GATA factor transcriptional activity: Insights from genome-wide binding profiles

GATA transcription factor in common bean: A comprehensive genome-wide functional characterization, identification, and abiotic stress response evaluation

The GATA transcription factors (TFs) have been extensively studied for its regulatory role in various biological processes in many plant species. The functional and molecular mechanism of GATA TFs in regulating tolerance to abiotic stress has not yet been studied in the common bean. This study analyzed the functional identity of the GATA gene family in the P. vulgaris genome under different abiotic and phytohormonal stress. The GATA gene family was systematically investigated in the P. vulgaris genome, and 31 PvGATA TFs were identified. The study found that 18 out of 31 PvGATA genes had undergone duplication events, emphasizing the role of gene duplication in GATA gene expansion. All the PvGATA genes were classified into four significant subfamilies, with 8, 3, 6, and 13 members in each subfamily (subfamilies I, II, III, and IV), respectively. All PvGATA protein sequences contained a single GATA domain, but subfamily II members had additional domains such as CCT and tify. A total of 799 promoter cis-regulatory elements (CREs) were predicted in the PvGATAs. Additionally, we used qRT-PCR to investigate the expression profiles of five PvGATA genes in the common bean roots under abiotic conditions. The results suggest that PvGATA01/10/25/28 may play crucial roles in regulating plant resistance against salt and drought stress and may be involved in phytohormone-mediated stress signaling pathways. PvGATA28 was selected for overexpression and cloned into N. benthamiana using Agrobacterium-mediated transformation. Transgenic lines were subjected to abiotic stress, and results showed a significant tolerance of transgenic lines to stress conditions compared to wild-type counterparts. The seed germination assay suggested an extended dormancy of transgenic lines compared to wild-type lines. This study provides a comprehensive analysis of the PvGATA gene family, which can serve as a foundation for future research on the function of GATA TFs in abiotic stress tolerance in common bean plants.

GATA6 inhibits the biological function of non-small cell lung cancer by modulating glucose metabolism

PURPOSE

This study aims to explore the role of GATA6 in lung cancer, with a focus on its impact on metabolic processes.

METHODS

We assessed GATA6 expression in lung cancer tissues and its association with patient prognosis. In vitro cell function experiments were conducted to investigate the effects of altered GATA6 levels on lung cancer cell proliferation and migration. Mechanistic insights were gained by examining GATA6's influence on glucose metabolism-related genes, particularly its effect on c-Myc mRNA expression.

RESULTS

Our study revealed significant down-regulation of GATA6 in lung cancer tissues, and this down-regulation was strongly correlated with unfavorable patient prognosis. Elevating GATA6 levels effectively inhibited the proliferation and migration of lung cancer cells in our cell function experiments. Mechanistically, we found that GATA6 suppressed the expression of c-Myc mRNA, impacting genes related to glucose metabolism. As a result, glucose uptake and metabolism in lung cancer cells were disrupted, ultimately impeding their malignant behaviors.

CONCLUSION

Our study provides crucial insights into the metabolic regulation of GATA6 in lung cancer cells. These findings have the potential to offer a solid theoretical foundation for the development of novel clinical treatments for lung cancer.

Growth hormone directly stimulates GATA2 expression

OBJECTIVE

GATA2 is a key transcription factor involved in the differentiation and determination of thyrotrophs and gonadotrophs in pituitary and hematopoietic development. However, studies on the upstream ligands of the GATA2 signal transduction pathway have been limited. To identify upstream ligands, we examined growth hormone (GH) as a plausible stimulator.

DESIGN

We evaluated GH-induced GATA2 expression in murine TtT/GF thyrotrophic pituitary tumor cells and its direct impact on the GHR/JAK/STAT5 pathway using a combination of a reporter assay, real-time quantitative polymerase chain reaction, and western blotting.

RESULTS

GATA2 expression increased with activated STAT5B in a dose-dependent manner and was inhibited by a STAT5 specific inhibitor. Moreover, we found functional STAT5B binding site consensus sequences at -359 bp in the GATA2 promoter region.

