Showing papers on "Transcription factor published in 2022"

Cell cycle regulation: p53-p21-RB signaling

Abstract: The retinoblastoma protein RB and the transcription factor p53 are central tumor suppressors. They are often found inactivated in various tumor types. Both proteins play central roles in regulating the cell division cycle. RB forms complexes with the E2F family of transcription factors and downregulates numerous genes. Among the RB-E2F target genes, a large number code for key cell cycle regulators. Their transcriptional repression by the RB-E2F complex is released through phosphorylation of RB, leading to expression of the cell cycle regulators. The release from repression can be prevented by the cyclin-dependent kinase inhibitor p21/CDKN1A. The CDKN1A gene is transcriptionally activated by p53. Taken together, these elements constitute the p53-p21-RB signaling pathway. Following activation of p53, for example by viral infection or induction of DNA damage, p21 expression is upregulated. High levels of p21 then result in RB-E2F complex formation and downregulation of a large number of cell cycle genes. Thus, p53-dependent transcriptional repression is indirect. The reduced expression of the many regulators leads to cell cycle arrest. Examination of the p53-p21-RB targets and genes controlled by the related p53-p21-DREAM signaling pathway reveals that there is a large overlap of the two groups. Mechanistically this can be explained by replacing RB-E2F complexes with the DREAM transcriptional repressor complex at E2F sites in target promoters. In contrast to RB-E2F, DREAM can downregulate genes also through CHR transcription factor binding sites. This results in a distinct gene set controlled by p53-p21-DREAM signaling independent of RB-E2F. Furthermore, RB has non-canonical functions without binding to E2F and DNA. Such a role of RB supporting DREAM formation may be exerted by the RB-SKP2-p27-cyclin A/E-CDK2-p130-DREAM link. In the current synopsis, the mechanism of regulation by p53-p21-RB signaling is assessed and the overlap with p53-p21-DREAM signaling is examined.

Human gut bacteria produce ΤΗ17-modulating bile acid metabolites

Abstract: The microbiota modulates gut immune homeostasis. Bacteria influence the development and function of host immune cells, including T helper cells expressing interleukin-17A (TH17 cells). We previously reported that the bile acid metabolite 3-oxolithocholic acid (3-oxoLCA) inhibits TH17 cell differentiation1. Although it was suggested that gut-residing bacteria produce 3-oxoLCA, the identity of such bacteria was unknown, and it was unclear whether 3-oxoLCA and other immunomodulatory bile acids are associated with inflammatory pathologies in humans. Here we identify human gut bacteria and corresponding enzymes that convert the secondary bile acid lithocholic acid into 3-oxoLCA as well as the abundant gut metabolite isolithocholic acid (isoLCA). Similar to 3-oxoLCA, isoLCA suppressed TH17 cell differentiation by inhibiting retinoic acid receptor-related orphan nuclear receptor-γt, a key TH17-cell-promoting transcription factor. The levels of both 3-oxoLCA and isoLCA and the 3α-hydroxysteroid dehydrogenase genes that are required for their biosynthesis were significantly reduced in patients with inflammatory bowel disease. Moreover, the levels of these bile acids were inversely correlated with the expression of TH17-cell-associated genes. Overall, our data suggest that bacterially produced bile acids inhibit TH17 cell function, an activity that may be relevant to the pathophysiology of inflammatory disorders such as inflammatory bowel disease. Bacterially produced bile acids inhibit TH17 cell function, which may be relevant to the pathophysiology of inflammatory disorders such as inflammatory bowel disease.

