewal and differentiation of ESCs through promoting P body formation and RNA storage. In summary, our study identified 66 MEK substrates supporting the extracellular signal-regulated kinase (ERK)-independent function of MEK and revealed that DCP1A, phosphorylated by MEK, regulates ESC self-renewal and differentiation through modulating P body formation.

Machine learning analysis of the orbitofrontal cortex transcriptome of human opioid users identifies Shisa7 as a translational target relevant for heroin-seeking leveraging a male rat model

BACKGROUND

Identifying neurobiological targets predictive of the molecular neuropathophysiological signature of human opioid use disorder (OUD) could expedite new treatments. OUD is characterized by dysregulated cognition and goal-directed behavior mediated by the orbitofrontal cortex (OFC), and next-generation sequencing could provide insights regarding novel targets.

METHODS

Here, we used machine learning to evaluate human post-mortem OFC RNA-sequencing datasets from heroin-users and controls to identify transcripts predictive of heroin use. To determine a causal link to OUD-related behaviors, we examined the effects of overexpressing the top target gene in a translational rat model of heroin-seeking and behavioral updating. Additionally, we determined the effects of overexpression on the rat OFC transcriptome compared to that of human heroin users. Co-immunoprecipitation/mass-spectrometry from rat OFC elucidated the protein complex of the novel target.

RESULTS

Our machine learning approach identified SHISA7 as predictive of human heroin users. Shisa7 is understudied but appears to be an auxiliary protein of GABAA or AMPA receptors. In rats, Shisa7 expression positively-correlated with heroin-seeking behavior. Overexpressing Shisa7 in the OFC augmented heroin-seeking and impaired behavioral updating for sucrose-based operant contingency. RNA-sequencing of rat OFC revealed gene co-expression networks regulated by Shisa7-overexpression similar to human heroin-users. Finally, co-immunoprecipitation/mass-spectrometry showed that heroin influences Shisa7 binding to glutamatergic and GABAergic receptor subunits. Both gene expression signatures and Shisa7 protein complex emphasized perturbations of neurodegenerative and neuroimmune processes.

CONCLUSIONS

Our findings suggest that OFC Shisa7 is a critical driver of neurobehavioral pathology related to drug-seeking behavior and behavioral updating, identifying a potential therapeutic target for OUD.

Cucumber JASMONATE ZIM-DOMAIN 8 interaction with transcription factor MYB6 impairs waterlogging-triggered adventitious rooting

Waterlogging is a serious abiotic stress that drastically decreases crop productivity by damaging the root system. Jasmonic acid (JA) inhibits waterlogging-induced adventitious root (AR) formation in cucumber (Cucumis sativus L.). However, we still lack a profound mechanistic understanding of how JA governs AR formation under waterlogging stress. JASMONATE ZIM-DOMAIN (JAZ) proteins are responsible for repressing JA signaling in a transcriptional manner. In this study, we showed that overexpressing CsJAZ8 inhibited the formation of ARs triggered by waterlogging. Molecular analyses revealed that CsJAZ8 inhibited the activation of the R2R3-MYB transcription factor CsMYB6 via direct interaction. Additionally, silencing of CsMYB6 negatively impacted AR formation under waterlogging stress, as CsMYB6 could directly bind to the promoters of 1-aminocyclopropane-1-carboxylate oxidase 2 gene CsACO2 and gibberellin 20-oxidase gene CsGA20ox2, facilitating the transcription of these genes. The overexpression of CsACO2 and CsGA20ox2 led to increased levels of ethylene and gibberellin, which facilitated AR formation under waterlogging conditions. On the contrary, silencing these genes resulted in contrasting phenotypes of AR formation. These results highlight that the transcriptional cascade of CsJAZ8 and CsMYB6 plays a critical role in regulating hormonal-mediated cucumber waterlogging-triggered AR formation by inhibiting ethylene and gibberellin accumulation. We anticipate that our findings will provide insights into the molecular mechanisms that drive the emergence of AR in cucumber plants under waterlogging stress.

Transcriptome-derived evidence reveals the regulatory network in the skeletal muscle of the fast-growth mstnb-/- male tilapia

Myostatin (Mstn) negatively regulates muscle growth and Mstn deficiency induced "double-skeletal muscle" development in vertebrates, including tilapias. In this study, we performed a transcriptomic analysis of skeletal muscle from both wild-type and mstnb-/- males to investigate the molecular mechanisms underlying skeletal muscle hypertrophy in mstnb-/- mutants. We identified 4697 differentially expressed genes (DEGs), 113 differentially expressed long non-coding RNAs (DE lncRNAs), 211 differentially expressed circular RNAs (DE circRNAs), and 98 differentially expressed microRNAs (DE miRNAs). The DEGs were significantly enriched in proteasome and ubiquitin-mediated proteolysis pathways. Cis- and trans-targeting genes of DE lncRNAs were also notably enriched in the above two pathways. The putative host genes of DE circRNAs linked to myofibrils, contractile fibers, and so on. Additionally, DE miRNAs were associated with ubiquitin-mediated proteolysis and key signaling pathways, including AMPK, FoxO, and mTOR. Furthermore, the core competing endogenous RNA (ceRNA) network was constructed comprising 31 DEGs, 37 DE miRNAs, 14 DE circRNAs, and 45 DE lncRNAs. The key roles of ubiquitin-proteasome system were highlighted in the ceRNA network. Taken together, this study provides a novel perspective on muscle mass increase in Mstn mutants through the repression of protein degradation and facilitates our understanding of the molecular mechanisms of skeletal muscle hypertrophy in fish.