CONCLUSION

These findings suggest that GH directly stimulates GATA2 via the GHR/JAK/STAT pathway and participates in various developmental phenomena mediated by GATA2.

GATA binding protein 6 regulates apoptosis in silkworms through interaction with poly (ADP-ribose) polymerase

The GATA family of genes plays various roles in crucial biological processes, such as development, cell differentiation, and disease progression. However, the roles of GATA in insects have not been thoroughly explored. In this study, a genome-wide characterization of the GATA gene family in the silkworm, Bombyx mori, was conducted, revealing lineage-specific expression profiles. Notably, GATA6 is ubiquitously expressed across various developmental stages and tissues, with predominant expression in the midgut, ovaries, and Malpighian tubules. Overexpression of GATA6 inhibits cell growth and promotes apoptosis, whereas, in contrast, knockdown of PARP mitigates the apoptotic effects driven by GATA6 overexpression. Co-immunoprecipitation (co-IP) has demonstrated that GATA6 can interact with Poly (ADP-ribose) polymerase (PARP), suggesting that GATA6 may induce cell apoptosis by activating the enzyme's activity. These findings reveal a dynamic and regulatory relationship between GATA6 and PARP, suggesting a potential role for GATA6 as a key regulator in apoptosis through its interaction with PARP. This research deepens the understanding of the diverse roles of the GATA family in insects, shedding light on new avenues for studies in sericulture and pest management.

Evolutionary Change in Gut Specification in Caenorhabditis Centers on the GATA Factor ELT-3 in an Example of Developmental System Drift

Cells in a developing animal embryo become specified by the activation of cell-type-specific gene regulatory networks. The network that specifies the gut in the nematode Caenorhabditis elegans has been the subject of study for more than two decades. In this network, the maternal factors SKN-1/Nrf and POP-1/TCF activate a zygotic GATA factor cascade consisting of the regulators MED-1,2 → END-1,3 → ELT-2,7, leading to the specification of the gut in early embryos. Paradoxically, the MED, END, and ELT-7 regulators are present only in species closely related to C. elegans, raising the question of how the gut can be specified without them. Recent work found that ELT-3, a GATA factor without an endodermal role in C. elegans, acts in a simpler ELT-3 → ELT-2 network to specify gut in more distant species. The simpler ELT-3 → ELT-2 network may thus represent an ancestral pathway. In this review, we describe the elucidation of the gut specification network in C. elegans and related species and propose a model by which the more complex network might have formed. Because the evolution of this network occurred without a change in phenotype, it is an example of the phenomenon of Developmental System Drift.

Systematic Characterization of GATA Transcription Factors in Liriodendron chinense and Functional Validation in Abiotic Stresses

The Liriodendron chinense in the Magnoliaceae family is an endangered tree species useful for its socio-economic and ecological benefits. Abiotic stresses (cold, heat, and drought stress), among other factors, affect its growth, development, and distribution. However, GATA transcription factors (TFs) respond to various abiotic stresses and play a significant role in plant acclimatization to abiotic stresses. To determine the function of GATA TFs in L. chinense, we investigated the GATA genes in the genome of L. chinense. In this study, a total of 18 GATA genes were identified, which were randomly distributed on 12 of the total 17 chromosomes. These GATA genes clustered together in four separate groups based on their phylogenetic relationships, gene structures, and domain conservation arrangements. Detailed interspecies phylogenetic analyses of the GATA gene family demonstrated a conservation of the GATAs and a probable diversification that prompted gene diversification in plant species. In addition, the LcGATA gene family was shown to be evolutionarily closer to that of O. sativa, giving an insight into the possible LcGATA gene functions. Investigations of LcGATA gene duplication showed four gene duplicate pairs by the segmental duplication event, and these genes were a result of strong purified selection. Analysis of the cis-regulatory elements demonstrated a significant representation of the abiotic stress elements in the promoter regions of the LcGATA genes. Additional gene expressions through transcriptome and qPCR analyses revealed a significant upregulation of LcGATA17, and LcGATA18 in various stresses, including heat, cold, and drought stress in all time points analyzed. We concluded that the LcGATA genes play a pivotal role in regulating abiotic stress in L. chinense. In summary, our results provide new insights into understanding of the LcGATA gene family and their regulatory functions during abiotic stresses.

