Putative Transcription Factor Research Articles

Integrative multi-omics increase resolution of the sea urchin posterior gut gene regulatory network at single cell level.

Drafting gene regulatory networks (GRNs) requires embryological knowledge pertaining to the cell type families, information on the regulatory genes, causal data from gene knockdown experiments and validations of the identified interactions by cis-regulatory analysis. We use multi-omics involving next-generation sequencing (-seq) to obtain the necessary information for drafting Strongylocentrotus purpuratus posterior gut GRN. Here we present an update to the GRN using i) a single cell RNA-seq derived cell atlas highlighting the 2 day post fertilization (dpf) sea urchin gastrula cell type families, as well as the genes expressed at single cell level, ii) a set of putative cis-regulatory modules and transcription factor (TF) binding sites obtained from chromatin accessibility ATAC-seq data, and iii) interactions directionality obtained from differential bulk RNA-seq following knockdown of the TF Sp-Pdx1, a key regulator of gut patterning in sea urchins. Combining these datasets, we draft the GRN for the hindgut Sp-Pdx1 positive cells in the 2 dpf gastrula embryo. Overall, our data suggests the complex connectivity of the posterior gut GRN and increases the resolution of gene regulatory cascades operating within it.

AtDREB2G is involved in the regulation of riboflavin biosynthesis in response to low-temperature stress and abscisic acid treatment in Arabidopsis thaliana

Riboflavin (RF) serves as a precursor to flavin mononucleotide and flavin adenine dinucleotide, which are crucial cofactors in various metabolic processes. Strict regulation of cellular flavin homeostasis is imperative, yet information regarding the factors governing this regulation remains largely elusive. In this study, we first examined the impact of external flavin treatment on the Arabidopsis transcriptome to identify novel regulators of cellular flavin levels. Our analysis revealed alterations in the expression of 49 putative transcription factors. Subsequent reverse genetic screening highlighted a member of the dehydration-responsive element binding (DREB) family, AtDREB2G, as a potential regulator of cellular flavin levels. Knockout mutants of AtDREB2G (dreb2g) exhibited reduced flavin levels and decreased expression of RF biosynthetic genes compared to wild-type plants. Conversely, conditional overexpression of AtDREB2G led to an increase in the expression of RF biosynthetic genes and elevated flavin levels. In wild-type plants, exposure to low temperatures and abscisic acid treatment stimulated enhanced flavin levels and upregulated the expression of RF biosynthetic genes, concomitant with the induction of AtDREB2G. Notably, these responses were significantly attenuated in dreb2g mutants. Our findings establish AtDREB2G is involved in the positive regulation of flavin biosynthesis in Arabidopsis, particularly under conditions of low temperature and abscisic acid treatment.

Expression of Transposable Elements throughout the Fasciola hepatica Trematode Life Cycle.

Transposable elements (TEs) are major components of eukaryotic genomes. The extensive body of evidence suggests that although they were once considered "genomic parasites", transposons and their transcripts perform specific functions, such as regulation of early embryo development. Understanding the role of TEs in such parasites as trematodes is becoming critically important. Fasciola hepatica, a parasite affecting humans and livestock, undergoes a complex life cycle in diverse environments and hosts, and knowledge about its life cycle regulation is scarce so far. We summarized the data regarding the repetitive elements in F. hepatica and conducted bulk RNA-seq analysis across its life cycle stages. TE expression profiles were analyzed, focusing on differential expression and potential homology with previously described long non-coding RNAs (lncRNAs). Differential expression analysis revealed stage-specific TE transcription patterns, notably peaking during egg and metacercariae stages. Some TEs showed homology with known lncRNAs and contained putative transcription factor binding sites. Interestingly, TE transcription levels were highest in eggs and metacercariae compared to adults, suggesting regulatory roles in trematode life cycle transitions. These findings suggest that TEs may play roles in regulating trematode life cycle transitions. Moreover, TE homology with lncRNAs underscores their significance in gene regulation.