Increased nuclear factor I-mediated chromatin access drives transition to androgen receptor splice variant dependence in prostate cancer

Androgen receptor (AR) splice variants, of which ARv7 is the most common, are increased in castration-resistant prostate cancer, but the extent to which they drive AR activity is unclear. We generated a subline of VCaP cells (VCaP16) that is resistant to the AR inhibitor enzalutamide (ENZ). AR activity in VCaP16 is driven by ARv7, independently of full-length AR (ARfl), and its cistrome and transcriptome mirror those of ARfl in VCaP cells. ARv7 expression increases rapidly in response to ENZ, but there is a delay in gaining chromatin binding and transcriptional activity, which is associated with increased chromatin accessibility. AR and nuclear factor I (NFI) motifs are most enriched at more accessible sites, and NFIB/X knockdown greatly diminishes ARv7 function. These findings indicate that ARv7 can drive the AR program but that its activity is dependent on adaptations that increase chromatin accessibility to enhance its intrinsically weak chromatin binding.

A negatively charged region within carboxy-terminal domain maintains proper CTCF DNA binding

As an essential regulator of higher-order chromatin structures, CCCTC-binding factor (CTCF) is a highly conserved protein with a central DNA-binding domain of 11 tandem zinc fingers (ZFs), which are flanked by amino (N-) and carboxy (C-) terminal domains of intrinsically disordered regions. Here we report that CRISPR deletion of the entire C-terminal domain of alternating charge blocks decreases CTCF DNA binding but deletion of the C-terminal fragment of 116 amino acids results in increased CTCF DNA binding and aberrant gene regulation. Through a series of genetic targeting experiments, in conjunction with electrophoretic mobility shift assay (EMSA), circularized chromosome conformation capture (4C), qPCR, chromatin immunoprecipitation with sequencing (ChIP-seq), and assay for transposase-accessible chromatin with sequencing (ATAC-seq), we uncovered a negatively charged region (NCR) responsible for weakening CTCF DNA binding and chromatin accessibility. AlphaFold prediction suggests an autoinhibitory mechanism of CTCF via NCR as a flexible DNA mimic domain, possibly competing with DNA binding for the positively charged ZF surface area. Thus, the unstructured C-terminal domain plays an intricate role in maintaining proper CTCF-DNA interactions and 3D genome organization.

Transcriptomic analysis of male diamondback moth antennae: Response to female semiochemicals and allyl isothiocyanate

Female semiochemicals and allyl isothiocyanate (AITC) attract moths, and the moths use odorant-degrading enzymes (ODEs) to break down the excess odor. By identifying antennae-specific ODEs, researchers have established the molecular foundation for odorant degradation and signal inactivation in insects. This enables further exploration of new pest control methods. Currently, the degradation of female semiochemicals and AITC has received limited attention, inspiring this study to identify target ODEs in diamondback moths through transcriptome analysis. Sequencing of antennae from male adults (MA) exposed to female adults (FA) and AITC yielded a substantial 54.18 Gb of clean data, revealing 2276 differentially expressed genes (DEGs) between the MA and MA-FA treatments, and 629 DEGs between MA and MA-AITC treatments. The analysis of MAs exposed to FAs and AITC identified 29 and 17 ODEs, respectively, mainly involving aldehyde dehydrogenases (ALDHs), alcohol dehydrogenases (ADs), cytochrome P450s (CYPs), and UDP-glucuronosyltransferases (UGTs). Pathway analysis revealed primary enrichment in glycolysis/gluconeogenesis and fatty acid degradation in female adult treatments. In contrast, AITC treatments showed major enrichment in pathways related to pentose and glucuronate interconversions, retinol metabolism, and ascorbate and aldarate metabolism. Additionally, qRT-PCR analysis validated the expression patterns of 10 ODE genes in response to these treatments, with varying results observed among the genes. These findings indicate significant changes in ODE expression levels, providing a molecular foundation for identifying potential targets for behavioral inhibitors.

Exploring the mechanism of seed shattering in Psathyrostachys juncea through histological analysis and comparative transcriptomics

BACKGROUND

Seed shattering (SS) negatively impacts seed yield in Psathyrostachys juncea. Understanding and improving the SS trait requires elucidating the regulatory mechanisms of SS and identifying the key genes involved.

RESULTS

This study presents a comprehensive analysis of the abscission zone (AZ) structures at four developmental stages in two P. juncea genotypes. High-SS P. juncea (H) exhibited a significantly higher SS rate than low-SS P. juncea (L) at all four developmental stages. Anatomical analysis revealed that the degree of lignification in the AZ cell walls is related to the integrity of the abscission structure. The degradation of the AZ in H occurred earlier and was more severe compared to L. At different developmental stages of the AZ, H exhibited higher cellulase and polygalacturonase activities and higher abscisic acid contents compared to L. Conversely, L showed higher lignin, cytokinin, auxin, and gibberellin contents than H. Transcriptomic analysis identified key metabolic pathways related to SS in P. juncea, such as phenylpropanoid biosynthesis, fructose and mannose metabolism, galactose metabolism, and pentose and glucuronate interconversions. The integration of morphological, histological, physiochemical, and metabolic data led to the identification of critical genes, including AUX1, CKX, ABF, GH3, 4CL, CCoAOMT, BGAL, Gal, and PG. The roles of these genes were involved in the regulation of plant hormones and in the synthesis and degradation of cell walls within the AZ.

CONCLUSIONS

This study provides an in-depth understanding of the regulatory mechanisms of SS in P. juncea through comparative transcriptomic analysis. The SS in P. juncea may result from the degradation of the cell wall regulated by cell wall hydrolases genes. The genes identified in this study provide a basis for the genetic improvement of SS traits and serve as a reference for research on other grass species.

Tissue-specific chromatin accessibility and transcriptional regulation in maize cold stress response

Maize, a vital crop globally, faces significant yield losses due to its sensitivity to cold stress, especially in temperate regions. Understanding the molecular mechanisms governing maize response to cold stress is crucial for developing strategies to enhance cold tolerance. However, the precise chromatin-level regulatory mechanisms involved remain largely unknown. In this study, we employed DNase-seq and RNA-seq techniques to investigate chromatin accessibility and gene expression changes in maize root, stem, and leaf tissues subjected to cold treatment. We discovered widespread changes in chromatin accessibility and gene expression across these tissues, with strong tissue specificity. Cold stress-induced DNase I hypersensitive sites (coiDHSs) were associated with differentially expressed genes, suggesting a direct link between chromatin accessibility and gene regulation under cold stress. Motif enrichment analysis identified ERF transcription factors (TFs) as central regulators conserved across tissues, with ERF5 emerging as pivotal in the cold response regulatory network. Additionally, TF co-localization analysis highlighted six TF pairs (ERF115-SHN3, ERF9-LEP, ERF7-SHN3, LEP-SHN3, LOB-SHN3, and AS2-LOB) conserved across tissues but showing tissue-specific binding preferences. These findings indicate intricate regulatory networks in maize cold response. Overall, our study provides insights into the chromatin-level regulatory mechanisms underpinning maize adaptive response to cold stress, offering potential targets for enhancing cold tolerance in agricultural contexts.

