Promoter Region Research Articles

A 6.49-Mb inversion associated with the purple embryo spot trait in potato

Abstract The embryo spot trait leads to a deep purple or reddish coloration at the base of the cotyledons of the embryo, visible on both sides of flat potato (Solanum tuberosum) seeds. This trait has long been used by potato researchers and breeders as a morphological marker during dihaploid induction. The formation of embryo spots reflects the accumulation of anthocyanins, but the genetic basis of this trait remains unclear. In this study, we mapped the embryo spot trait to a 6.78-Mb region at the end of chromosome 10 using an F2 population derived from a cross between spotted and spotless plants. The recombination rate in the candidate region is severely suppressed, posing challenges for the map-based cloning of the underlying gene and suggesting large-scale rearrangements in this region. A de novo genome assembly of the spotted individual and a comparative genomic analysis to the reference genome of spotless potato revealed a 6.49-Mb inversion present in the spotted plant genome. The left breakpoint of this inversion occurred in the promoter region of an R2R3 MYB transcription factor gene that is highly expressed in the cotyledon base of spotted embryos but is not expressed in that of spotless embryos. This study elucidated the genetic basis for embryo spot formation in potato and provides a foundation for future cloning of the causative gene.

The transcription factor GmFULc regulates soybean plant height by binding the promoter of a gibberellin-responsive gene.

Plant height is a crucial agronomic characteristic that substantially influences soybean [Glycine max (L.) Merr.] yield. FRUITFULLc (GmFULc) is a MADS-box transcription factor that acts as a growth promoter in soybean; however, the mechanism by which GmFULc regulates soybean height is unknown. This study revealed that GmFULc:GmFULc (the expression of the GmFULc gene driven by its native promoter) soybeans exhibit increased plant height and longer internodes. Conversely, soybean plants containing fulc mutations showed reduced plant height and shortened internodes. Chromatin immunoprecipitation-qPCR revealed GmFULc promotes the expression of gibberellic acid-stimulated Arabidopsis 14 (GmGASA14) and GmGASA32 by directly binding to G-boxes in their promoter regions, leading to notably increased expression of GmGASA14 and GmGASA32 in GmFULc:GmFULc soybean plants and reduced expression in soybean plants containing the fulc-2 mutation. The GmFULc-mediated enhanced expression of GmGASA14 and GmGASA32 increased the gibberellin signal, which may have inhibited gibberellin synthesis by increasing gibberellin 2-oxidase (GmGA2ox) expression and decreasing GA20ox expression. Our findings suggest that GmFULc promoted the expression of GmGASA genes by directly binding to G-boxes in their promoters to regulate soybean plant height.

Liraglutide mitigates dexamethasone-induced fatty acid synthase (FASN) and the cluster of differentiation36 (CD36) expression: a potential treatment for glucocorticoid-induced non-alcoholic fatty liver disease (NAFLD).

The clinical use of dexamethasone (DXM) is associated with the development of non-alcoholic fatty liver disease (NAFLD). However, the mechanisms by which DXM-induced NAFLD is still incompletely known. Therefore, the current study aims to test the hypothesis that DXM-induced NAFLD is mediated by dysregulation of key genes involved in lipid metabolism and liraglutide (LG) can ameliorate these effects. The histopathological and biochemical analysis assessed the effects of DXM and/or LG in liver tissue. The computational analysis was performed to detect the glucocorticoid response elements (GRE) in the promotor regions of FASN and CD36 genes. The effects of DXM and LG on the expression of FASN and CD36 were determined by real-time quantitative reverse transcription PCR (RT-qPCR), western blot (WB) and immunohistochemical (IHC) analyses. The NAFLD induced by high-fat diet (HFD) and DXM was manifested by increased levels of liver enzymes, deterioration of histological architecture of the liver tissue and accumulation of fat droplets. Computational analysis revealed that the promotor regions of FASN and CD36 harper several GRE. Most importantly, treatment with DXM decreased phosphorylated adenosine monophosphate-activated protein kinase (p-AMPK) levels, while LG upregulate it. In addition, treatment with DXM increased expression of FASN and CD36, whereas LG ameliorated these effects in a dose-dependent manner. DXM-induced NAFLD is mediated by upregulation of FASN and CD36 expression which may be attributed to GRE. LG coupling with DXM mitigates this induction by downregulating FASN and CD36 levels and therefore mitigates the development of NAFLD.

