Abiotic stresses including cold, drought, salt, and iron deficiency severely impair plant development, crop productivity, and geographic distribution. Several bodies of research have shed light on the pleiotropic functions of BASIC HELIX-LOOP-HELIX (bHLH) proteins in plant responses to these abiotic stresses. In this review, we mention the regulatory roles of bHLH TFs in response to stresses such as cold, drought, salt resistance, and iron deficiency, as well as in enhancing grain yield in plants, especially crops. The bHLH proteins bind to E/G-box motifs in the target promoter and interact with various other factors to form a complex regulatory network. Through this network, they cooperatively activate or repress the transcription of downstream genes, thereby regulating various stress responses. Finally, we present some perspectives for future research focusing on the molecular mechanisms that integrate and coordinate these abiotic stresses. Understanding these molecular mechanisms is crucial for the development of stress-tolerant crops.

Endogenous retroviruses (ERVs) became a part of the eukaryotic genome through endogenization millions of years ago. Moreover, they have lost their innate capability of virulence or replication. Nevertheless, in eukaryotic cells, they actively engage in various activities that may be advantageous or disadvantageous to the cells. The mechanisms by which transcription is triggered and implicated in cellular processes are complex. Owing to the diversity in the expression of transcription factors (TFs) in cells and the TF-binding motifs of viruses, the comprehensibility of ERV initiation and its impact on cellular functions are unclear. Currently, several factors are known to be related to their initiation. TFs that bind to the viral long-terminal repeat (LTR) are critical initiators. This review discusses the TFs shown to actively associate with ERV stimulation across species such as humans, mice, pigs, monkeys, zebrafish, Drosophila, and yeast. A comprehensive summary of the expression of previously reported TFs may aid in identifying similarities between animal species and endogenous viruses. Moreover, an in-depth understanding of ERV expression will assist in elucidating their physiological roles in eukaryotic cell development and in clarifying their relationship with endogenous retrovirus-associated diseases.

WRKY as the name suggests, are the transcription factors (TFs) that contain the signature WRKY domains, hence named after it. Since their discovery in 1994, they have been well studied in plants with exploration of approximately 74 WRKY genes in the model plant, Arabidopsis alone. However, the study of these transcription factors (TFs) is not just limited to model plant now. They have been studied widely in crop plants as well, because of their tremendous contribution in stress as well as in growth and development. Here, in this review, we describe the story of WRKY TFs from their identification to their origin, the binding mechanisms, structure and their contribution in regulating plant development and stress physiology. High throughput transcriptomics-based data also opened a doorway to understand the comprehensive and detailed functioning of WRKY TFs in plants. Indeed, the detailed functional role of each and every WRKY member in regulating the gene expression is required to pave the path to develop holistic understanding of their role in stress physiology and developmental processes in plants.

UNASSIGNED: Sterol regulatory element-binding proteins (SREBPs) are a family of membrane-binding transcription factors that activate genes encoding enzymes required for cholesterol and unsaturated fatty acid synthesis. Overactivation of SREBP is related to the occurrence and development of diabetes, nonalcoholic fatty liver, tumor, and other diseases. In the past period, many SREBP inhibitors have been found.
UNASSIGNED: This manuscript is a patent review of SREBP inhibitors. We searched 2008 to date for all data from the US patent database (https://www.uspto.gov/) and the European patent database (https://www.epo.org/) with \'SREBP\' and \'inhibitor\' as keywords and analyzed the search results.
UNASSIGNED: Both synthetic and natural SREBP inhibitors have been reported. Despite the lack of cocrystal structure of SREBP inhibitor, the mechanisms of several compounds have been clarified. Importantly, some SREBP inhibitors have been proved to have good activity in preclinical studies. As the characteristics of lipid metabolism reprogramming in cardio-cerebrovascular diseases and tumors are gradually revealed, more and more attention will be focused on SREBP.

Reactive oxygen species (ROS) is a term encompassing a group of highly reactive oxygen-derived molecules. In physiological systems, ROS production exists in concert with antioxidant defenses, which safeguard cells against higher, toxic levels of ROS. Oxidative stress, coined as \"oxidative distress\", is \"a serious imbalance between the generation of ROS and antioxidant defenses in favor of ROS, causing excessive oxidative damage to biomolecules\". At physiological levels, ROS are essential for many cellular processes, which is known as \"oxidative eustress\". Oxidants like hydrogen peroxide (H2O2) activate signaling pathways like mitogen-activated protein kinases (MAPK)s and phosphoinositide 3-kinase (PI3K)/protein kinase B (Akt). ROS activate transcription factors like nuclear factor erythroid 2-related factor 2 (Nrf2), hypoxia-inducible factor 1α (HIF-1α), activator protein 1 (AP-1), and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB). Redox signaling through H2O2 mainly occurs through reversible oxidation of protein cysteine thiolate residues (RS-) to form sulfenic acids (RSOH). An unresolved question is that the reaction rate of H2O2 with protein thiols is very low. In cells, the reaction of H2O2 with protein thiols is likely to be outcompeted by faster reactions of H2O2 with peroxiredoxins and glutathione peroxidases. A novel mechanism being explored is that H2O2 could react with peroxiredoxins that act as reactive redox sensor proteins, leading to peroxiredoxin-mediated relays. Very few redox signaling pathways have been well characterized. Improved understanding of precise mechanisms by which ROS regulate signaling pathways and the role of cellular sensors, is essential for deciphering their roles in physiological and pathological conditions.