Partial replacement by ammonium nutrition enhances Brassica napus growth by promoting root development, photosynthesis, and nitrogen metabolism

Nitrogen (N) is crucial for plant growth, available primarily as nitrate (NO3-) and ammonium (NH4+). However, its presence in soil is often limited, necessitating strategies to augment N availability. This study delves into the enigmatic interplay between NO3- and NH4+ in fostering the growth of Brassica napus, an important oil crop worldwide. Here, we examined the growth responses of 49 B. napus varieties to five NH4+:NO3- ratios (12:0, 9:3, 3:9, 1:11, 0:12). In general, the biomass of 49 rapeseed varieties increased with the decrease of NH4+ to NO3- ratios in the growth environment. However, different varieties may respond diversely to the mixed N sources, or sole NO3- or NH4+ condition. For some cultivars, the mixed N supply significantly enhanced the plant growth compared with the sole NO3- conditions. Thus, we further investigate the morphological, physiological and molecular response of rapeseed to the mixed N source condition using sole NO3- as a control. The results show that partial replacement by ammonium nutrition in the environment can promote rapeseed root development, net photosynthetic rate and NO3- reduction compared to NO3--only conditions. Using transcriptome analysis, we found a total of 399 and 465 genes which were differentially expressed in root and shoot under A1N11 compared to A0N12 treatments, respectively. Genes involved in photosynthesis, N uptake and assimilation were upregulated by mixed N supplies. These findings highlight that the mixed N supply primarily stimulates B. napus growth by enhancing root development, photosynthesis and N metabolism in the shoot. Such insights are crucial for optimizing N form selection in B. napus to enhance plant performance and N use efficiency.

Differentially Expressed Genes (DEGs) in Umbelliferone (UMB) Producing Endophytic Fusarium oxysporum (ZzEF8) Following Epigenetic Modification

Despite several studies documenting secondary metabolite (SM) production by endophytes, their commercial use is often limited owing to the research lacunae in the underlying biosynthetic pathway and the corresponding metabolic flux. Combining epigenetic modulation with RNA-Seq analysis constitutes a promising approach for inducing regulatory gene(s) and thereby identifying their role in SM biosynthesis. Our earlier studies had identified the hypomethylating effects of prednisone in umbelliferone (UMB) (7-hydroxyl coumarin) producing endophytic Fusarium oxysporum isolate, ZzEF8 isolated from Zingiber zerumbet rhizomes. Hypomethylating effect of prednisone (300 μM) in ZzEF8 was validated in present experiments revealing decrease in 5-mC content (0.09 ± 0.01%) in prednisone treated ZzEF8 (PrZzEF8) compared to untreated control (UtZzEF8) (0.36 ± 0.01%). Subsequent RNA-Seq analysis detected transcriptional alterations in PrZzEF8 compared to UtZzEF8. Transcripts with significant differential expression (-2 ≥ fold change (FC) ≥ 2; q-value < 0.05) were detected for 64 transcripts, with 60 upregulated and four downregulated in PrZzEF8. Upregulated differentially expressed genes (DEGs) were annotated as transmembrane transporters, non-ribosomal peptide synthetase (NRPS), Type I and III polyketide synthase (PKS), phytoene dehydrogenase, bifunctional lycopene cyclase/phytoene synthase, geranylgeranyl pyrophosphate synthase and various genes involved in nutrient assimilation, transcription factors and transporters regulating metabolite export. Expression analysis of the selected DEGs were validated by qRT-PCR. Present study proposes UMB biosynthesis through acetate-malonate pathway from acetate units via a pentaketide intermediate in ZzEF8 instead of the phenylpropanoid pathway reported in plants. Study is of relevance as the insights gained into the UMB biosynthetic pathway in ZzEF8 will help in strategizing scale-up of UMB production.

Characteristics of Gracilariopsis lemaneiformis hydrocolloids and their effects on intestine PPAR signaling and liver lipid metabolism in Oreochromis niloticus: A multiomics analysis

This study evaluated the effects of Gracilariopsis lemaneiformis hydrocolloids on Nile tilapia (Oreochromis niloticus) using an advanced multiomics approach (transcriptome and proteome) linked with genomic isoform structure to elucidate the biofunctions of G. lemaneiformis hydrocolloids. The results showed that G. lemaneiformis hydrocolloids did not affect growth, as indicated by the nonsignificant differences in growth and blood biochemical indicators. Regarding the response, both intestine and liver tissues were assessed. These findings indicate that 20 % G. lemaneiformis hydrocolloids enhanced cytokine expression, which may contribute to a biological function in the intestine and liver of O. niloticus. Genome and proteome profiles indicated that G. lemaneiformis hydrocolloids upregulated the intestine and liver peroxisome proliferator-activated receptor (PPAR) signaling pathway, nucleocytoplasmic transport, steroid biosynthesis, and histidine metabolism. In contrast, co-factor biosynthesis, nucleocytoplasmic transport, tryptophan metabolism, arginine and proline metabolism, arginine biosynthesis, and ribosome activity were downregulated. These findings indicate that G. lemaneiformis hydrocolloids significantly affect liver lipid and carbohydrate metabolism. Proteomics analysis revealed that G. lemaneiformis hydrocolloids upregulated the PPAR signaling pathway, playing a crucial role in lipid metabolism. In summary, 20 % G. lemaneiformis hydrocolloids are primarily involved in modulating the intestine and liver PPAR signaling pathway to regulate lipid metabolism.

