Promoter Region Of Gene Research Articles

The evaluation of transcription factor binding site prediction tools in human and Arabidopsis genomes

BackgroundThe precise prediction of transcription factor binding sites (TFBSs) is pivotal for unraveling the gene regulatory networks underlying biological processes. While numerous tools have emerged for in silico TFBS prediction in recent years, the evolving landscape of computational biology necessitates thorough assessments of tool performance to ensure accuracy and reliability. Only a limited number of studies have been conducted to evaluate the performance of TFBS prediction tools comprehensively. Thus, the present study focused on assessing twelve widely used TFBS prediction tools and four de novo motif discovery tools using a benchmark dataset comprising real, generic, Markov, and negative sequences. TFBSs of Arabidopsis thaliana and Homo sapiens genomes downloaded from the JASPAR database were implanted in these sequences and the performance of tools was evaluated using several statistical parameters at different overlap percentages between the lengths of known and predicted binding sites.ResultsOverall, the Multiple Cluster Alignment and Search Tool (MCAST) emerged as the best TFBS prediction tool, followed by Find Individual Motif Occurrences (FIMO) and MOtif Occurrence Detection Suite (MOODS). In addition, MotEvo and Dinucleotide Weight Tensor Toolbox (DWT-toolbox) demonstrated the highest sensitivity in identifying TFBSs at 90% and 80% overlap. Further, MCAST and DWT-toolbox managed to demonstrate the highest sensitivity across all three data types real, generic, and Markov. Among the de novo motif discovery tools, the Multiple Em for Motif Elicitation (MEME) emerged as the best performer. An analysis of the promoter regions of genes involved in the anthocyanin biosynthesis pathway in plants and the pentose phosphate pathway in humans, using the three best-performing tools, revealed considerable variation among the top 20 motifs identified by these tools.ConclusionThe findings of this study lay a robust groundwork for selecting optimal TFBS prediction tools for future research. Given the variability observed in tool performance, employing multiple tools for identifying TFBSs in a set of sequences is highly recommended. In addition, further studies are recommended to develop an integrated toolbox that incorporates TFBS prediction or motif discovery tools, aiming to streamline result precision and accuracy.

N6-methyladenosine (m6A)-circHECA from secondary hair follicle of cashmere goats: identification, regulatory network and expression regulated potentially by methylation of its host gene promoter.

The objective of this study was to identify the N6-methyladenosine (m6A)- circHECA molecule in secondary hair follicles (SHFs) of cashmere goats, and generate its potential regulatory network, as well as explore the potential relationship between transcriptional pattern of m6A-circHECA and promoter methylation of its host gene (HECA). The validation of circHECA m6A sites was performed using methylation immunoprecipitation (Me-RIP) along with reverse transcription-quantitative polymerase chain reaction (RT-qPCR) technique. The nucleus and cytoplasm localizations of m6AcircHECA were performed using SHF stem cells of cashmere goats with RT-qPCR analysis. Based on in-silico analysis, the regulatory networks of m6A-circHECA were generated with related signal pathway enrichment. The methylation level of promoter region of m6A-circHECA host gene (HECA) was assessed by the bisulfite sequencing PCR (BSPPCR) technique. The m6A-circHECA was confirmed to contain four m6A modification sites including m6A-213, m6A-297, m6A-780, and m6A-927, and it was detected mainly in cytoplasm of the SHF stem cells of cashmere goats. The integrated regulatory network analysis showed directly or indirectly complex regulatory relationships between m6A-circHECA of cashmere goats and its potential target molecules: miRNAs, mRNAs, and proteins. The regulatory network and pathway enrichment indicated that m6A-circHECA might play multiple roles in the SHF physiology process of cashmere goats through directly or indirectly interacting or regulating its potential target molecules. A higher methylation level of promoter region of HECA gene in SHFs of cashmere goats might cause the lower expression of m6A-circHECA. The m6A-circHECA might play multiple roles in SHF physiology process of cashmere goats through miRNA mediated pathways along with directly or indirectly interaction with its target proteins. The promoter methylation of m6A-circHECA host gene (HECA) most likely was implicated in its expression inhibition in SHFs of cashmere goats.