Nonlinear control of transcription through enhancer–promoter interactions

Abstract: Abstract Chromosome structure in mammals is thought to regulate transcription by modulating three-dimensional interactions between enhancers and promoters, notably through CTCF-mediated loops and topologically associating domains (TADs) 1–4 . However, how chromosome interactions are actually translated into transcriptional outputs remains unclear. Here, to address this question, we use an assay to position an enhancer at large numbers of densely spaced chromosomal locations relative to a fixed promoter, and measure promoter output and interactions within a genomic region with minimal regulatory and structural complexity. A quantitative analysis of hundreds of cell lines reveals that the transcriptional effect of an enhancer depends on its contact probabilities with the promoter through a nonlinear relationship. Mathematical modelling suggests that nonlinearity might arise from transient enhancer–promoter interactions being translated into slower promoter bursting dynamics in individual cells, therefore uncoupling the temporal dynamics of interactions from those of transcription. This uncovers a potential mechanism of how distal enhancers act from large genomic distances, and of how topologically associating domain boundaries block distal enhancers. Finally, we show that enhancer strength also determines absolute transcription levels as well as the sensitivity of a promoter to CTCF-mediated transcriptional insulation. Our measurements establish general principles for the context-dependent role of chromosome structure in long-range transcriptional regulation.

Nrf2/Keap1/ARE signaling: Towards specific regulation

Abstract: The Nrf2 transcription factor governs the expression of hundreds genes involved in cell defense against oxidative stress, the hallmark of numerous diseases such as neurodegenerative, cardiovascular, some viral pathologies, diabetes and others. The main route for Nrf2 activity regulation is via interactions with the Keap1 protein. Under the normoxia the Keap1 binds the Nrf2 and targets it to the proteasomal degradation, while the Keap1 is regenerated. Upon oxidative stress the interactions between Nrf2 and Keap1 are interrupted and the Nrf2 activates the transcription of the protective genes. Currently, the Nrf2 system activation is considered as a powerful cytoprotective strategy for treatment of different pathologies, which pathogenesis relies on oxidative stress including viral diseases of pivotal importance such as COVID-19. The implementation of this strategy is accomplished mainly through the inactivation of the Keap1 "guardian" function. Two approaches are now developing: the Keap1 modification via electrophilic agents, which leads to the Nrf2 release, and direct interruption of the Nrf2:Keap1 protein-protein interactions (PPI). Because of theirs chemical structure, the Nrf2 electrophilic inducers could non-specifically interact with others cellular proteins leading to undesired effects. Whereas the non-electrophilic inhibitors of the Nrf2:Keap1 PPI could be more specific, thereby widening the therapeutic window.

Genome organization controls transcriptional dynamics during development

Abstract: Past studies offer contradictory claims for the role of genome organization in the regulation of gene activity. Here, we show through high-resolution chromosome conformation analysis that the Drosophila genome is organized by two independent classes of regulatory sequences, tethering elements and insulators. Quantitative live imaging and targeted genome editing demonstrate that this two-tiered organization is critical for the precise temporal dynamics of Hox gene transcription during development. Tethering elements mediate long-range enhancer-promoter interactions and foster fast activation kinetics. Conversely, the boundaries of topologically associating domains (TADs) prevent spurious interactions with enhancers and silencers located in neighboring TADs. These two levels of genome organization operate independently of one another to ensure precision of transcriptional dynamics and the reliability of complex patterning processes. Description Organization shapes expression The role of genome organization in the regulation of gene activity during development has been the subject of considerable controversy. Batut et al. present evidence that dedicated “tethering elements” help to establish long-range enhancer-promoter interactions in the Drosophila genome (see the Perspective by Gaskill and Harrison). Single-cell imaging of transcription in living embryos shows the importance of these elements in determining the timing of Hox gene activation during development. Tethers operate independently of boundary elements, which mediate the opposite function of blocking spurious regulatory interactions between neighboring loci. This work sheds light on how genome organization controls the dynamics of gene expression underlying complex developmental processes. —BAP Tethering elements foster long-range regulatory interactions to promote rapid activation of Hox genes in developing Drosophila embryos.