Fibroblast-specific TGF-β signaling mediates cardiac dysfunction, fibrosis, and hypertrophy in obese diabetic mice

AIMS

Transforming growth factor (TGF)-β is up-regulated in the diabetic myocardium and may mediate fibroblast activation. We aimed at examining the role of TGF-β-induced fibroblast activation in the pathogenesis of diabetic cardiomyopathy.

METHODS AND RESULTS

We generated lean and obese db/db mice with fibroblast-specific loss of TbR2, the Type 2 receptor-mediating signaling through all three TGF-β isoforms, and mice with fibroblast-specific Smad3 disruption. Systolic and diastolic function, myocardial fibrosis, and hypertrophy were assessed. Transcriptomic studies and in vitro experiments were used to dissect mechanisms of fibroblast activation. Fibroblast-specific TbR2 loss attenuated systolic and diastolic dysfunction in db/db mice. The protective effects of fibroblast TbR2 loss in db/db mice were associated with attenuated fibrosis and reduced cardiomyocyte hypertrophy, suggesting that in addition to their role in fibrous tissue deposition, TGF-β-stimulated fibroblasts may also exert paracrine actions on cardiomyocytes. Fibroblast-specific Smad3 loss phenocopied the protective effects of fibroblast TbR2 loss in db/db mice. Db/db fibroblasts had increased expression of genes associated with oxidative response (such as Fmo2, encoding flavin-containing monooxygenase 2), matricellular genes (such as Thbs4 and Fbln2), and Lox (encoding lysyl oxidase). Ingenuity pathway analysis (IPA) predicted that neurohumoral mediators, cytokines, and growth factors (such as AGT, TGFB1, and TNF) may serve as important upstream regulators of the transcriptomic profile of diabetic mouse fibroblasts. IPA of scRNA-seq data identified TGFB1, p53, MYC, PDGF-BB, EGFR, and WNT3A/CTNNB1 as important upstream regulators underlying fibroblast activation in db/db hearts. Comparison of the transcriptome of fibroblasts from db/db mice with fibroblast-specific Smad3 loss and db/db Smad3 fl/fl controls identified Thbs4 [encoding thrombospondin-4 (TSP-4), a marker of activated fibroblasts] as a candidate diabetes-induced fibrogenic mediator. However, in vitro experiments showed no significant activating effects of matricellular or intracellular TSP-4 on cardiac fibroblasts.

CONCLUSION

Fibroblast-specific TGF-β/Smad3 signaling mediates ventricular fibrosis, hypertrophy, and dysfunction in Type 2 diabetes.

Exploration of key mechanisms underlying the therapeutic effects of AMD3100 on attenuating lipopolysaccharide-induced acute lung injury in mice

Context

AMD3100, a CXCR4 antagonist, has beneficial effects immaculate in the treatment of acute lung injury (ALI).

Objective

ALI is a severe inflammatory condition associated with poor prognosis and limited treatment options. AMD3100, has therapeutic effects that reduce ALI. Our study explored the regulatory mechanisms of AMD3100 in alleviating the injury of lipopolysaccharide (LPS)-induced ALI in mice.

Materials and Methods

Male ICR mice were randomly divided into control, LPS-treated, AMD3100-treated, and LPS + AMD3100-treatment groups. The histological changes of lung tissues from different groups were evaluated using hematoxylin and eosin staining. Lung injury was measured by ELISA and lung wet/dry ratio. Moreover, lung tissues from the four groups were subjected to transcriptome sequencing followed by differential expression, functional enrichment, protein-protein interaction (PPI) networks, and transcription factor analyses. The validation of mRNAs and protein levels were conducted with qRT-PCR and ELISA.

Results

Hematoxylin and eosin staining combined with the concentration of IL-1 and IL1-β and lung wet/dry ratios revealed that AMD3100 reduced the level of LPS-induced lung injury. Analysis of the transcriptome sequencing data identified 294 differentially expressed genes in the LPS-induced ALI mouse model. Based on the PPI network and module analysis, hub targets of AMD3100, such as Cxcl10 and Cxcl9, were identified in module 1, and hub targets, such as Cxcl12 and Cxcl1, were identified in module 2. Cxcl10 and Cxcl9 are involved in the Toll-like receptor signaling pathway, and Cxcl12 and Cxcl1 arae enriched in the nuclear factor-kappa B signaling pathway. Cxcl19, Cxcl10, and Cxcl1 are targeted by transcription factors like NF-κB. The validation of mRNAs and protein levels conducted by PCR and ELISA supported our transcriptome data.

Conclusions

Our findings indicate that AMD3100 may exhibit a therapeutic effect on LPS-induced ALI in mice by modulating multiple chemokines to inhibit the Toll-like receptor/nuclear factor-kappa B signaling pathway.

The SlDLK2 receptor, involved in the control of arbuscular mycorrhizal symbiosis, regulates hormonal balance in roots

Arbuscular mycorrhiza (AM) represents a symbiotic mutualistic association between most land plants and Glomeromycota fungi. AM fungi develops specialized intraradical and highly branched structures, called arbuscules, where bidirectional exchange of nutrients between plant and fungi partners occurs, improving plant growth and fitness. Transcriptional reprogramming and hormonal regulation are necessary for the formation of the arbuscules. SlDLK2, a member of the third clade from the DWARF14 family of α, β-hydrolases closely related to the strigolactone receptor D14, is a negative regulator of arbuscule branching in tomato, but the underlying mechanisms are unknown. We explored the possible role of SlDLK2 on the regulation of hormonal balance. RNA-seq analysis was performed on roots from composite tomato plants overexpressing SlDLK2 and in control plants transformed with the empty vector. Analysis of transcriptomic data predicted that significantly repressed genes were enriched for genes related to hormone biosynthesis pathways, with a special relevance of carotenoid/apocarotenoid biosynthesis genes. Stable transgenic SlDLK2 overexpressing (OE) tomato lines were obtained, and hormone contents were analyzed in their roots and leaves. Interesting significant hormonal changes were found in roots of SlDLK2 OE lines with respect to the control lines, with a strong decrease on jasmonic acid and ABA. In addition, SlDLK2 OE roots showed a slight reduction in auxin contents and in one of the major strigolactones in tomato, solanacol. Overall, our results suggest that the negative regulation of AM symbiosis by SlDLK2 is associated with the repression of genes involved in the biosynthesis of AM-promoting hormones.