Systematic identification of pathogenic variants of non-small cell lung cancer in the promoters of DNA-damage repair genes

Deficiency in DNA-damage repair (DDR) genes, often due to disruptive coding variants, is linked to higher cancer risk. Our previous study has revealed the association between rare loss-of-function variants in DDR genes and the risk of lung cancer. However, it is still challenging to study the predisposing role of rare regulatory variants of these genes. Based on whole-genome sequencing data from 2984 patients with non-small cell lung cancer (NSCLC) and 3020 controls, we performed massively parallel reporter assays on 1818 rare variants located in the promoters of DDR genes. Pathway- or gene-level burden analyses were performed using Firth's logistic regression or generalized linear model. We identified 750 rare functional regulatory variants (frVars) that showed allelic differences in transcriptional activity within the promoter regions of DDR genes. Interestingly, the burden of frVars was significantly elevated in cases (odds ratio [OR]=1.17, p=0.026), whereas the burden of variants prioritized solely based on bioinformatics annotation was comparable between cases and controls (OR=1.04, p=0.549). Among the frVars, 297 were down-regulated transcriptional activity (dr-frVars) and 453 were up-regulated transcriptional activity (ur-frVars); especially, dr-frVars (OR=1.30, p=0.008) rather than ur-frVars (OR=1.06, p=0.495) were significantly associated with risk of NSCLC. Individuals with NSCLC carried more dr-frVars from Fanconi anemia, homologous recombination, and nucleotide excision repair pathways. In addition, we identified seven genes (i.e., BRCA2, GTF2H1, DDB2, BLM, ALKBH2, APEX1, and RAD51B) with promoter dr-frVars that were associated with lung cancer susceptibility. Our findings indicate that functional promoter variants in DDR genes, in addition to protein-truncating variants, can be pathogenic and contribute to lung cancer susceptibility. National Natural Science Foundation of China, Youth Foundation of Jiangsu Province, Research Unit of Prospective Cohort of Cardiovascular Diseases and Cancer of Chinese Academy of Medical Sciences, and Natural Science Foundation of Jiangsu Province.

RSF1 orchestrates p53 transcriptional activity by coordinating p300 acetyltransferase and FACT complex.

The transcriptional regulation of p53-dependent genes in response to DNA damage is critical for effective DNA repair and cell survival. We previously established that RSF1 (remodeling and spacing factor 1) is necessary for p53-dependent gene transcription in response to DNA strand breaks. Here, we further elucidate that the role of RSF1 in p53 regulation by demonstrating that its depletion results in a reduction in the acetylated-Lys(K)382 level of p53, which governs its transcriptional activity. RSF1 was co-precipitated with p300 acetyltransferase upon etoposide treatment. Chromatin immunoprecipitation assays on the upstream region of CDKN1A gene revealed reduced p300 and TBP accumulation, which were accompanied with low H3H27ac and H3K4me1 levels in RSF1 knockout cells. Moreover, RSF1 depletion led to a reduced accumulation of SSRP1 and SPT16, subunits of FACT complex at the promoter of CDKN1A gene. These findings suggest that RSF1 promotes p53-dependent p21 gene transcription by facilitating the accumulation of p300 acetyltransferase at the enhancer and FACT at the promoter region of CDKN1A gene, respectively.

Transcriptional and post-transcriptional regulation of whiB6 by a response regulator PhoP and a small noncoding RNA MTS1338 in Mycobacterium tuberculosis

WhiB6 in pathogenic mycobacteria is highly upregulated during NO stress, hypoxia, and macrophage infection. Its expression primarily results from transcriptional control by a two-component response regulator PhoP in response to the various stresses exerted on mycobacterial cells inside phagosomes. Herein, we investigated the transcriptional and posttranscriptional regulatory mechanism of whiB6 expression. We found that PhoP binds to the PhoP-signature sequences located upstream to the core promoter region of whiB6 gene and controls its expression at the transcriptional level. Phosphorylation of PhoP is obligatory for binding to whiB6 promoter. A dormancy regulatory factor DosR, although doesn’t bind to whiB6 gene, can bind to the PhoP-bound whiB6 gene implicating its potential role in whiB6 expression. A virulence-associated sRNA MTS1338 directly binds to the coding region of whiB6 gene presumably protecting it from cellular ribonucleases. Induction of MTS1338 in response to low pH and oxidative stress increases whiB6 accumulation likely through the stabilization of whiB6 transcript at the posttranscriptional level. This study substantially increases our knowledge of the regulation of whiB6 expression in M. tuberculosis.

