Expression Profiles Of Transcription Factors Research Articles

P0106 Profiling inflammation-associated T helper subsets in Inflammatory Bowel Disease

Abstract Background Microbiota-specific CD4+ T cells drive chronic inflammation in Inflammatory Bowel Disease (IBD), comprising Crohn’s Disease (CD) and Ulcerative Colitis (UC). In previous projects we have identified several CD4+ T cell subsets enriched in the inflamed mucosa from naïve IBD patients, especially a colon-specific increase of HLA-DR+CD38+CD4+ memory T cells1. However, the functional properties remained to be elucidated. We therefore aimed to characterize CD4+ helper T cell lineage-specifying transcription factor (TF) expression and cytokine profiles in mucosa and circulation from IBD patients. Methods We collected intestinal samples and peripheral blood from patients and healthy controls undergoing diagnostic ileocolonoscopy, and subsequently employed 5-laser spectral flow cytometry to analyse single-cell data. Results For phenotypic characterization, a 37-antibody panel including TF and chemokine receptors was applied to 70 intestinal samples from 16 CD and 12 UC patients (including 22 non-inflamed, 22 inflamed samples and 16 samples in remission), as well as 5 healthy controls. Unbiased tSNE-based analysis revealed an increase of Foxp3+ Treg cells in inflamed biopsies. Particularly, in Ki-67+RORγt+ cells, we identified a cluster co-expressing Foxp3 and Helios, and a cluster expressed T-bet were enriched in inflamed colonic biopsies. As described before, two clusters of activated RORγt+HLA-DR+CD38+ T cell subset, one CD103+ and another CD103-, were increased in frequency in inflamed biopsies. Both clusters expressed CTLA-4, CD39 and Ki-67. In contrast, the frequencies of RORγt+ NKT-like cells (CD161+CD69+CD103-) were decreased in inflamed tissues. Next, we measured cytokine production in CD4+ T intestinal cells upon anti-CD3/CD28 stimulation of non-inflamed (healthy controls=8, IBD in active stage=8, IBD in remission=4) and inflamed samples (IBD in active stage=7). Frequencies of multifunctional CD103+ and CD103- CD154+ cells simultaneously producing IFNγ, TNFα and IL-2 were decreased in inflamed biopsies. On the contrary, CXCL-13 expression was elevated in the inflamed group. Conclusion In conclusion, we observed that a Th17/Treg and a Th17/Th1 subset were increased in inflamed biopsies, which we hypothesize to represent a transformation of Th17 to Treg or Th1. In addition, the HLA-DR+CD38+ subset displaying a Th17 profile was proliferating in inflamed mucosa, indicative of an active role in the disease pathogenesis. Simultaneously, Tregs were upregulated while CD4+ T cells produced less cytokines in inflamed mucosa, potentially indicating that Treg cells suppress the pro-inflammatory CD4+ T cell response in IBD patients. Thus, our results provide new clues about the functional contribution of CD4+ T cells to inflammation in IBD.

Genome-Wide Study of Plant-Specific PLATZ Transcription Factors and Functional Analysis of OsPLATZ1 in Regulating Caryopsis Development of Rice (Oryza sativa L.).

Plant A/T-rich sequence- and zinc-binding protein (PLATZ) is a type of plant-specific zinc-dependent DNA-binding protein that binds to A/T-rich DNA sequences. This family is essential for plant growth, development, and stress response. In this study, 15 OsPLATZs were identified in the rice genome with complete PLATZ-conserved domains by CD-search, similar to those found in angiosperms. Multi-species phylogenetic analysis showed that PLATZs were conserved in photosynthetic organisms, and an evolutionary branch unique to angiosperms was identified among members of the PLATZ family. Fifteen OsPLATZs were represented by five groups, each with distinct characteristics. An analysis of protein structures and sequence motifs showed that OsPLATZs were similar within groups, but varied between them. The expression profile and qRT-PCR results showed that OsPLATZs had distinct expression patterns in different tissues, with some responding to stress induction. Most of the OsPLATZs localized to the nuclei, and were predicted to bind to DNA sequences by AlphaFold3, suggesting that they likely function as conventional transcription factors. We also identified OsPLATZ1, a caryopsis-specific gene that regulates grain filling and caryopsis development in rice. This research lays the foundation for exploring the structural diversity, evolutionary traits, expression profile, and possible roles of PLATZ transcription factors in rice.