ICE-CBF-COR Signaling Cascade and Its Regulation in Plants Responding to Cold Stress

Abstract: Cold stress limits plant geographical distribution and influences plant growth, development, and yields. Plants as sessile organisms have evolved complex biochemical and physiological mechanisms to adapt to cold stress. These mechanisms are regulated by a series of transcription factors and proteins for efficient cold stress acclimation. It has been established that the ICE-CBF-COR signaling pathway in plants regulates how plants acclimatize to cold stress. Cold stress is perceived by receptor proteins, triggering signal transduction, and Inducer of CBF Expression (ICE) genes are activated and regulated, consequently upregulating the transcription and expression of the C-repeat Binding Factor (CBF) genes. The CBF protein binds to the C-repeat/Dehydration Responsive Element (CRT/DRE), a homeopathic element of the Cold Regulated genes (COR gene) promoter, activating their transcription. Transcriptional regulations and post-translational modifications regulate and modify these entities at different response levels by altering their expression or activities in the signaling cascade. These activities then lead to efficient cold stress tolerance. This paper contains a concise summary of the ICE-CBF-COR pathway elucidating on the cross interconnections with other repressors, inhibitors, and activators to induce cold stress acclimation in plants.

A transcriptional regulator that boosts grain yields and shortens the growth duration of rice

Abstract: Complex biological processes such as plant growth and development are often under the control of transcription factors that regulate the expression of large sets of genes and activate subordinate transcription factors in a cascade-like fashion. Here, by screening candidate photosynthesis-related transcription factors in rice, we identified a DREB (Dehydration Responsive Element Binding) family member, OsDREB1C, in which expression is induced by both light and low nitrogen status. We show that OsDREB1C drives functionally diverse transcriptional programs determining photosynthetic capacity, nitrogen utilization, and flowering time. Field trials with OsDREB1C-overexpressing rice revealed yield increases of 41.3 to 68.3% and, in addition, shortened growth duration, improved nitrogen use efficiency, and promoted efficient resource allocation, thus providing a strategy toward achieving much-needed increases in agricultural productivity. Description Genetic improvement drives rice yield Improvements in agricultural productivity could lessen the impact of agriculture on the environment and perhaps supply more food from less land. Working in rice, Wei et al. identified a transcription factor that, when overexpressed, has a variety of useful effects (see the Perspective by Kelly). The gene’s expression is induced by both light and low-nitrogen status, and it regulates photosynthetic capacity, nitrogen utilization, and flowering time. In field trials, plants overexpressing this gene delivered greater yield, shortened growth duration, and improved nitrogen use efficiency. —PJH Overexpression of a single transcription factor improves the agricultural productivity of rice. INTRODUCTION Rapid population growth, rising meat consumption, and the expanding use of crops for nonfood and nonfeed purposes increase the pressure on global food production. At the same time, the excessive use of nitrogen fertilizer to enhance agricultural production poses serious threats to both human health and the environment. To achieve the required yield increases and make agriculture more sustainable, intensified breeding and genetic engineering efforts are needed to obtain new crop varieties with higher photosynthetic capacity and improved nitrogen use efficiency (NUE). However, progress has been slow, largely due to the limited knowledge about regulator genes that potentially can coordinately optimize carbon assimilation and nitrogen utilization. RATIONALE Transcription factors control diverse biological processes by binding to the promoters (or intragenic regions) of target genes, and a number of transcription factors have been identified that control carbon fixation and nitrogen assimilation. A previous comparative analysis of maize and rice leaf transcriptomes and metabolomes revealed a set of 118 candidate transcription factors that may act as regulators of C4 photosynthesis. We screened these transcription factors for their responsiveness to light and nitrogen supply in rice, and found that the gene Dehydration-Responsive Element-Binding Protein 1C (OsDREB1C), a member of the APETALA2/ethylene-responsive element binding factor (AP2/ERF) family, exhibits properties expected of a regulator that can simultaneously modulate photosynthesis and nitrogen utilization. RESULTS OsDREB1C expression is induced in rice by both light and low-nitrogen status. We generated overexpression lines (OsDREB1C-OE) and knockout mutants (OsDREB1C-KO) in rice, and conducted field trials in northern, southeastern, and southern China from 2018 to 2021. OsDREB1C-OE plants exhibited 41.3 to 68.3% higher yield than wild-type (WT) plants due to increased grain number per panicle, elevated grain weight, and enhanced harvest index. We observed that light-induced growth promotion of OsDREB1C-OE plants was accompanied by enhanced photosynthetic capacity and concomitant increases in photosynthetic assimilates. In addition, 15N feeding experiments and field studies with different nitrogen fertilization regimes revealed that NUE was improved in OsDREB1C-OE plants due to elevated nitrogen uptake and transport activity. Moreover, OsDREB1C overexpression led to more efficient carbon and nitrogen allocation from source to sink, thus boosting grain yield, particularly under low-nitrogen conditions. Additionally, the OsDREB1C-OE plants flowered 13 to 19 days earlier and accumulated higher biomass at the heading stage than WT plants under long-day conditions. OsDREB1C is localized in the nucleus and the cytosol and functions as a transcriptional activator that directly binds to cis elements in the DNA, including dehydration-responsive element (DRE)/C repeat (CRT), GCC, and G boxes. Chromatin immunoprecipitation sequencing (ChIP-seq) and transcriptomic analyses identified a total of 9735 putative OsDREB1C-binding sites at the genome-wide level. We discovered that five genes targeted by OsDREB1C [ribulose-l,5-bisphosphate carboxylase/oxygenase small subunit 3 (OsRBCS3), nitrate reductase 2 (OsNR2), nitrate transporter 2.4 (OsNRT2.4), nitrate transporter 1.1B (OsNRT1.1B), and flowering locus T-like 1 (OsFTL1)] are closely associated with photosynthesis, nitrogen utilization, and flowering, the key traits altered by OsDREB1C overexpression. ChIP-quantitative polymerase chain reaction (ChIP-qPCR) and DNA affinity purification sequencing (DAP-seq) assays confirmed that OsDREB1C activates the transcription of these genes by binding to the promoter of OsRBCS3 and to exons of OsNR2, OsNRT2.4, OsNRT1.1B, and OsFTL1. By showing that biomass and yield increases can also be achieved by OsDREB1C overexpression in wheat and Arabidopsis, we have demonstrated that the mode of action and the biological function of the transcription factor are evolutionarily conserved. CONCLUSION Overexpression of OsDREB1C not only boosts grain yields but also confers higher NUE and early flowering. Our work demonstrates that by genetically modulating the expression of a single transcriptional regulator gene, substantial yield increases can be achieved while the growth duration of the crop is shortened. The existing natural allelic variation in OsDREB1C, the highly conserved function of the transcription factor in seed plants, and the ease with which its expression can be altered by genetic engineering suggest that this gene could be the target of future crop improvement strategies toward more efficient and more sustainable food production. OsDREB1C coordinates yield and growth duration. OsDREB1C was identified by its responsiveness to light and low nitrogen in a screen of 118 transcription factors related to C4 photosynthesis. Transcriptional activation of multiple downstream target genes by OsDREB1C confers enhanced photosynthesis, improved nitrogen utilization, and early flowering. Together, the activated genes cause substantial yield increases in rice and wheat.