Hepatic GATA4 regulates cholesterol and triglyceride homeostasis in collaboration with LXRs

GATA4 is a transcription factor known for its crucial role in the development of many tissues, including the liver; however, its role in adult liver metabolism is unknown. Here, using high-throughput sequencing technologies, we identified GATA4 as a transcriptional regulator of metabolism in the liver. GATA4 expression is elevated in response to refeeding, and its occupancy is increased at enhancers of genes linked to fatty acid and lipoprotein metabolism. Knocking out GATA4 in the adult liver (Gata4LKO) decreased transcriptional activity at GATA4 binding sites, especially during feeding. Gata4LKO mice have reduced plasma HDL cholesterol and increased liver triglyceride levels. The expression of a panel of GATA4 binding genes involved in hepatic cholesterol export and triglyceride hydrolysis was down-regulated in Gata4LKO mice. We further demonstrate that GATA4 collaborates with LXR nuclear receptors in the liver. GATA4 and LXRs share a number of binding sites, and GATA4 was required for the full transcriptional response to LXR activation. Collectively, these results show that hepatic GATA4 contributes to the transcriptional control of hepatic and systemic lipid homeostasis.

The GATA factor ELT-3 specifies endoderm in Caenorhabditis angaria in an ancestral gene network

Endoderm specification in Caenorhabditis elegans occurs through a network in which maternally provided SKN-1/Nrf, with additional input from POP-1/TCF, activates the GATA factor cascade MED-1,2→END-1,3→ELT-2,7. Orthologues of the MED, END and ELT-7 factors are found only among nematodes closely related to C. elegans, raising the question of how gut is specified in their absence in more distant species in the genus. We find that the C. angaria, C. portoensis and C. monodelphis orthologues of the GATA factor gene elt-3 are expressed in the early E lineage, just before their elt-2 orthologues. In C. angaria, Can-pop-1(RNAi), Can-elt-3(RNAi) and a Can-elt-3 null mutation result in a penetrant ‘gutless’ phenotype. Can-pop-1 is necessary for Can-elt-3 activation, showing that it acts upstream. Forced early E lineage expression of Can-elt-3 in C. elegans can direct the expression of a Can-elt-2 transgene and rescue an elt-7 end-1 end-3; elt-2 quadruple mutant strain to viability. Our results demonstrate an ancestral mechanism for gut specification and differentiation in Caenorhabditis involving a simpler POP-1→ELT-3→ELT-2 gene network.

Preliminary Interpretations of Epigenetic Profiling of Cord Blood in Preeclampsia

Preeclampsia (PE) is characterized by new-onset hypertension after 20 weeks of pregnancy and results in high maternal and fetal mortality worldwide. It has been reported that PE is associated with abnormalities in the umbilical cord and cord blood. However, previous studies were focused primarily on the transcriptomics level, while the underlying gene regulatory landscapes are still unclear. Thus, we performed the Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) using the umbilical cord blood samples collected from a patient with superimposed PE and three healthy donors to uncover the chromatin accessibility changes attributed to PE. We have identified genes associated with immunomodulation and hypoxia response that have higher chromatin accessibility close to their transcription start sites. Motif analysis indicated that the GATA family transcription factor binding was enriched in PE and may play an essential regulatory role in the disease progression. Overall, our findings provide an overview of gene regulatory programs and the corresponding downstream pathways associated with PE that may influence the placenta function and fetal growth.