Genome‑wide identifcation and expression analysis of growth-regulating factors under drought in Brassica juncea

Growth-regulating factors (GRFs) are plant-specific transcription factors involved in the regulation of plant growth, development, and abiotic stress processes. However, the function of Brassica juncea (L.) Czern & Coss GRFs remain largely unknown. In this study, 34 BjGRF genes were identified in B. juncea. BjGRF members of the same subfamily were found to share a similar motif composition and gene structure. In total, 663 cis-acting elements were found in the promoter regions of BjGRF genes, which were related to light response, hormone response, environmental stresses, and plant growth/development. Additionally, 48 pairs of segmental duplication genes were identified during gene duplication events, and no tandemly duplicated genes were identified. qRT-PCR analysis showed that the 34 BjGRF genes were primarily expressed in the roots, followed by the leaves. Furthermore, the 10 BjGRF genes were screened in response to drought stress, and the expression patterns of the genes were relatively consistent, with a maximum expression level at 3 or 24 h, and the selected BjGRF03 and BjGRF32 might be involved in drought stress. This preliminary study clarifies the response of the BjGRF gene family to drought stress and provides ideas for further analyses of the biological functions of BjGRF genes.

Genome-wide survey and expression analysis of JAZ genes in watermelon (Citrullus lanatus).

BACKGROUND JAZ: (Jasmonate ZIM-domain) genes play important roles in plant growth and JA signaling pathway which is correlated with fruit ripening process. However, there have been few reports on the genome-wide identification of JAZ genes in watermelon and its relationship with fruit ripening. METHODS AND RESULTS: In this study, bioinformatics approaches were employed to identify ClaJAZ genes of watermelon at the genome-wide levels. Further exploration delved into the phylogenetic relationships, chromosomal mappings, promoter dynamics, expression, and architectural features of the JAZ genes. The results showed that a total of 9 ClaJAZ genes unevenly distributed across six chromosomes were identified in the watermelon genome, and they all have conserved Jas and TIFY domains. These JAZ genes were divided into four distinct groups with five genes involved in inter-chromosomal tandem duplication events, and members of the same subgroup exhibited a high degree of similarity in their gene structure and protein motif patterns. Analysis of the promoter regions of the ClaJAZ genes indicated the presence of cis-acting elements associated with hormonal responses, stress, and developmental processes. Gene expression analysis through real-time quantitative PCR (qRT-PCR) showed that there were spatiotemporal differences in the expression of ClaJAZ genes at various stages of fruit development. Among them, ClaJAZ7 has the highest level of transcriptional expression and showed strong promoter activity. CONCLUSIONS: This study conducted a comprehensive analysis of the ClaJAZ genes and provided insights into the role of ClaJAZ in the development and ripening of watermelon fruit.

Genomic Features of Taiwanofungus gaoligongensis and the Transcriptional Regulation of Secondary Metabolite Biosynthesis