Bioinformatics Analysis in Predicting Transcription Factors of Robo3 Gene in Drosophila melanogaster

In bilaterian animals, axon guidance decisions are regulated by many transmembrane receptor proteins called Roundabout (Robo) family members. During the developmental stages of fruit flies (Drosophila melanogaster), three Robo family members play unique roles in the central nervous system. Robo3 is revolutionarily conserved among taxa and studies show that Robo3 regulates mediolateral axonal navigation. Recent studies suggest that Robo3 guides longitudinal axons in a manner independent of its ligand (slit). The expression patterns of Robo3 are controlled by transcription factors (TFs) that play a significant role in gene regulation, and it is not a fully understood mechanism. Knowing the transcription factor binding sites (TFBS) of Robo3 would help to predict TFs that regulate Robo3. In this study, bioinformatics tools MEME Suite, TOMTOM, and MAST were utilized to analyze the Robo3 DNA sequence to identify putative TFs that assist as docking regions for TFs involved in the regulation of Robo3 gene expression. We found seven putative TFs: Btd, Opa, Mad, Odd, Twi, CF2, and h. Mapping these TF motifs against the Robo3 sequence showed that these motifs are located in many regions of the Robo3 gene. Understanding the roles of these TFs in Robo3 gene regulation would help to implement novel strategies to control and overcome disorders related to the Robo3 gene. This study aims to identify the unknown TFs that may play a critical role in Robo3 gene expression.

In vivo transgenic studies confirm the critical acylation function of LeBAHD56 for shikonin in Lithospermum erythrorhizon.

LeBAHD56 is preferentially expressed in tissues where shikonin and its derivatives are biosynthesized, and it confers shikonin acylation in vivo. Two WRKY transcriptional factors might regulate LeBAHD56's expression. Shikonin and its derivatives, found in the roots of Lithospermum erythrorhizon, have extensive application in the field of medicine, cosmetics, and other industries. Prior research has demonstrated that LeBAHD1(LeSAT1) is responsible for the biochemical process of shikonin acylation both in vitro and in vivo. However, with the exception of its documented in vitro biochemical function, there is no in vivo genetic evidence supporting the acylation function of the highly homologous gene of LeSAT1, LeBAHD56(LeSAT2), apart from its reported role. Here, we validated the critical acylation function of LeBAHD56 for shikonin using overexpression (OE) and CRISPR/Cas9-based knockout (KO) strategies. The results showed that the OE lines had a significantly higher ratio of acetylshikonin, isobutyrylshikonin or isovalerylshikonin to shikonin than the control. In contrast, the KO lines had a significantly lower ratio of acetylshikonin, isobutyrylshikonin or isovalerylshikonin to shikonin than controls. As for its detailed expression patterns, we found that LeBAHD56 is preferentially expressed in roots and callus cells, which are the biosynthesis sites for shikonin and its derivatives. In addition, we anticipated that a wide range of putative transcription factors might control its transcription and verified the direct binding of two crucial WRKY members to the LeBAHD56 promoter's W-box. Our results not only confirmed the in vivo function of LeBAHD56 in shikonin acylation, but also shed light on its transcriptional regulation.

Functional annotation and meta-analysis of maize transcriptomes reveal genes involved in biotic and abiotic stress

BackgroundEnvironmental stress factors, such as biotic and abiotic stress, are becoming more common due to climate variability, significantly affecting global maize yield. Transcriptome profiling studies provide insights into the molecular mechanisms underlying stress response in maize, though the functions of many genes are still unknown. To enhance the functional annotation of maize-specific genes, MaizeGDB has outlined a data-driven approach with an emphasis on identifying genes and traits related to biotic and abiotic stress.ResultsWe mapped high-quality RNA-Seq expression reads from 24 different publicly available datasets (17 abiotic and seven biotic studies) generated from the B73 cultivar to the recent version of the reference genome B73 (B73v5) and deduced stress-related functional annotation of maize gene models. We conducted a robust meta-analysis of the transcriptome profiles from the datasets to identify maize loci responsive to stress, identifying 3,230 differentially expressed genes (DEGs): 2,555 DEGs regulated in response to abiotic stress, 408 DEGs regulated during biotic stress, and 267 common DEGs (co-DEGs) that overlap between abiotic and biotic stress. We discovered hub genes from network analyses, and among the hub genes of the co-DEGs we identified a putative NAC domain transcription factor superfamily protein (Zm00001eb369060) IDP275, which previously responded to herbivory and drought stress. IDP275 was up-regulated in our analysis in response to eight different abiotic and four different biotic stresses. A gene set enrichment and pathway analysis of hub genes of the co-DEGs revealed hormone-mediated signaling processes and phenylpropanoid biosynthesis pathways, respectively. Using phylostratigraphic analysis, we also demonstrated how abiotic and biotic stress genes differentially evolve to adapt to changing environments.ConclusionsThese results will help facilitate the functional annotation of multiple stress response gene models and annotation in maize. Data can be accessed and downloaded at the Maize Genetics and Genomics Database (MaizeGDB).