Decoding gene regulation in the fly brain

Abstract: The Drosophila brain is a frequently used model in neuroscience. Single-cell transcriptome analysis1–6, three-dimensional morphological classification7 and electron microscopy mapping of the connectome8,9 have revealed an immense diversity of neuronal and glial cell types that underlie an array of functional and behavioural traits in the fly. The identities of these cell types are controlled by gene regulatory networks (GRNs), involving combinations of transcription factors that bind to genomic enhancers to regulate their target genes. Here, to characterize GRNs at the cell-type level in the fly brain, we profiled the chromatin accessibility of 240,919 single cells spanning 9 developmental timepoints and integrated these data with single-cell transcriptomes. We identify more than 95,000 regulatory regions that are used in different neuronal cell types, of which 70,000 are linked to developmental trajectories involving neurogenesis, reprogramming and maturation. For 40 cell types, uniquely accessible regions were associated with their expressed transcription factors and downstream target genes through a combination of motif discovery, network inference and deep learning, creating enhancer GRNs. The enhancer architectures revealed by DeepFlyBrain lead to a better understanding of neuronal regulatory diversity and can be used to design genetic driver lines for cell types at specific timepoints, facilitating their characterization and manipulation. A chromatin accessibility atlas of 240,919 cells in the adult and developing Drosophila brain reveals 95,000 enhancers, which are integrated in cell-type specific enhancer gene regulatory networks and decoded into combinations of functional transcription factor binding sites using deep learning.

