Transcription Factor Gene Expression Research Articles

Ensemble learning based assessment of the role of transcription factors in gene expression

Cancer cells are formed when the associated, active genes fail to function the way they are meant to function. Multiple genes collectively control cell growth by activating a proper set of genes. Regulation of gene expression is controlled through the combined effort of multiple regulatory elements. Transcription of each gene is affected differently according to the combinatorial patterns of regulatory elements bound in the nearby regions. Identifying and analysing such patterns will give a better insight into the cell function. The main focus of this study is on developing a computational model to predict the functional role of transcriptional factors residing between divergent gene pairs. Acute Myeloid Leukaemia (AML) gene expression data from GEO and the two TFs EP300 and CTCF binding data calibrated in k562 cell line from ENCODE consortium are taken as a case study.

FOXA1/2 depletion drives global reprogramming of differentiation state and metabolism in a human liver cell line and inhibits differentiation of human stem cell-derived hepatic progenitor cells.

FOXA factors are critical members of the developmental gene regulatory network (GRN) composed of master transcription factors (TF) which regulate murine cell fate and metabolism in the gut and liver. How FOXA factors dictate human liver cell fate, differentiation, and simultaneously regulate metabolic pathways is poorly understood. Here, we aimed to determine the role of FOXA2 (and FOXA1 which is believed to compensate for FOXA2) in controlling hepatic differentiation and cell metabolism in a human hepatic cell line (HepG2). siRNA mediated knockdown of FOXA1/2 in HepG2 cells significantly downregulated albumin (p < .05) and GRN TF gene expression (HNF4α, HEX, HNF1ß, TBX3) (p < .05) and significantly upregulated endoderm/gut/hepatic endoderm markers (goosecoid [GSC], FOXA3, and GATA4), gut TF (CDX2), pluripotent TF (NANOG), and neuroectodermal TF (PAX6) (p < .05), all consistent with partial/transient reprograming. shFOXA1/2 targeting resulted in similar findings and demonstrated evidence of reversibility of phenotype. RNA-seq followed by bioinformatic analysis of shFOXA1/2 knockdown HepG2 cells demonstrated 235 significant downregulated genes and 448 upregulated genes, including upregulation of markers for alternate germ layers lineages (cardiac, endothelial, muscle) and neurectoderm (eye, neural). We found widespread downregulation of glycolysis, citric acid cycle, mitochondrial genes, and alterations in lipid metabolism, pentose phosphate pathway, and ketogenesis. Functional metabolic analysis agreed with these findings, demonstrating significantly diminished glycolysis and mitochondrial respiration, with concomitant accumulation of lipid droplets. We hypothesized that FOXA1/2 inhibit the initiation of human liver differentiation in vitro. During human pluripotent stem cells (hPSC)-hepatic differentiation, siRNA knockdown demonstrated de-differentiation and unexpectedly, activation of pluripotency factors and neuroectoderm. shRNA knockdown demonstrated similar results and activation of SOX9 (hepatobiliary). These results demonstrate that FOXA1/2 controls hepatic and developmental GRN, and their knockdown leads to reprogramming of both differentiation and metabolism, with applications in studies of cancer, differentiation, and organogenesis.

BTH-induced joint regulation of wound healing at the wounds of apple fruit by JA and its downstream transcription factors

Jasmonic acids (JAs) are important injury signaling molecules, which participate in the process of wound healing in plants. However, how JA and its downstream transcription factors involve in wound healing in apple fruit mediated by BTH has not been reported yet. In the present study, BTH treatment up-regulated gene expression of MdLOX3.1, MdAOS1, MdAOC, and MdOPR3, promoting JA synthesis at fruit wounds. Moreover, BTH up-regulated the gene expression of MdMYC2, MdGAIPB, and MdMYB108 transcription factors and increased MdPAL1, Md4CL2, MdCOMT1, and MdCAD6 expression. In addition, BTH facilitated the synthesis of phenylpropanoid metabolism products and accelerated suberin polyphenolics deposition at the wounds, which effectively reduced fruit weight loss and lesion diameter of apple fruit inoculated with Penicillium expansum during healing. It is suggested that BTH induced wound healing in apple fruit by the stimulating JA and its downstream transcription factors, and phenylpropanoid metabolism.