Transcriptional landscape and dynamics involved in sugar and acid accumulation during apple fruit development.

In fleshy fruit, sugars and acids are central components of fruit flavor and quality. To date, the mechanisms underlying transcriptional regulation of sugar and acid during fruit development remain largely unknown. Here, we combined ATAC-seq with RNA-seq to investigate the genome-wide chromatin accessibility and to identify putative transcription factors related to sugar and acid accumulation during apple (Malus domestica) fruit development. By integrating the differentially accessible regions and differentially expressed genes, we generated a global data set of promoter-accessibility and expression-increased genes. Using this strategy, we constructed a transcriptional regulatory network enabling screening for key transcription factors and target genes involved in sugar and acid accumulation. Among these transcription factors, 5 fruit-specific DNA binding with one finger genes were selected to confirm their regulatory effects, and our results showed that they could affect sugar or acid concentration by regulating the expression of sugar or acid metabolism-related genes in apple fruits. Our transcriptional regulatory network provides a suitable platform to identify candidate genes that control sugar and acid accumulation. Meanwhile, our data set will aid in analyzing other characteristics of apple fruit that have not been illuminated previously. Overall, these findings support a better understanding of the regulatory dynamics during apple fruit development and lay a foundation for quality improvement of apple.

Abstract 1099: Single-cell Transcriptomic And Epigenic Profiling Identifies Sox6 As A Key Regulator Of Arterial Endothelial Cell Phenotype In Systemic Sclerosis-associated Pulmonary Hypertension

Background: Pulmonary hypertension (PH) frequently arises as a complication of systemic sclerosis (SSc), and is a major cause of death among patients with this condition. Pulmonary vasculopathy in SSc is characterized by endothelial dysfunction with subsequent remodeling of the pulmonary vasculature, especially arterioles and small arteries. Characterization of transcriptional regulators driving the pathological changes in arterial endothelial cells (ECs) is critical to understanding pathogenic mechanisms underlying SSc-associated vasculopathy. Methods and Results: We performed single-cell multiome sequencing to simultaneously profile the transcriptome and epigenome of explanted lung tissue from SSc-PH patients (n = 9) and healthy donors (n = 6). We identified co-regulated genes and candidate enhancer regions associated with transcription factors (TFs) across different EC cell states using SCENIC+. Gene regulatory network analysis revealed SOX6 as a key transcription factor for the arterial EC phenotype associated with SSc-PH. 71 genes and 153 regions were predicted to be regulated by SOX6. Notably, SOX6 was the only SOX family member significantly upregulated in SSc-PH arterial ECs (fold change = 40.0, adjusted p-value = 6.1*10 -21 ). Putative bound TF motif instances accounting for chromatin accessibility in the candidate enhancer regions were identified using the base-resolution deep learning model, ChromBPNet. Consistent with SCENIC+ predictions, cell-state specific ChromBPNet models revealed higher putative TF occupancy at SOX motif instances across the genome. In addition, we identified SOX/ETS composite motif instances showing higher putative occupancy in SSc-PH arterial ECs, which may support cooperative binding of SOX proteins with ETS family members. Conclusions: These data provide novel insight into transcriptional regulatory programs of arterial ECs in SSc-PH and highlight SOX6 as a key contributor.

Full-length transcriptome analysis of a bloom-forming dinoflagellate Prorocentrum shikokuense (Dinophyceae)

Prorocentrum shikokuense (formerly P. donghaiense) is a pivotal dinoflagellate species associating with the HABs in the East China Sea. The complexity of its large nuclear genome hindered us from understanding its genomic characteristics. Full-length transcriptome sequencing offers a practical solution to decipher the physiological mechanisms of a species without the reference genome. In this study, we employed single-molecule real-time (SMRT) sequencing technology to sequence the full-length transcriptome of Prorocentrum shikokuense. We successfully generated 41.73 Gb of clean SMRT sequencing reads and isolated 105,249 non-redundant full-length non-chimeric reads. Our trial has led to the identification of 11,917 long non-coding RNA transcripts, 514 alternative splicing events, 437 putative transcription factor genes from 17 TF gene families, and 34,723 simple sequence repeats. Additionally, a total of 78,265 open reading frames were identified, of them 15,501 were the protein coding sequences. This dataset is valuable for annotating P. shikokuense genome, and will contribute significantly to the in-depth studies on the molecular mechanisms underlining the dinoflagellate bloom formation.