Emerging Signatures of Hematological Malignancies from Gene Expression and Transcription Factor-Gene Regulations.

Hematological malignancies are a diverse group of cancers developing in the peripheral blood, the bone marrow or the lymphatic system. Due to their heterogeneity, the identification of novel and advanced molecular signatures is essential for enhancing their characterization and facilitate its translation to new pharmaceutical solutions and eventually to clinical applications. In this study, we collected publicly available microarray data for more than five thousand subjects, across thirteen hematological malignancies. Using PANDA to estimate gene regulatory networks (GRNs), we performed hierarchical clustering and network analysis to explore transcription factor (TF) interactions and their implications on biological pathways. Our findings reveal distinct clustering patterns among leukemias and lymphomas, with notable differences in gene and TF expression profiles. Gene Set Enrichment Analysis (GSEA) identified 57 significantly enriched KEGG pathways, highlighting both common and unique biological processes across HMs. We also identified potential drug targets within these pathways, emphasizing the role of TFs such as CEBPB and NFE2L1 in disease pathophysiology. Our comprehensive analysis enhances the understanding of the molecular landscape of HMs and suggests new avenues for targeted therapeutic strategies. These findings also motivate the adoption of regulatory networks, combined with modern biotechnological possibilities, for insightful pan-cancer exploratory studies.

Uncovering Key Transcription Factors Driving Chilling Stress Tolerance in Rice Germination

Background: Rice, one of the main foods in Brazil and the world, is sensitive to chilling (0–15 °C), especially in the germination and reproductive stages. Chilling causes delayed germination and affects coleoptile elongation at the S3 stage (needlepoint), causing poor plant establishment, stunted growth, and non-vigorous plants, also impacting weed management. Elucidating the mechanisms responsible for resilience under cold conditions helps the development of tolerant cultivars. Transcription factors (TFs) act in stress response signaling, making them indispensable in the tolerance mechanism. Objective: Thus, this study aimed to identify and characterize the expression profile of transcription factors in the response to chilling stress in rice at the germination stage. Methods: To determine the transcriptional profile of 2408 genes belonging to 56 TF families, RNAseq was performed on the shoot tissue of seedlings of Oro (chilling-tolerant) and Tio Taka (chilling-sensitive) genotypes grown under control conditions (25 °C) and chilling stress (13 °C) until the S3 stage. Results: Of the total genes analyzed, 22% showed significant differential expression in the analyzed cultivars. There were 117 genes that showed significant differential expression in the tolerant cultivar, 60 of which were downregulated and 57 upregulated. In the sensitive cultivar, 248 genes had a significant differential expression, of which 98 genes were downregulated and 150 genes were upregulated. A total of 170 genes encoding TFs were commonly and significantly differentially expressed in the tolerant and sensitive genotypes. Conclusions: Here, we revealed potential new targets involved in the regulation of chilling stress in rice at the S3 stage.

Comprehensive Genome-Wide Identification and Expression Profiling of bHLH Transcription Factors in Areca catechu Under Abiotic Stress.

The basic helix-loop-helix (bHLH) transcription factor (TF) family, the second-largest among eukaryotes, is known for its evolutionary and functional diversity across plant species. However, bHLH genes have not yet been characterized in Areca catechu. In this study, we identified 76 AcbHLH genes, which exhibit a variety of physicochemical properties. Phylogenetic analysis revealed evolutionary relationships between Arabidopsis thaliana bHLH genes (AtbHLH) and their counterparts in A. catechu (AcbHLH). These analyses also highlighted conserved amino acid motifs (S, R, K, P, L, A, G, and D), conserved domains, and evolutionary changes, such as insertions, deletions, and exon gains or losses. Promoter analysis of AcbHLH genes revealed 76 cis-elements related to growth, phytohormones, light, and stress. Gene duplication analysis revealed four tandem duplications and twenty-three segmental duplications, while AcbHLH63 in the Areca genome exhibited significant synteny with bHLH genes from A. thaliana, Vitis vinifera, Solanum lycopersicum, Brachypodium distachyon, Oryza sativa, and Zea mays. Furthermore, relative expression analysis showed that under drought stress (DS), AcbHLH22, AcbHLH39, AcbHLH45, and AcbHLH58 showed distinct upregulation in leaves at specific time points, while all nine AcbHLH genes were upregulated in roots. Under salt stress (SS), AcbHLH22, AcbHLH39, AcbHLH45, and AcbHLH58 were upregulated in leaves, and AcbHLH22, AcbHLH34, and AcbHLH39 exhibited differential expression in roots at various time points. This study provides valuable insights into the bHLH superfamily in A. catechu, offering a solid foundation for further investigation into its role in responding to abiotic stresses.