Impact of 10-day bed rest on serum levels of irisin and markers of musculoskeletal metabolism.

The bed rest (BR) is a ground-based model to simulate microgravity mimicking skeletal-muscle alterations as in spaceflight. Molecular coupling between bone and muscle might be involved in physiological and pathological conditions. Thus, the new myokine irisin and bone-muscle turnover markers have been studied during and after 10 days of BR. Ten young male individuals were subjected to 10 days of horizontal BR. Serum concentrations of irisin, myostatin, sclerostin, and haptoglobin were assessed, and muscle tissue gene expression on vastus lateralis biopsies was determined. During 10-days BR, we observed no significant fluctuation levels of irisin, myostatin, and sclerostin. Two days after BR (R+2), irisin serum levels significantly decreased while myostatin, sclerostin, and haptoglobin were significantly increased compared with BR0. Gene expression of myokines, inflammatory molecules, transcription factors, and markers of muscle atrophy and senescence on muscle biopsies were not altered, suggesting that muscle metabolism of young, healthy subjects is able to adapt to the hypomobility condition during 10-day BR. However, when subjects were divided according to irisin serum levels at BR9, muscle ring finger-1 mRNA expression was significantly lower in subjects with higher irisin serum levels, suggesting that this myokine may prevent the triggering of muscle atrophy. Moreover, the negative correlation between p21 mRNA and irisin at BR9 indicated a possible inhibitory effect of the myokine on the senescence marker. In conclusion, irisin could be a prognostic marker of hypomobility-induced muscle atrophy, and its serum levels could protect against muscle deterioration by preventing and/or delaying the expression of atrophy and senescence cellular markers.

Rotenone-induced oxidative stress in THP-1 cells: biphasic effects of baicalin.

Several results demonstrated that microglia and peripheral monocytes/macrophages infiltrating the central nervous system (CNS) are involved in cell response against toxic compounds. It has been shown that rotenone induces neurodegeneration in various in vitro experimental models. Baicalin, a natural compound, is able to attenuate cell damage through anti-oxidant, anti-microbial, anti-inflammatory, and immunomodulatory action. Using THP-1 monocytes, we investigated rotenone effects on mitochondrial dysfunction and apoptosis, as well as baicalin ability to counteract rotenone toxicity. THP-1 cells were exposed to rotenone (250nM), in the presence/absence of baicalin (10-500μM) for 2-24h. Reactive Oxygen Species production (ROS), mitochondrial activity and transmembrane potential (Δψm), DNA damage, and caspase-3 activity were assessed. Moreover, gene expression of mitochondrial transcription factor a (mtTFA), interleukin-1β (IL-1β), B-cell lymphoma 2 (Bcl2) and BCL2-associated X protein (Bax), together with apoptotic morphological changes, were evaluated. After 2h of rotenone incubation, increased ROS production and altered Δψm were observed, hours later resulting in DNA oxidative damage and apoptosis. Baicalin treatment at 50µM counteracted rotenone toxicity by modulating the expression levels of some proteins involved in mitochondrial biogenesis and apoptosis. Interestingly, at higher baicalin concentrations, rotenone-induced alterations persisted. These results give evidence that exposure to rotenone may promote the activation of THP-1 monocytes contributing to enhanced neurodegeneration. In this context, baicalin at low concentration exerts beneficial effects on mitochondrial function, and thus may prevent the onset of neurotoxic processes.

Transcriptional mapping of the macaque retina and RPE-choroid reveals conserved inter-tissue transcription drivers and signaling pathways.