SmERF6 Promotes the Expression of Terpenoid Pathway in Salvia officinalis and Improves the Production of High Value Abietane Diterpenes, Carnosol and Carnosic acid.

Carnosol (CO) and carnosic acid (CA) are pharmaceutically important diterpenes predominantly produced in members of Lamiaceae, Salvia officinalis (garden sage), Salvia fruticosa and Rosmarinus officinalis. Nevertheless, availability of these compounds in plant system is very low. In an effort to improve the in planta content of these diterpenes in garden sage, SmERF6 (Salvia miltiorrhiza Ethylene Responsive Factor 6) transcription factor was expressed heterologously. Bai et al. (2018) proved that SmERF6 binds to the promoter regions of Copalyl pyrophosphate synthase (CPS) and Kaurene synthase like (KSL) genes, and improves transcription, thereby, augmenting ferruginol levels, a common precursor for abietane diterpenes in Salvia genus, moreover, transgenic hairy roots of S. miltiorrhiza displayed four fold improved tanshinone content. In our study, heterologous transient expression of SmERF6 in S. officinalis exhibited inter-specific activity in promoting differential accumulation of diterpenes. Overexpression studies showed elevation in the levels of CO (2-fold) and CA (5-fold). Further, in infiltrated leaves levels of ferruginol (50%) and CA derivatives (rosmanol, epirosmanol, methyl carnosic acid) were significantly upregulated along with the other signature terpenes. Finally, stable transgenic lines of S. officinalis developed through Agrobacterium mediated in planta genetic transformation accumulated significant amounts of CO (4-folds), CA (3-folds) as compared to wild plants. Overall, the present study is the first report on improving the content of pharmaceutically important diterpenes in S. officinalis by overexpressing pathway specific transcription factors. The current findings showed convincing evidence for the concept of improving specialized metabolite(s) content in medicinal plants by manipulating the expression of transcriptional regulators.

Evidence of DNA methylation heterogeneity and epipolymorphism in kidney cancer tissue samples.

Clear cell renal cell carcinoma (ccRCC) is characterised by significant genetic heterogeneity, which has diagnostic and prognostic implications. Very limited evidence is available regarding DNA methylation heterogeneity. We therefore generate sequence level DNA methylation data on 136 multi-region tumour and normal kidney tissue from 18 ccRCC patients, along with matched whole exome sequencing (85 samples) and gene expression (47 samples) data on a subset of samples. We perform a comprehensive systematic analysis of heterogeneity between patients, within a patient and within a sample. We demonstrate that bulk methylation data may be deconvoluted into cell-type-specific latent methylation components (LMCs), and that LMC1, which is likely to represent T cells, is associated with prognostic parameters. Differential epipolymorphism was noted between ccRCC and normal tissue in the promoter region of genes which are known to be associated with kidney cancer. This was externally validated in an independent cohort of 71 ccRCC and normal kidney tissues. Differential epipolymorphism in the gene promoter was a predictor of gene expression, after adjusting for average methylation. This represents the first evaluation of epipolymorphism in ccRCC and suggests that gains and losses in methylation disorder may have a functional relevance, gleaning important information on tumourigenesis.

Aging-dependent temporal regulation of MIR156 epigenetic silencing by CiLDL1 and CiNF-YB8 in chrysanthemum.

