Transcription of eukaryotic protein-coding genes

Characterization and functional analysis of novel α-bisabolol synthase (MrBAS) promoter from Matricaria recutita

Matricaria recutita is widely used in industry and as a medicinal plant because it contains α-bisabolol. Alpha-bisabolol has broad application prospects due to its healthy function and medical value. The activity of the α-bisabolol synthase (MrBAS) promoter determines the expression of the MrBAS gene, which in turn influences the synthesis and accumulation of α-bisabolol. However, the activity and tissue specificity of the MrBAS promoter have not yet been characterized. In this study, a 1327-base pair (bp) region upstream of the MrBAS of the translation start site was cloned from the genome of M. recutita. MrBAS promoter sequence analysis revealed multiple light-responsive elements, and further dark treatment reduced α-bisabolol content in flowers. The α-bisabolol content and MrBAS expression levels in various flower tissues showed a strong correlation. The 5' deletion analysis revealed that the MrBAS promoter sequence could drive β-glucuronidase (GUS) gene expression in Nicotiana benthamiana leaves, with activity decreasing as the fragment shortened. Transgenic experiments demonstrated that the MrBAS promoter could specifically drive GUS gene expression in Arabidopsis anthers, pollen tubes, and petals. Thus, the MrBAS promoter has the potential to be a tool for directing transgene expression specifically in flower organs, offering new research avenues for cultivar development.

Regulation of eukaryotic transcription initiation in response to cellular stress

Transcription initiation is a vital step in the regulation of eukaryotic gene expression. It can be dysregulated in response to various cellular stressors which is associated with numerous human diseases including cancer. Transcription initiation is facilitated via many gene-specific trans-regulatory elements such as transcription factors, activators, and coactivators through their interactions with transcription pre-initiation complex (PIC). These trans-regulatory elements can uniquely facilitate PIC formation (hence, transcription initiation) in response to cellular nutrient stress. Cellular nutrient stress also regulates the activity of other pathways such as target of rapamycin (TOR) pathway. TOR pathway exhibits distinct regulatory mechanisms of transcriptional activation in response to stress. Like TOR pathway, the cell cycle regulatory pathway is also found to be linked to transcriptional regulation in response to cellular stress. Several transcription factors such as p53, C/EBP Homologous Protein (CHOP), activating transcription factor 6 (ATF6α), E2F, transforming growth factor (TGF)-β, Adenomatous polyposis coli (APC), SMAD, and MYC have been implicated in regulation of transcription of target genes involved in cell cycle progression, apoptosis, and DNA damage repair pathways. Additionally, cellular metabolic and oxidative stressors have been found to regulate the activity of long non-coding RNAs (lncRNA). LncRNA regulates transcription by upregulating or downregulating the transcription regulatory proteins involved in metabolic and cell signaling pathways. Numerous human diseases, triggered by chronic cellular stressors, are associated with abnormal regulation of transcription. Hence, understanding these mechanisms would help unravel the molecular regulatory insights with potential therapeutic interventions. Therefore, here we emphasize the recent advances of regulation of eukaryotic transcription initiation in response to cellular stress.

The regulatory landscape of interacting RNA and protein pools in cellular homeostasis and cancer

Biological systems encompass intricate networks governed by RNA-protein interactions that play pivotal roles in cellular functions. RNA and proteins constituting 1.1% and 18% of the mammalian cell weight, respectively, orchestrate vital processes from genome organization to translation. To date, disentangling the functional fraction of the human genome has presented a major challenge, particularly for noncoding regions, yet recent discoveries have started to unveil a host of regulatory functions for noncoding RNAs (ncRNAs). While ncRNAs exist at different sizes, structures, degrees of evolutionary conservation and abundances within the cell, they partake in diverse roles either alone or in combination. However, certain ncRNA subtypes, including those that have been described or remain to be discovered, are poorly characterized given their heterogeneous nature. RNA activity is in most cases coordinated through interactions with RNA-binding proteins (RBPs). Extensive efforts are being made to accurately reconstruct RNA-RBP regulatory networks, which have provided unprecedented insight into cellular physiology and human disease. In this review, we provide a comprehensive view of RNAs and RBPs, focusing on how their interactions generate functional signals in living cells, particularly in the context of post-transcriptional regulatory processes and cancer.

African swine fever virus RNA polymerase subunits C315R and H359L inhibition host translation by activating the PKR-eIF2a pathway and suppression inflammatory responses

ASFV C315R is homologous to the transcription factor TFIIB of large unclassified DNA viruses, and H359L is identical to the subunit 3 (RPB3) of eukaryotic RNA polymerase II. The C315R and H359L may play an important role in ASFV replication and transcription. Here, we evaluated the biological function of the C315R and H359L genes during virus replication in vitro and during infection in pigs. Results showed that C315R and H359L are highly conserved among ASFV genotype II strains; quantitative PCR (qPCR) and western blotting analyses revealed that C315R and H359L are early transcribed genes prior to viral DNA replication, but their protein expression is delayed. The immunofluorescence and western blotting analysis revealed that both proteins localized in the cell cytoplasm and nucleus at 24 h post infection, however, pH359L was mainly detected in the cell cytoplasm. Furthermore, overexpression of pH359L in MA104 cells significantly increased viral titer, RNA transcription levels, and viral protein expression levels, while overexpression of pC315R slightly enhanced ASFV replication. In contrast, siRNA targeting ASFV-H359L or C315R reduced replication efficiency in porcine macrophage culture compared to the parent ASFV-CN/SC/2019, demonstrating that C315R and H359L genes are necessary for ASFV replication. Finally, the functional role of C315R or H359L on PKR and eIF2α phosphorylation status and SG formation, as well as cytokine production were evaluated. These studies demonstrated that C315R and H359L are involved in virus replication processes in swine and play important roles in ASFV replication.

The temporal dynamics of lncRNA Firre-mediated epigenetic and transcriptional regulation

Numerous studies have now demonstrated that lncRNAs can influence gene expression programs leading to cell and organismal phenotypes. Typically, lncRNA perturbations and concomitant changes in gene expression are measured on the timescale of many hours to days. Thus, we currently lack a temporally grounded understanding of the primary, secondary, and tertiary relationships of lncRNA-mediated transcriptional and epigenetic regulation-a prerequisite to elucidating lncRNA mechanisms. To begin to address when and where a lncRNA regulates gene expression, we genetically engineer cell lines to temporally induce the lncRNA Firre. Using this approach, we are able to monitor lncRNA transcriptional regulatory events from 15 min to four days. We observe that upon induction, Firre RNA regulates epigenetic and transcriptional states in trans within 30 min. These early regulatory events result in much larger transcriptional changes after 12 h, well before current studies monitor lncRNA regulation. Moreover, Firre-mediated gene expression changes are epigenetically remembered for days. Overall, this study suggests that lncRNAs can rapidly regulate gene expression by establishing persistent epigenetic and transcriptional states.

Reduction of ZFX levels decreases histone H4 acetylation and increases Pol2 pausing at target promoters

The ZFX transcriptional activator binds to CpG island promoters, with a major peak at ∼200-250 bp downstream from transcription start sites. Because ZFX binds within the transcribed region, we investigated whether it regulates transcriptional elongation. We used GRO-seq to show that loss or reduction of ZFX increased Pol2 pausing at ZFX-regulated promoters. To further investigate the mechanisms by which ZFX regulates transcription, we determined regions of the protein needed for transactivation and for recruitment to the chromatin. Interestingly, although ZFX has 13 grouped zinc fingers, deletion of the first 11 fingers produces a protein that can still bind to chromatin and activate transcription. We next used TurboID-MS to detect ZFX-interacting proteins, identifying ZNF593, as well as proteins that interact with the N-terminal transactivation domain (which included histone modifying proteins), and proteins that interact with ZFX when it is bound to the chromatin (which included TAFs and other histone modifying proteins). Our studies support a model in which ZFX enhances elongation at target promoters by recruiting H4 acetylation complexes and reducing pausing.

Multilevel Regulation of Membrane Proteins in Response to Metal and Metalloid Stress: A Lesson from Yeast

In the face of flourishing industrialization and global trade, heavy metal and metalloid contamination of the environment is a growing concern throughout the world. The widespread presence of highly toxic compounds of arsenic, antimony, and cadmium in nature poses a particular threat to human health. Prolonged exposure to these toxins has been associated with severe human diseases, including cancer, diabetes, and neurodegenerative disorders. These toxins are known to induce analogous cellular stresses, such as DNA damage, disturbance of redox homeostasis, and proteotoxicity. To overcome these threats and improve or devise treatment methods, it is crucial to understand the mechanisms of cellular detoxification in metal and metalloid stress. Membrane proteins are key cellular components involved in the uptake, vacuolar/lysosomal sequestration, and efflux of these compounds; thus, deciphering the multilevel regulation of these proteins is of the utmost importance. In this review, we summarize data on the mechanisms of arsenic, antimony, and cadmium detoxification in the context of membrane proteome. We used yeast Saccharomyces cerevisiae as a eukaryotic model to elucidate the complex mechanisms of the production, regulation, and degradation of selected membrane transporters under metal(loid)-induced stress conditions. Additionally, we present data on orthologues membrane proteins involved in metal(loid)-associated diseases in humans.