Genome-Wide Identification and Expression Profiles of Nuclear Factor Y A Transcription Factors in Blueberry Under Abiotic Stress.

Nuclear Factor Y A (NF-YA) transcription factors are widely involved in multiple plant biological processes, such as embryogenesis, abscisic acid signaling, and abiotic stress response. This study presents a comprehensive genome-wide identification and expression profiling of NF-YA transcription factors in blueberry (Vaccinium corymbosum), an important economic crop with good adaptability, under abiotic stress conditions. Given the economic significance and health benefits of blueberries, understanding their responses to environmental stresses, such as salt, drought, and temperature extremes, is crucial. A total of 24 NF-YA transcription factors were identified through bioinformatics analyses, including sequence alignment, phylogenetic tree construction, and conserved motif analysis. The expression patterns of these NF-YA genes were evaluated in various tissues (roots, stems, and leaves) and under different stress treatments (abscisic acid, salt, and cold) using quantitative real-time PCR (qRT-PCR). The results indicated that most VcNF-YA genes exhibited higher expression levels in stems and leaves compared to roots. Most VcNF-YAs were responsive to the stress treatment. Furthermore, cis-acting element analysis revealed that the promoters of VcNF-YAs were enriched with elements responsive to abiotic stress, suggesting their pivotal role in stress adaptation. This research unveils the expressional responses of NF-YA transcription factors in blueberry upon abiotic stresses and lays the groundwork for future studies on improving crop adaptation.

Single cell analysis identified a basal cell transition state associated with the development and progression of bladder cancer

BackgroundBladder cancer (BC) is a prevalent malignancy characterized by significant cellular heterogeneity. While single-cell multi-omics studies have provided valuable insights, much of the existing data remains underexplored, limiting our understanding of BC’s molecular mechanisms. Uncovering the pathogenesis of BC and finding new treatment methods are urgent problems to be solved. This study aims to address this gap by re-analyzing available single-cell datasets to uncover novel insights into BC.MethodsIn this study, we retrieved three single-cell transcriptome datasets by searching the Gene Expression Omnibus (GEO) database, focusing on single-cell sequencing of normal mouse bladder within the past 5 years. Through quality control and batch effect elimination, we obtained a total of 24,930 cells including epithelial, stromal, and immune cells. Subgroup analysis, pseudotemporal analysis, cell–cell communication, and transcription factor analysis were conducted specifically on epithelial cells to identify a transitional state during basal cell differentiation. We further compared the expression profiles of key transcription factors in cancer and normal tissues. In addition, we also performed immunohistochemical staining and survival analysis for key transcription factors.ResultsSubgroup analysis revealed multiple subtypes of epithelial cells, including basal, umbrella, and intermediate cells. Through pseudotemporal analysis, we discovered the developmental trajectory from basal cells to umbrella cells and further found that Basal_I is a transitional state for basal cell differentiation. Cell-to-cell communication analyses highlighted the pivotal role of Basal_I in cell–cell interactions, and key ligand-receptor pairs associated with cancer progression were also identified. Furthermore, elevated expression levels of key transcription factors in Basal_I were found to be closely associated with the stage and prognosis of BC. Immunohistochemical staining results further confirmed the upregulated expression of these transcription factors in BC.ConclusionsCollectively, we found a transitional state of basal cells in normal bladder epithelial cells in mice, which may be related to the occurrence and development of BC, providing important clues for further understanding of the pathogenesis of BC. Our study provided possible molecular mechanisms or target for the research and treatment of BC.