Compatibility rules of human enhancer and promoter sequences

Abstract: Gene regulation in the human genome is controlled by distal enhancers that activate specific nearby promoters1. A proposed model for this specificity is that promoters have sequence-encoded preferences for certain enhancers, for example, mediated by interacting sets of transcription factors or cofactors2. This ‘biochemical compatibility’ model has been supported by observations at individual human promoters and by genome-wide measurements in Drosophila3–9. However, the degree to which human enhancers and promoters are intrinsically compatible has not yet been systematically measured, and how their activities combine to control RNA expression remains unclear. Here we design a high-throughput reporter assay called enhancer × promoter self-transcribing active regulatory region sequencing (ExP STARR-seq) and applied it to examine the combinatorial compatibilities of 1,000 enhancer and 1,000 promoter sequences in human K562 cells. We identify simple rules for enhancer–promoter compatibility, whereby most enhancers activate all promoters by similar amounts, and intrinsic enhancer and promoter activities multiplicatively combine to determine RNA output (R2 = 0.82). In addition, two classes of enhancers and promoters show subtle preferential effects. Promoters of housekeeping genes contain built-in activating motifs for factors such as GABPA and YY1, which decrease the responsiveness of promoters to distal enhancers. Promoters of variably expressed genes lack these motifs and show stronger responsiveness to enhancers. Together, this systematic assessment of enhancer–promoter compatibility suggests a multiplicative model tuned by enhancer and promoter class to control gene transcription in the human genome. A new high-throughput assay applied to 1,000 enhancers and 1,000 promoters in human cells reveals how different classes of enhancers and promoters control RNA expression.

Sequence determinants of human gene regulatory elements

Abstract: DNA can determine where and when genes are expressed, but the full set of sequence determinants that control gene expression is unknown. Here, we measured the transcriptional activity of DNA sequences that represent an ~100 times larger sequence space than the human genome using massively parallel reporter assays (MPRAs). Machine learning models revealed that transcription factors (TFs) generally act in an additive manner with weak grammar and that most enhancers increase expression from a promoter by a mechanism that does not appear to involve specific TF-TF interactions. The enhancers themselves can be classified into three types: classical, closed chromatin and chromatin dependent. We also show that few TFs are strongly active in a cell, with most activities being similar between cell types. Individual TFs can have multiple gene regulatory activities, including chromatin opening and enhancing, promoting and determining transcription start site (TSS) activity, consistent with the view that the TF binding motif is the key atomic unit of gene expression.

Increasing the resilience of plant immunity to a warming climate

Abstract: Abstract Extreme weather conditions associated with climate change affect many aspects of plant and animal life, including the response to infectious diseases. Production of salicylic acid (SA), a central plant defence hormone 1–3 , is particularly vulnerable to suppression by short periods of hot weather above the normal plant growth temperature range via an unknown mechanism 4–7 . Here we show that suppression of SA production in Arabidopsis thaliana at 28 °C is independent of PHYTOCHROME B 8,9 (phyB) and EARLY FLOWERING 3 10 (ELF3), which regulate thermo-responsive plant growth and development. Instead, we found that formation of GUANYLATE BINDING PROTEIN-LIKE 3 (GBPL3) defence-activated biomolecular condensates 11 (GDACs) was reduced at the higher growth temperature. The altered GDAC formation in vivo is linked to impaired recruitment of GBPL3 and SA-associated Mediator subunits to the promoters of CBP60g and SARD1 , which encode master immune transcription factors. Unlike many other SA signalling components, including the SA receptor and biosynthetic genes, optimized CBP60g expression was sufficient to broadly restore SA production, basal immunity and effector-triggered immunity at the elevated growth temperature without significant growth trade-offs. CBP60g family transcription factors are widely conserved in plants 12 . These results have implications for safeguarding the plant immune system as well as understanding the concept of the plant–pathogen–environment disease triangle and the emergence of new disease epidemics in a warming climate.