Systems level analysis of time and stimuli specific signaling through PKA

It is well known that eukaryotic cells create gradients of cAMP across space and time to regulate the cAMP dependent protein kinase (PKA) and, in turn, growth and metabolism. However, it is unclear how PKA responds to different concentrations of cAMP. Here, to address this question, we examine PKA signaling in Saccharomyces cerevisiae in different conditions, timepoints, and concentrations of the chemical inhibitor 1-NM-PP1, using phosphoproteomics. These experiments show that there are numerous proteins that are only phosphorylated when cAMP and PKA activity are at/near their maximum level, while other proteins are phosphorylated even when cAMP levels and PKA activity are low. The data also show that PKA drives cells into distinct growth states by acting on proteins with different thresholds for phosphorylation in different conditions. Analysis of the sequences surrounding the 118 PKA-dependent phosphosites suggests that the phosphorylation thresholds are set, at least in part, by the affinity of PKA for each site.

Unveiling the impact of CDK8 on tumor progression: mechanisms and therapeutic strategies

CDK8 is an important member of the cyclin-dependent kinase family associated with transcription and acts as a key "molecular switch" in the Mediator complex. CDK8 regulates gene expression by phosphorylating transcription factors and can control the transcription process through Mediator complex. Previous studies confirmed that CDK8 is an important oncogenic factor, making it a potential tumor biomarker and a promising target for tumor therapy. However, CDK8 has also been confirmed to be a tumor suppressor, indicating that it not only promotes the development of tumors but may also be involved in tumor suppression. Therefore, the dual role of CDK8 in the process of tumor development is worth further exploration and summary. This comprehensive review delves into the intricate involvement of CDK8 in transcription-related processes, as well as its role in signaling pathways related to tumorigenesis, with a focus on its critical part in driving cancer progression.

Differences in transcription initiation directionality underlie distinctions between plants and animals in chromatin modification patterns at genes and cis-regulatory elements

Transcriptional initiation is among the first regulated steps controlling eukaryotic gene expression. High-throughput profiling of fungal and animal genomes has revealed that RNA Polymerase II often initiates transcription in both directions at the promoter transcription start site, but generally only elongates productively into the gene body. Additionally, Pol II can initiate transcription in both directions at cis-regulatory elements such as enhancers. These bidirectional RNA Polymerase II initiation events can be observed directly with methods that capture nascent transcripts, and they are also revealed indirectly by the presence of transcription-associated histone modifications on both sides of the transcription start site or cis-regulatory elements. Previous studies have shown that nascent RNAs and transcription-associated histone modifications in the model plant Arabidopsis thaliana accumulate mainly in the gene body, suggesting that transcription does not initiate widely in the upstream direction from genes in this plant. We compared transcription-associated histone modifications and nascent transcripts at both transcription start sites and cis-regulatory elements in A. thaliana, Drosophila melanogaster, and Homo sapiens. Our results provide evidence for mostly unidirectional RNA Polymerase II initiation at both promoters and gene-proximal cis-regulatory elements of A. thaliana, whereas bidirectional transcription initiation is observed widely at promoters in both D. melanogaster and H. sapiens, as well as cis-regulatory elements in Drosophila. Furthermore, the distribution of transcription-associated histone modifications around transcription start sites in the Oryza sativa (rice) and Glycine max (soybean) genomes suggests that unidirectional transcription initiation is the norm in these genomes as well. These results suggest that there are fundamental differences in transcriptional initiation directionality between flowering plant and metazoan genomes, which are manifested as distinct patterns of chromatin modifications around RNA polymerase initiation sites.

Cornelian Cherry (Cornus mas L.) Fruit Extract Lowers SREBP-1c and C/EBPα in Liver and Alters Various PPAR-α, PPAR-γ, LXR-α Target Genes in Cholesterol-Rich Diet Rabbit Model

Cornelian cherry (Cornus mas L.) fruits, abundant in iridoids and anthocyanins, are natural products with proven beneficial impacts on the functions of the cardiovascular system and the liver. This study aims to assess and compare whether and to what extent two different doses of resin-purified cornelian cherry extract (10 mg/kg b.w. or 50 mg/kg b.w.) applied in a cholesterol-rich diet rabbit model affect the levels of sterol regulatory element-binding protein 1c (SREBP-1c) and CCAAT/enhancer binding protein α (C/EBPα), and various liver X receptor-α (LXR-α), peroxisome proliferator-activated receptor-α (PPAR-α), and peroxisome proliferator-activated receptor-γ (PPAR-γ) target genes. Moreover, the aim is to evaluate the resistive index (RI) of common carotid arteries (CCAs) and aortas, and histopathological changes in CCAs. For this purpose, the levels of SREBP-1c, C/EBPα, ATP-binding cassette transporter A1 (ABCA1), ATP-binding cassette transporter G1 (ABCG1), fatty acid synthase (FAS), endothelial lipase (LIPG), carnitine palmitoyltransferase 1A (CPT1A), and adiponectin receptor 2 (AdipoR2) in liver tissue were measured. Also, the levels of lipoprotein lipase (LPL), visceral adipose tissue-derived serine protease inhibitor (Vaspin), and retinol-binding protein 4 (RBP4) in visceral adipose tissue were measured. The RI of CCAs and aortas, and histopathological changes in CCAs, were indicated. The oral administration of the cornelian cherry extract decreased the SREBP-1c and C/EBPα in both doses. The dose of 10 mg/kg b.w. increased ABCA1 and decreased FAS, CPT1A, and RBP4, and the dose of 50 mg/kg b.w. enhanced ABCG1 and AdipoR2. Mitigations in atheromatous changes in rabbits' CCAs were also observed. The obtained outcomes were compared to the results of our previous works. The beneficial results confirm that cornelian cherry fruit extract may constitute a potentially effective product in the prevention and treatment of obesity-related disorders.

Differences in transcription initiation directionality underlie distinctions between plants and animals in chromatin modification patterns at genes and cis-regulatory elements

Transcriptional initiation is among the first regulated steps controlling eukaryotic gene expression. High-throughput profiling of fungal and animal genomes has revealed that RNA Polymerase II (Pol II) often initiates transcription in both directions at the promoter transcription start site (TSS), but generally only elongates productively into the gene body. Additionally, Pol II can initiate transcription in both directions at cis-regulatory elements (CREs) such as enhancers. These bidirectional Pol II initiation events can be observed directly with methods that capture nascent transcripts, and they are also revealed indirectly by the presence of transcription-associated histone modifications on both sides of the TSS or CRE. Previous studies have shown that nascent RNAs and transcription-associated histone modifications in the model plant Arabidopsis thaliana accumulate mainly in the gene body, suggesting that transcription does not initiate widely in the upstream direction from genes in this plant. We compared transcription-associated histone modifications and nascent transcripts at both TSSs and CREs in Arabidopsis thaliana, Drosophila melanogaster, and Homo sapiens. Our results provide evidence for mostly unidirectional Pol II initiation at both promoters and gene-proximal CREs of Arabidopsis thaliana, whereas bidirectional transcription initiation is observed widely at promoters in both Drosophila melanogaster and Homo sapiens, as well as CREs in Drosophila. Furthermore, the distribution of transcription-associated histone modifications around TSSs in the Oryza sativa (rice) and Glycine max (soybean) genomes suggests that unidirectional transcription initiation is the norm in these genomes as well. These results suggest that there are fundamental differences in transcriptional initiation directionality between flowering plant and metazoan genomes, which are manifested as distinct patterns of chromatin modifications around RNA polymerase initiation sites.

A snapshot of Bothrops jararaca snake venom gland subcellular proteome

Snake venom protein synthesis undergoes finely regulated processes in the specialized secretory epithelium within the venom gland. Such processes occur within a defined period in the cell and at specific cellular locations. Thus, the determination of subcellular proteomes allows the characterization of protein groups for which the site may be relevant to their biological roles, thereby allowing the deconvolution of complex biological circuits into functional information. In this regard, we performed subcellular fractionation of proteins from B. jararaca venom gland, focusing on nuclear proteins since this cellular compartment comprises key effectors that shape gene expression. Our results provided a snapshot of B. jararaca's subcellular venom gland proteome and pointed to a 'conserved' proteome core among different life stages (newborn and adult) and between sexes (adult male and female). Overall, the top 15 highly abundant proteins identified in B. jararaca venom glands mirrored the panel of highly expressed genes in human salivary glands. Therefore, the expression profile observed for such a protein set could be considered a conserved core signature of salivary gland secretory epithelium. Moreover, the newborn venom gland displayed a unique expression signature of transcription factors involved in regulating transcription and biosynthetic processes and may mirror biological constraints of the ontogenetic development of B. jararaca, contributing to venom proteome diversity.