Comprehensive Annotation and Expression Profiling of C2H2 Zinc Finger Transcription Factors across Chicken Tissues.

As the most abundant class of transcription factors in eukaryotes, C2H2-type zinc finger proteins (C2H2-ZFPs) play critical roles in various biological processes. Despite being extensively studied in mammals, C2H2-ZFPs remain poorly characterized in birds. Recent accumulation of multi-omics data for chicken enables the genome-wide investigation of C2H2-ZFPs in birds. The purpose of this study is to reveal the genomic occurrence and evolutionary signature of chicken C2H2-ZFPs, and further depict their expression profiles across diverse chicken tissues. Here, we annotated 301 C2H2-ZFPs in chicken genome, which are associated with different effector domains, including KRAB, BTB, HOMEO, PHD, SCAN, and SET. Among them, most KRAB-ZFPs lack orthologues in mammals and tend to form clusters by duplication, supporting their fast evolution in chicken. We also annotated a unique and previously unidentified SCAN-ZFP, which is lineage-specific and highly expressed in ovary and testis. By integrating 101 RNA-seq datasets for 32 tissues, we found that most C2H2-ZFPs have tissue-specific expression. Particularly, 74 C2H2-ZFPs-including 27 KRAB-ZFPs-show blastoderm-enriched expression, indicating their association with early embryo development. Overall, this study performs comprehensive annotation and expression profiling of C2H2 ZFPs in diverse chicken tissues, which gives new insights into the evolution and potential function of C2H2-ZFPs in avian species.

Changes in T-cell subsets occur in interstitial lung disease and may contribute to pathology via complicated immune cascade.

The study aimed to investigate the expression profiles of transcription factors, cytokines, and co-stimulatory molecules in helper T (Th)-cell subsets within bronchoalveolar lavage (BAL) samples of patients with interstitial lung diseases (ILDs). Twenty ILDs patients were included in the study, comprising those with idiopathic pulmonary fibrosis (IPF) (n:8), autoimmune-related ILDs (auto-ILD) (n:4), and orphan diseases (O-ILD) (n:8), alongside five control subjects. Flow cytometry was employed to evaluate the Th to cytotoxic Tcell (CTL) ratio in BAL fluid, while cytopathological examination assessed macrophages, lymphocytes, and neutrophils. Quantitative real-time polymerase chain reaction was utilized to investigate the expressions in Th1, Th2, Th17, and regulatory T (Treg) cells. Results revealed elevated Th cell to CTL ratios across all patient groups compared to controls. Furthermore, upregulation of Th1, Th2, Th17, and T-cell factors was observed in all patient groups compared to controls. Interestingly, upregulation of CD28 and downregulation of CTLA-4 and PD-1 gene expression were consistent across all ILDs groups, highlighting potential immune dysregulation. This study provides a comprehensive exploration of molecular immunological mechanisms in ILDs patients, underscoring the dominance of Th2 and Th17 responses and revealing novel findings regarding the dysregulation of CD28, CTLA-4, and PD-1 expressions in ILDs for the first time.

Expression profiling of Nuclear Factor-Y (NF-Y) transcription factors during dehydration and salt stress in finger millet reveals potential candidate genes for multiple stress tolerance.