The macula and fovea comprise a highly sensitive visual detection tissue that is susceptible to common disease processes like age-related macular degeneration (AMD). Our understanding of the molecular determinants of high acuity vision remains unclear, as few model organisms possess a human-like fovea. We explore transcription factor networks and receptor-ligand interactions to elucidate tissue interactions in the macula and peripheral retina and concomitant changes in the underlying retinal pigment epithelium (RPE)/choroid. Poly-A selected, 100bp paired-end RNA-sequencing (RNA-seq) was performed across the macular/foveal, perimacular, and temporal peripheral regions of the neural retina and RPE/choroid tissues of four adult Rhesus macaque eyes to characterize region- and tissue-specific gene expression. RNA-seq reads were mapped to both the macaque and human genomes for maximum alignment and analyzed for differential expression and Gene Ontology (GO) enrichment. Comparison of the neural retina and RPE/choroid tissues indicated distinct, contiguously changing gene expression profiles from fovea through perimacula to periphery. Top GO enrichment of differentially expressed genes in the RPE/choroid included cell junction organization and epithelial cell development. Expression of transcriptional regulators and various disease-associated genes show distinct location-specific preference and retina-RPE/choroid tissue-tissue interactions. Regional gene expression changes in the macaque retina and RPE/choroid is greater than that found in previously published transcriptome analysis of the human retina and RPE/choroid. Further, conservation of human macula-specific transcription factor profiles and gene expression in macaque tissues suggest a conservation of programs required for retina and RPE/choroid function and disease susceptibility.

Immediate stress dissipation in dual cross-link hydrogels controls osteogenic commitment of mesenchymal stem cells

In vitro studies of mesenchymal stem cells (MSCs) differentiation have been predominantly performed with non-physiologically elastic materials. Here we report the effect of different viscoplastic ECM mimics on the osteogenic engagement of MSCs in 2D. We have developed soft hydrogels, composed of a lactose-modified chitosan, using a combination of permanent and temporary cross-links. The presence of temporary cross-links has a minor effect on the shear modulus of the hydrogels, but causes an immediate relaxation (dissipation) of the applied stress. This material property leads to early osteogenic commitment of MSCs, as evidenced by gene expression of runt-related transcription factor 2 (RUNX2), type 1 collagen (COL1A1), osteocalcin (OCN), alkaline phosphatase enzyme activity (ALP) and calcium deposit formation. In contrast, cells cultured on purely elastic hydrogels with only permanent cross-link begin to differentiate only after a longer period of time, indicating a dissipation-mediated mechano-sensing in the osteogenic commitment of MSCs.

Deep learning approaches for noncoding variant prioritization in neurodegenerative diseases.

Determining how noncoding genetic variants contribute to neurodegenerative dementias is fundamental to understanding disease pathogenesis, improving patient prognostication, and developing new clinical treatments. Next generation sequencing technologies have produced vast amounts of genomic data on cell type-specific transcription factor binding, gene expression, and three-dimensional chromatin interactions, with the promise of providing key insights into the biological mechanisms underlying disease. However, this data is highly complex, making it challenging for researchers to interpret, assimilate, and dissect. To this end, deep learning has emerged as a powerful tool for genome analysis that can capture the intricate patterns and dependencies within these large datasets. In this review, we organize and discuss the many unique model architectures, development philosophies, and interpretation methods that have emerged in the last few years with a focus on using deep learning to predict the impact of genetic variants on disease pathogenesis. We highlight both broadly-applicable genomic deep learning methods that can be fine-tuned to disease-specific contexts as well as existing neurodegenerative disease research, with an emphasis on Alzheimer's-specific literature. We conclude with an overview of the future of the field at the intersection of neurodegeneration, genomics, and deep learning.

Upregulated Expression of Runt-related Transcription Factor 3 and Interferon Regulatory Factor 4 Genes in Patients With Ankylosing Spondylitis

Background: Ankylosing spondylitis (AS) is a debilitating autoimmune disease presented by chronic inflammation of large joints and central skeleton. The role of various immune cells, including T cell subsets, has been studied in the pathogenesis of AS. Two critical transcription factors, runtrelated transcription factor 3 (RUNX3) and interferon regulatory factor 4 (IRF4), are involved in the differentiation and function of T lymphocytes. This study compared the gene expression level ofRUNX3 and IRF4 between patients with AS and healthy subjects to understand the impact of these factors in the immunopathogenesis of the disease. Methods: Thirty patients with AS and 30 age- and gender-matched healthy individuals were recruited to the study, and expression of RUNX3 and IRF4 genes was evaluated using the reverse transcription polymerase chain reaction (RT-PCR) technique in their peripheral blood. Results: The expression of RUNX3 and IRF4 genes in AS patients was significantly upregulated compared to the healthy controls (P=0.03 and 0.025, respectively). In addition, there was a direct correlation between IRF4 gene expression and bath ankylosing spondylitis global score (BAS-G) (correlation coefficient=0.38, P=0.04) Conclusion: Gene expression of RUNX3 and IRF4 transcription factors involved in T cells’ differentiation and function was increased in AS. These findings might have prognostic and therapeutic value.