Regulation of the RNA polymerase II pre-initiation complex by its associated coactivators

The RNA polymerase II (Pol II) pre-initiation complex (PIC) is a critical node in eukaryotic transcription regulation, and its formation is the major rate-limiting step in transcriptional activation. Diverse cellular signals borne by transcriptional activators converge on this large, multiprotein assembly and are transduced via intermediary factors termed coactivators. Cryogenic electron microscopy, multi-omics and single-molecule approaches have recently offered unprecedented insights into both the structure and cellular functions of the PIC and two key PIC-associated coactivators, Mediator and TFIID. Here, we review advances in our understanding of how Mediator and TFIID interact with activators and affect PIC formation and function. We also discuss how their functions are influenced by their chromatin environment and selected cofactors. We consider how, through its multifarious interactions and functionalities, a Mediator-containing and TFIID-containing PIC can yield an integrated signal processing system with the flexibility to determine the unique temporal and spatial expression pattern of a given gene.

Transcription activation of SPINK4 by ELF-1 augments progression of colon cancer by regulating biological behaviors

BACKGROUND

SPINK4 was highly expressed in colorectal cancer and resulted in worse prognosis of colorectal cancer patients. However, the expression and function of SPINK4 in colon cancer have not been revealed.

METHODS

Analysis from GEPIA website showed the expression and function of SPINK4 in colon cancer samples. Colon cancer cell lines were applied to detect the biological function of SPINK4. Functionally, the transcriptional factor of SPINK4 has been predicted and verified. Finally, the associations between transcriptional factor and SPINK4 have been confirmed.

RESULTS

SPINK4 expression was obviously increased in colon cancer samples. HCT-116 and DXH-1 cells in si-SPINK4-1 or si-SPINK4-2 group displayed an obvious reduction in its proliferation, cell cycle, invasion and migration compared to those in the si-control group. Moreover, transcriptional factor ELF-1 bound to the promoter of SPINK4 and affected its expression in colon cancer cells. High ELF-1 expression was presented in colon cancer samples and resulted in worse prognosis of colon cancer patients. Additionally, si-SPINK4 antagonized the function of ELF-1 overexpression in modulating colon cancer cell proliferation, cell cycle and mobility.

CONCLUSIONS

Our findings afforded a theoretical basis for further research on the treatment of colon cancer based on the control of ELF-1/SPINK4 expression.

BmTBP upregulates the transcription of BmSuc1 in silkworm (Bombyx mori) by binding to BmTfΙΙA-S

The BmSuc1 gene, which encodes a novel animal-type β-fructofuranosidase (EC 3.2.1.26), was first cloned and identified in silkworm (Bombyx mori). As an essential sucrase, the activity of BmSUC1 is unaffected by alkaloidal sugar mimics in mulberry leaves. This enzyme may also directly regulate the degree of sucrose hydrolysis in the silkworm midgut. In addition, BmSUC1 is involved in the synthesis of sericin 1 in the silk gland tissue. However, the mechanism underlying the regulation of BmSuc1 transcription remains unclear. In this study, we analyzed the BmSuc1 promoter activity using a dual-luciferase reporter assay and identified 4 regions that are critical for transcriptional activation. The gene encoding a predicted transcription factor (TATA-box-binding protein; BmTBP) capable of binding to the core promoter regions was cloned. A quantitative real-time polymerase chain reaction analysis indicated the gene was highly expressed in the midgut. Downregulating BmTBP expression via RNA interference decreased the expression of BmSuc1 at the transcript and protein levels. An electrophoretic mobility shift analysis and chromatin immunoprecipitation indicated that BmTBP can bind to the TATA-box cis-regulatory element in the BmSuc1 promoter. Furthermore, a bioinformatics-based analysis and a far-western blot revealed the interaction between BmTBP and another transcription factor (BmTfIIA-S). The luciferase reporter gene assay results confirmed that the BmTBP-BmTfIIA-S complex increases the BmSuc1 promoter activity. Considered together, these findings suggest that BmTBP regulates BmSuc1 expression through its interaction with BmTfIIA-S.

Combined SPT and FCS methods reveal a mechanism of RNAP II oversampling in cell nuclei

Gene expression orchestration is a key question in fundamental and applied research. Different models for transcription regulation were proposed, yet the dynamic regulation of RNA polymerase II (RNAP II) activity remains a matter of debate. To improve our knowledge of this topic, we investigated RNAP II motility in eukaryotic cells by combining single particle tracking (SPT) and fluorescence correlation spectroscopy (FCS) techniques, to take advantage of their different sensitivities in order to analyze together slow and fast molecular movements. Thanks to calibrated samples, we developed a benchmark for quantitative analysis of molecular dynamics, to eliminate the main potential instrumental biases. We applied this workflow to study the diffusion of RPB1, the catalytic subunit of RNAP II. By a cross-analysis of FCS and SPT, we could highlight different RPB1 motility states and identifyed a stationary state, a slow diffusion state, and two different modes of subdiffusion. Interestingly, our analysis also unveiled the oversampling by RPB1 of nuclear subdomains. Based on these data, we propose a novel model of spatio-temporal transcription regulation. Altogether, our results highlight the importance of combining microscopy approaches at different time scales to get a full insight into the real complexity of molecular kinetics in cells.

Tailored machine learning models for functional RNA detection in genome-wide screens

The in silico prediction of non-coding and protein-coding genetic loci has received considerable attention in comparative genomics aiming in particular at the identification of properties of nucleotide sequences that are informative of their biological role in the cell. We present here a software framework for the alignment-based training, evaluation and application of machine learning models with user-defined parameters. Instead of focusing on the one-size-fits-all approach of pervasive in silico annotation pipelines, we offer a framework for the structured generation and evaluation of models based on arbitrary features and input data, focusing on stable and explainable results. Furthermore, we showcase the usage of our software package in a full-genome screen of Drosophila melanogaster and evaluate our results against the well-known but much less flexible program RNAz.

An insight into Pisum sativum HSF gene family-Genome-wide identification, phylogenetic, expression, and analysis of transactivation potential of pea heat shock transcription factor

Field pea (Pisum sativum L, 2n = 14) is a popular temperate legume with high economic value. Heat shock factors (HSFs) are the core element in the regulatory mechanism of heat stress responses. HSFs in pea (P. sativum) have not been characterized and their role remains unclear in different abiotic stresses. To address this knowledge gap, the current study aimed to characterize the HSF gene family in pea. We identified 38 PsHsf members in P. sativum, which are distributed on the seven chromosomes, and based on phylogenetic analysis, we classified them into three representative classes i.e. A, B, and C. Conserved motif and gene structure analysis confirmed a high degree of similarity among the members of the same class. Additionally, identified cis-acting regulatory elements (CAREs) related to abiotic responses, development, growth, and hormone signaling provides crucial insights into the regulatory mechanisms of PsHsfs. Our research revealed instances of gene duplication in PsHsf gene family, suggesting that this mechanism could be driving the expansion of the PsHsf gene family. Moreover, Expression analysis of PsHsfs exhibited upregulation under heat stress (HS), salt stress (SS), and drought stress (DS) showing their phenomenal role in stress conditions. PsHsfs protein interaction network suggested their involvement in stress-responsive mechanisms. Further transactivation potential was checked for spliced variant of PsHsfA2a (PsHsfA2aI, PsHsfA2aII, and PsHsfA2aIII), PsHsfA3, PsHsfA6b, PsHsfA9, PsHsfB1a, and PsHsfB2a. Overall, these findings provide valuable insight into the evolutionary relationship of PsHsf gene family and their role in abiotic stress responses.