Expression profiling of NF-Y transcription factors during dehydration and salt stress in finger millet genotypes contrastingly differing in tolerance levels identifies candidate genes for further characterization and functional studies. The Nuclear Factor-Y (NF-Y) transcription factors are known for imparting abiotic stress tolerance in different plant species. However, there is no information on the role of this transcription factor family in naturally drought-tolerant crop finger millet (Eleusine coracana L.). Therefore, interpretation of expression profiles against drought and salinity stress may provide valuable insights into specific and/or overlapping expression patterns of Eleusine coracana Nuclear Factor-Y (EcNF-Y) genes. Given this, we identified 59 NF-Y (18 NF-YA, 23 NF-YB, and 18 NF-YC) encoding genes and designated them EcNF-Y genes. Expression profiling of these genes was performed in two finger millet genotypes, PES400 (dehydration and salt stress tolerant) and VR708 (dehydration and salt stress sensitive), subjected to PEG-induced dehydration and salt (NaCl) stresses at different time intervals (0, 6, and 12h). The qRT-PCR expression analysis reveals that the six EcNF-Y genes namely EcNF-YA1, EcNF-YA5, EcNF-YA16, EcNF-YB6, EcNF-YB10, and EcNF-YC2 might be associated with tolerance to both dehydration and salinity stress in early stress condition (6h), suggesting the involvement of these genes in multiple stress responses in tolerant genotype. In contrast, the transcript abundance of finger millet EcNF-YA5 genes was also observed in the sensitive genotype VR708 under late stress conditions (12h) of both dehydration and salinity stress. Therefore, the EcNF-YA5 gene might be important for adaptation to salinity and dehydration stress in sensitive finger millet genotypes. Therefore, this gene could be considered as a susceptibility determinant, which can be edited to impart tolerance. The phylogenetic analyses revealed that finger millet NF-Y genes share strong evolutionary and functional relationship to NF-Ys governing response to abiotic stresses in rice, sorghum, maize, and wheat. This is the first report of expression profiling of EcNF-Ys genes identified from the finger millet genome and reveals potential candidate for enhancing dehydration and salt tolerance.

The landscape of transcription factor promoter activity during vegetative development in Marchantia.

Transcription factors (TFs) are essential for the regulation of gene expression and cell fate determination. Characterizing the transcriptional activity of TF genes in space and time is a critical step toward understanding complex biological systems. The vegetative gametophyte meristems of bryophytes share some characteristics with the shoot apical meristems of flowering plants. However, the identity and expression profiles of TFs associated with gametophyte organization are largely unknown. With only ∼450 putative TF genes, Marchantia (Marchantia polymorpha) is an outstanding model system for plant systems biology. We have generated a near-complete collection of promoter elements derived from Marchantia TF genes. We experimentally tested reporter fusions for all the TF promoters in the collection and systematically analyzed expression patterns in Marchantia gemmae. This allowed us to build a map of expression domains in early vegetative development and identify a set of TF-derived promoters that are active in the stem-cell zone. The cell markers provide additional tools and insight into the dynamic regulation of the gametophytic meristem and its evolution. In addition, we provide an online database of expression patterns for all promoters in the collection. We expect that these promoter elements will be useful for cell-type-specific expression, synthetic biology applications, and functional genomics.

PbrWRKY62-PbrADC1 module involves in superficial scald development of Pyrus bretschneideri Rehd.fruit via regulating putrescine biosynthesis

Putrescine plays a role in superficial scald development during the cold storage of pear fruit. However, the molecular mechanism behind this phenomenon has not been un-fully clarified until recently. In this study, a conjoint analysis of metabolites and gene expression profiles in the putrescine-metabolic pathway of P. bretschneideri Rehd. fruit followed by experimental validation revealed that PbrADC1, forming a homodimer in the chloroplast, was involved in putrescine biosynthesis and thus fruit chilling resistance. Additionally, the substrate-binding residue Cys546 in PbrADC1, whose activity was modified by H2O2, played a crucial role in arginine decarboxylation into agmatine. Through a combined analysis of the distribution of cis-acting elements in the PbrADC1 promoter as well as the expression profiles of related transcription factors (TFs), several TFs were identified as upstream regulators of PbrADC1 gene. Further investigation revealed that the nuclear PbrWRKY62 could directly bind to the W-box elements in the PbrADC1 promoter, activate its expression, enhance putrescine accumulation, and thus increase fruit chilling tolerance. In conclusion, our results suggest that the PbrWRKY62-PbrADC1 module is involved in the development of superficial scald in P. bretschneideri Rehd. fruit via regulating putrescine biosynthesis. Consequently, these findings could serve as valuable genetic resources for breeding scald-resistant pear fruit.Graphical

Expression patterns of E2Fs identify tumor microenvironment features in human gastric cancer.

