Haloxylon ammodendron (C.A. Mey.), an endangered desert tree with excellent drought and salinity tolerance, provides a unique genotype to characterize and understand the tolerance mechanisms. In this study, four RNA-Seq libraries were constructed and sequenced from H. ammodendron under salinity stress. Total 12 027 differentially expressed genes (DEGs) were identified, in which 4 023, 3 517, 4 487 genes were differentially expressed under light salinity stress (200 mM NaCl), moderate salinity stress (400 mM NaCl), and severe salinity stress (800 mM NaCl), respectively. The up-regulated DEGs included several transcription factors (e.g., MYB and bHLH), hormone-related genes (e.g., cytochrome P450), protein kinases (e.g., Atpk2-Atpk19 like), and genes involved in carbon metabolism (e.g., UDP glycosyltransferase), osmotic regulation (e.g., proline transporter), and ubiquitin proteasome system (e.g., ubiquitin-conjugating enzymes). Heat shock proteins were identified as positive regulators of salinity tolerance in H. ammodendron. The expression patterns of 13 DEGs verified by real-time quantitative PCR were identically consistent with the variations in transcript abundance identified by RNA-Seq. Our results provide new insights into molecular mechanism of H. ammodendron in response to salinity stress.
Analyzing the vast amount of omics data generated comprehensively by high-throughput sequencing technology is of utmost importance for scientists. In this context, we propose HiOmics, a cloud-based platform equipped with nearly 300 plugins designed for the comprehensive analysis and visualization of omics data. HiOmics utilizes the Element Plus framework to craft a user-friendly interface and harnesses Docker container technology to ensure the reliability and reproducibility of data analysis results. Furthermore, HiOmics employs the Workflow Description Language and Cromwell engine to construct workflows, ensuring the portability of data analysis and simplifying the examination of intricate data. Additionally, HiOmics has developed DataCheck, a tool based on Golang, which verifies and converts data formats. Finally, by leveraging the object storage technology and batch computing capabilities of public cloud platforms, HiOmics enables the storage and processing of large-scale data while maintaining resource independence among users.
Background: In recent years, miR-152 has been dysregulated in a variety of tumors and used as a tumor suppressor. Nevertheless, its role in nasopharyngeal carcinoma (NPC) remains unidentified. Materials and methods: Real-time quantitative PCR (polymerase chain reaction) was performed to analyze the expression of miR-152 in NPC cell lines. MiR-152 expression profiles in NPC tissues were obtained from Gene Expression Omnibus (GEO GSE36682). The effect of miR-152 on the invasion and proliferation of NPC cells was determined through cell invasion, wound healing, and cell viability assays. Apoptosis was examined by flow cytometry, and Western blot was performed to measure expression of the target gene. Pyrosequencing was used to detect the methylation level of NPC cells. Results: In this study, miR-152 was downregulated in the NPC tissues and cell lines. When miR-152 was enhanced, the invasion and migration of NPC cells were inhibited. However, miR-152 had no effect on the proliferation of NPC cells. Luciferase reporter gene analysis was performed, and the results showed that DNMT1 (DNA (cytosine-5)-methyltransferase 1) is a direct target of miR-152 in NPC cells. DNMT1 downregulation and miR-152 overexpression both reversed the effects of miR-152 inhibition on the NPC cells. In addition, miR-152 expression increased as a result of the inhibition of the methylation level of miR-152 when DNMT1 expression was downregulated. Conclusion: The overexpression of miR-152 inhibited the migration and invasion of NPC cells by targeting DNMT1. Furthermore, DNMT1 regulated miR-152 expression through DNA methylation. Overall, the novel miR-152-DNMT1 regulatory circuit may provide better understanding of the pathogenesis of NPC and new epigenetic therapeutic target in NPC. Keywords: miR-152, DNMT1, NPC, methylation
Metabolite can regulate stem cell (SC) function in vitro and in vivo. But very little is known about whether or not metabolites function as signaling mediators of SC and niche cross talk during tissue regeneration. The hair follicle stem cells (HFSCs) and melanocyte stem cells (McSC) reside in a shared niche and collaborate in the regeneration of pigmented hair follicles. We show here that deletion of the Notch pathway co-factor RBP-J specifically in mouse HFSCs triggers adjacent McSCs to precociously differentiate in the niche at the beginning of hair regeneration stage. Transcriptome screen revealed elevated expression of retinoic acid (RA) metabolic process genes as a result of RBP-J deletion in HFSCs. The increased level of RA in the niche sensitizes McSCs to differentiation signal KIT-ligand by increasing its c-Kit receptor protein level in vivo. Using genetic approach, we further pinpointed HFSCs as the source of KIT-ligand in the niche, which normally increases at the beginning of hair regeneration cycle. We discovered that RA mediates the cross talk of two different types of SCs in a shared niche. And HFSCs play an essential role of safeguarding the differentiation refractory niche environment for neighboring McSCs by regulating metabolite level in vivo.