Overexpression of ZmEULD1b enhances maize seminal root elongation and drought tolerance

Drought stress damages the growth and development of maize, which results in the maize yield reduction. A strong root system improves the drought tolerance in maize. A previous genome-wide association study for the maize seminal root length under drought stress conditions identified a significant SNP, which was located in the ZmEULD1b gene. Here, we show that enhancing ZmEULD1b expression in transgenic maize increases seminal root length, as well as plant tolerance to water deficit. Meanwhile, ZmEULD1b overexpression influences the stomatal development and promotes water-use efficiency of maize. Further, transcriptome analysis of wild type and ZmEULD1b-OE plants show that several peroxidases and ABA-related pathway genes are upregulated in the ZmEULD1b-OE plants under drought stress conditions. Additionally, rhizosphere microbiota analyses of plant root confirm that overexpression of ZmEULD1b improves the abundance of growth-promoting microbes in the maize root system under drought stress conditions. Collectively, the data presented in this work suggest that ZmEULD1b could be a valuable gene resource or selection target for the drought-tolerant genetic improvement of maize.

Maize ZmWRKY71 gene positively regulates drought tolerance through reactive oxygen species homeostasis

Drought stress severely affects plant growth and yield. The plant-specific WRKY transcription factors play an important role in regulating the plant response to abiotic stresses. In this study, we identified a group I WRKY gene from maize, designated ZmWRKY71. Real-time quantitative reverse transcription-PCR analysis revealed that ZmWRKY71 was predominantly expressed in the roots and was induced by drought. ZmWRKY71 was localized in the nucleus and showed transcriptional activity in yeast. Heterologous overexpression of ZmWRKY71 improved drought tolerance in yeast and Arabidopsis. Compared with the wild type, the overexpression lines showed a higher survival rate under drought stress with reduced malondialdehyde content and elevated antioxidant enzyme activities. In contrast, mutation of ZmWRKY71 in maize leads to increased sensitivity to drought stress, reduced survival, elevated concentrations of reactive oxygen species, and increased malondialdehyde content. RNA-sequencing analysis revealed that the expression patterns of genes associated with translation, membrane, and oxidoreductase activity pathways were altered under drought stress. Yeast one-hybrid, dual-luciferase, and electrophoretic mobility shift assays confirmed that ZmWRKY71 was capable of directly binding to the W-box element in the promoter region of ZmPOD42 (Zm00001eb330550). Taken together, the results show that ZmWRKY71 positively regulates maize drought tolerance. This research enriches the drought tolerance gene pool for maize and provides a theoretical basis for maize drought tolerance breeding.

Integrated Transcriptomic and Metabolomic Analyses Reveal Changes in Aroma- and Taste-Related Substances During the Withering Process of Black Tea

Withering is one of the major processing steps critical for the quality of black tea. In this study, we investigated the mechanisms underlying the physicochemical changes in metabolites and gene expression during the withering process of black tea using metabolomic and transcriptomic approaches, respectively. Based on gas chromatography/mass spectrometry non-targeted metabolomic approaches (GC-MS) and ultra-high performance liquid chromatograph-tandem mass spectrometry (UHPLC-MS/MS), a total of 76 volatile compounds and 160 non-volatile compounds were identified from tea leaves, respectively. RNA-seq analysis revealed that the number of differentially expressed genes (DEGs) for the comparative combination of withering time (i.e., W4h, W6h, W8h, W10h, and W12h) compared with CK (i.e., fresh leaves) were 3634, 2906, 4127, 5736, and 7650, respectively. The core genes in starch metabolism, namely alpha-amylase (AMY) and beta-amylase (BAM), were upregulated as withering time increased. AMY and BAM contributed to the decomposition of starch to increase the soluble sugars. The content of tea leaf alcohols and aldehydes, which are the vital contributors for greenish aroma, gradually decreased as withering time increased due to the downregulation of associated genes while the compounds related to sweet and fruity characteristics increased due to the upregulated expression of related genes. Most DEGs involved in amino acids were significantly upregulated, leading to the increase in free amino acids content. However, DEGs involved in catechins metabolism were generally downregulated during withering, and resulted in a reduction in catechins content and the accumulation of theaflavins. The same trend was observed in alpha-linolenic acid metabolism-related genes that were downregulated and enhanced the reduction in grassy aroma in black tea. The weighted gene co-expression network analysis (WGCNA) of DEGs showed that one module can be associated with more components and one component can be regulated by various modules. Our findings provide new insights into the quality formation of black tea during the withering process.

Analysis of gonadal transcriptome reveals core long non-coding RNA-mRNA regulatory network in sea cucumber Apostichopus japonicus