E2F transcription factors are associated with tumor development, but their underlying mechanisms in gastric cancer (GC) remain unclear. This study explored whether E2Fs determine the prognosis or immune and therapy responses of GC patients. E2F regulation patterns from The Cancer Genome Atlas (TCGA) were systematically investigated and E2F patterns were correlated with the characteristics of cellular infiltration in the tumor microenvironment (TME). A principal component analysis was used to construct an E2F scoring model based on prognosis-related differential genes to quantify the E2F regulation of a single tumor. This scoring model was then tested in patient cohorts to predict effects of immunotherapy. Based on the expression profiles of E2F transcription factors in GC, two different regulatory patterns of E2F were identified. TME and survival differences emerged between the two clusters. Lower survival rates in the Cluster2 group were attributed to limited immune function due to stromal activation. The E2F scoring model was then constructed based on the E2F-related prognostic genes. Evidence supported the E2F score as an independent and effective prognostic factor and predictor of immunotherapy response. A gene-set analysis correlated E2F score with the characteristics of immune cell infiltration within the TME. The immunotherapy cohort database showed that patients with a higher E2F score demonstrated better survival and immune responses. This study found that differences in GC prognosis might be related to the E2F patterns in the TME. The E2F scoring system developed in this study has practical value as a predictor of survival and treatment response in GC patients.

Viable tendon neotissue from adult adipose-derived multipotent stromal cells.

Background: Tendon healing is frequently prolonged, unpredictable, and results in poor tissue quality. Neotissue formed by adult multipotent stromal cells has the potential to guide healthy tendon tissue formation. Objectives: The objective of this study was to characterize tendon neotissue generated by equine adult adipose-derived multipotent stromal cells (ASCs) on collagen type I (COLI) templates under 10% strain in a novel bioreactor. The tested hypothesis was that ASCs assume a tendon progenitor cell-like morphology, express tendon-related genes, and produce more organized extracellular matrix (ECM) in tenogenic versus stromal medium with perfusion and centrifugal fluid motion. Methods: Equine ASCs on COLI sponge cylinders were cultured in stromal or tenogenic medium within bioreactors during combined perfusion and centrifugal fluid motion for 7, 14, or 21days under 10% strain. Viable cell distribution and number, tendon-related gene expression, and micro- and ultra-structure were evaluated with calcein-AM/EthD-1 staining, resazurin reduction, RT-PCR, and light, transmission, and scanning electron microscopy. Fibromodulin was localized with immunohistochemistry. Cell number and gene expression were compared between culture media and among culture periods (p < 0.05). Results: Viable cells were distributed throughout constructs for up to 21days of culture, and cell numbers were higher in tenogenic medium. Individual cells had a round or rhomboid shape with scant ECM in stromal medium in contrast to clusters of parallel, elongated cells surrounded by highly organized ECM in tenogenic medium after 21days of culture. Transcription factor, extracellular matrix, and mature tendon gene expression profiles confirmed ASC differentiation to a tendon progenitor-like cell in tenogenic medium. Construct micro- and ultra-structure were consistent with tendon neotissue and fibromodulin was present in the ECM after culture in tenogenic medium. Conclusion: Long-term culture in custom bioreactors with combined perfusion and centrifugal tenogenic medium circulation supports differentiation of equine adult ASCs into tendon progenitor-like cells capable of neotissue formation.

Genome-wide analysis of sugar transporter gene family in Erianthus rufipilus and Saccharum officinarum, expression profiling and identification of transcription factors.