Temporal decline in microRNA miR156 expression is crucial for the transition to, and maintenance of, the adult phase and flowering competence in flowering plants. However, the molecular mechanisms underlying the temporal regulation of miR156 reduction remain largely unknown. Here, we investigated the epigenetic mechanism regulating the temporal silencing of cin-MIR156 in wild chrysanthemum (Chrysanthemum indicum), focusing on the role of the lysine-specific demethylase CiLDL1 and the nuclear factor Y complex. CiLDL1 and CiNF-YB8 interact with the classical histone-like fold domain (HFD) of CiNF-YC1 and CiNF-YA3, which form distinct heterotrimers binding to the 'CCAAT' box in the promoter region of cin-MIR156ab. CiLDL1 and CiNF-YB8 have opposing effects on cin-MIR156ab expression, with influencing histone 3 lysine 4 demethylation (H3K4me2) levels at the cin-MIR156ab locus. During aging, decreased CiNF-YB8 expression leads to a quantitative switch from the CiNF-YA3-CiNF-YC1-CiNF-YB8 heterotrimer to the CiNF-YA3-CiNF-YC1-CiLDL1 heterotrimer, which reduces H3K4me2 levels at the cin-MIR156ab locus, thus temporal silencing its expression. Our results thus reveal that the dynamic regulatory shift between CiLDL1 and CiNF-YB8 ensures proper aging-dependent flowering in chrysanthemum.

Natural variation in the GmVPE1 promoter contributes to phosphorus re-translocation to seeds and improves soybean yield.

Phosphorus (P) is an essential yet frequently deficient plant nutrient. Optimizing P distribution and recycling between tissues is vital for improving P utilization efficiency (PUE). Yet, the mechanisms underlying the transport and re-translocation of P within plants remain unclear. Here, wide-ranging natural diversity in seed P allocation and positive correlations among yield traits were found using 190 soybean accessions in field trials. Among them, the P-efficient genotype BX10 outperformed BD2 in assessments of PUE that were largely explained through differences in P redistribution from pods to seeds under low P stress. Pods of BX10 were therefore subjected to transcriptome analysis, and GmVPE1 was identified as a vacuolar Pi transporter to investigate further. Importantly, significant DNA polymorphism in GmVPE1 promoter regions was remarkably associated with seed weight among soybean accessions grown on P-deficient soils. Further analyses suggested that mRNA abundance of GmVPE1 in haplotype 2 (Hap) is significantly higher than that GmVPE1Hap1. GmVPE1 was highly upregulated by P deficiency and preferentially expressed in pods, seeds, and seed coats, which was consistent with GUS staining using transgenic soybean plants carrying pGmVPE1Hap2::GUS. Near-isogenic lines carrying the GmVPE1Hap2 allele, along with stable transgenic soybeans overexpressing GmVPE1 in a GmVPE1Hap1 background, had increases in PUE, more seed setting, and greater yields in both greenhouse and field trials than control plants. In summary, natural variation among GmVPE1 alleles determines genetic expression and subsequent P re-translocation phenotypes, which impacts PUE and yield, and thereby makes this an important genetic resource for soybean molecular breeding.

Cohesin Complex Interacting with Promoters of MMP Genes for in Pterygium Occurrence

Purpose Pterygium is a common ocular surface disease characterized by a high recurrence rate and unknown etiology. Methods In this study, we investigated the upregulation of matrix metalloproteinase genes, including MMP1, MMP2, MMP3, MMP7, MMP9, MMP11, MMP12, MMP13, MMP23B, and MMP28, in pterygium tissue using RNA sequencing, Western blotting, and immunohistochemistry. Results Employing the MEME tool, we identified a conserved DNA motif within the promoter regions of these matrix metalloproteinase genes. Mass spectrometry analysis revealed an interaction between the cohesin complex and this motif. Disrupting the cohesin complex through RNA interference of RAD21 cohesin complex component or structural maintenance of chromosomes 3 in primary pterygial fibroblasts led to decreased matrix metalloproteinase gene expression and reduced recruitment of twist family bHLH transcription factor 1 and transcription factor 4 to matrix metalloproteinase gene promoters. Conclusion Overall, our findings suggest a novel epigenetic mechanism regulating matrix metalloproteinase transcription in pterygium.