Apostichopus japonicus is a representative temperate sea cucumber species, that mainly inhabits in coastal zone of the continental shelf. With high nutritional value and important medical value, A. japonicus become an important commercial aquaculture species and produce significant economic value in recent years. A. japonicus has no sexual dimorphism that can be used to distinguish female and male individuals by external appearance and morphology. The phenotype sex can be only detected by dissecting and observing gonad tissue, thus the breeding efficiency could be greatly reduced. This limitation has hindered the advancement of selective breeding programs and sea cucumber industry. To investigate the genetic basis of reproductive biology in A. japonicus, advanced sequencing techniques, such as next- and third-generation sequencing, have been employed to explore the roles of non-coding RNAs and other genetic factors, offering new insights into sex determination mechanisms. To further gain a deeper understanding of the knowledge underlying lncRNAs in gonadal differentiation, we conducted a comparative transcriptome sequencing analysis of gonadal tissues from both sexes. In our research, a total of 3990 novel lncRNAs and 1441 differentially expressed lncRNAs were identified between female and male gonads. Additionally, a molecular regulatory network indicating lncRNA-mRNA interactions was constructed based on transcriptional profiles, which provide insights into the potential cis- and trans- target genes of lncRNAs. The gonadal transcriptome analysis identified a number of novel long non-coding RNAs involved in female and male reproduction process. Both cis- and trans-acting regulatory networks indicating lncRNA-mRNA interaction were constructed based on transcriptional profiles. These findings provide new insights into the lncRNA-mediated regulation of reproductive biology in marine invertebrates, indicating the crucial roles of long non-coding sequences in regulating expression profiles. Further, the GO and KEGG enrichment analyses of cis- and trans- targeted mRNA for differentially expressed lncRNA indicated that sexual reproduction (GO:0019953), germ cell development (GO:0007281), and negative regulation of hormone secretion (GO:0046888) are potentially involved in gonadal differentiation through the regulation of long non-coding sequences. Notably, besides the classical reproduction related signaling pathway like Gonadotropin-releasing hormone (GnRH) secretion (ko04929), several regulatory pathways, such as Epidermal growth factor receptor (ErbB) signaling pathway (ko04012), TGF-beta signaling pathway (ko04350), and neurotrophin signaling pathway (ko04722) were also enriched and potentially involved in sex differentiation and gonadal development.

Barbatula nuda: an economically valuable freshwater fish that accepts phytoplankton as first food

Barbatula nuda is considered a promising emerging species to diversify small cold-water fish aquaculture worldwide due to its rapid growth and delicious flesh. However, limited information on larval development and nutrition is available. In this study, 7-day feeding experiments were performed to evaluate three different initial diets (zooplankton, phytoplankton, and artificial microdiet) in the zoo group, algae group, and AD group on growth, development, and digestion of larvae B. nuda. The results showed that there was no significant difference in survival rate among the three groups (p > 0.05). The algae group exhibited the highest feed intake success rate and body weight (p < 0.05), the best intestinal development with the protruded intestinal mucosa, and visible intestinal microvillus. Pepsase and trypsin enzyme activities in the algae group larvae were significantly higher than those in the other two groups (p < 0.05). Transcriptome data showed that the mechanistic target of rapamycin pathway of B. nuda fed with phytoplankton was activated, and the metabolisms of carbohydrate were significantly more active than those in the other two groups. As omnivorous fish, B. nuda could accept zooplankton, phytoplankton, and microdiet as initial diets with its survival unaffected, but B. nuda fed with phytoplankton exhibited better growth status and digestive tract development and higher digestive enzyme activities than those fed with other two diets. Therefore, phytoplankton was a suitable initial diet for B. nuda. Our findings provide guidance for the artificial breeding of B. nuda and a theoretical basis for research on fish initial diet.

PagHAM4a-PagSCL21 and PagHAM4b-PagTCP20 modules positively regulate cambial activity and its differentiation into secondary xylem in poplar

Stem secondary xylem produced by cambial division and differentiation is the main source of tree biomass. Secondary xylem formation involves a complex transcriptional regulatory network; however, the underlying mechanism is still being explored. Here, we report that PagHAM4a and PagHAM4b are positive regulators of cambial differentiation into secondary xylem in hybrid poplar (Populus alba × Populus glandulosa clone 84K). Overexpression of PagHAM4a and PagHAM4b enhanced cambial activity and increased the number of secondary xylem cells in the stems of poplar. By contrast, single or double mutations of PagHAM4a and PagHAM4b generated by CRISPR/Cas9 decreased cambial activity, leading to a significant reduction of secondary xylem. Neither overexpression nor mutation of the two genes affected the size of vessels and fibers in xylem. Both PagHAM4a- and PagHAM4b-regulated gene networks were mainly centered at the stage when cambium had just initiated secondary growth, but the molecular networks regulated by the two genes were distinct. Further analysis revealed that PagSCL21 and PagTCP20 are direct targets of PagHAM4a and PagHAM4b, respectively, and their overexpression also promoted cambial differentiation into secondary xylem. Taken together, we identified two novel key regulatory modules in poplar, PagHAM4a-PagSCL21 and PagHAM4b-PagTCP20, which provide new insights into the mechanism of secondary xylem formation in trees.

Muscle tissue transcriptome of F1 Angus-Nellore bulls and steers feedlot finished: impacts on intramuscular fat deposition

BACKGROUND

Castration is a common practice in beef cattle production systems to manage breeding and enhance meat quality by promoting intramuscular fat (IMF) deposition, known as marbling. However, the molecular mechanisms that are influenced by castration in beef cattle are poorly understood. The aim of this study was to identify differentially expressed genes (DEGs) and metabolic pathways that regulate IMF deposition in crossbred cattle by RNA sequencing (RNA-Seq) of skeletal muscle tissue. Six hundred and forty F1 Angus-Nellore bulls and steers (n = 320/group) were submitted to feedlot finishing for 180 days. Sixty Longissimus thoracis muscle samples were collected randomly from each group in the hot carcass (at slaughter) and 48 h post-mortem (at deboning), at between 12th and 13th thoracic vertebrae. Three muscle samples of each group were randomly selected for RNA-Seq analysis, while the post-deboning meat samples were submitted to determination of IMF content.

RESULTS

Steers had a 2.7-fold greater IMF content than bulls (5.59 vs. 2.07%; P < 0.01). A total of 921 DEGs (FDR < 0.05) were identified in contrast between Bulls versus Steers; of these, 371 were up-regulated, and 550 were down-regulated. Functional transcriptome enrichment analysis revealed differences in biological processes and metabolic pathways related to adipogenesis and lipogenesis, such as insulin resistance, AMPK, cAMP, regulation of lipolysis in adipocytes, and PI3K-Akt signaling pathways. Candidate genes such as FOXO1, PPARG, PCK2, CALM1, LEP, ADIPOQ, FASN, FABP4, PLIN1, PIK3R3, ROCK2, ADCY5, and ADORA1 were regulated in steers, which explains the expressive difference in IMF content when compared to bulls.