Sugar, the primary product of photosynthesis, is a vital requirement for cell activities. Allocation of sugar from source to sink tissues is facilitated by sugar transporters (ST). These STs belong to the Major Facilitator Superfamily (MFS), the largest family of STs in plants. In this study, we performed genome wide and gene expression data analysis to identify the putative ST genes in Erianthus rufipilus (E. rufipilus) and in Saccharum officinarum (S. officinarum). We identified 78 ST gene families in E. rufipilus and 86 ST gene families in S. officinarum. Phylogenetic analysis distributed the ST genes into eight distinct subfamilies (INT, MST, VGT, pGlcT, PLT, STP, SFP and SUT). Chromosomal distribution of ST genes clustered them on 10 respective chromosomes. Furthermore, synteny analysis with S. spontaneum and Sorghum bicolor (S. bicolor) revealed highly colinear regions. Synonymous and non-synonymous ratio (Ka/Ks) showed purifying selection in gene evolution. Promoter analysis identified several cis-regulatory elements, mainly associated with light responsiveness. We also examined the expression pattern of ST genes in different developing tissues (mature leaf, pre-mature stem, mature stem and seedling stem). Under sugar stress, we identified the significant ST genes showing differential expression patterns. Moreover, our yeast one-hybrid (Y1H) assays identified NAM, ATAF and CUC (NAC) and Lesion Simulating Disease (LSD) potential transcription factors (TFs) that may bind to the SUT1-T1 promoter in S. officinarum, showing negative correlation pattern with SUT1-T1. Our results deepen our understanding of ST gene evolution in Saccharum species and will facilitate the future investigation of functional analysis of the ST gene family.

PbrWRKY42-PbrSOT13 module regulated sorbitol accumulation in the developing ‘Yali’ fruit after three-layer-paper bagging treatment

As a conventional preharvest handling practice, fruit bagging could control insects and diseases, and therefore improve the visual quality of pear, but suppress the accumulation of soluble sugar. However, the molecular mechanism underlying this phenomenon has not been fully elucidated until recently. In this study, the three-layer-paper bagging treatment considerably suppressed the accumulation of four soluble sugars in the developing ‘Yali’ fruit. In combination with the expression profiles of the differently expressed sugar-metabolism-related genes, PbrSOT13, encoding a plasma membrane-located protein, was selected and confirmed to participate in sorbitol influx and accumulation in pear. Notably, molecular dynamic simulation indicated that the Asp52 and Arg132 residues were pivotal in this process. After a conjoined analysis of cis-acting elements in PbrSOT13 promoter and the expression profiles of transcription factors, PbrWRKY42 was identified as a candidate upstream regulator of PbrSOT13. The nuclear PbrWRKY42 could bind to the W-box element of PbrSOT13 promoter and then activate its transcription, as evidenced by yeast one-hybrid assay and dual-luciferase assay, thus enhancing sorbitol accumulation in fruit. Further study found that the transcription of PbrSOT13 and PbrWRKY42 was suppressed by the elevated temperature and the reduced light-exposure period, which was the consequence of bagging treatment. Taken together, our results implied that three-layer-paper bagging treatment would alter temperature and light exposure around the developing ‘Yali’ fruit, and thus suppress sorbitol accumulation via the PbrWRKY42-PbrSOT13 module.

Expression Profiling of Salt-Responsive Genes and Transcription Factors in Leaf Transcriptome of Arabidopsis thaliana

This investigation discerns the expression profiles of genes within the leaf transcriptome of Arabidopsis thaliana subjected to salt stress (200 mM NaCl). Notably, the pivotal role of indole acetic acid emerged as a keystone orchestrating a multifaceted cascade of regulatory events aimed at enhancing the plant’s adaptability under salt-induced stress. Cluster analysis elucidated upregulation of gene families with pivotal roles in supporting the availability of carbon dioxide, ameliorating photosynthetic processes and mitigating the deleterious effects of reactive oxygen species under salt stress. Analysis also unveiled the participation of several transcription factor families in the orchestration of a multitude of genes under salt stress. The investigation singled out a solitary TF, denominated as BH100, which was validated through RNA-Seq and qPCR, utilizing a VIGS line featuring the knockdown of the BH100 gene. This transcription factor was implicated in the upregulation of the FRO gene, thereby establishing a link between the synchronized expression of these two genes and their role in promoting iron acquisition under salt stress. In summation, our study unveiled the regulatory frameworks and salt-responsive genes underpinning the response of Arabidopsis to salt stress. We present compelling arguments for the potential applicability of this information in the realm of molecular breeding programs.

Genome-Wide Identification and Expression Profiles of C-Repeat Binding Factor Transcription Factors in Betula platyphylla under Abiotic Stress.