Integrative analysis of transcriptomic and epigenomic data reveals distinct patterns for developmental and housekeeping gene regulation

BackgroundRegulation of transcription is central to the emergence of new cell types during development, and it often involves activation of genes via proximal and distal regulatory regions. The activity of regulatory elements is determined by transcription factors (TFs) and epigenetic marks, but despite extensive mapping of such patterns, the extraction of regulatory principles remains challenging.ResultsHere we study differentially and similarly expressed genes along with their associated epigenomic profiles, chromatin accessibility and DNA methylation, during lineage specification at gastrulation in mice. Comparison of the three lineages allows us to identify genomic and epigenomic features that distinguish the two classes of genes.We show that differentially expressed genes are primarily regulated by distal elements, while similarly expressed genes are controlled by proximal housekeeping regulatory programs. Differentially expressed genes are relatively isolated within topologically associated domains, while similarly expressed genes tend to be located in gene clusters. Transcription of differentially expressed genes is associated with differentially open chromatin at distal elements including enhancers, while that of similarly expressed genes is associated with ubiquitously accessible chromatin at promoters.ConclusionBased on these associations of (linearly) distal genes’ transcription start sites (TSSs) and putative enhancers for developmental genes, our findings allow us to link putative enhancers to their target promoters and to infer lineage-specific repertoires of putative driver transcription factors, within which we define subgroups of pioneers and co-operators.

The Putative GATA Transcription Factor SbGATA22 as a Novel Regulator of Dhurrin Biosynthesis.

Cyanogenic glucosides are specialized metabolites produced by over 3000 species of higher plants from more than 130 families. The deployment of cyanogenic glucosides is influenced by biotic and abiotic factors in addition to being developmentally regulated, consistent with their roles in plant defense and stress mitigation. Despite their ubiquity, very little is known regarding the molecular mechanisms that regulate their biosynthesis. The biosynthetic pathway of dhurrin, the cyanogenic glucoside found in the important cereal crop sorghum (Sorghum bicolor (L.) Moench), was described over 20 years ago, and yet no direct regulator of the biosynthetic genes has been identified. To isolate regulatory proteins that bind to the promoter region of the key dhurrin biosynthetic gene of sorghum, SbCYP79A1, yeast one-hybrid screens were performed. A bait fragment containing 1204 base pairs of the SbCYP79A1 5' regulatory region was cloned upstream of a reporter gene and introduced into Saccharomyces cerevisiae. Subsequently, the yeast was transformed with library cDNA representing RNA from two different sorghum developmental stages. From these screens, we identified SbGATA22, an LLM domain B-GATA transcription factor that binds to the putative GATA transcription factor binding motifs in the SbCYP79A1 promoter region. Transient assays in Nicotiana benthamiana show that SbGATA22 localizes to the nucleus. The expression of SbGATA22, in comparison with SbCYP79A1 expression and dhurrin concentration, was analyzed over 14 days of sorghum development and in response to nitrogen application, as these conditions are known to affect dhurrin levels. Collectively, these findings suggest that SbGATA22 may act as a negative regulator of SbCYP79A1 expression and provide a preliminary insight into the molecular regulation of dhurrin biosynthesis in sorghum.

Abstract 4406: Single cell multiomic analysis reveals how genomic, epigenomic and transcriptomic events drive progression of multiple myeloma precursor states