CONCLUSIONS

The current findings suggest the importance of these pathways and genes for lipid metabolism in steers with greater IMF. Notably, this study reveals for the first time the involvement of the PI3K-Akt pathway and associated genes in regulating IMF deposition in F1 Angus-Nellore cattle. Castration influenced DEGs linked to energy metabolism and lipid biosynthesis, highlighting key molecular players responsible for IMF accumulation post-castration in beef cattle.

MiR-26a Inhibits Porcine Adipogenesis by Regulating ACADM and ACSL1 Genes and Cell Cycle Progression

MicroRNAs play essential roles in biological processes by regulating gene expression at the post-transcriptional level. Our previous studies suggested the role of miR-26a in porcine fat accumulation. Here, through gain- and loss-of-function analyses, we first showed that miR-26a increased the proliferation of porcine preadipocytes by promoting cell division and that miR-26a inhibited the preadipocyte differentiation. Next, acyl-CoA dehydrogenase, medium chain (ACADM) was revealed to promote the proliferation and differentiation of preadipocytes for the first time. Then, it was revealed that miR-26a regulates adipogenesis by directly binding to the 3' untranslated region of ACADM and the long-chain acyl-Co A synthetase 1 (ACSL1) gene, a previously known regulator of adipogenesis. Finally, RNA-sequencing, performed on preadipocytes overexpressing miR-26a, identified 337 differentially expressed genes in the early stage of adipogenesis; among them, nine genes were characterized as potential targets of miR-26a. The 337 genes were mainly involved in Gene Ontology terms related to cell division, indicating that cell cycle progression was also a major event regulated by miR-26a during adipogenesis. We provide novel data for understanding the molecular mechanisms underlying adipogenesis, which will contribute to controlling fat accumulation in animals.

Differential gene expression analysis pipelines and bioinformatic tools for the identification of specific biomarkers: A review

In recent years, the role of bioinformatics and computational biology together with omics techniques and transcriptomics has gained tremendous importance in biomedicine and healthcare, particularly for the identification of biomarkers for precision medicine and drug discovery. Differential gene expression (DGE) analysis is one of the most used techniques for RNA-sequencing (RNA-seq) data analysis. This tool, which is typically used in various RNA-seq data processing applications, allows the identification of differentially expressed genes across two or more sample sets. Functional enrichment analyses can then be performed to annotate and contextualize the resulting gene lists. These studies provide valuable information about disease-causing biological processes and can help in identifying molecular targets for novel therapies. This review focuses on differential gene expression (DGE) analysis pipelines and bioinformatic techniques commonly used to identify specific biomarkers and discuss the advantages and disadvantages of these techniques.

Citric acid treatment inhibits fading of sorghum (Sorghum bicolor) by modulating the accumulation of flavonoids

Sorghum seeds can discolor during storage. Treatment of seeds with citric acid improves sensory quality and antioxidant activity. This study compared the differences in phenotypic and antioxidant activity between citric acid-treated and water-treated sorghum seeds. The study used transcriptomics and metabolomics approaches to investigate the regulatory mechanisms. The ∆a, ∆b and ∆l values of citric acid-treated sorghum seeds significantly increased after 6 months of storage. The SOD, POD and CAT enzyme activities of the citric acid-treated group were 1.94, 1.91 and 2.45 times higher than those of the control, respectively. The joint transcriptome and metabolome analysis showed that the citric acid-induced changes were mainly focused on the flavonoid biosynthetic pathway. Citric acid treatment up-regulated CHS, ANR, MYB and bHLH genes and promoted flavonoid accumulation. In conclusion, citric acid treatment promotes flavonoid accumulation, delays sorghum seed discoloration, and enhances antioxidant activity and storage life.

miR1432 negatively regulates cold tolerance by targeting OsACAs

miRNAs function as negative regulators that significantly influence plant growth and stress responses. Within rice and other monocotyledonous plants, miR1432 plays a conserved role in seed development and disease resistance. However, its involvement in the response to abiotic stresses remains unclear. Our study aimed to elucidate this mechanism by predicting the targeting of the rice P-type IIB Ca2+ ATPase gene OsACAs by miR1432 and identifying its cleavage sites via 5'RACE. We observed induced expression of miR1432 and its target gene, OsACA6, under abiotic stresses. Overexpression (OX) of miR1432 and suppression of OsACA6 resulted in reduced cold, salt, and drought tolerance, while OsACA6 suppression/knockout and OX had opposite effects on cold tolerance. Additionally, miR1432 may target other OsACA6 homologs. RNA-sequencing data highlighted the differential expression of stress-related genes in miR1432-overexpressing rice. Furthermore, miR1432-overexpressing rice exhibited weakened vigor, dwarfism, yellowing leaves and reduced fertility. Collectively, our results strongly suggest that miR1432 not only negatively modulates abiotic stress tolerance by suppressing Ca2+ ATPase gene(s) but also influences plant growth and development.

RNA binding protein ZCCHC24 promotes tumorigenicity in triple-negative breast cancer

Triple-negative breast cancer (TNBC) lacks the expression of hormone and HER2 receptors and is highly malignant with no effective therapeutic targets. In TNBC, the cancer stem-like cell (CSC) population is considered to be the main cause of resistance to treatment. Thus, the therapeutic targeting of this population could substantially improve patient survival. Here, we identify the RNA-binding protein ZCCHC24 as enriched in the mesenchymal-like TNBC population. ZCCHC24 promotes the expression of a set of genes related to tumorigenicity and treatment resistance by directly binding to the cis-element "UGUWHWWA" in their mRNAs, thereby stabilizing them. One of the ZCCHC24 targets, ZEB1, is a transcription factor that promotes the expression of cancer stemness genes and reciprocally induces ZCCHC24 expression. ZCCHC24 knockdown by siRNAs shows a therapeutic effect and reduces the mesenchymal-like cell population in TNBC patient-derived xenografts. ZCCHC24 knockdown also has additive effects with the BET inhibitor JQ1 in suppressing tumor growth in TNBC patient-derived xenografts.