Genome-wide analysis and characterization of the LRR-RLK gene family provides insights into anthracnose resistance in common bean

Anthracnose, caused by the hemibiotrophic fungus Colletotrichum lindemuthianum, is a damaging disease of common beans that can drastically reduce crop yield. The most effective strategy to manage anthracnose is the use of resistant cultivars. There are many resistance loci that have been identified, mapped and associated with markers in common bean chromosomes. The Leucine-rich repeat kinase receptor protein (LRR-RLK) family is a diverse group of transmembrane receptors, which potentially recognizes pathogen-associated molecular patterns and activates an immune response. In this study, we performed in silico analyses to identify, classify, and characterize common bean LRR-RLKs, also evaluating their expression profile in response to the infection by C. lindemuthianum. By analyzing the entire genome of Phaseolus vulgaris, we could identify and classify 230 LRR-RLKs into 15 different subfamilies. The analyses of gene structures, conserved domains and motifs suggest that LRR-RLKs from the same subfamily are consistent in their exon/intron organization and composition. LRR-RLK genes were found along the 11 chromosomes of the species, including regions of proximity with anthracnose resistance markers. By investigating the duplication events within the LRR-RLK family, we associated the importance of such a family with an expansion resulting from a strong stabilizing selection. Promoter analysis was also performed, highlighting cis-elements associated with the plant response to biotic stress. With regard to the expression pattern of LRR-RLKs in response to the infection by C. lindemuthianum, we could point out several differentially expressed genes in this subfamily, which were associated to specific molecular patterns of LRR-RLKs. Our work provides a broad analysis of the LRR-RLK family in P. vulgaris, allowing an in-depth structural and functional characterization of genes and proteins of this family. From specific expression patterns related to anthracnose response, we could infer a direct participation of RLK-LRR genes in the mechanisms of resistance to anthracnose, highlighting important subfamilies for further investigations.

Ada2 and Ada3 Regulate Hyphal Growth, Asexual Development, and Pathogenicity in Beauveria bassiana by Maintaining Gcn5 Acetyltransferase Activity

The histone acetyltransferase (HAT) Gcn5 ortholog is essential for a variety of fungi. Here, we characterize the roles of Ada2 and Ada3, which are functionally linked to Gcn5, in the insect-pathogenic fungus Beauveria bassiana. Loss of Ada2 and Ada3 led to severe hyphal growth defects on rich and minimal media and drastic decreases in blastospore yield and conidiation capacity, with abnormal conidia-producing structures. ΔAda2 and ΔAda3 exhibited a delay in conidial germination and increased sensitivity to multiple chemical stresses and heat shock. Nearly all their pathogenicity was lost, and their ability to secrete extracellular enzymes, Pr1 proteases and chitinases for cuticle degradation was reduced. A yeast two-hybrid assay demonstrated that Ada2 binds to Ada3 and directly interacts with Gcn5, confirming the existence of a yeast-like Ada3-Ada2-Gcn5 HAT complex in this fungus. Additionally, deletion of the Ada genes reduced the activity of Gcn5, especially in the ΔAda2 strain, which was consistent with the acetylation level of histone H3 determined by Western blotting. These results illustrate the dependence of Gcn5 enzyme activity on Ada2 and Ada3 in fungal hyphal growth, asexual development, multiple stress responses, and pathogenicity in B. bassiana. IMPORTANCE The histone acetyltransferase Gcn5 ortholog contributes significantly to the growth and development of various fungi. In this study, we found that Ada2 and Ada3 have critical regulatory effects on Gcn5 enzyme activity and influence the acetylation of histone H3. Deletion of Ada2 or Ada3 decreased the fungal growth rate and asexual conidial yield and increased susceptibility to multiple stresses in Beauveria bassiana. Importantly, Ada genes are vital virulence factors, and their deletion caused the most virulence loss, mainly by inhibiting the activity of a series of hydrolytic enzymes and the dimorphic transition ability. These findings provide a new perspective on the function of the Gcn5 acetyltransferase complex in pathogens.

Gene expression variability across cells and species shapes the relationship between renal resident macrophages and infiltrated macrophages

BACKGROUND

Two main subclasses of macrophages are found in almost all solid tissues: embryo-derived resident tissue macrophages and bone marrow-derived infiltrated macrophages. These macrophage subtypes show transcriptional and functional divergence, and the programs that have shaped the evolution of renal macrophages and related signaling pathways remain poorly understood. To clarify these processes, we performed data analysis based on single-cell transcriptional profiling of renal tissue-resident and infiltrated macrophages in human, mouse and rat.

RESULTS

In this study, we (i) characterized the transcriptional divergence among species and (ii) illustrated variability in expression among cells of each subtype and (iii) compared the gene regulation network and (iv) ligand-receptor pairs in human and mouse. Using single-cell transcriptomics, we mapped the promoter architecture during homeostasis.

CONCLUSIONS

Transcriptionally divergent genes, such as the differentially TF-encoding genes expressed in resident and infiltrated macrophages across the three species, vary among cells and include distinct promoter structures. The gene regulatory network in infiltrated macrophages shows comparatively better species-wide consistency than resident macrophages. The conserved transcriptional gene regulatory network in infiltrated macrophages among species is uniquely enriched in pathways related to kinases, and TFs associated with largely conserved regulons among species are uniquely enriched in kinase-related pathways.

Genome-wide inference reveals that feedback regulations constrain promoter-dependent transcriptional burst kinetics

Gene expression in mammalian cells is highly variable and episodic, resulting in a series of discontinuous bursts of mRNAs. A challenge is to understand how static promoter architecture and dynamic feedback regulations dictate bursting on a genome-wide scale. Although single-cell RNA sequencing (scRNA-seq) provides an opportunity to address this challenge, effective analytical methods are scarce. We developed an interpretable and scalable inference framework, which combined experimental data with a mechanistic model to infer transcriptional burst kinetics (sizes and frequencies) and feedback regulations. Applying this framework to scRNA-seq data generated from embryonic mouse fibroblast cells, we found Simpson's paradoxes, i.e. genome-wide burst kinetics exhibit different characteristics in two cases without and with distinguishing feedback regulations. We also showed that feedbacks differently modulate burst frequencies and sizes and conceal the effects of transcription start site distributions on burst kinetics. Notably, only in the presence of positive feedback, TATA genes are expressed with high burst frequencies and enhancer-promoter interactions mainly modulate burst frequencies. The developed inference method provided a flexible and efficient way to investigate transcriptional burst kinetics and the obtained results would be helpful for understanding cell development and fate decision.

Histone modifications and DNA methylation act cooperatively in regulating symbiosis genes in the sea anemone Aiptasia

Background

The symbiotic relationship between cnidarians and dinoflagellates is one of the most widespread endosymbiosis in our oceans and provides the ecological basis of coral reef ecosystems. Although many studies have been undertaken to unravel the molecular mechanisms underlying these symbioses, we still know little about the epigenetic mechanisms that control the transcriptional responses to symbiosis.

Results

Here, we used the model organism Exaiptasia diaphana to study the genome-wide patterns and putative functions of the histone modifications H3K27ac, H3K4me3, H3K9ac, H3K36me3, and H3K27me3 in symbiosis. While we find that their functions are generally conserved, we observed that colocalization of more than one modification and or DNA methylation correlated with significantly higher gene expression, suggesting a cooperative action of histone modifications and DNA methylation in promoting gene expression. Analysis of symbiosis genes revealed that activating histone modifications predominantly associated with symbiosis-induced genes involved in glucose metabolism, nitrogen transport, amino acid biosynthesis, and organism growth while symbiosis-suppressed genes were involved in catabolic processes.

Conclusions

Our results provide new insights into the mechanisms of prominent histone modifications and their interaction with DNA methylation in regulating symbiosis in cnidarians.

Network reconstruction for trans acting genetic loci using multi-omics data and prior information

BACKGROUND

Molecular measurements of the genome, the transcriptome, and the epigenome, often termed multi-omics data, provide an in-depth view on biological systems and their integration is crucial for gaining insights in complex regulatory processes. These data can be used to explain disease related genetic variants by linking them to intermediate molecular traits (quantitative trait loci, QTL). Molecular networks regulating cellular processes leave footprints in QTL results as so-called trans-QTL hotspots. Reconstructing these networks is a complex endeavor and use of biological prior information can improve network inference. However, previous efforts were limited in the types of priors used or have only been applied to model systems. In this study, we reconstruct the regulatory networks underlying trans-QTL hotspots using human cohort data and data-driven prior information.

METHODS

We devised a new strategy to integrate QTL with human population scale multi-omics data. State-of-the art network inference methods including BDgraph and glasso were applied to these data. Comprehensive prior information to guide network inference was manually curated from large-scale biological databases. The inference approach was extensively benchmarked using simulated data and cross-cohort replication analyses. Best performing methods were subsequently applied to real-world human cohort data.

RESULTS

Our benchmarks showed that prior-based strategies outperform methods without prior information in simulated data and show better replication across datasets. Application of our approach to human cohort data highlighted two novel regulatory networks related to schizophrenia and lean body mass for which we generated novel functional hypotheses.

CONCLUSIONS

We demonstrate that existing biological knowledge can improve the integrative analysis of networks underlying trans associations and generate novel hypotheses about regulatory mechanisms.