Fungal secondary metabolites (SMs) have broad applications in biomedicine, biocontrol, and the food industry. In this study, whole-genome sequencing and annotation of Taiwanofungus gaoligongensis were conducted, followed by comparative genomic analysis with 11 other species of Polyporales to examine genomic variations and secondary metabolite biosynthesis pathways. Additionally, transcriptome data were used to analyze the differential expression of polyketide synthase (PKS), terpene synthase (TPS) genes, and transcription factors (TFs) under different culture conditions. The results show that T. gaoligongensis differs from other fungal species in genome size (34.58 Mb) and GC content (50.72%). The antibiotics and Secondary Metabolites Analysis Shell (AntiSMASH) analysis reveals significant variation in the number of SM biosynthetic gene clusters (SMBGCs) across the 12 species (12–29), with T. gaoligongensis containing 25 SMBGCs: 4 PKS, 6 non-ribosomal peptide synthetase (NRPS), and 15 TPS clusters. The TgPKS1 gene is hypothesized to be involved in the biosynthesis of orsellinic acid or its derivatives, while TgPKS2 might catalyze the synthesis of 6-methylsalicylic acid (6MSA) and its derivatives. The TgTRI5 genes are suggested to synthesize tetracyclic sesquiterpene type B trichothecene compounds, while TgPentS may be involved in the synthesis of δ-cadinol, β-copaene, and α-murolene analogs or derivatives. Comparative genomic analysis shows that the genome size of T. gaoligongensis is similar to that of T. camphoratus, with comparable SMs. Both species share four types of PKS domains and five distinct types of TPS. Additionally, T. gaoligongensis exhibits a high degree of similarity to Laetiporus sulphureus, despite belonging to a different genus within the same family. Transcriptome analysis reveals significant variation in the expression levels of PKS and TPS genes across different cultivation conditions. The TgPKS1 and TgPKS4 genes, along with nine TgTFs, are significantly upregulated under three solid culture conditions. In contrast, under three different liquid culture conditions, the TgPKS3, TgTRI5-1, and TgTRI5-2 genes, along with twelve TgTFs, exhibit higher activity. Co-expression network analysis and TgTFs binding site prediction in the promoter regions of TgPKS and TgTPS genes suggest that TgMYB9 and TgFTD4 regulate TgPKS4 expression. TgHOX1, TgHSF2, TgHSF3, and TgZnF4 likely modulate TgPKS3 transcriptional activity. TgTRI5-1 and TgTRI5-5 expression is likely regulated by TgbZIP2 and TgZnF15, respectively. This study provides new insights into the regulatory mechanisms of SMs in T. gaoligongensis and offers potential strategies for enhancing the biosynthesis of target compounds through artificial intervention.

Epigenetic mechanisms mediate cytochrome P450 1A1 expression and lung endothelial injury caused by MRSA invitro and invivo.

Methicillin-resistant Staphylococcus aureus (MRSA) is a common cause of severe pneumonia and acute respiratory distress syndrome (ARDS). To advance our mechanistic understanding of this important pathogen, we characterized the effects of MRSA-induced epigenetic modification of histone 3 lysine 9 acetylation (H3K9ac), an activator of gene transcription, on lung endothelial cells (EC), a critical site of ARDS pathophysiology. Chromatin immunoprecipitation and sequencing (ChIP-seq) analysis revealed that MRSA induces H3K9ac in the promoter regions of multiple genes, with the highest ranked peak annotated to the CYP1A1 gene. Subsequent experiments confirm that MRSA increases CYP1A1 protein and mRNA expression, and its enzymatic activity in EC. Epigenetic inhibitors (C646, RVX-208) reduce MRSA-induced CYP1A1 expression and inflammatory responses, including cytokine release and adhesion molecule expression. Inhibition of the Aryl hydrocarbon receptor (Ahr), a known mediator of CYP1A1 expression, blocks MRSA-induced upregulation of CYP1A1 mRNA and protein expression, enzyme activity, and cytokine release. Reduction of CYP1A1 protein expression by siRNA or inhibition of its activity by rhapontigenin attenuated MRSA-induced EC permeability and inflammatory responses. In a mouse model of MRSA-induced acute lung injury (ALI), inhibition of CYP1A1 activity by rhapontigenin improved multiple indices of ALI, including bronchoalveolar lavage (BAL) protein concentration, cytokine levels, and markers of endothelial damage. Analysis of publicly available data suggests upregulation of CYP1A1 expression in ARDS patients compared to ICU controls. In summary, these studies provide new insights into MRSA-induced lung injury and identify a novel functional role for epigenetic upregulation of CYP1A1 in lung EC during ARDS pathogenesis.

Tracing the intraspecies expansion of glyoxalase genes and their expanding roles across the genus Oryza.