Abstract In this study we have leveraged Moffitt Cancer Center’s cohort of over 1,000 bone marrow (BMBX) aspirates from normal donors, MM precursor diseases (MGUS, SMOL), active therapy naïve disease (NDMM), as well as early (post 1-3 lines of therapy, ERMM) and late-relapse (3+ lines of therapy, LRMM) MM patients, characterized clinically, cytogenetically (FISH), genetically (WES), and transcriptomically (RNA-seq).Transcriptomic analysis identified a subset of cancer hallmarks differentially expressed between MGUS and NDMM samples (e.g. cell identity, adhesion and inflammatory signaling, etc.).Dimensionality reduction analysis, followed by unsupervised segmentation, identified clusters of co-expressing genes across this dataset. Enrichment analysis of aforementioned gene clusters, differentially expressed between MGUS and NDMM states, identified a number of putative transcription factors (GATA1/2, SUZ12, RUNX1, SOX2, TP63, NFE2L2, FOXM1 and NANOG), as well as polycomb complex and H3K27me3 as main drivers. Single cell ATAC-seq in 11 BMBX (4 SMOL, 4 NDMM, 1 ERMM, 2 LRMM) and single cell multiomics (simultaneous scATAC-seq/scRNA-seq) in additional 10 BMBX (2 healthy, 3 MGUS, 3 SMOL and 2 NDMM) confirmed that the H3K27me3 putatively regulated gene clusters were the only ones with significant chromatin accessibility changes. Single cell analysis confirmed differential expression and accessibility of cancer hallmarks identified in larger cohort, as well as putative driver TFs. Correlation between TF expression and motif accessibility produced an additional list of pioneer TFs putatively involved in progression from MM precursor states (ZEB1, EBF1, SPI1, PAX5, etc.).Investigation of scMultiomic data demonstrated that NDMM and SMOL samples contain subpopulations of cells in MGUS and normal “states” (cell clusters in scMultiomics UMAP), confirming intra-sample heterogeneity, and that divergence within the multiomic plane occurs in the transition between MGUS and SMOL. Through pseudotime and single cell copy number analysis (epiAneufinder/scATAC-seq and inferCNV/scRNA-seq) we were able to reconstruct how MM FISH cytogenetic abnormalities alter the multiome of these cells, creating aforementioned intra-sample heterogeneity. Despite different initiating events, all samples shared a common biology putatively regulated by epigenetic dysregulation, suggesting polycomb complex hijacking as a therapeutic opportunity for precursor MM. Citation Format: Rafael Canevarolo, Praneeth Sudalagunta, Maria Silva, Mark Meads, Rachid Baz, Melissa Alsina, Kenneth H. Shain, Ariosto Siqueira Silva. Single cell multiomic analysis reveals how genomic, epigenomic and transcriptomic events drive progression of multiple myeloma precursor states [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4406.

The exp2 gene, which encodes a protein with two zinc finger domains, regulates cap expansion and autolysis in Coprinopsis cinerea

Cap expansion in agaricoid mushroom species is an important event for sexual reproduction because meiosis occurs in basidia under the cap, and basidiospores can be released by opening the cap. However, molecular mechanisms underlying cap expansion in basidiomycetes remain poorly understood. We aimed to elucidate the molecular mechanisms of cap expansion in basidiomycetes by analyzing the unique cap-expansionless UV mutant #13 (exp2–1) in Coprinopsis cinerea. Linkage analysis and consequent genome sequence analysis revealed that the gene responsible for the mutant phenotypes encodes a putative transcription factor with two C2H2 zinc finger motifs. The mutant that was genome-edited to lack exp2 exhibited an expansionless phenotype. Some of the genes encoding cell wall degradation-related enzymes showed decreased expression during cap expansion and autolysis in the exp2 UV and genome-edited mutant. The exp2 gene is widely conserved in Agaricomycetes, suggesting that Exp2 homologs regulate fruiting body maturation in Agaricomycetes, especially cap expansion in Agaricoid-type mushroom-forming fungi. Therefore, exp2 homologs could be a target for mushroom breeding to maintain shape after harvest for some cultivating mushrooms, presenting a promising avenue for further research in breeding techniques.

Single-cell transcriptomics of the human parasite Schistosoma mansoni first intra-molluscan stage reveals tentative tegumental and stem-cell regulators

Schistosomiasis is a major Neglected Tropical Disease, caused by the infection with blood flukes in the genus Schistosoma. To complete the life cycle, the parasite undergoes asexual and sexual reproduction within an intermediate snail host and a definitive mammalian host, respectively. The intra-molluscan phase provides a critical amplification step that ensures a successful transmission. However, the cellular and molecular mechanisms underlying the development of the intra-molluscan stages remain poorly understood. Here, single cell suspensions from S. mansoni mother sporocysts were produced and sequenced using the droplet-based 10X Genomics Chromium platform. Six cell clusters comprising two tegument, muscle, neuron, parenchyma and stem/germinal cell clusters were identified and validated by in situ hybridisation. Gene Ontology term analysis predicted key biological processes for each of the clusters, including three stem/germinal sub-clusters. Furthermore, putative transcription factors predicted for stem/germinal and tegument clusters may play key roles during parasite development and interaction with the intermediate host.