Ubiquitin regulatory X (UBX) domain-containing protein 6 is essential for autophagy induction and inflammation control in macrophages

Ubiquitin regulatory X (UBX) domain-containing protein 6 (UBXN6) is an essential cofactor for the activity of the valosin-containing protein p97, an adenosine triphosphatase associated with diverse cellular activities. Nonetheless, its role in cells of the innate immune system remains largely unexplored. In this study, we report that UBXN6 is upregulated in humans with sepsis and may serve as a pivotal regulator of inflammatory responses via the activation of autophagy. Notably, the upregulation of UBXN6 in sepsis patients was negatively correlated with inflammatory gene profiles but positively correlated with the expression of Forkhead box O3, an autophagy-driving transcription factor. Compared with those of control mice, the macrophages of mice subjected to myeloid cell-specific UBXN6 depletion exhibited exacerbated inflammation, increased mitochondrial oxidative stress, and greater impairment of autophagy and endoplasmic reticulum-associated degradation pathways. UBXN6-deficient macrophages also exhibited immunometabolic remodeling, characterized by a shift to aerobic glycolysis and elevated levels of branched-chain amino acids. These metabolic shifts amplify mammalian target of rapamycin pathway signaling, in turn reducing the nuclear translocation of the transcription factor EB and impairing lysosomal biogenesis. Together, these data reveal that UBXN6 serves as an activator of autophagy and regulates inflammation to maintain immune system suppression during human sepsis.

The Spatial-Temporal Alternative Splicing Profile Reveals the Functional Diversity of FXR1 Isoforms in Myogenesis

Alternative splicing (AS) is a fundamental mechanism contributing to proteome diversity, yet its comprehensive landscape and regulatory dynamics during skeletal muscle development remain largely unexplored. Here, the temporal AS profiles are investigated during myogenesis in five vertebrates, conducting comprehensive profiling across 27 developmental stages in skeletal muscle and encompassing ten tissues in adult pigs. The analysis reveals a pervasive and evolutionarily conserved pattern of alternative exon usage throughout myogenic differentiation, with hundreds of skipped exons (SEs) showing developmental regulation, particularly within skeletal muscle. Notably, this study identifies a muscle-specific SE (exon 15) within the Fxr1 gene, whose AS generates two dynamically expressed isoforms with distinct functions: the isoform without exon 15 (Fxr1E15 -) regulates myoblasts proliferation, while the isoform incorporating exon 15 (Fxr1E15+) promotes myogenic differentiation and fusion. Transcriptome analysis suggests that specifically knocking-down Fxr1E15+ isoform in myoblasts modulates differentiation by influencing gene expression and splicing of specific targets. The increased inclusion of exon 15 during differentiation is mediated by the binding of Rbm24 to the intron. Furthermore, in vivo experiments indicate that the Fxr1E15+ isoform facilitates muscle regeneration. Collectively, these findings provide a comprehensive resource for AS studies in skeletal muscle development, underscoring the diverse functions and regulatory mechanisms governing distinct Fxr1 isoforms in myogenesis.

Transcriptomics reveals the regulation of the immune system of the mushroom-forming fungus Schizophyllum commune during interaction with four competitors

Mushroom-forming fungi frequently encounter competitors during their lifecycle, but their defense mechanisms remain largely unexplored. We studied the response of the mushroom-forming fungus Schizophyllum commune during interaction with the fungal competitors Trichoderma harzianum, Trichoderma aggressivum and Purpureocillium lilacinum and the bacterial competitor Serratia quinivorans. Transcriptomics revealed 632 up-regulated genes in the direct interaction zone, which were enriched in small secreted proteins and transporters. A set of 26 genes were up-regulated during all interactions, indicating a core transcriptomic defense response. In the non-interacting edge of the mycelium of S. commune, there were 154 up-regulated genes, suggesting that there is a systemic response due to a signal that reaches unaffected areas. The GATA zinc finger transcription factor gene gat1 was up-regulated during interaction and a Δgat1 strain displayed increased colonization by T. harzianum. Previously linked to mushroom development, this transcription factor apparently has a dual role. Moreover, 138 genes were up-regulated during both interaction and mushroom development, indicating priming of the defense response during development to prepare the fruiting body for future interactions. Overall, we unveiled a defensive response of S. commune during interaction with fungal and bacterial competitors and identified a regulator of this response.

Brain Specific RagA Overexpression Triggers Depressive-Like Behaviors in Mice via Activating ADORA2A Signaling Pathway

Neuroinflammation hallmarks the pathology of depression although the etiological complexity has not yet been resolved. Previous studies demonstrate that bacterial lipopolysaccharide induces depressive-like behaviors by activating RagA-mTOR-p70S6K signaling pathway. The current project aims to investigate whether and how brain-specific RagA overexpression triggers depressive-like behaviors in mice. Full-length RagA cDNA is cloned into the mammalian expression vector under the control of brain specific promoter, and subsequently overexpressed in the brain of mouse embryos. Indeed, RagA transgenic mice exhibit depressive-like behaviors and memory impairments. RNA-seq profiling of the prefrontal cortex (PFC) transcriptome highlights adenosine A2a receptor (ADORA2A) as a key differentially expressed gene (DEG). Western blotting confirms that ADORA2A and phospho-p70S6K are markedly elevated in RagA transgenic mice. Behavioral assessments demonstrate that ADORA2A inhibitor istradefylline markedly attenuates depressive-like behaviors. Further metabolomics reveals that N-acetylserotonin and several depression-related metabolites are downregulated while proteomic profiling showed that OLIG1 and other proteins are significantly regulated in RagA transgenic mice. Collectively, RagA overexpression alters the expression patterns of signaling proteins and the metabolism of depression-associated metabolites. RagA may cause depressive-like behaviors in mice via activating p70S6K/ADORA2A signaling pathway. Thus, RagA-p70S6K-ADORA2A signaling pathway may be a target for the development of new antidepressant therapies.