X-linked deafness (DFNX) is estimated to account for up to 2% of cases of hereditary hearing loss and occurs in both syndromic and non-syndromic forms. POU3F4 is the gene most commonly associated with X-linked deafness (DFNX2, DFN3) and accounts for about 50% of the cases of X-linked non-syndromic hearing loss. This gene codes for a transcription factor of the POU family that plays a major role in the development of the middle and inner ear. The clinical features of POU3F4-related hearing loss include a pathognomonic malformation of the inner ear defined as incomplete partition of the cochlea type 3 (IP-III). Often, a perilymphatic gusher is observed upon stapedectomy during surgery, possibly as a consequence of an incomplete separation of the cochlea from the internal auditory canal. Here we present an overview of the pathogenic gene variants of POU3F4 reported in the literature and discuss the associated clinical features, including hearing loss combined with additional phenotypes such as cognitive and motor developmental delays. Research on the transcriptional targets of POU3F4 in the ear and brain is in its early stages and is expected to greatly advance our understanding of the pathophysiology of POU3F4-linked hearing loss.

In eukaryotes, dynamic regulation enables DNA polymerases to catalyze a variety of RNA products in spatial and temporal patterns. Dynamic gene expression is regulated by transcription factors (TFs) and epigenetics (DNA methylation and histone modification). The applications of biochemical technology and high-throughput sequencing enhance the understanding of mechanisms of these regulations and affected genomic regions. To provide a searchable platform for retrieving such metadata, numerous databases have been developed based on the integration of genome-wide maps (e.g., ChIP-seq, whole-genome bisulfite sequencing, RNA-seq, ATAC-seq, DNase-seq, and MNase-seq data) and functionally genomic annotation. In this mini review, we summarize the main functions of TF-related databases and outline the prevalent approaches used in inferring epigenetic regulations, their associated genes, and functions. We review the literature on crosstalk between TF and epigenetic regulation and the properties of non-coding RNA regulation, which are challenging topics that promise to pave the way for advances in database development.

Seeds are a major source of nutrients for humans and animal livestock worldwide. With improved living standards, high nutritional quality has become one of the main targets for breeding. Storage protein content in seeds, which is highly variable depending on plant species, serves as a pivotal criterion of seed nutritional quality. In the last few decades, our understanding of the molecular genetics and regulatory mechanisms of storage protein synthesis has greatly advanced. Here, we systematically and comprehensively summarize breakthroughs on the conservation and divergence of storage protein synthesis in dicot and monocot plants. With regard to storage protein accumulation, we discuss evolutionary origins, developmental processes, characteristics of main storage protein fractions, regulatory networks, and genetic modifications. In addition, we discuss potential breeding strategies to improve storage protein accumulation and provide perspectives on some key unanswered problems that need to be addressed.

Forkhead box K2 (FOXK2) is a central transcriptional regulator of embryonic development and cell homeostasis. Since its discovery, evidence has shown that FOXK2 mediates a variety of biological processes involving in genomic stability, DNA repair, cancer stem cell maintenance, cell proliferation, apoptosis and cell metabolism. The inherent structural characteristics of FOXK2 enable it as a transcriptional factor (TF) to cooperate with other active molecules in cancer development. FOXK2 mediates several significant chromatin events that are necessary for some chromatin accessibility and protein-protein interaction. FOXK2 is involved in the pathogenesis of a number of types of cancer as an oncoprotein or tumor suppressor depending on its interactive partners. Therefore, the loss of FOXK2 and its functions directly or indirectly affect the fate of cells. FOXK2 expresses differentially in a number of types of cancer and is involved in a number of aspects of carcinogenesis. However, its roles in tumorigenesis remain largely unexplored. The present review focused on the latest findings and evidence on the broad roles and possible mediating mechanisms of FOXK2 in carcinogenesis. The recent findings about FOXK2 may shed light on the direction of future FOXK2 research in tumorigenesis.

Reactive oxygen species (ROS) are signaling molecules that regulate many biological processes in plants. However, excess ROS induced by biotic and abiotic stresses can destroy biological macromolecules and cause oxidative damage to plants. As the global environment continues to deteriorate, plants inevitably experience abiotic stress. Therefore, in-depth exploration of ROS metabolism and an improved understanding of its regulatory mechanisms are of great importance for regulating cultivated plant growth and developing cultivars that are resilient to abiotic stresses. This review presents current research on the generation and scavenging of ROS in plants and summarizes recent progress in elucidating transcription factor-mediated regulation of ROS metabolism. Most importantly, the effects of applying exogenous substances on ROS metabolism and the potential regulatory mechanisms at play under abiotic stress are summarized. Given the important role of ROS in plants and other organisms, our findings provide insights for optimizing cultivation patterns and for improving plant stress tolerance and growth regulation.