Orphan Nuclear Receptor Family 4A (NR4A) Members NR4A2 and NR4A3 Selectively Modulate Elements of the Monocyte Response to Buffered Hypercapnia.

Hypercapnia occurs when the partial pressure of carbon dioxide (CO2) in the blood exceeds 45 mmHg. Hypercapnia is associated with several lung pathologies and is transcriptionally linked to suppression of immune and inflammatory signalling through poorly understood mechanisms. Here we propose Orphan Nuclear Receptor Family 4A (NR4A) family members NR4A2 and NR4A3 as potential transcriptional regulators of the cellular response to hypercapnia in monocytes. Using a THP-1 monocyte model, we investigated the sensitivity of NR4A family members to CO2 and the impact of depleting NR4A2 and NR4A3 on the monocyte response to buffered hypercapnia (10% CO2) using RNA-sequencing. We observed that NR4A2 and NR4A3 are CO2-sensitive transcription factors and that depletion of NR4A2 and NR4A3 led to reduced CO2-sensitivity of mitochondrial and heat shock protein (Hsp)-related genes, respectively. Several CO2-sensitive genes were, however, refractory to depletion of NR4A2 and NR4A3, indicating that NR4As regulate certain elements of the cellular response to buffered hypercapnia but that other transcription factors also contribute. Bioinformatic analysis of conserved CO2-sensitive genes implicated several novel putative CO2-sensitive transcription factors, of which the ETS Proto-Oncogene 1 Transcription Factor (ETS-1) was validated to show increased nuclear expression in buffered hypercapnia. These data give significant insights into the understanding of immune responses in patients experiencing hypercapnia.

Physiological role of genes involved in taurine biosynthesis in fishes and in silico approach to determine transcription factors in their promoters’ zone

Taurine, an amino sulfonic acid that is sometimes referred to as an amino acid, is endogenously synthesized by the action of the key genes/enzymes: cysteine dioxygenase (cdo), cysteine sulfonate decarboxylase (csad), glutamate decarboxylase (gad), and 2-amino ethanethiol dioxygenase (ado). The taurine transporter (taut) also distributes this taurine formation across the plasma. These genes have been identified as important in different physiological processes such as reproduction, digestion, olfactory, visual, circulatory, and muscular systems. Thus, a literature review of these genes in fish has been described in the present work. Moreover, there is null information regarding the study of regulatory elements such as transcription factors (TFs) in taurine biosynthesis and transportation genes of fishes. In this interest and taking advantage of the availability of different sequence databases, bioinformatics can be applied as a first approach for an in silico identification of the putative TFs and transcription factor binding sites (TFBS) that might play an important role in regulating these genes. The results showed that some are commonly shared, whereas TFs and TFBs vary among fish species. Hence, binding sites for homeobox protein BarH-like 1 (BARX1), brain-specific homeobox protein homolog (BSX), helicase-like transcription factor (HLTF), homeobox protein Hox-A7 (HOXA7), homeobox protein Hox-B3 (HOXB3), homeobox protein Hox-B6 (HOXB6), homeobox protein Meis1 (MEIS1), homeobox protein Meis3 (MEIS3), nuclear factor of activated T cells 1 (NFATC1), and homeobox protein Nkx-6.2 (NKX6-2) were commonly found in the promoter regions of genes involved in taurine transportation and biosynthesis. Additionally, our results suggested that the frequency of HOXB3, a transcription factor involved in development, has repetitive TFBS sites in the promoter region of all species analyzed in the present study. Although bioinformatics gives us an approach to determine putative TFs and TFBS, further work is needed to verify how the found regulatory elements play a key role in taurine biosynthesis and transportation.

Transcriptome and comparative chloroplast genome analysis of Taxus yunnanensis individuals with high and low paclitaxel yield