Physiological and molecular mechanisms of the response of roots of Pinus massoniana Lamb. to low-temperature stress

Pinus massoniana Lamb. is the timber species with the widest distribution and the largest afforestation area in China, providing a large amount of timber, turpentine and ecological products. but low temperature limits its growth and geographical distribution. Physiological and molecular studies can well explain the mechanism of P. massoniana response to low temperature. In this study, physiological and biochemical indexes, cell morphology, lignin content, gene regulatory networks, and gene expression patterns of different P. massoniana varieties (cold-tolerant and cold-sensitive) were studied from physiological, biochemical, and molecular perspectives. The results indicated that under low-temperature stress, the cold-tolerant cultivar maintained high contents of osmoregulatory substances, and the root morphology and structure remained intact. In the initial stage of low-temperature stress, the number of differentially expressed genes was 7148, and with the extension of stress time, the number of differentially expressed genes decreased to 1991. P. massoniana might direct its responses to low temperature by regulating phenylpropane metabolism, starch and sucrose metabolism, hormone signaling pathways, and transcription factors. BAM, 4CL, CCoAOMT, PRX5, WRKYs, and hormone synthesis related genes play important roles. P. massoniana cultivars may vary in response mechanisms. In this study, physiological and analytical techniques were used to study the root tip response mechanism of Masson's pine to low temperature stress. The results of this study lay a foundation for in-depth research on the molecular functions of P. massoniana under low-temperature stress conditions.

A remodeled RNA polymerase II complex catalyzing viroid RNA-templated transcription

Viroids, a fascinating group of plant pathogens, are subviral agents composed of single-stranded circular noncoding RNAs. It is well-known that nuclear-replicating viroids exploit host DNA-dependent RNA polymerase II (Pol II) activity for transcription from circular RNA genome to minus-strand intermediates, a classic example illustrating the intrinsic RNA-dependent RNA polymerase activity of Pol II. The mechanism for Pol II to accept single-stranded RNAs as templates remains poorly understood. Here, we reconstituted a robust in vitro transcription system and demonstrated that Pol II also accepts minus-strand viroid RNA template to generate plus-strand RNAs. Further, we purified the Pol II complex on RNA templates for nano-liquid chromatography-tandem mass spectrometry analysis and identified a remodeled Pol II missing Rpb4, Rpb5, Rpb6, Rpb7, and Rpb9, contrasting to the canonical 12-subunit Pol II or the 10-subunit Pol II core on DNA templates. Interestingly, the absence of Rpb9, which is responsible for Pol II fidelity, explains the higher mutation rate of viroids in comparison to cellular transcripts. This remodeled Pol II is active for transcription with the aid of TFIIIA-7ZF and appears not to require other canonical general transcription factors (such as TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH, and TFIIS), suggesting a distinct mechanism/machinery for viroid RNA-templated transcription. Transcription elongation factors, such as FACT complex, PAF1 complex, and SPT6, were also absent in the reconstituted transcription complex. Further analyses of the critical zinc finger domains in TFIIIA-7ZF revealed the first three zinc finger domains pivotal for RNA template binding. Collectively, our data illustrated a distinct organization of Pol II complex on viroid RNA templates, providing new insights into viroid replication, the evolution of transcription machinery, as well as the mechanism of RNA-templated transcription.

Transcription factor SS18L1 regulates the proliferation, migration and differentiation of Schwann cells in peripheral nerve injury

Transcription factors bind to specific DNA sequences, modulate the transcription of target genes, and regulate various biological processes, including peripheral nerve regeneration. Our previous analysis showed that SS18L1, a gene encoding the transcription factor SS18-like protein 1, was differentially expressed in the distal sciatic nerve stumps after rat sciatic nerve transection injury, but its effect on peripheral nerve injury has not been reported. In the current study, we isolated and cultured primary Schwann cells, and examined the role of SS18L1 for the biological functions of the cells. Depletion of SS18L1 by siRNA in Schwann cells enhanced cell proliferation and inhibited cell migration, as determined by EdU assay and transwell migration assay, respectively. In addition, silencing of SS18L1 inhibited Schwann cell differentiation induced by HRG and cAMP. Bioinformatics analyses revealed an interaction network of SS18L1, including DF2, SMARCD1, SMARCA4, and SMARCE1, which may be implicated in the regulatory functions of SS18L1 on the proliferation, migration and differentiation of Schwann cells. In conclusion, our results revealed a temporal expression profile of SS18L1 in peripheral nerve injury and its potential roles during the process of nerve recovery.

Identification of essential element determining fruit-specific transcriptional activity in the tomato HISTIDINE DECARBOXYLASE A gene promoter

In SlHDC-A promoter, SlHDC-A core-ES is an essential region for fruit-specific expression and interacts with GATA, HSF and AP1. Triplication of essential region was proposed as a minimal fruit-specific promoter. In plant biotechnology, fruit-specific promoter is an important tool for the improvement and utilization of tomato fruit. To expand our understanding on fruit-specific expression, it is necessary to determine the promoter region involved in fruit-specific transcriptional activity and transcriptional regulations of the promoter. In previous study, we isolated a fruit-specific SlHDC-A core promoter specifically expressed during tomato ripening stages. In this study, we identified SlHDC-A promoter region (SlHDC-A core-ES) that is essential for fruit-specific expression of the SlHDC-A. To understand the molecular mechanisms of fruit-specific expression of the SlHDC-A promoter, we first identified the putative transcription factor binding elements in the SlHDC-A core promoter region and corresponding putative transcription factors which are highly expressed during fruit maturation. Yeast one hybrid analysis confirmed that GATA, HSF, and AP1 interact with the SlHDC-A core-ES promoter region. Further transactivation analysis revealed that expression of the three transcription factors significantly activated expression of a reporter gene driven by SlHDC-A core-ES promoter. These results suggest that GATA, HSF, and AP1 are involved in the fruit-specific expression of SlHDC-A promoter. Furthermore, the synthetic promoter composed of three tandem repeats of SlHDC-A core-ES showed relatively higher activity than the constitutive 35S promoter in the transgenic tomato fruits at the orange stage. Taken together, we propose a new synthetic promoter that is specifically expressed during fruit ripening stage.

Transcriptional and post-transcriptional regulation of checkpoint genes on the tumour side of the immunological synapse

Cancer is a disease of the genome, therefore, its development has a clear Mendelian component, demonstrated by well-studied genes such as BRCA1 and BRCA2 in breast cancer risk. However, it is known that a single genetic variant is not enough for cancer to develop leading to the theory of multistage carcinogenesis. In many cases, it is a sequence of events, acquired somatic mutations, or simply polygenic components with strong epigenetic effects, such as in the case of brain tumours. The expression of many genes is the product of the complex interplay between several factors, including the organism's genotype (in most cases Mendelian-inherited), genetic instability, epigenetic factors (non-Mendelian-inherited) as well as the immune response of the host, to name just a few. In recent years the importance of the immune system has been elevated, especially in the light of the immune checkpoint genes discovery and the subsequent development of their inhibitors. As the expression of these genes normally suppresses self-immunoreactivity, their expression by tumour cells prevents the elimination of the tumour by the immune system. These discoveries led to the rapid growth of the field of immuno-oncology that offers new possibilities of long-lasting and effective treatment options. Here we discuss the recent advances in the understanding of the key mechanisms controlling the expression of immune checkpoint genes in tumour cells.

Identification of aberrant transcription termination at specific gene loci with DNA hypomethylated transcription termination sites caused by DNA methyltransferase deficiency

CpG methylation of genomic DNA is a well-known repressive epigenetic marker in eukaryotic transcription, and DNA methylation of promoter regions is correlated with gene silencing. In contrast to the promoter regions, the function of DNA methylation during transcription termination remains to be elucidated. A recent study revealed that mouse DNA methyltransferase 3a (Dnmt3a) mainly functions in de novo methylation in the promoter and gene body regions, including transcription termination sites (TTSs), during development. To investigate the relationship between DNA methylation overlapping the TTSs and transcription termination, we performed bioinformatics analysis using six pre-existing Dnmt^-/- mouse cell datasets: four types of neurons (three Dnmt3a^-/- and one Dnmt1^-/- mutants) and two types of embryonic fibroblasts (MEFs) (Dnmt3a^-/- and Dnmt3b^-/- mutants). Combined analyses using methylome and transcriptome data revealed that read counts downstream of hypomethylated TTSs were increased in three types of neurons (two Dnmt3a^-/- and one Dnmt1^-/- mutants). Among these, an increase in chimeric transcripts downstream of the TTSs was observed in Dnmt3a^-/- mature olfactory sensory neurons and Dnmt3a^-/- agouti-related peptide (protein)-producing neurons, thereby indicating that read-through occurs in hypomethylated TTSs at specific gene loci in these two mutants. Conversely, in Dnmt3a^-/- MEFs, we detected reductions in read counts downstream of hypomethylated TTSs. These results indicate that the hypomethylation of TTSs can both positively and negatively regulate transcription termination, dependent on Dnmt and cell types. This study is the first to identify the aberrant termination of transcription at specific gene loci with DNA hypomethylated TTSs attributable to Dnmt deficiency.