ABSTRACT Hypoxic preconditioning (HPC) alleviates the selective and delayed neuronal death in the hippocampal CA1 region induced by transient global cerebral ischemia (tGCI). This type of cell death may include different programmed cell death mechanisms, namely, apoptosis and necroptosis. Although apoptotic signaling is well defined, the mechanisms that underlie neuronal necroptosis are yet to be fully elucidated. In this study, we investigated whether HPC protects neurons from cerebral ischemia‐induced necroptosis. We observed that tGCI up‐regulated the expression of receptor‐interacting protein (RIP) 3 and increased the interaction of RIP1‐RIP3 in CA1 at the early stage of reperfusion. The pretreatment with HPC or necrostatin‐1 decreased the expression of RIP3 and the formation of RIP1–RIP3 after tGCI. We also found that HPC decreased the expression and the activity of caspase‐8 in CA1 after tGCI, and notably, the pretreatment with Z‐VAD‐FMK, a pan‐caspase inhibitor, did not trigger necroptosis but attenuated the tGCI‐induced neuronal damage. Furthermore, we demonstrated that HPC decreased the activation of calcium‐calmodulin kinase (CaMK) IIa and the interaction of RIP1 and CaMKIIα induced by tGCI. Intriguingly, the pretreatment with a CaMKs inhibitor KN‐93 before tGCI resulted in significantly reduced RIP1–3 interaction and tGCI‐induced neuronal damage. Finally, we ascertained that HPC prevented the dephosphorylation of dynamin‐related protein 1 (Drp1)–Ser637 (serine 637) and inhibited the translocation of Drp1 to mitochondria induced by tGCI. Importantly, the treatment with a Drp1 inhibitor Mdivi‐1 or necrostatin‐1 before tGCI also abolished Drp1 dephosphorylation at Ser637 and mitochondrial translocation. Taken together, our results highlight that HPC attenuates necroptotic neuronal death induced by tGCI via Drp1‐dependent mitochondrial signaling pathways mediated by CaMKIIα inactivation.—Zhan, L., Lu, Z., Zhu, X., Xu, W., Li, L., Li, X., Chen, S., Sun, W., Xu, E. Hypoxic preconditioning attenuates necroptotic neuronal death induced by global cerebral ischemia via Drp1‐dependent signaling pathway mediated by CaMKIIα inactivation in adult rats. FASEB J. 33, 1313–1329 (2019). www.fasebj.org
Abstract The subfamily Agavoideae comprises crassulacean acid metabolism (CAM), C3, and C4 plants with a young age of speciation and slower mutation accumulation, making it a model crop for studying CAM evolution. However, the genetic mechanism underlying CAM evolution remains unclear because of lacking genomic information. This study assembled the genome of Agave hybrid NO.11648, a constitutive CAM plant belonging to subfamily Agavoideae, at the chromosome level using data generated from high-throughput chromosome conformation capture, Nanopore, and Illumina techniques, resulting in 30 pseudo-chromosomes with a size of 4.87 Gb and scaffold N50 of 186.42 Mb. The genome annotation revealed 58 841 protein-coding genes and 76.91% repetitive sequences, with the dominant repetitive sequences being the I-type repeats (Copia and Gypsy accounting for 18.34% and 13.5% of the genome, respectively). Our findings also provide support for a whole genome duplication event in the lineage leading to A. hybrid, which occurred after its divergence from subfamily Asparagoideae. Moreover, we identified a gene duplication event in the phosphoenolpyruvate carboxylase kinase (PEPCK) gene family and revealed that three PEPCK genes (PEPCK3, PEPCK5, and PEPCK12) were involved in the CAM pathway. More importantly, we identified transcription factors enriched in the circadian rhythm, MAPK signaling, and plant hormone signal pathway that regulate the PEPCK3 expression by analysing the transcriptome and using yeast one-hybrid assays. Our results shed light on CAM evolution and offer an essential resource for the molecular breeding program of Agave spp.
The prokaryotic CRISPR/Cas9 system has recently emerged as a powerful tool for genome editing in mammalian cells with the potential to bring curative therapies to patients with genetic diseases. However, efficient in vivo delivery of this genome editing machinery and indeed the very feasibility of using these techniques in vivo remain challenging for most tissue types. Here, we show that nonreplicable Cas9/sgRNA ribonucleoproteins can be used to correct genetic defects in skin stem cells of postnatal recessive dystrophic epidermolysis bullosa (RDEB) mice. We developed a method to locally deliver Cas9/sgRNA ribonucleoproteins into the skin of postnatal mice. This method results in rapid gene editing in epidermal stem cells. Using this method, we show that Cas9/sgRNA ribonucleoproteins efficiently excise exon80, which covers the point mutation in our RDEB mouse model, and thus restores the correct localization of the collagen VII protein in vivo. The skin blistering phenotype is also significantly ameliorated after treatment. This study provides an in vivo gene correction strategy using ribonucleoproteins as curative treatment for genetic diseases in skin and potentially in other somatic tissues.
Summary Drought and salt stresses impose major constraints on soybean production worldwide. However, improving agronomically valuable soybean traits under drought conditions can be challenging due to trait complexity and multiple factors that influence yield. Here, we identified a nuclear factor Y C subunit (NF‐YC) family transcription factor member, GmNF‐YC14, which formed a heterotrimer with GmNF‐YA16 and GmNF‐YB2 to activate the GmPYR1‐mediated abscisic acid (ABA) signalling pathway to regulate stress tolerance in soybean. Notably, we found that CRISPR/Cas9‐generated GmNF‐YC14 knockout mutants were more sensitive to drought than wild‐type soybean plants. Furthermore, field trials showed that overexpression of GmNF‐YC14 or GmPYR1 could increase yield per plant, grain plumpness, and stem base circumference, thus indicating improved adaptation of soybean plants to drought conditions. Taken together, our findings expand the known functional scope of the NF‐Y transcription factor functions and raise important questions about the integration of ABA signalling pathways in plants. Moreover, GmNF‐YC14 and GmPYR1 have potential for application in the improvement of drought tolerance in soybean plants.
'/%3e%3cuse xlink:href='%23a' transform='rotate(23.036 .093 25.536)'/%3e%3cuse xlink:href='%23a' transform='rotate(45.87 1.273 16.18)'/%3e%3cuse xlink:href='%23a' transform='rotate(69.945 .996 12.078)'/%3e%3cuse xlink:href='%23a' transform='rotate(20.66 -19.689 31.932)'/%3e%3c/svg%3e)