The genus Oryza is of utmost importance to human civilization as two of its species became agronomically productive and widely cultivated, and also because wild rice is a treasure trove of beneficial alleles that can be used for crop improvement. Most of the wild rice genotypes are known for their stress tolerance several times more than the domesticated rice varieties. In this study, we aimed to carry out an exhaustive genomic survey to identify glyoxalase I (GLYI) and glyoxalase II (GLYII) genes across the 11 rice genomes sequenced so far. Notably, we found the putatively functional metal-dependent GLYI and GLYII enzymes to be conserved throughout domestication and a few homologous pairs to have undergone beneficial mutations to drive positive selection, and thus, acquire newer functions. Interestingly, we also report four newly identified GLYII members in O. sativa subsp. japonica in addition to the three previously reported GLYII genes. The presence of different types of cis-elements in the promoter region of the glyoxalase genes gives insights into their role and regulation under various developmental processes besides stress adaptation. Publicly available data suggests the role of glyoxalase genes particularly in salinity stress in both wild and cultivated rice as is also confirmed through qRT-PCR. Interestingly, we found less accumulation of MG and concurrently higher enzymatic activity of GLYI and GLYII proteins in stressed seedlings of selected wild rice genotypes indicating that glyoxalases indeed contribute to the intrinsic stress tolerance of wild rice.

Lactate promotes H3K18 lactylation in human neuroectoderm differentiation

In mammals, early embryonic gastrulation process is high energy demanding. Previous studies showed that, unlike endoderm and mesoderm cells, neuroectoderm differentiated from human embryonic stem cells relied on aerobic glycolysis as the major energy metabolic process, which generates lactate as the final product. Here we explored the function of intracellular lactate during neuroectoderm differentiation. Our results revealed that the intracellular lactate level was elevated in neuroectoderm and exogenous lactate could further promote hESCs differentiation towards neuroectoderm. Changing intracellular lactate levels by sodium lactate or LDHA inhibitors had no obvious effect on BMP or WNT/β-catenin signaling during neuroectoderm differentiation. Notably, histone lactylation, especially H3K18 lactylation was significant upregulated during this process. We further performed CUT&Tag experiments and the results showed that H3K18la is highly enriched at gene promoter regions. By analyzing data from CUT&Tag and RNA-seq experiments, we further identified that four genes, including PAX6, were transcriptionally upregulated by lactate during neuroectoderm differentiation. A H3K18la modification site at PAX6 promoter was verified and exogenous lactate could also rescue the level of PAX6 after shPAX6 inhibition.

Systematic regulation of immune checkpoint molecules by redox regulators CNC-bZIP transcription factors

BackgroundAlthough oxidative stress is strongly connected to the initiation and progression of cancer, the underlying molecular pathways remain unknown. The redox regulator CNC-bZIPs are important transcription factor groups that mediate the interplay of environmental cues and intercellular homeostasis. Immune checkpoint molecules (ICMs) are key molecules that mediate the communication between immune cells and tumor cells. This research sought to explore the transcriptional regulatory effects of CNC-bZIPs on ICMs.MethodsThe potential role of CNC-bZIPs in tumors and the correlation between CNC-bZIPs and ICMs were analyzed by the gene expression characteristics, survival analysis, and correlation analysis in TCGA data. And the transcriptional regulatory effects of CNC-bZIPs on ICMs were verified through cis acting element analysis and promoter activity reporter experiments.ResultsIn this study, we found that high expression of CNC-bZIPs predicted poor prognosis, and we determined that CNC-bZIPs are universally connected to ICMs by analyzing gene expression correlation in TCGA tumor data. Specifically, CD47 and CD274 exhibit universally positive correlation with CNC-bZIPs in various tumor tissues. Promoter analysis revealed that there are several ARE elements, which are specifically recognized by CNC-bZIPs, in the promoter regions of CD47 and CD274 genes. Overexpression of NFE2L1 and NFE2L2 was used to explore the regulation of common ICM genes, such as CD47 and CD274, and the transcriptional regulatory effect of CNC-bZIPs on ICMs was confirmed using promoter activity reporter experiments.ConclusionIn this study, the universal and systematic transcriptional regulatory role of the CNC-bZIP transcription factor family on ICMs was discovered. According to this study, the results and conclusions drawn are based on gene expression correlation and promoter activity assays, the CNC-bZIPs/ICMs transcriptional regulatory axis was revealed to be a potential regulatory axis that may drive redox signaling and anti-tumor immune responses.