Paclitaxel is a potent anti-cancer drug that is mainly produced through semi-synthesis, which still requires plant materials as precursors. The content of paclitaxel and 10-deacetyl baccatin III (10-DAB) in Taxus yunnanensis has been found to differ from that of other Taxus species, but there is little research on the mechanism underlying the variation in paclitaxel content in T. yunnanensis of different provenances. In this experiment, the contents of taxoids and precursors in twigs between a high paclitaxel-yielding individual (TG) and a low paclitaxel-yielding individual (TD) of T. yunnanensis were compared, and comparative analyses of transcriptomes as well as chloroplast genomes were performed. High-performance liquid chromatography (HPLC) detection showed that 10-DAB and baccatin III contents in TG were 18 and 47 times those in TD, respectively. Transcriptomic analysis results indicated that genes encoding key enzymes in the paclitaxel biosynthesis pathway, such as taxane 10-β-hydroxylase (T10βH), 10-deacetylbaccatin III 10-O-acetyltransferase (DBAT), and debenzoyl paclitaxel N-benzoyl transferase (DBTNBT), exhibited higher expression levels in TG. Additionally, qRT-PCR showed that the relative expression level of T10βH and DBAT in TG were 29 and 13 times those in TD, respectively. In addition, six putative transcription factors were identified that may be involved in paclitaxel biosynthesis from transcriptome data. Comparative analysis of plastid genomes showed that the TD chloroplast contained a duplicate of rps12, leading to a longer plastid genome length in TD relative to TG. Fifteen mutation hotspot regions were identified between the two plastid genomes that can serve as candidate DNA barcodes for identifying high-paclitaxel-yield individuals. This experiment provides insight into the difference in paclitaxel accumulation among different provenances of T. yunnanensis individuals.

In Silico Comparison of WRKY Transcription Factors in Wild and Cultivated Soybean and Their Co-expression Network Arbitrating Disease Resistance.

WRKY Transcription factors (TFs) play critical roles in plant defence mechanisms that are activated in response to biotic and abiotic stresses. However, information on the Glycine soja WRKYs (GsoWRKYs) is scarce. Owing to its importance in soybean breeding, here we identified putative WRKY TFs in wild soybean, and compared the results with Glycine max WRKYs (GmaWRKYs) by phylogenetic, conserved motif, and duplication analyses. Moreover, we explored the expression trends of WRKYs in G. max (oomycete, fungi, virus, bacteria, and soybean cyst nematode) and G. soja (soybean cyst nematode), and identified commonly expressed WRKYs and their co-expressed genes. We identified, 181 and 180 putative WRKYs in G. max and G. soja, respectively. Though the number of WRKYs in both studied species is almost the same, they differ in many ways, i.e., the number of WRKYs on corresponding chromosomes, conserved domain structures, WRKYGQK motif variants, and zinc-finger motifs. WRKYs in both species grouped in three major clads, i.e., I-III, where group-II had sub-clads IIa-IIe. We found that GsoWRKYs expanded mostly through segmental duplication. A large number of WRKYs were expressed in response to biotic stresses, i.e., Phakospora pachyrhizi, Phytoplasma, Heterodera glycines, Macrophomina phaseolina, andSoybean mosaic virus; 56 GmaWRKYs were commonly expressed in soybean plants infected with these diseases. Finally, 30 and 63 GmaWRKYs and GsoWRKYs co-expressed with 205 and 123 non-WRKY genes, respectively, indicating that WRKYs play essential roles in biotic stress tolerance in Glycine species.

Molecular insights into a non-lethal yellow bud mutant in Ilex × ‘Nellie R. Stevens’

While the mechanisms behind the yellow phenotype have been widely investigated in model plant seedlings, research on leaf mutations in woody species has been restricted. The purpose of this research is to characterize a holly bud mutant of Ilex × ‘Nellie R. Stevens’ with a non-lethal yellow phenotype. Through cytological, physiological, metabolomic, and transcriptomic analyses, we identified remarkable differences between the mutant and its wild-type. The mutant exhibited abnormal chloroplasts, reduced chlorophyll levels, and elevated carotenoid/chlorophyll ratios. Metabolomic and transcriptomic analyses identified differentially expressed genes (DEGs) associated with chlorophyll and heme biosynthesis disruption, contributing to the chlorophyll-deficient phenotype. Moreover, genes associated with carotenoid metabolism were significantly down-regulated, linking to decreased carotenoid content and impacting photoprotection. Down-regulated DEGs in photosynthesis-related underscored the mutant's diminished photosynthetic activity. Additionally, the study identified 382 DEGs encoding putative transcription factors such as bHLHs, NACs, and GLKs. The study suggests an intricate interplay between chlorophyll, heme and carotenoid metabolism as major regulators of leaf mutation in I. × ‘Nellie R. Stevens.’ These insights contribute to the understanding of leaf color variation, enabling targeted strategies for developing desirable ornamental cultivars.

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

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