N-WASP Attenuates Cell Proliferation and Migration through ERK2-Dependent Enhanced Expression of TXNIP

Simple Summary

Neural Wiskott–Aldrich Syndrome Protein (N-WASP) regulates actin cytoskeleton remodeling and can, it has been suggested, suppress several cancers. In this study, HSC-5 cells, a mammalian cell line with reduced N-WASP expression, were used to generate control cells and HSC-5 cells with increased N-WASP expression that is comparable to that of normal keratinocytes. The two cell lines were used to elucidate the regulation of cell proliferation and migration by N-WASP. Our findings suggest that N-WASP increases ERK2-dependent phosphorylation of FOXO1 and increases TXNIP expression, which reduces cell proliferation and migration. This study is the first to propose an antiproliferative role of N-WASP, which is mediated via ERK2, and it suggests new avenues for cancer therapeutic research and treatment.

Abstract

Neural Wiskott–Aldrich Syndrome Protein (N-WASP) regulates actin cytoskeleton remodeling. It has been known that reduced N-WASP expression in breast and colorectal cancers is associated with poor prognosis. Here, we found reduced N-WASP expression in squamous cell carcinoma (SCC) patient samples. The SCC cell line HSC-5 with reduced N-WASP expression was used to generate HSC-5^CN (control) and HSC-5^NW (N-WASP overexpression) cells. HSC-5^NW cells had reduced cell proliferation and migration compared to HSC-5^CN cells. HSC-5^NW cells had increased phospho-ERK2 (extracellular signal-regulated kinase 2), phosphorylated Forkhead box protein class O1 (FOXO1) and reduced nuclear FOXO1 staining compared to HSC-5^CN cells. Proteasome inhibition stabilized total FOXO1, however, not nuclear staining, suggesting that FOXO1 could be degraded in the cytoplasm. Inhibition of ERK2 enhanced nuclear FOXO1 levels and restored cell proliferation and migration of HSC-5^NW to those of HSC-5^CN cells, suggesting that ERK2 regulates FOXO1 activity. The expression of thioredoxin-interacting protein (TXNIP), a FOXO1 target that inhibits thioredoxin and glucose uptake, was higher in HSC-5^NW cells than in HSC-5^CN cells. Knockdown of TXNIP in HSC-5^NW cells restored cell proliferation and migration to those of HSC-5^CN cells. Thus, we propose that N-WASP regulates cell proliferation and migration via an N-WASP-ERK2-FOXO1-TXNIP pathway.

ProbC: joint modeling of epigenome and transcriptome effects in 3D genome

BACKGROUND

Hi-C and its high nucleosome resolution variant Micro-C provide a window into the spatial packing of a genome in 3D within the cell. Even though both techniques do not directly depend on the binding of specific antibodies, previous work has revealed enriched interactions and domain structures around multiple chromatin marks; epigenetic modifications and transcription factor binding sites. However, the joint impact of chromatin marks in Hi-C and Micro-C interactions have not been globally characterized, which limits our understanding of 3D genome characteristics. An emerging question is whether it is possible to deduce 3D genome characteristics and interactions by integrative analysis of multiple chromatin marks and associate interactions to functionality of the interacting loci.

RESULT

We come up with a probabilistic method PROBC to decompose Hi-C and Micro-C interactions by known chromatin marks. PROBC is based on convex likelihood optimization, which can directly take into account both interaction existence and nonexistence. Through PROBC, we discover histone modifications (H3K27ac, H3K9me3, H3K4me3, H3K4me1) and CTCF as particularly predictive of Hi-C and Micro-C contacts across cell types and species. Moreover, histone modifications are more effective than transcription factor binding sites in explaining the genome's 3D shape through these interactions. PROBC can successfully predict Hi-C and Micro-C interactions in given species, while it is trained on different cell types or species. For instance, it can predict missing nucleosome resolution Micro-C interactions in human ES cells trained on mouse ES cells only from these 5 chromatin marks with above 0.75 AUC. Additionally, PROBC outperforms the existing methods in predicting interactions across almost all chromosomes.

CONCLUSION

Via our proposed method, we optimally decompose Hi-C interactions in terms of these chromatin marks at genome and chromosome levels. We find a subset of histone modifications and transcription factor binding sites to be predictive of both Hi-C and Micro-C interactions and TADs across human, mouse, and different cell types. Through learned models, we can predict interactions on species just from chromatin marks for which Hi-C data may be limited.

Expression Profile of Sorghum Genes and Cis-Regulatory Elements under Salt-Stress Conditions

Salinity stress is one of the most important abiotic stresses that causes great losses in crop production worldwide. Identifying the molecular mechanisms of salt resistance in sorghum will help develop salt-tolerant crops with high yields. Sorghum (Sorghum bicolor (L.) Moench) is one of the world’s four major grains and is known as a plant with excellent adaptability to salt stress. Among the various genotypes of sorghum, a Korean cultivar Nampungchal is also highly tolerant to salt. However, little is known about how Nampungchal responds to salt stress. In this study, we measured various physiological parameters, including Na⁺ and K⁺ contents, in leaves grown under saline conditions and investigated the expression patterns of differentially expressed genes (DEGs) using QuantSeq analysis. These DEG analyses revealed that genes up-regulated in a 150 mM NaCl treatment have various functions related to abiotic stresses, such as ERF and DREB. In addition, transcription factors such as ABA, WRKY, MYB, and bZip bind to the CREs region of sorghum and are involved in the regulation of various abiotic stress-responsive transcriptions, including salt stress. These findings may deepen our understanding of the mechanisms of salt tolerance in sorghum and other crops.

The zinc cluster transcription factor Rha1 is a positive filamentation regulator in Candida albicans

Zinc cluster transcription factors (TFs) are essential fungal regulators of gene expression. In the pathogen Candida albicans, the gene orf19.1604 encodes a zinc cluster TF regulating filament development. Hyperactivation of orf19.1604, which we have named RHA1 for Regulator of Hyphal Activity, generates wrinkled colony morphology under nonhyphal growth conditions, triggers filament formation, invasiveness, and enhanced biofilm formation and causes reduced virulence in the mouse model of systemic infection. The strain expressing activated Rha1 shows up-regulation of genes required for filamentation and cell-wall-adhesion-related proteins. Increased expression is also seen for the hyphal-inducing TFs Brg1 and Ume6, while the hyphal repressor Nrg1 is downregulated. Inactivation of RHA1 reduces filamentation under a variety of filament-inducing conditions. In contrast to the partial effect of either single mutant, the double rha1 ume6 mutant strain is highly defective in both serum- and Spider-medium-stimulated hyphal development. While the loss of Brg1 function blocks serum-stimulated hyphal development, this block can be significantly bypassed by Rha1 hyperactivity, and the combination of Rha1 hyperactivity and serum addition can generate significant polarization even in brg1 ume6 double mutants. Thus, in response to external signals, Rha1 functions with other morphogenesis regulators including Brg1 and Ume6, to mediate filamentation.

The Evolution and Expression Profiles of EC1 Gene Family during Development in Cotton

Fertilization is essential to sexual reproduction of flowering plants. EC1 (EGG CELL 1) proteins have a conserved cysteine spacer characteristic and play a crucial role in double fertilization process in many plant species. However, to date, the role of EC1 gene family in cotton is fully unknown. Hence, detailed bioinformatics analysis was explored to elucidate the biological mechanisms of EC1 gene family in cotton. In this study, we identified 66 genes in 10 plant species in which a total of 39 EC1 genes were detected from cotton genome. Phylogenetic analysis clustered the identified EC1 genes into three families (I-III) and all of them contain Prolamin-like domains. A good collinearity was observed in the synteny analysis of the orthologs from cotton genomes. Whole-genome duplication was determined to be one of the major impetuses for the expansion of the EC1 gene family during the process of evolution. qRT-PCR analysis showed that EC1 genes were highly expressed in reproductive tissues under multiple stresses, signifying their potential role in enhancing stress tolerance or responses. Additionally, gene interaction networks showed that EC1 genes may be involved in cell stress and response transcriptional regulator in the synergid cells and activate the expression of genes required for pollen tube guidance. Our results provide novel functional insights into the evolution and functional elucidation of EC1 gene family in cotton.