Whole-Genome Identification of the Flax Fatty Acid Desaturase Gene Family and Functional Analysis of the LuFAD2.1 Gene Under Cold Stress Conditions.

Fatty acid desaturase (FAD) is essential for plant growth and development and plant defence response. Although flax (Linum usitatissimum L.) is an important oil and fibre crop, but its FAD gene remains understudied. This study identified 43 LuFAD genes in the flax genome. The phylogenetic analysis divided the FAD genes into seven subfamilies. LuFAD is unevenly distributed on 15 chromosomes, and fragment duplication is the only driving force for the amplification of the LuFAD gene family. In the LuFAD gene promoter region, most elements respond to plant hormones (MeJA, ABA) and abiotic stresses (anaerobic and low temperature). The expression pattern analysis showed that the temporal and spatial expression patterns of all LuFAD genes in different tissues and the response patterns to abiotic stresses (heat and salt) were identified. Subcellular localisation showed that all LuFAD2-GFP were expressed in the endoplasmic reticulum membrane. RT-qPCR analysis revealed that LuFAD2 was significantly upregulated under cold, salt and drought stress, and its overexpression in Arabidopsis thaliana enhanced cold tolerance genes and reduced ROS accumulation. This study offers key insights into the FAD gene family's role in flax development and stress adaptation.

Genome wide identification of BjSWEET gene family and drought response analysis of BjSWEET12 and BjSWEET17 genes in Brassica juncea

BackgroundSugars Will Eventually be Exported Transporter (SWEET) gene family is a unique type of sugar transporter that plays a vital role in metabolic regulation, growth, development, and stress response in multiple species. This study aimed to systematically identify the SWEET gene family members and detect the regulation of gene expression and their potential roles of the SWEET gene family in Brassica juncea.ResultsA total of 66 BjSWEET (Brassica juncea Sugar Will Eventually be Exported Transporter) genes distributed across 17 chromosomes were identified. The gene structure and motifs were relatively conserved, with all members containing the MtN3/saliva domain. Phylogenetic analysis revealed that the SWEET gene family can be classified into four subfamilies (Clades I, II, III, and IV). Collinearity analysis revealed that there were 118 pairs of segment duplicates, indicating that some BjSWEET genes were obtained via segmental duplication. The promoter regions of the BjSWEET genes contained many plant hormone-related response elements, stress-related response elements, growth and development elements, and light-responsive regulatory elements. Furthermore, analysis of the expression profiles revealed that the expression levels of the BjSWEET genes differed among the eight different tissues. qRT‒PCR analysis of six selected BjSWEET genes revealed that the expression levels of BjSWEET17.2, BjSWEET17.4, BjSWEET12.2, and BjSWEET12.3 were significantly upregulated under drought treatment, suggesting that these genes may respond to drought stress in B. juncea.ConclusionThis study systematically identified and analyzed the SWEET gene family members in B. juncea for the first time, laying the foundation for further research on the molecular mechanisms of drought resistance in B. juncea and providing theoretical guidance for the application of these genes in other species.

Minimally Invasive and Emerging Diagnostic Approaches in Endometrial Cancer: Epigenetic Insights and the Promise of DNA Methylation.

Endometrial cancer (EC) is the most common gynecological malignancy, with rising incidence and mortality rates. Key risk factors, including obesity, prolonged estrogen exposure, and metabolic disorders, underscore the urgent need for non-invasive, early diagnostic tools. This review focuses on the role of DNA methylation as a potential biomarker for early EC detection. Aberrant DNA methylation in the promoter regions of tumor suppressor genes can lead to gene silencing and cancer progression. We examine recent studies utilizing minimally invasive samples, such as urine, cervicovaginal, and cervical scrapes, to detect early-stage EC through DNA methylation patterns. Markers such as RASSF1A, HIST1H4F, GHSR, SST, and ZIC1 have demonstrated high diagnostic accuracy, with AUC values up to 0.95, effectively distinguishing EC from non-cancerous conditions. This review highlights the potential of DNA methylation-based testing as a non-invasive alternative to traditional diagnostic methods, offering earlier detection, better risk stratification, and more personalized treatment plans. These innovations hold the promise of transforming clinical practice by enabling more timely and effective management of endometrial cancer.