Identification and Analysis of Melon (Cucumis melo L.) SHMT Gene Family Members and Their Functional Studies on Tolerance to Low-Temperature Stress

Melon (Cucumis melo L.) is a significant cash crop globally and is cherished for its sweet and flavorful fruits, as well as its high nutritional values. However, its yield and quality are limited by various factors, including drought, salinity, and low temperatures. Low temperatures are one of the primary factors influencing the growth and development of melons, diminishing the viability, germination, and growth rate of melon seeds. Concurrently, low temperatures also reduce light absorption efficiency and fruit yields, thereby affecting melon growth and development. Serine hydroxymethyltransferase (SHMT), a conserved phosphopyridoxal-dependent enzyme, plays a crucial role in plant resistance to abiotic stressors. In this study, eight CmSHMT family genes were identified from the melon genome. We predicted their chromosomal locations, physicochemical properties, gene structures, evolutionary relationships, conserved motifs, cis-acting elements of promoters, and tissue-specific expression patterns. The expression levels of CmSHMT family genes in response to low-temperature stress was then analyzd using qRT-PCR. The phylogenetic results indicated that these CmSHMT genes were classified into four subfamilies and were unevenly distributed across five chromosomes, with relatively high conservation among them. Furthermore, our investigation revealed that the promoter regions of the CmSHMT family genes contain many cis-acting elements related to phytohormones, growth, and various stress responses. The relative expression levels of CmSHMT3, CmSHMT4, CmSHMT6, and CmSHMT7 were higher under low-temperature stress compared to the control group. Notably, the promoter region of CmSHMT3 contains cis-acting elements associated with low-temperature response (LTR) and abscisic acid response (ABRE). It is suggested that the mechanism through which CmSHMT3 responds to low-temperature stress treatments may be associated with hormonal regulation. These findings provide a foundation for the further exploration of CmSHMT family genes in melon and their functional roles in response to low-temperature stress, and they provide a theoretical basis for the targeted breeding of superior melon varieties with enhanced tolerance to low temperatures.

IL-17 triggers PD-L1 gene transcription in NSCLC cells via TRIM31-dependent MEF2C K63-linked polyubiquitination

BackgroundNon-small cell lung cancer (NSCLC) is a disease related to inflammation. Proinflammatory cytokines such as interleukin 17 (IL-17) can induce cancer cell proliferation, metastasis and immune escape. Although NSCLC immune escape is partly due to the interaction between PD-1 and PD-L1 and PD-L1 expression can be upregulated in cancer cells upon stimulation with IL-17, the underlying mechanism of IL-17-triggered PD-L1 gene transcription in NSCLC cells remains elusive.MethodsRT‒PCR, real-time PCR, and IB were used to assess the levels of PD-L1, MEF2C, and TRIM31 in NSCLC tissues as well as in IL-17–stimulated H1299 or PC9 cells. Bioinformatics analysis, luciferase assays, and ChIP were utilized to investigate the transcriptional mechanism of the PD-L1 gene. Co-IP/IB was used to examine the interaction between MEF2C and PD-L1, including MEF2C ubiquitination. IHC staining was carried out to analyse the expression of IL-17RA, MEF2C, TRIM31, and PD-L1 in NSCLC tissue arrays. The corresponding plasmids were constructed and identified. An isograft model was used to verify the findings in vitro.ResultsPD-L1, MEF2C and TRIM31 expression levels were increased in NSCLC tissues and NSCLC cells exposed to IL-17. Mechanistically, MEF2C could bind to the − 778 to -475 nt and − 336 to -97 nt regions of the PD-L1 promoter. TRIM31 could mediate MEF2C K63-linked polyubiquitination at Lys 25, increasing MEF2C recruitment to the PD-L1 promoter and PD-L1 gene transcription. MEF2C, TRIM31 or PD-L1 gene silencing effectively suppressed MEF2C K63-linked polyubiquitination, PD-L1 induction and NSCLC growth in mice inoculated with Lewis lung cancer (LLC) cells transfected with the corresponding shRNA and treated with IL-17.ConclusionIL-17 induces PD-L1 gene transcription in NSCLC cells through TRIM31-dependent MEF2C K63-linked polyubiquitination.