Stem cell-derived extracellular vesicles reduce the expression of molecules involved in cardiac hypertrophy-In a model of human-induced pluripotent stem cell-derived cardiomyocytes.

Cardiac pathological hypertrophy is the major risk factor that usually progresses to heart failure. We hypothesized that extracellular vesicles (EVs), known to act as important mediators in regulating physiological and pathological functions, could have the potential to reduce the cardiac hypertrophy and the ensuing cardiovascular diseases. Herein, the effects of mesenchymal stem cell-derived extracellular vesicles (EV-MSCs) on cardiac hypertrophy were investigated. EVs were isolated from the secretome of human adipose tissue-derived stem cells (EV-ADSCs) or bone marrow-derived stem cells (EV-BMMSCs). Human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) were stimulated with AngII and TGF-β1, in absence or presence of EVs. The results showed that exposure of hiPSC-CMs to AngII and TGF-β1 generated in vitro model of hypertrophic cardiomyocytes characterized by increases in surface area, reactive oxygen species production, protein expression of cardiac-specific biomarkers atrial natriuretic factor, migration inhibitory factor, cTnI, COL1A1, Cx43, α-SMA and signalling molecules SMAD2 and NF-kBp50. The presence of EV-ADSCs or EV-BMMSCs in the hiPSC-CM culture along with hypertrophic stimuli reduced the protein expressions of hypertrophic specific markers (ANF, MIF, cTnI, COL1A1) and the gene expressions of IL-6 molecule involved in inflammatory process associated with cardiac hypertrophy and transcription factors SMAD2, SMAD3, cJUN, cFOS with role in cardiomyocyte hypertrophic response induced by AngII and TGF-β1. The EV-ADSCs were more effective in reducing the protein expressions of hypertrophic and inflammatory markers, while EV-BMMSCs in reducing the gene expressions of transcription factors. Notably, neither EV-ADSCs nor EV-BMMSCs induced significant changes in cardiac biomarkers Cx43, α-SMA and fibronectin. These different effects of stem cell-derived EVs could be attributed to their miRNA content: some miRNAs (miR-126-3p, miR-222-3p, miR-30e-5p, miR-181b-5p, miR-124-3p, miR-155-5p, miR-210-3p hsa-miR-221-3p) were expressed in both types of EVs and others only in EV-ADSCs (miR-181a-5p, miR-185-5p, miR-21-5p) or in EV-BMMSCs (miR-143-3p, miR-146a-5p, miR-93-5p), some of these attenuating the cardiac hypertrophy while others enhance it. In conclusion, in hiPSC-CMs the stem cell-derived EVs through their cargo reduced the expression of hypertrophic specific markers and molecules involved in inflammatory process associated with cardiac hypertrophy. The data suggest the EV potential to act as therapeutic mediators to reduce cardiac hypertrophy and possibly the subsequent cardiovascular events.

DynDeepDRIM: a dynamic deep learning model to infer direct regulatory interactions using time-course single-cell gene expression data.

Time-course single-cell RNA sequencing (scRNA-seq) data have been widely used to explore dynamic changes in gene expression of transcription factors (TFs) and their target genes. This information is useful to reconstruct cell-type-specific gene regulatory networks (GRNs). However, the existing tools are commonly designed to analyze either time-course bulk gene expression data or static scRNA-seq data via pseudo-time cell ordering. A few methods successfully utilize the information from multiple time points while also considering the characteristics of scRNA-seq data. We proposed dynDeepDRIM, a novel deep learning model to reconstruct GRNs using time-course scRNA-seq data. It represents the joint expression of a gene pair as an image and utilizes the image of the target TF-gene pair and the ones of the potential neighbors to reconstruct GRNs from time-course scRNA-seq data. dynDeepDRIM can effectively remove the transitive TF-gene interactions by considering neighborhood context and model the gene expression dynamics using high-dimensional tensors. We compared dynDeepDRIM with six GRN reconstruction methods on both simulation and four real time-course scRNA-seq data. dynDeepDRIM achieved substantially better performance than the other methods in inferring TF-gene interactions and eliminated the false positives effectively. We also applied dynDeepDRIM to annotate gene functions and found it achieved evidently better performance than the other tools due to considering the neighbor genes.