CBF (C-repeat binding factor) transcription factor subfamily belongs to AP2/ERF (Apetala 2/ethylene-responsive factor) transcription factor family, known for playing a vital role in plant abiotic stress response. Although some CBF transcription factors have been identified in several species, such as Arabidopsis, tobacco, tomato and poplar, research of CBF focus mainly on model plant Arabidopsis and have not been reported in Betula platyphylla yet. In this study, a total of 20 BpCBF subfamily members were identified. The conserved domains, physicochemical properties, exon-intron gene structure and the structure of conserved protein motifs of BpCBFs were analyzed via bioinformatic tools. The collinearity analysis of CBF genes was performed between Betula platyphylla and Arabidopsis thaliana, Betula platyphylla, and Populus trichocarpa. The cis-acting elements in the promoter region of BpCBFs were identified, which were mainly environmental stress-related and hormone-related element components. In this case, the expression patterns of the 20 BpCBFs upon ABA or salt treatment were investigated. Most of these transcription factors were responsive to ABA or salt stress in different plant tissues. The up-regulation trend upon cold treatment of the six cold-responsive genes validated by qRT-PCR was consistent with the result of RNA-seq. BpCBF7 showed transcription activating activity. This study sheds light on the responses of BpCBFs to abiotic stress and provides a reference for further study of CBF transcription factors in woody plants.

Whole-body gene expression atlas of an adult metazoan.

Gene activity defines cell identity, drives intercellular communication, and underlies the functioning of multicellular organisms. We present the single-cell resolution atlas of gene activity of a fertile adult metazoan: Caenorhabditis elegans. This compendium comprises 180 distinct cell types and 19,657 expressed genes. We predict 7541 transcription factor expression profile associations likely responsible for defining cellular identity. We predict thousands of intercellular interactions across the C. elegans body and the ligand-receptor pairs that mediate them, some of which we experimentally validate. We identify 172 genes that show consistent expression across cell types, are involved in basic and essential functions, and are conserved across phyla; therefore, we present them as experimentally validated housekeeping genes. We developed the WormSeq application to explore these data. In addition to the integrated gene-to-systems biology, we present genome-scale single-cell resolution testable hypotheses that we anticipate will advance our understanding of the molecular mechanisms, underlying the functioning of a multicellular organism and the perturbations that lead to its malfunction.

Upregulation of the Oct3/4 Network in Basal Breast Cancer Is Associated with Its Metastatic Potential and Shows Tissue Dependent Variability.

Adaptive plasticity of Breast Cancer stem cells (BCSCs) is strongly correlated with cancer progression and resistance, leading to a poor prognosis. In this study, we report the expression profile of several pioneer transcription factors of the Oct3/4 network associated with tumor initiation and metastasis. In the triple negative breast cancer cell line (MDA-MB-231) stably transfected with human Oct3/4-GFP, differentially expressed genes (DEGs) were identified using qPCR and microarray, and the resistance to paclitaxel was assessed using an MTS assay. The tumor-seeding potential in immunocompromised (NOD-SCID) mice and DEGs in the tumors were also assessed along with the intra-tumor (CD44+/CD24-) expression using flow cytometry. Unlike 2-D cultures, the Oct3/4-GFP expression was homogenous and stable in 3-D mammospheres developed from BCSCs. A total of 25 DEGs including Gata6, FoxA2, Sall4, Zic2, H2afJ, Stc1 and Bmi1 were identified in Oct3/4 activated cells coupled with a significantly increased resistance to paclitaxel. In mice, the higher Oct3/4 expression in tumors correlated with enhanced tumorigenic potential and aggressive growth, with metastatic lesions showing a >5-fold upregulation of DEGs compared to orthotopic tumors and variability in different tissues with the highest modulation in the brain. Serially re-implanting tumors in mice as a model of recurrence and metastasis highlighted the sustained upregulation of Sall4, c-Myc, Mmp1, Mmp9 and Dkk1 genes in metastatic lesions with a 2-fold higher expression of stem cell markers (CD44+/CD24-). Thus, Oct3/4 transcriptome may drive the differentiation and maintenance of BCSCs, promoting their tumorigenic potential, metastasis and resistance to drugs such as paclitaxel with tissue-specific heterogeneity.