Elevated SREBP1 accelerates the initiation and growth of pancreatic cancer by targeting SOX9

Pancreatic cancer is a lethal disease with an insidious onset, and little is known about its early molecular events. Here, we found that the sterol regulatory element-binding protein 1 (SREBP1) expression is gradually upregulated during the initiation of pancreatic cancer. Through in vitro 3D culture of pancreatic acinar cells and experiments in LSL-KrasG12D/+;Pdx1-Cre (KC) mice, we found that pharmacological inhibition of SREBP1 suppressed pancreatic tumorigenesis. In vitro, either knockdown or pharmacological inhibition of SREBP1 suppressed tumor proliferation but SREBP1 overexpression promoted tumor proliferation. In LSL-KrasG12D/+;Trp53fl/+;Pdx1-Cre (KPC) mice, we confirmed the tumor-promoting role of SREBP1 in pancreatic cancer progression. Mechanistically, we revealed SOX9 as a downstream target of SREPB1. SREBP1 inhibition decreased SOX9 expression in both acinar cells and pancreatic cancer cells. Indeed, we identified SREBP1 binding sites in the SOX9 promoter region and reported that SOX9 is transcriptionally regulated by SREBP1. Taken together, our findings demonstrate that SREBP1/SOX9 inhibition suppresses pancreatic cancer initiation and growth, suggesting that SREBP1 could serve as a potential target for cancer screening and treatment.

H3K14la drives endothelial dysfunction in sepsis-induced ARDS by promoting SLC40A1/transferrin-mediated ferroptosis.

Pulmonary endothelial cell (EC) activation is a key factor in acute respiratory distress syndrome (ARDS). In sepsis, increased glycolysis leads to lactate buildup, which induces lysine lactylation (Kla) on histones and other proteins. However, the role of protein lactylation in EC dysfunction during sepsis-induced ARDS remains unclear. Integrative lactylome and proteome analyses were performed to identify the global lactylome profile in the lung tissues of septic mice. Cut&Tag analysis was used to identify the transcriptional targets of histone H3 lysine 14 lactylation (H3K14la) in ECs. Septic mice presented elevated levels of lactate and H3K14la in lung tissues, particularly in pulmonary ECs. Suppressing glycolysis reduced both H3K14la and EC activation, suggesting a link between glycolysis and lactylation. Moreover, H3K14la was enriched at promoter regions of ferroptosis-related genes such as transferrin receptor (TFRC) and solute carrier family 40 member 1 (SLC40A1), which contributed to EC activation and lung injury under septic conditions. For the first time, we reported the role of lactate-dependent H3K14 lactylation in regulating EC ferroptosis to promote vascular dysfunction during sepsis-induced lung injury. Our findings suggest that manipulation of the glycolysis/H3K14la/ferroptosis axis may provide novel therapeutic approaches for sepsis-associated ARDS.

Plant Coping with Cold Stress: Molecular and Physiological Adaptive Mechanisms with Future Perspectives

Cold stress strongly hinders plant growth and development. However, the molecular and physiological adaptive mechanisms of cold stress tolerance in plants are not well understood. Plants adopt several morpho-physiological changes to withstand cold stress. Plants have evolved various strategies to cope with cold stress. These strategies included changes in cellular membranes and chloroplast structure, regulating cold signals related to phytohormones and plant growth regulators (ABA, JA, GA, IAA, SA, BR, ET, CTK, and MET), reactive oxygen species (ROS), protein kinases, and inorganic ions. This review summarizes the mechanisms of how plants respond to cold stress, covering four main signal transduction pathways, including the abscisic acid (ABA) signal transduction pathway, Ca2+ signal transduction pathway, ROS signal transduction pathway, and mitogen-activated protein kinase (MAPK/MPK) cascade pathway. Some transcription factors, such as AP2/ERF, MYB, WRKY, NAC, and bZIP, not only act as calmodulin-binding proteins during cold perception but can also play important roles in the downstream chilling-signaling pathway. This review also highlights the analysis of those transcription factors such as bHLH, especially bHLH-type transcription factors ICE, and discusses their functions as phytohormone-responsive elements binding proteins in the promoter region under cold stress. In addition, a theoretical framework outlining plant responses to cold stress tolerance has been proposed. This theory aims to guide future research directions and inform agricultural production practices, ultimately enhancing crop resilience to cold stress.