Creating burdock polysaccharide-oleanolic acid-ursolic acid nanoparticles to deliver enhanced anti-inflammatory effects: fabrication, structural characterization and property evaluation

This study explored the potential of polysaccharides from Actium lappa (ALPs) as natural wall materials for producing ALP-based nanoparticles to deliver poorly water-soluble oleanolic acid (OA) and ursolic acid (UA). Encapsulating OA+UA with ALPs (ALP:OA+UA, 50:1; OA:UA, 1:1) changed the crystalline nature to a more amorphous state through hydrogen bonding and involving O–H/C–O/O–C–O groups. ALP-OA/UA nanoparticles had a particle size and zeta potential (in water) of 199.1 nm/–7.15 mV, with a narrow unimodal size distribution, and excellent pH, salt solution, temperature and storage stability. Compared with ALPs, ALP-OA/UA nanoparticles showed enhanced anti-inflammatory activity (especially at a dose of 100 μg/mL) in a CuSO4-induced zebrafish inflammation model via down-regulating the NF-κB signalling pathway and gene expression of associated transcription factors and cytokines (TNF-α, IL-1β and IL-8). Therefore, ALP-based nanoparticles are natural and anti-inflammatory carriers for hydrophobic bioactive molecules.

Morpho-physiological responses and expression analysis of MYB94 transcription factor gene in four groundnut cultivars under drought and salinity stress

Aim: The present study aimed to evaluate the impact of salinity stress on morpho-physiological parameters and relative expression of the MYB94 transcription factor gene among four widely cultivated groundnut cultivars. Methodology: A comparative analysis of morpho-physiological parameters was studied in four groundnut cultivars (Kadiri-Amaravati, Kadiri-Lepakshi, Kadiri-6, and Kadiri-9) subjected to different concentrations of NaCl prepared in half-strength Arnon’s nutrient growth medium. The relative expression analysis of a stress responsive transcription factor gene, MYB94 was studied in four groundnut cultivars subjected to drought and NaCl stress by qRT PCR. Results: NaCl stress resulted in a significant increase in proline content, MDA content in cultivar Kadiri-9 compared to other cultivar studied. On the contrary, plant growth, shoot dry weight, root dry weight, leaf relative water content, cell membrane injury decreased to lesser extent in cultivar Kadiri-9 than Kadiri-Amaravati, Kadiri-Lepakshi, Kadiri-6 under salinity stress. qRT-PCR based relative expression analysis of the MYB94 gene revealed a significant increase of transcript expression levels in cultivar Kadiri-9 compared to other three cultivars under both drought and salinity stress. Interpretation: Groundnut cultivar Kadiri-9 showed better tolerance to NaCl stress as evidenced from enhanced proline content, better relative water content and lesser extent of membrane damage when compared with other groundnut cultivars under given NaCl stress treatments. In addition, relative expression of MYB94 gene was significantly higher due to NaCl stress as compared to drought stress conditions in cultivar Kadiri-9 suggested that the MYB94 could be involved in salt stress tolerance. Key words: Groundnut, MYB94 transcription factor, qRT-PCR, Salinity stress

Differentiation of endostyle cells by Nkx2-1 and FoxE in the ascidian Ciona intestinalis type A: insights into shared gene regulation in glandular- and thyroid-equivalent elements of the chordate endostyle.