Maternal exercise represses FGF21 via SIRT1 to improve the phenotypic transformation of vascular smooth muscle in hypertensive offspring.

Maternal exercise during pregnancy is widely recognized as an effective means of promoting cardiovascular health in offspring. Few studies have explored how maternal exercise impacts vascular function and phenotypic switching in hypertensive offspring, despite the known involvement of vascular structural and functional remodeling in hypertension pathogenesis. Research indicates a significant relationship between elevated blood pressure and fibroblast growth factor 21 (FGF21) levels. It remains unclear whether maternal exercise during pregnancy can improve vascular function in hypertensive offspring by regulating FGF21 and its underlying mechanisms. In this study, pregnant spontaneously hypertensive rats and Wistar-Kyoto rats were randomly assigned to either a sedentary or exercise group. The exercise group underwent weightless swimming exercise from gestation day 1 (GD1) to GD20. The aim was to investigate the epigenetic modifications mediated by histone deacetylase sirtuin 1 (SIRT1) during the fetal period and the phenotypic changes in the mesenteric arteries (MAs) of hypertensive offspring. We found that maternal exercise significantly improved vascular remodeling in hypertensive offspring. Specifically, maternal exercise upregulated SIRT1 expression, which led to decreased H3K9ac (histone H3 lysine 9 acetylation) in the promoter region of the FGF21 gene. This epigenetic modification resulted in the transcriptional downregulation of FGF21 in the MAs of hypertensive fetuses. These results suggest that maternal exercise may lower blood pressure in hypertensive offspring by regulating deacetylation of the FGF21 gene promoter region through SIRT1, thereby reversing phenotypic switching and vascular structural remodeling.

Identification of two transcription factors that work coordinately to regulate early development in Entamoeba.

The protozoan parasite Entamoeba has a life cycle that switches between infective cysts and invasive trophozoites. Encystation, a crucial process in parasite biology, is controlled by different mechanisms including transcriptional control. We identified two nuclear proteins in Entamoeba invadens, EIN_066100 and EIN_085620, that regulate parasite development by binding to a DNA motif (TCACTTTC) in the promoter regions of genes upregulated in the first 8 h of stage conversion. Overexpression of EIN_066100, a homolog of MAK16 protein, resulted in reduced amoebic proliferation without affecting encystation efficiency. Overexpression of EIN_085620, a protein with an RNA-recognition motif (RRM), led to increased encystation efficiency. Glutathione S-transferase (GST) pull down assays revealed that EIN_066100 interacts with EIN_085620 both in vivo and in vitro, and this interaction is mediated by the EIN_085620 RRM domain. By evaluating truncated proteins with deletions at either the N-terminal or C-terminal regions of EIN_066100, we elucidated the importance of its N-terminal region in proper protein localization, proliferation, encystation, and interaction with EIN_085620. Taken together, these results indicate a coordinated role of EIN_066100 and EIN_085620 in regulating Entamoeba development. This work sheds light on the molecular mechanisms in the earliest stages of Entamoeba encystation.IMPORTANCEAn important biological process in the biology of Entamoeba is stage conversion, which plays a crucial role in disease propagation, facilitating parasite survival outside the host and spreading to new hosts. Multiple mechanisms contribute to controlling the expression of amebic stage-specific genes such as epigenetic and transcriptional control. Identification of early transcriptional control regulators is crucial to understanding the initiation of the encystation cascade. We identified two nuclear proteins, EIN_066100 and EIN_085620, involved in the proliferation and developmental regulation of E. invadens. These proteins work by direct binding to each other and mediating encystation efficiency. Study of new regulators involved in Entamoeba development represents an important advance in a critical aspect of parasite biology.

Identification and functional validation of variants in the promoter region of HAND1 gene in sporadic tetralogy of Fallot.