Genome-Wide Analysis and Expression Profiling of Watermelon VQ Motif-Containing Genes Under Abiotic and Biotic Stresses

Valine-glutamine (VQ) motif-containing proteins play important roles in diverse plant developmental processes and signal transduction in response to biotic and abiotic stresses. However, no systematic investigation has been conducted on VQ genes in watermelon. In this study, we identified 31 watermelon VQ genes, which were classified into six subfamilies (I–VI). All of the deduced proteins contained a conserved FxxxVQxL/F/VTG motif. Eleven ClVQs were involved in segment duplication, which was the main factor in the expansion of the VQ family in watermelon. Numerous stress- and hormone-responsive cis-elements were detected in the putative promoter region of the ClVQ genes. Green fluorescent protein fusion proteins for ten selected ClVQs were localized in the nucleus, but three ClVQs also showed signals in cell membranes and the cell wall, thus confirming their predicted divergent functionality. Quantitative real-time PCR (qRT-PCR) analysis indicated that the majority of ClVQ genes were specifically or preferentially expressed in certain tissues or organs, especially in the male flower. Analyses of RNA-sequencing data under osmotic, cold, and drought stresses and Cucumber green mottle mosaic virus (CGMMV) infection revealed that the majority of ClVQ genes, especially those from subfamily IV, were responsive to these stresses. The results provide useful information for the functional characterization of watermelon ClVQ genes to unravel their biological roles.

ATF3 triggers M2 macrophage polarization to protect against pulp inflammation through WNT4 regulation.

Pulpitis is a common inflammatory oral disease that can lead to pulp necrosis. The aim of this study is to investigate the expression and regulatory mechanisms of ATF3, a potential therapeutic marker, in pulpitis. A mouse pulpitis model with different degrees of inflammation is established, and the expression of ATF3 in pulpitis is explored. The histological features of healthy pulp and pulpitis are analyzed by HE staining, and classical inflammatory factors are detected by immunohistochemistry (IHC). In an in vitro study, we investigate the role of ATF3 in the regulation of WNT4 transcription and explore the effects of the ATF3/WNT4 axis on the polarization of RAW264.7 macrophages, the inflammatory response and the osteogenic differentiation of human dental pulp stem/stromal cells (hDPSCs). Our results show that ATF3 is expressed at low levels in inflamed pulp tissues; overexpression of ATF3 reduces the area of pulp necrosis, decreases the level of pro-inflammatory factors, and promotes macrophage polarization toward the M2 type. Furthermore, we reveal that ATF3 binds to the WNT4 promoter region and positively regulates the expression of WNT4 and that ATF3 downregulates M1 markers and increases the expression of M2 markers by regulating WNT4 expression. In addition, ATF3 promotes the osteogenic differentiation of dental pulp stem cells. In summary, this study reveals that ATF3 promotes M2 macrophage polarization by regulating WNT4, which in turn inhibits pulpal inflammatory responses and promotes the osteogenic differentiation of dental pulp stem cells. These findings suggest that ATF3 may be a potential target for pulpitis treatment.

Protein Phosphatase 2A B'α and B'β promote pollen wall construction partially through BZR1-activated CEP1 in Arabidopsis.

A well-constructed pollen wall is essential for pollen fertility, which relies on the contribution of tapetum. Our results demonstrate an essential role of the tapetum-expressed protein phosphatase 2A (PP2A) B'α and B'β in pollen wall formation. The b'aβ double mutant pollen grains harbored sticky remnants and tectum breakages, resulting in failed release. B'α and B'β function partially through dephosphorylating and activating BZR1. The bzr1 bes1 double and higher-order mutants of this family displayed similar defects in pollen wall, while bzr1-1D, having an active mBZR1 exhibited fertile pollen grains in a B'α and B'β dependent manner. Correspondingly, the level of phospho-BZR1 is increased and dephospho-BZR1 is decreased in b'aβ and bzr1-1D/b'aβ at anther stages 8-9 as compared with Col-0 and bzr1-1D, respectively. A cysteine protease gene CEP1 was identified as a BZR1 target, whose transcriptional activation necessitates BRREs in the promoter region and BZR1 DNA binding domain. The mRNA level of CEP1 at stages 8-9 was extremely low in bzr1 and bzr1 bes1, while higher in Col-0 and bzr1-1D depending on B'α and B'β. Furthermore, cep1 mutants displayed similar defects in pollen wall. In brief, this study uncovered a PP2A-BZR1-CEP1 regulatory module, providing a new insight into pollen maturation mechanism.