Brassinosteroids (BRs) Role in Plant Development and Coping with Different Stresses

Abstract: Plants are vulnerable to a number of abiotic and biotic stresses that cause a substantial decrease in the production of plants. Plants respond to different environmental stresses by experiencing a series of molecular and physiological changes coordinated by various phytohormones. The use of phytohormones to alleviate stresses has recently achieved increasing interest. Brassinosteroids (BRs) are a group of polyhydroxylated steroidal phytohormones that are required for the development, growth, and productivity of plants. These hormones are involved in regulating the division, elongation, and differentiation of numerous cell types throughout the entire plant life cycle. BR studies have drawn the interest of plant scientists over the last few decades due to their flexible ability to mitigate different environmental stresses. BRs have been shown in numerous studies to have a positive impact on plant responses to various biotic and abiotic stresses. BR receptors detect the BR at the cell surface, triggering a series of phosphorylation events that activate the central transcription factor (TF) Brassinazole-resistant 1 (BZR1), which regulates the transcription of BR-responsive genes in the nucleus. This review discusses the discovery, occurrence, and chemical structure of BRs in plants. Furthermore, their role in the growth and development of plants, and against various stresses, is discussed. Finally, BR signaling in plants is discussed.

Inhibition of nonalcoholic fatty liver disease in mice by selective inhibition of mTORC1