Due to similarities in iodine concentrations and peroxidase activities, the thyroid in vertebrates is considered to originate from the endostyle of invertebrate chordates even though it is a glandular (mucus-producing) organ for aquatic suspension feeding. Among chordates with an endostyle, urochordates are useful evolutionary research models for the study of vertebrate traits. The ascidian Ciona intestinalis forms an endostyle with specific components of glandular- and thyroid-related elements, and molecular markers have been identified for these components. Since we previously examined a simple endostyle in the larvacean Oikopleura dioica, the expression of the thyroid-related transcription factor genes, Ciona Nkx2-1 and FoxE, was perturbed by TALEN-mediated gene knockout in the present study to elucidate the shared and/or divergent features of a complex ascidian endostyle. The knockout of Ciona Nkx2-1 and FoxE exerted different effects on the morphology of the developing endostyle. The knockout of Nkx2-1 eliminated the expression of both glandular and thyroidal differentiation marker genes, e.g., vWFL1, vWFL2, CiEnds1, TPO, and Duox, while that of FoxE eliminated the expression of the differentiation marker genes, TPO and CiEnds1. The supporting element-related expression of Pax2/5/8a, Pax2/5/8b, FoxQ1, and β-tubulin persisted in the hypoplastic endostyles of Nkx2-1- and FoxE-knockout juveniles. Although the gene regulation of ascidian-specific CiEnds1 remains unclear, these results provide insights into the evolution of the vertebrate thyroid as well as the urochordate endostyle.

Genome-wide identification and comprehensive analyses of NAC transcription factor gene family and expression analysis under Fusarium kyushuense and drought stress conditions in Passiflora edulis.

The NAC gene family is one of the largest plant transcription factors (TFs) families and plays important roles in plant growth, development, metabolism, and biotic and abiotic stresses. However, NAC gene family has not been reported in passion fruit (Passiflora edulis). In this study, a total of 105 NAC genes were identified in the passion fruit genome and were unevenly distributed across all nine-passion fruit chromomere, with a maximum of 48 PeNAC genes on chromosome one. The physicochemical features of all 105 PeNAC genes varied including 120 to 3,052 amino acids, 3 to 8 conserved motifs, and 1 to 3 introns. The PeNAC genes were named (PeNAC001–PeNAC105) according to their chromosomal locations and phylogenetically grouped into 15 clades (NAC-a to NAC-o). Most PeNAC proteins were predicted to be localized in the nucleus. The cis-element analysis indicated the possible roles of PeNAC genes in plant growth, development, light, hormones, and stress responsiveness. Moreover, the PeNAC gene duplications including tandem (11 gene pairs) and segmental (12 gene pairs) were identified and subjected to purifying selection. All PeNAC proteins exhibited similar 3D structures, and a protein–protein interaction network analysis with known Arabidopsis proteins was predicted. Furthermore, 17 putative ped-miRNAs were identified to target 25 PeNAC genes. Potential TFs including ERF, BBR-BPC, Dof, and bZIP were identified in promoter region of all 105 PeNAC genes and visualized in a TF regulatory network. GO and KEGG annotation analysis exposed that PeNAC genes were related to different biological, molecular, and cellular terms. The qRT-PCR expression analysis discovered that most of the PeNAC genes including PeNAC001, PeNAC003, PeNAC008, PeNAC028, PeNAC033, PeNAC058, PeNAC063, and PeNAC077 were significantly upregulated under Fusarium kyushuense and drought stress conditions compared to controls. In conclusion, these findings lay the foundation for further functional studies of PeNAC genes to facilitate the genetic improvement of plants to stress resistance.

A regulatory network of Sox and Six transcription factors initiate a cell fate transformation during hearing regeneration in adult zebrafish

SUMMARYUsing adult zebrafish inner ears as a model for sensorineural regeneration, we ablated the mechanosensory receptors and characterized the single-cell epigenome and transcriptome at consecutive time points during hair cell regeneration. We utilized deep learning on the regeneration-induced open chromatin sequences and identified cell-specific transcription factor (TF) motif patterns. Enhancer activity correlated with gene expression and identified potential gene regulatory networks. A pattern of overlapping Sox- and Six-family TF gene expression and binding motifs was detected, suggesting a combinatorial program of TFs driving regeneration and cell identity. Pseudotime analysis of single-cell transcriptomic data suggested that support cells within the sensory epithelium changed cell identity to a “progenitor” cell population that could differentiate into hair cells. We identified a 2.6 kb DNA enhancer upstream of the sox2 promoter that, when deleted, showed a dominant phenotype that resulted in a hair-cell-regeneration-specific deficit in both the lateral line and adult inner ear.

CHD4 acts as a critical regulator in the survival of spermatogonial stem cells in mice†.