Chromatin Accessibility Mediated by CHROMATIN REMODELING 11 Promotes Chilling Tolerance in Rice.

Chromatin remodeling plays a crucial role in controlling gene transcription by modifying chromatin structure. However, the involvement of chromatin remodeling in plant stress responses, especially cold tolerance, through chromatin accessibility remains largely unexplored. Here, we report that rice (Oryza sativa L.)CHROMATIN REMODELING 11 (OsCHR11) positively regulates chilling tolerance by enhancing chromatin accessibility and facilitating changes in gene expression. Loss-of-function mutants of OsCHR11 exhibited increased susceptibility to chilling stress compared to wild-type rice plants. Transcriptome analysis revealed that the chr11 mutant displays diminished transcriptomic responses to chilling. Additionally, assay for transposase-accessible chromatin (ATAC) indicated that chilling treatment increases chromatin accessibility in the promoter regions, and this process depended on OsCHR11 function. Chromatin immunoprecipitation sequencing (ChIP-seq) showed that OsCHR11 is physically associated with the promoters of cold-responsive genes. Integrated multi-omics analysis further demonstrated a correlation between OsCHR11 enrichment and chromatin accessibility, as well as a correlation between chromatin accessibility and gene expression. Furthermore, OsCHR11 is required for the full expression of key cold-response genes, including those involved in trehalose biosynthesis. The exogenous application of trehalose partially rescued the chilling-susceptible phenotype of the chr11 mutant, suggesting that trehalose biosynthesis contributes to the chilling tolerance promoted by OsCHR11. Collectively, these findings indicate that OsCHR11 enhances cold tolerance in plants, likely by increasing chromatin accessibility and elevating the expression levels of cold-response genes in response to chilling.

Transcription factor MAZ activates the transcription of hypomethylated TYMP in ccRCC.

Clear cell renalcell carcinoma (ccRCC) isa highly malignant tumor characterized by a significant propensity for recurrence and metastasis. DNA methylation has emerged as a critical epigenetic mechanism with substantial utility in cancer diagnosis. In this study, multi-omics data were utilized to investigate the target genes regulated by the transcription factor MYC-associated zinc finger protein (MAZ) in ccRCC, leading to the identification of thymidine phosphorylase (TYMP) as a gene with notably elevated expression in ccRCC. The interaction between MAZ and TYMP was confirmed through chromatin immunoprecipitation (ChIP) assays and bioinformatics analysis. It was found that the binding of MAZ to the TYMP promoter is associated with the methylation status of this promoter region. Furthermore, the methylation of the TYMP promoter appears to be correlated with both the clinicopathological stage and overall survival of ccRCC patients. Further exploration of genes within the "nucleotide metabolism" pathway, identified through Gene Ontology (GO) enrichment analysis, revealed that uridine phosphorylase 1 (UPP1) interacts with TYMP. Interestingly, UPP1 was also shown to be activated by MAZ, suggesting a coordinated regulatory mechanism. Based on these findings, we propose that the TYMP-UPP1 complex, co-regulated by MAZ, plays a pivotal role in nucleotide metabolism in ccRCC. These results suggest that TYMP may contribute to the pathophysiology of ccRCC and that promoter methylation offers potential as a prognostic indicator, providing novel insights into the molecular underpinnings of ccRCC and potential avenues for therapeutic intervention.