Tetralogy of Fallot (TOF) is a common congenital heart disease (CHD) but the impact of the variants of the HAND1 gene promoter region has not been explored. DNA from blood samples of 612 subjects (300 sporadic TOF patients and 312 healthy controls) was sequenced to identify variants in the HAND1 gene promoter region that were further tested by cellular function experiments including dual-luciferase reporter gene assays, electrophoretic mobility shift analysis (EMSA), and bioinformatics analysis using JASPAR, a transcription factor binding site database. Eight variants in HAND1 gene promoter region were identified with 3 only found in TOF patients including one novel g.3639 G > T. All 3 variants significantly reduced the transcriptional activity of HAND1 gene promoter in an in vitro reporter assay (p < 0.05). JASPAR analysis indicated that these variants may alter the binding sites of transcription factors, potentially associated with TOF formation. In the promoter region of HAND1gene of TOF patients, 3 variants were found only in the patients including one found for the first time. These variants decreased transcription factor activity. Therefore, the present study implies the role of HAND1 gene in the pathogenesis of TOF and further provides new insights into the genetic basis of TOF formation. Sequencing of DNA from 612 human subjects (300 TOF patients and 312 healthy controls) identified 8 variants in the promoter region of HAND1 gene with 3 found only in TOF including 1 newly identified. Reduced transcriptional activity at these 3 variants was confirmed by dual-luciferase reporter gene assay and EMSA assay. Predictions from the JASPAR database suggest altered binding sites of transcription factors by the variants. We for the first time demonstrate variants in the HAND1 promoter and that cause cellular dysfunction. The variants identified may have a pathological role in the formation of TOF.

Expression of the polyphenol oxidase gene MdPPO7 is modulated by MdWRKY3 to regulate browning in sliced apple fruit.

Browning is a pervasive problem in horticultural products, substantially diminishing the appearance, flavor and nutritional value of fruit, including important fruits like apple (Malus × domestica Borkh.). In this study, we compared the physiological characteristics of the browning-resistant line 'Rb-18' with the susceptible variety 'Fuji' and found that the polyphenol oxidase (PPO) enzyme activity and phenolic content of Rb-18 were significantly lower than those in Fuji. In addition, the PPO enzyme in Fuji showed a stronger affinity for its substrate, catechol, compared to Rb-18. Through transcriptome and RT-qPCR analyses, MdPPO7 expression was identified as contributing to flesh browning after cutting. Subsequent fruit injection and stable genetic transformation of the MdPPO7 gene into apple fruit and calli determined that syringic acid, procyanidin, phloridzin, chlorogenic acid, gallic acid, catechin, and caffeic act as its catalytic substrates in the process involved in browning. Furthermore, luciferase reporter, yeast one-hybrid, β-glucuronidase reporter assays and chip-qPCR analysis demonstrated that a WRKY transcription factor(MdWRKY3) binds to the promoter region of polyphenol oxidase gene (MdPPO7) and positively regulates its expression to promote apple flesh browning. This study provides insights into the molecular regulatory mechanisms of fruit browning in fresh-cut apples and provides a theoretical basis for the generation of high-quality apple germplasm resources.

Pangenome Reveals Gene Content Variations and Structural Variants Contributing to Pig Characteristics.

Pigs are among the most essential sources of high-quality protein in human diets. Structural variants (SVs) are a major source of genetic variants associated with diverse traits and evolutionary events. However, the current linear reference genome of pigs limits the presentation of position information for SVs. In this study, we generated a pangenome of pigs and a genome variation map of 599 deep-sequenced genomes across Eurasia. Moreover, a section-wide gene repertoire was constructed, which indicated that core genes were more evolutionarily conserved than variable genes. Subsequently, we identified 546,137 SVs, their enrichment regions, and relationships with genomic features and found significant divergence across Eurasian pigs. More importantly, the pangenome-detected SVs could complement heritability estimates and genome-wide association studies based only on single nucleotide polymorphisms. Among the SVs shaped by selection, we identified an insertion in the promoter region of the TBX19 gene, which may be related to the development, growth, and timidity traits of Asian pigs and may affect the gene expression. Our constructed pig pangenome and the identified SVs provide rich resources for future functional genomic research on pigs.