Genome-Wide Identification and Functional Characterization of GATA Transcription Factor Gene Family in Alternaria alternata

In the present study, we identified six GATA transcription factors (AaAreA, AaAreB, AaLreA, AaLreB, AaNsdD, and AaSreA) and characterized their functions in response to environmental stress and virulence in the tangerine pathotype of Alternaria alternata. The targeted gene knockout of each of the GATA-coding genes decreased the growth to varying degrees. The mutation of AaAreA, AaAreB, AaLreB, or AaNsdD decreased the conidiation. All the GATA transcription factors were found to be required for tolerance to cumyl hydroperoxide and tert-butyl-hydroperoxide (oxidants) and Congo red (a cell-wall-destructing agent). Pathogenicity assays assessed on detached citrus leaves revealed that mutations of AaAreA, AaLreA, AaLreB, or AaNsdD significantly decreased the fungal virulence. A comparative transcriptome analysis between the ∆AreA mutant and the wild-type strain revealed that the inactivation of AaAreA led to alterations in the expression of genes involved in a number of biological processes, including oxidoreductase activity, amino acid metabolism, and secondary metabolite biogenesis. Taken together, our findings revealed that GATA-coding genes play diverse roles in response to environmental stress and are important regulators involved in fungal development, conidiation, ROS detoxification, as well as pathogenesis. This study, for the first time, systemically underlines the critical role of GATA transcription factors in response to environmental stress and virulence in A. alternata.

A universal framework for detecting cis-regulatory diversity in DNA regulatory regions

High-throughput sequencing-based assays measure different biochemical activities pertaining to gene regulation, genome-wide. These activities include transcription factor (TF)–DNA binding, enhancer activity, open chromatin, and more. A major goal is to understand underlying sequence components, or motifs, that can explain the measured activity. It is usually not one motif but a combination of motifs bound by cooperatively acting proteins that confers activity to such regions. Furthermore, regions can be diverse, governed by different combinations of TFs/motifs. Current approaches do not take into account this issue of combinatorial diversity. We present a new statistical framework, cisDIVERSITY, which models regions as diverse modules characterized by combinations of motifs while simultaneously learning the motifs themselves. Because cisDIVERSITY does not rely on knowledge of motifs, modules, cell type, or organism, it is general enough to be applied to regions reported by most high-throughput assays. For example, in enhancer predictions resulting from different assays—GRO-cap, STARR-seq, and those measuring chromatin structure—cisDIVERSITY discovers distinct modules and combinations of TF binding sites, some specific to the assay. From protein–DNA binding data, cisDIVERSITY identifies potential cofactors of the profiled TF, whereas from ATAC-seq data, it identifies tissue-specific regulatory modules. Finally, analysis of single-cell ATAC-seq data suggests that regions open in one cell-state encode information about future states, with certain modules staying open and others closing down in the next time point.

High-throughput single-cell chromatin accessibility CRISPR screens enable unbiased identification of regulatory networks in cancer

Chromatin accessibility profiling can identify putative regulatory regions genome wide; however, pooled single-cell methods for assessing the effects of regulatory perturbations on accessibility are limited. Here, we report a modified droplet-based single-cell ATAC-seq protocol for perturbing and evaluating dynamic single-cell epigenetic states. This method (Spear-ATAC) enables simultaneous read-out of chromatin accessibility profiles and integrated sgRNA spacer sequences from thousands of individual cells at once. Spear-ATAC profiling of 104,592 cells representing 414 sgRNA knock-down populations reveals the temporal dynamics of epigenetic responses to regulatory perturbations in cancer cells and the associations between transcription factor binding profiles.

p63-related signaling at a glance

p63 (also known as TP63) is a transcription factor of the p53 family, along with p73. Multiple isoforms of p63 have been discovered and these have diverse functions encompassing a wide array of cell biology. p63 isoforms are implicated in lineage specification, proliferative potential, differentiation, cell death and survival, DNA damage response and metabolism. Furthermore, p63 is linked to human disease states including cancer. p63 is critical to many aspects of cell signaling, and in this Cell science at a glance article and the accompanying poster, we focus on the signaling cascades regulating TAp63 and ΔNp63 isoforms and those that are regulated by TAp63 and ΔNp63, as well the role of p63 in disease.