Genome-wide identification of CAMTA gene family in teak (Tectona grandis) and functional characterization of TgCAMTA1 and TgCAMTA3 in cold tolerance

BackgroundCalmodulin-binding transcription activator (CAMTA) proteins play significant roles in signal transduction, growth and development, as well as abiotic stress responses, in plants. Understanding their involvement in the low-temperature stress response of teak is vital for revealing cold resistance mechanisms.ResultsThrough bioinformatics analysis, the CAMTA gene family in teak was examined, and six CAMTA genes were identified in teak. The encoded proteins were predicted to be located in the nucleus and exhibited hydrophilic properties, with molecular weights ranging from 103.4 to 123.3 kDa and isoelectric points ranging from 5.49 to 7.55. On the basis of protein sequence homology, the CAMTA family could be divided into three subgroups. Domain and 3D structure analyses demonstrated that all the TgCAMTA proteins contained the typical CAMTA domain with the CaMBD binding domain, which was exposed on the surface. Expression analysis of different tissues revealed the expression of TgCAMTA genes in teak roots, stems, leaves, flowers, fruits, and branches. Furthermore, the promoter region contained various cis-acting elements related to light, hormone, and abiotic stress responses. After low-temperature stress treatment, different expression patterns of TgCAMTAs were observed in teak roots, stems, and leaves, with TgCAMTA1 showing the highest expression level in leaves compared with stems. Transgenic lines carrying the TgCAMTA1/3 promoter::GUS construct cold stress induction of TgCAMTA1/3 genes revealed the presence of multiple low-temperature responsive cis-acting elements in the TgCAMTA1/3 promoter region. Subcellular localization analysis indicated that these genes were functional predominantly in the nucleus. Compared with wild-type Arabidopsis, TgCAMTA1/3-overexpressing Arabidopsis presented increased tolerance to freezing stress, with increased expression of AtCOR genes. Moreover, under low-temperature conditions, TgCAMTA3-overexpressing Arabidopsis presented significantly elevated expression levels of genes related to the CBF signaling pathway, including AtCBF1/2/3.ConclusionsOur findings add significantly to the existing knowledge regarding cold stress tolerance and help elucidate cold response mechanisms in teak.

Decreased expression of LEF1 caused defective decidualization by inhibiting IL-11 expression in patients with adenomyosis

Reduced lymphoid enhancer-binding factor 1 (LEF1) expression in patients with adenomyosis during the mid-secretory phase leads to impaired endometrial receptivity, affecting embryo implantation. This study investigated the molecular mechanisms underlying reduced endometrial receptivity in 25 adenomyosis patients and 25 controls. Functional experiments were conducted using human endometrial stromal cells (HESCs) and TERT-immortalized HESCs(T-HESCs), with final validation performed using a mouse model. Western blot and quantitative real-time polymerase chain reaction (RT-qPCR) analyses revealed that patients with adenomyosis showed a marked decrease in LEF1 expression in the stromal cells of the endometrium during the mid-secretory phase. In vitro experiments demonstrated that LEF1 knockdown in stromal cells led to impaired decidualization. Transcriptome sequencing, dual-luciferase reporter assays, and chromatin immunoprecipitation (ChIP) experiments showed that LEF1 could bind to the promoter region of interleukin (IL)-11 and promote its transcription, and IL-11 expression was also found to be downregulated in adenomyosis patients. Overexpression of IL-11 rescued the impaired decidualization caused by decreased LEF1 expression. In the in vitro co-culture model, LEF1/IL-11 knockdown led to a reduction in embryo implantation area, which was partially restored upon IL-11 overexpression. In the adenomyosis mouse model, we observed a decrease in LEF1 expression and a reduction in implantation sites compared to control mice, accompanied by impaired decidualization and receptivity. Notably, supplementation with IL-11 restored the number of implantation sites. The decrease in fertility due to reduced endometrial receptivity in adenomyosis patients is a significant clinical issue in assisted reproductive technology. This research provides insights into one potential molecular mechanism underlying this decreased receptivity, with a specific focus on the reduced expression of LEF1 in the endometrial stromal cells during the mid-secretory phase in adenomyosis patients. Our findings offer new perspectives for clinical strategies to improve endometrial receptivity in patients with adenomyosis, potentially enhancing their chances of successful pregnancy.