Histone chaperone Nucleophosmin regulates transcription of key genes involved in oral tumorigenesis

Nucleophosmin (NPM1) is a multifunctional histone chaperone that can activate acetylation-dependent transcription from chromatin templates in vitro. Acetylation of NPM1 by p300 has been shown to further enhance its transcription activation potential. Moreover, its total and acetylated pools are increased in oral squamous cell carcinoma. However, the role of NPM1 or its acetylated form (AcNPM1) in transcriptional regulation in cells and oral tumorigenesis is not fully elucidated. Using ChIP-seq analyses, we provide the first genome-wide profile of AcNPM1 and show that AcNPM1 is enriched at transcriptional regulatory elements. AcNPM1 co-occupies marks of active transcription at promoters and DNase I hypersensitive sites at enhancers. In addition, using a high-throughput protein interaction profiling approach, we show that NPM1 interacts with RNA Pol II, general transcription factors, mediator subunits, histone acetyltransferase complexes, and chromatin remodelers. NPM1 histone chaperone activity also contributes to its transcription activation potential. Further, NPM1 depletion leads to decreased AcNPM1 occupancy and reduced expression of genes required for proliferative, migratory and invasive potential of oral cancer cells. NPM1 depletion also abrogates the growth of orthotopic tumors in mice. Collectively, these results establish that AcNPM1 functions as a coactivator during during RNA polymerase II-driven transcription and regulates the expression of genes that promote oral tumorigenesis.

Histone Acetyltransferases and Deacetylases Are Required for Virulence, Conidiation, DNA Damage Repair, and Multiple Stresses Resistance of Alternaria alternata

Histone acetylation, which is critical for transcriptional regulation and various biological processes in eukaryotes, is a reversible dynamic process regulated by HATs and HDACs. This study determined the function of 6 histone acetyltransferases (HATs) (Gcn5, RTT109, Elp3, Sas3, Sas2, Nat3) and 6 histone deacetylases (HDACs) (Hos2, Rpd3, Hda1, Hos3, Hst2, Sir2) in the phytopathogenic fungus Alternaria alternata by analyzing targeted gene deletion mutants. Our data provide evidence that HATs and HDACs are both required for mycelium growth, cell development and pathogenicity as many gene deletion mutants (ΔGcn5, ΔRTT109, ΔElp3, ΔSas3, ΔNat3, ΔHos2, and ΔRpd3) displayed reduced growth, conidiation or virulence at varying degrees. In addition, HATs and HDACs are involved in the resistance to multiple stresses such as oxidative stress (Sas3, Gcn5, Elp3, RTT109, Hos2), osmotic stress (Sas3, Gcn5, RTT109, Hos2), cell wall-targeting agents (Sas3, Gcn5, Hos2), and fungicide (Gcn5, Hos2). ΔGcn5, ΔSas3, and ΔHos2 displayed severe growth defects on sole carbon source medium suggesting a vital role of HATs and HDACs in carbon source utilization. More SNPs were generated in ΔGcn5 in comparison to wild-type when they were exposed to ultraviolet ray. Moreover, ΔRTT109, ΔGcn5, and ΔHos2 showed severe defects in resistance to DNA-damaging agents, indicating the critical role of HATs and HDACs in DNA damage repair. These phenotypes correlated well with the differentially expressed genes in ΔGcn5 and ΔHos2 that are essential for carbon sources metabolism, DNA damage repair, ROS detoxification, and asexual development. Furthermore, Gcn5 is required for the acetylation of H3K4. Overall, our study provides genetic evidence to define the central role of HATs and HDACs in the pathological and biological functions of A. alternata.

Advances in promoter engineering: novel applications and predefined transcriptional control

Synthetic biology continues to progress by relying on more robust tools for transcriptional control, of which promoters are the most fundamental component. Numerous studies have sought to characterize promoter function, determine principles to guide their engineering, and create promoters with stronger expression or tailored inducible control. In this review, we will summarize promoter architecture and highlight recent advances in the field, focusing on the novel applications of inducible promoter design and engineering towards metabolic engineering and cellular therapeutic development. Additionally, we will highlight how the expansion of new, machine learning techniques for modeling and engineering promoter sequences are enabling more accurate prediction of promoter characteristics. This article is protected by copyright. All rights reserved.

Cross-species Exon Capture and Whole Exome Sequencing: Application, Utility and Challenges for Genomic Resource Development in Non-model Species

Comprehending the genetic architecture of complex traits has many applications in evolution, ecology, conservation biology and plant and animal production systems. Underlying research questions in these fields are diverse species that often have limited genetic information available. In aquaculture, for example, genetic progress has been slow in many species due to a lack in such genetic information. In this study, zebrafish (as a well-studied model species) was used in cross-species transfer to develop genomic resources and identify candidate genes underling growth differentials in dusky kob. Dusky kob is a Sciaenid finfish and an emerging aquaculture species. The zebrafish All Exon Predesigned Probe-set capture protocol was used to enrich fractionated DNA samples from kob, classified as either large or small, before massive parallel sequencing on the Ion Torrent platform. Although vast quantities of sequence data were generated, only about 30% of contigs could be identified as zebrafish homologues. There were numerous species-specific sequences and inconsistent coverage of sequencing products across samples, likely due to non-specific binding of the probe-set as a result of the evolutionary divergence between zebrafish and kob. Nonetheless, more than 55,000 SNPs could be reliably identified and genotyped to the individual level. Using SNP genotypic divergence estimates, between large and small cohorts, a number of candidate genes associated with growth was also identified for future investigation. These findings contribute to the growing body of evidence demonstrating the utility of a cross-species capture approach in the development of important genomic resources for understanding traits of interest in species without reference genomes.

Prognostic signature composed of transcription factors accurately predicts the prognosis of gastric cancer patients

BACKGROUND

Transcription factors (TFs) are involved in important molecular biological processes of tumor cells and play an essential role in the occurrence and development of gastric cancer (GC).

METHODS

Combined The Cancer Genome Atlas Program and Genotype-Tissue Expression database to extract the expression of TFs in GC, analyzed the differences, and weighted gene co-expression network analysis to extract TFs related to GC. The cohort including the training and validation cohort. Univariate Cox, least absolute contraction and selection operator (LASSO) regression, and multivariate Cox analysis was used for screening hub TFs to construct the prognostic signature in the training cohort. The Kaplan-Meier (K-M) and the receiver operating characteristic curve (ROC) was drawn to evaluate the predictive ability of the prognostic signature. A nomogram combining clinical information and prognostic signatures of TFs was constructed and its prediction accuracy was evaluated through various methods. The target genes of the hub TFs was predicted and enrichment analysis was performed to understand its molecular biological mechanism. Clinical samples and public data of GC was collected to verify its expression and prognosis. 5-Ethynyl-2'-deoxyuridine and Acridine Orange/Ethidium Bromide staining, flow cytometry and Western-Blot detection were used to analyze the effects of hub-TF ELK3 on the proliferation and apoptosis of gastric cancer in vitro.

RESULTS

A total of 511 misaligned TFs were obtained and 200 GC-related TFs were exposed from them. After systematic analysis, a prognostic signature composed of 4 TFs (ZNF300, ELK3, SP6, MEF2B) were constructed. The KM and ROC curves demonstrated the good predictive ability in training, verification, and complete cohort. The areas under the ROC curve are respectively 0.737, 0.705, 0.700. The calibration chart verified that the predictive ability of the nomogram constructed by combining the prognostic signature of TFs and clinical information was accurate, with a C-index of 0.714. Enriching the target genes of hub TFs showed that it plays an vital role in tumor progression, and its expression and prognostic verification were consistent with the previous analysis. Among them, ELK3 was proved in vitro, and downregulation of its expression inhibited the proliferation of gastric cancer cells, induced proliferation, and exerted anti-tumor effects.

CONCLUSIONS

The 4-TFs prognostic signature accurately predicted the overall survival of GC, and ELK3 may be potential therapeutic targets for GC.

The Impact of Anthocyanins and Iridoids on Transcription Factors Crucial for Lipid and Cholesterol Homeostasis

Nutrition determines our health, both directly and indirectly. Consumed foods affect the functioning of individual organs as well as entire systems, e.g., the cardiovascular system. There are many different diets, but universal guidelines for proper nutrition are provided in the WHO healthy eating pyramid. According to the latest version, plant products should form the basis of our diet. Many groups of plant compounds with a beneficial effect on human health have been described. Such groups include anthocyanins and iridoids, for which it has been proven that their consumption may lead to, inter alia, antioxidant, cholesterol and lipid-lowering, anti-obesity and anti-diabetic effects. Transcription factors directly affect a number of parameters of cell functions and cellular metabolism. In the context of lipid and cholesterol metabolism, five particularly important transcription factors can be distinguished: liver X receptor (LXR), peroxisome proliferator-activated receptor-α (PPAR-α), peroxisome proliferator-activated receptor-γ (PPAR-γ), CCAAT/enhancer binding protein α (C/EBPα) and sterol regulatory element-binding protein 1c (SREBP-1c). Both anthocyanins and iridoids may alter the expression of these transcription factors. The aim of this review is to collect and systematize knowledge about the impact of anthocyanins and iridoids on transcription factors crucial for lipid and cholesterol homeostasis.