Spermatogenesis is sustained by homeostatic balance between the self-renewal and differentiation of spermatogonial stem cells, which is dependent on the strict regulation of transcription factor and chromatin modulator gene expression. Chromodomain helicase DNA-binding protein 4 is highly expressed in spermatogonial stem cells but roles in mouse spermatogenesis are not fully understood. Here, we report that the germ-cell-specific deletion of chromodomain helicase DNA-binding protein 4 resulted in complete infertility in male mice, with rapid loss of spermatogonial stem cells and excessive germ cell apoptosis. Chromodomain helicase DNA-binding protein 4-knockdown in cultured spermatogonial stem cells also promoted the expression of apoptosis-related genes and thereby activated the tumor necrosis factor signaling pathway. Mechanistically, chromodomain helicase DNA-binding protein 4 occupies the genomic regulatory region of key apoptosis-related genes, including Jun and Nfkb1. Together, our findings reveal the determinant role of chromodomain helicase DNA-binding protein 4 in spermatogonial stem cells survival in vivo, which will offer insight into the pathogenesis of male sterility and potential novel therapeutic targets.

Exposure of carbon nanotubes affects testis and brain of common carp

Carbon nanotubes production has been rapidly increasing for many potential applications, however, the environmental impact of this nanomaterial needs to be comprehended. The present work focused on unraveling the effects of single-walled carbon nanotubes (SWCNT) in the common carp, Cyprinus carpio. The physicochemical properties of SWCNT were analyzed with X-ray diffraction, Fourier transforms infra-red, UV-Vis absorption, transmission electron microscopy (TEM), and Raman spectroscopy before testing for exposure impact. The effects of SWCNT, were investigated by exposing to two doses viz., 10 and 50 μg/L, for 7 days in adult common carp, in vivo. Expression of key steroidogenic and transcription factor genes related to testis and brain were downregulated after the treatment. The concomitant decreases in serum testosterone and 11-ketotestosterone levels revealed the impact of SWCNT after exposure. Further, SWCNT exposure induced antioxidant enzymes namely glutathione-S-transferases, superoxide dismutase, and catalase in both testis and brain. Concurrently, histological and TEM analysis of testis revealed structural disarray. In addition, SWCNT treatment, in testicular and brain primary cell cultures decreased cell viability with an increase of reactive oxygen species levels, leading to a significant elevation of apoptotic cells. In line with this, low mitochondrial membrane potential and DNA damage were also observed during post SWCNT treatment. Taken together, transient exposure of SWCNT causes toxic effects and alters testicular and brain function in the common carp. Thus, the discharge of carbon nanotubes poses a greater risk to the aquatic environment warranting regulatory measures.

Streptomyces strains can improve the quality properties and antifungal bioactivities of tomato fruits by impacting WRKY70 transcription factor gene and nitrate accumulation

The current study evaluated the effect of plant growth-promoting (PGP) strains of Streptomyces on yield, quality, and nitrate content of fruits, plant-microbe responses, and antifungal effect against blight disease caused by fungus pathogen Alternaria solani on tomato fruits in commercial greenhouse conditions. Greenhouse trials were done with four treatments including strains Y28, IC10, IT25, and commercial bio-fertilizer (Barvar NPK®) on tomato plants. In PGP treatments, the number of infected fruits significantly reduced (60%) compared to Barvar and control. Strain Y28 improved the quality of tomatoes more than other treatments. All three PGP treatments contained a higher level of total sugar concentration and antioxidant enzyme activities than Barvar and control. In contrast, PGP strains, especially Y28, significantly reduced nitrate accumulation (25%) compared to Barvar and control tomatoes. Streptomyces treatments induced more than a 20-fold increase in UDP and WRKY70 transcription factor gene expression relative to the control (P < 0.01). Based on the results, microbe-dependent plant defense induced by these strains is positively correlated to WRKY70 expression and nitrate reduction in commercial greenhouse conditions. These findings suggest that the commercial application of specific strains not only can illustrate an eco-friendly solution to induce resistance against fungal pathogens but also improve the quality properties of food plants with lower nitrate content.

Role of Polycomb Repressive Complex 2 in Regulation of Human Transcription Factor Gene Expression

For instance, this was the case with 16 of 20 TF families. The results are interpreted to indicate that while individual TFs such as EZH2 may be specific for broadly expressed or tissue targeted genes, this is not a property of most TF families. Most have both broadly expressed and tissue targeted members