Mathematical Algorithm for Identification of Eukaryotic Promoter Sequences

Identification of promoter sequences in the eukaryotic genome, by computer methods, is an important task of bioinformatics. However, this problem has not been solved since the best algorithms have a false positive probability of 10−3–10−4 per nucleotide. As a result of full genome analysis, there may be more false positives than annotated gene promoters. The probability of a false positive should be reduced to 10−6–10−8 to reduce the number of false positives and increase the reliability of the prediction. The method for multi alignment of the promoter sequences was developed. Then, mathematical methods were developed for calculation of the statistically important classes of the promoter sequences. Five promoter classes, from the rice genome, were created. We developed promoter classes to search for potential promoter sequences in the rice genome with a false positive number less than 10−8 per nucleotide. Five classes of promoter sequences contain 1740, 222, 199, 167 and 130 promoters, respectively. A total of 145,277 potential promoter sequences (PPSs) were identified. Of these, 18,563 are promoters of known genes, 87,233 PPSs intersect with transposable elements, and 37,390 PPSs were found in previously unannotated sequences. The number of false positives for a randomly mixed rice genome is less than 10−8 per nucleotide. The method developed for detecting PPSs was compared with some previously used approaches. The developed mathematical method can be used to search for genes, transposable elements, and transcript start sites in eukaryotic genomes.

Advances in targeting 'undruggable' transcription factors with small molecules

Transcription factors (TFs) represent key biological players in diseases including cancer, autoimmunity, diabetes and cardiovascular disease. However, outside nuclear receptors, TFs have traditionally been considered 'undruggable' by small-molecule ligands due to significant structural disorder and lack of defined small-molecule binding pockets. Renewed interest in the field has been ignited by significant progress in chemical biology approaches to ligand discovery and optimization, especially the advent of targeted protein degradation approaches, along with increasing appreciation of the critical role a limited number of collaborators play in the regulation of key TF effector genes. Here, we review current understanding of TF-mediated gene regulation, discuss successful targeting strategies and highlight ongoing challenges and emerging approaches to address them.

Mediator structure and conformation change

Mediator is a universal adaptor for transcription control. It serves as an interface between gene-specific activator or repressor proteins and the general RNA polymerase II (pol II) transcription machinery. Previous structural studies revealed a relatively small part of Mediator and none of the gene activator-binding regions. We have determined the cryo-EM structure of the Mediator at near-atomic resolution. The structure reveals almost all amino acid residues in ordered regions, including the major targets of activator proteins, the Tail module, and the Med1 subunit of the Middle module. Comparison of Mediator structures with and without pol II reveals conformational changes that propagate across the entire Mediator, from Head to Tail, coupling activator- and pol II-interacting regions.

Generating Ensembles of Gene Regulatory Networks to Assess Robustness of Disease Modules

The use of biological networks such as protein-protein interaction and transcriptional regulatory networks is becoming an integral part of genomics research. However, these networks are not static, and during phenotypic transitions like disease onset, they can acquire new "communities" (or highly interacting groups) of genes that carry out cellular processes. Disease communities can be detected by maximizing a modularity-based score, but since biological systems and network inference algorithms are inherently noisy, it remains a challenge to determine whether these changes represent real cellular responses or whether they appeared by random chance. Here, we introduce Constrained Random Alteration of Network Edges (CRANE), a method for randomizing networks with fixed node strengths. CRANE can be used to generate a null distribution of gene regulatory networks that can in turn be used to rank the most significant changes in candidate disease communities. Compared to other approaches, such as consensus clustering or commonly used generative models, CRANE emulates biologically realistic networks and recovers simulated disease modules with higher accuracy. When applied to breast and ovarian cancer networks, CRANE improves the identification of cancer-relevant GO terms while reducing the signal from non-specific housekeeping processes.

Sequencing, de novo assembly and annotation of Digitalis ferruginea subsp. schischkinii transcriptome

There is an increasing demand for elucidating the biosynthetic pathway of medicinal plants, which are capable of producing several metabolites with great potentials for industrial drug production. Digitalis species are important medicinal plants for the production of cardenolide compounds. Advancement on culture techniques is strictly related to our understanding of the genomic background of species. There are a limited number of genomic studies on Digitalis species. The goal of this study is to contribute to the genomic data of Digitalis ferruginea subsp. schischkinii by presenting transcriptome annotation. Digitalis ferruginea subsp. schischkinii has a limited distribution in Turkey and Transcaucasia, and has a high level of lanatoside C, an important cardenolide. In the study, we sequenced the cDNA library prepared from RNA pools of D. ferruginea subsp. schischkinii tissues treated with various stress conditions. Comprehensive bioinformatics approaches were used for de novo assembly and functional annotation of D. ferruginea subsp. schischkinii transcriptome sequence data along with TF families predictions and phylogenetic analysis. In the study, 58,369 unigenes were predicted and unigenes were annotated by analyzing the sequence data in the non-redundant (NR) protein database, the non-redundant nucleotide (NT) database, Gene Orthology (GO), EuKaryotic Orthologous Groups (KOG), Kyoto Encyclopedia of Genes and Genomes (KEGG), SwissProt, and InterPro databases. This study is the first transcriptome data for D. ferruginea subsp. schischkinii.

Functional roles of antisense enhancer RNA for promoting prostate cancer progression

Rationale: Enhancer RNA (eRNA) bi-directionally expresses from enhancer region and sense eRNA regulates adjacent mRNA in cis and in trans. However, it has remained unclear whether antisense eRNAs in different direction are functional or merely a reflection of enhancer activation. Methods: Strand-specific, ribosome-minus RNA sequencing (RNA-seq) were performed in AR positive prostate cancer cells. RNA-seq, GRO-seq, ChIP-seq, 4C-seq and DNA-methylation-seq that published in our and other labs were re-analyzed to define bi-directional enhancer RNA and DNA methylation regions. Molecular mechanisms were demonstrated by 3C, ChIP, ChIRP, CLIP, RT-PCR and western blot assays. The biological functions of antisense-eRNA were assessed using mice xenograft model and RT-PCR analysis in human tissues. Results: In this study, we identified that antisense eRNA was regulated by androgen receptor (AR) activity in prostate cancer cells. Antisense eRNA negatively regulated antisense ncRNA in AR-related target genes' loci, through recruiting DNMT1 on the antisense enhancer in the gene-ending regions and elevating DNA methylation. Importantly, the chromatin exhibited a double looping manner that facilitated sense-eRNA to promoter and antisense-eRNA to gene-ending region in cis. Depletion of antisense eRNA impaired its neighbor mRNA expression, cancer growth and invasion. The expressions of antisense eRNA were correlated with biochemical recurrence and clinical marker PSA's levels in patients' tissues. Conclusions: The findings indicated that antisense eRNA was a functional RNA and may be a novel target that when suppressed improved prostate cancer therapy and diagnosis. New chromatin interaction among enhancer, promoter and gene-ending region might provide new insight into the spatiotemporal mechanism of the gene transcription and acting of bi-directional eRNAs.

The G4 resolvase RHAU modulates mRNA translation and stability to sustain postnatal heart function and regeneration

Post-transcriptional regulation of mRNA translation and stability is primarily achieved by RNA-binding proteins, which are of increasing importance for heart function. Furthermore, G-quadruplex (G4) and G4 resolvase activity are involved in a variety of biological processes. However, the role of G4 resolvase activity in heart function remains unknown. The present study aims to investigate the role of RNA helicase associated with adenylate- and uridylate-rich element (RHAU), an RNA-binding protein with G4 resolvase activity in postnatal heart function through deletion of Rhau in the cardiomyocytes of postnatal mice. RHAU-deficient mice displayed progressive pathological remodeling leading to heart failure and mortality and impaired neonatal heart regeneration. RHAU ablation reduced the protein levels but enhanced mRNA levels of Yap1 and Hexim1 that are important regulators for heart development and postnatal heart function. Furthermore, RHAU was found to associate with both the 5' and 3' UTRs of these genes to destabilize mRNA and enhance translation. Thus, we have demonstrated the important functions of RHAU in the dual regulation of mRNA translation and stability, which is vital for heart physiology.