Abstract: Nonalcoholic fatty liver disease (NAFLD) and nonalcoholic steatohepatitis (NASH) remain without effective therapies. The mechanistic target of rapamycin complex 1 (mTORC1) pathway is a potential therapeutic target, but conflicting interpretations have been proposed for how mTORC1 controls lipid homeostasis. We show that selective inhibition of mTORC1 signaling in mice, through deletion of the RagC/D guanosine triphosphatase–activating protein folliculin (FLCN), promotes activation of transcription factor E3 (TFE3) in the liver without affecting other mTORC1 targets and protects against NAFLD and NASH. Disease protection is mediated by TFE3, which both induces lipid consumption and suppresses anabolic lipogenesis. TFE3 inhibits lipogenesis by suppressing proteolytic processing and activation of sterol regulatory element–binding protein-1c (SREBP-1c) and by interacting with SREBP-1c on chromatin. Our data reconcile previously conflicting studies and identify selective inhibition of mTORC1 as a potential approach to treat NASH and NAFLD. Description mTORC1 as fatty liver disease target Inappropriate accumulation of fat in the liver causes serious life-threatening disease in humans. In mice, Gosis et al. explored the potential beneficial effects of controlling lipid metabolism by preventing signaling by the mTORC1 (mechanistic target of rapamycin complex 1) protein kinase complex (see the Perspective by Ginsberg and Mani). The authors inhibited some, but not all, signaling by mTORC1 by depleting the folliculin protein in the liver. Such mice had increased lipid consumption and decreased lipogenesis and were protected when fed a diet that normally induces nonalcoholic fatty liver disease. These effects appear to result in part from activation of the TFE3 transcription factor. Similar strategies might thus be useful in treating liver disease. —LBR Inhibiting a particular signal from the mTORC1 protein kinase complex protects mice from fatty liver disease. INTRODUCTION As many as 100 million people in the US have nonalcoholic fatty liver disease (NAFLD), characterized by increased liver lipid accumulation, which often leads to hepatocyte injury and fibrosis, characteristics of nonalcoholic steatohepatitis (NASH). NASH in turn can progress to cirrhosis and hepatocellular carcinoma. There are currently no US Food and Drug Administration–approved therapies for NAFLD or NASH. NAFLD occurs when there is disequilibrium between the processes of hepatic lipid synthesis and consumption. The nutrient sensor mechanistic target of rapamycin complex 1 (mTORC1) regulates several of these pathways. mTORC1 is thus an attractive target to modulate lipid homeostasis in the liver. However, mTORC1 also regulates numerous other cellular pathways, and blunting of mTORC1 modulation can lead to unexpected feedback loops and unwanted effects. RATIONALE We hypothesized that selective modulation of hepatic mTORC1 signaling could benefit liver lipid metabolism and prevent NAFLD. In non-liver cell types, the protein folliculin (FLCN) has been shown to confer substrate specificity to mTORC1. Deletion of FLCN inhibits mTORC1-mediated phosphorylation of the transcription factor E3/B (TFE3/B) family of transcription factors, without affecting mTORC1-driven phosphorylation of its canonical substrates ribosomal protein S6 kinase beta-1 (S6K1) and eukaryotic translation initiation factor 4E–binding protein 1 (4E-BP1). Unphosphorylated TFE3 translocates to the nucleus and activates genes that promote lysosomal biogenesis, mitochondrial biogenesis, and oxidative metabolism. We reasoned that suppression of FLCN in the liver might promote fatty acid oxidation and lipid clearance without untoward effects of generalized mTORC1 inhibition. RESULTS Hepatocyte-specific genetic deletion of Flcn in adult mice selectively inhibited mTORC1-mediated cytoplasmic sequestration of TFE3, with little effect on other mTORC1 targets, including S6K, 4E-BP1, and Lipin1. Hepatocyte loss of Flcn protected mice from both NAFLD and NASH and partially reversed these processes when already established. The protection against NAFLD and NASH required TFE3, which activated lipid clearance. Unleashed TFE3 additionally suppressed de novo lipogenesis. The latter was mediated in part by TFE3-mediated induction of insulin-induced gene 2 (Insig2) to inhibit proteolytic activation of sterol regulatory element–binding protein-1c (SREBP-1c), a critical lipogenic transcription factor. CONCLUSION Our data establish FLCN as a critical regulator of lipid homeostasis in the liver. Flcn deletion affords selective inhibition of mTORC1, leading to nuclear translocation and activation of the transcription factor TFE3, which coordinates hepatic lipid metabolic pathways to protect against NAFLD and NASH in mice. Thus, our data reveal FLCN as a promising target for the treatment of NAFLD and NASH. The data also illuminate previously published and seemingly conflicting data, which likely reflected different effects on each arm of mTORC1 signaling. There have been numerous attempts by many to develop disease-specific treatments for NAFLD and NASH, thus far without success. A recurrent problem has been the many compensatory responses by the liver to targeting any one pathway; for example, inhibitors of acetyl–coenzyme A carboxylase led to compensatory activation of SREBP-1c and consequent hyperlipidemia. Targeting FLCN is thus particularly attractive, in that loss of FLCN simultaneously and favorably affects multiple aspects of hepatic lipid homeostasis, including promoting fatty acid oxidation and lysosomal biogenesis and inhibiting de novo lipogenesis. Deletion of Flcn in the liver protects mice from NAFLD and NASH through selective suppression of mTORC1. Diets high in fat, carbohydrates, and cholesterol lead to NAFLD and NASH. When Flcn is simultaneously deleted, mTORC1 is selectively inhibited, preserving phosphorylation of canonical substrates S6K and 4E-BP1 while blocking phosphorylation of the transcription factor TFE3. Unphosphorylated TFE3 is released to the nucleus, where it activates lipid catabolism genes while suppressing de novo lipogenesis genes. [Image created using Biorender]

Hypoxia-inducible factors: cancer progression and clinical translation

Abstract: Hypoxia-inducible factors (HIFs) are master regulators of oxygen homeostasis that match O2 supply and demand for each of the 50 trillion cells in the adult human body. Cancer cells co-opt this homeostatic system to drive cancer progression. HIFs activate the transcription of thousands of genes that mediate angiogenesis, cancer stem cell specification, cell motility, epithelial-mesenchymal transition, extracellular matrix remodeling, glucose and lipid metabolism, immune evasion, invasion, and metastasis. In this Review, the mechanisms and consequences of HIF activation in cancer cells are presented. The current status and future prospects of small-molecule HIF inhibitors for use as cancer therapeutics are discussed.

Enhancer–promoter interactions and transcription are largely maintained upon acute loss of CTCF, cohesin, WAPL or YY1

Abstract: It remains unclear why acute depletion of CTCF (CCCTC-binding factor) and cohesin only marginally affects expression of most genes despite substantially perturbing three-dimensional (3D) genome folding at the level of domains and structural loops. To address this conundrum, we used high-resolution Micro-C and nascent transcript profiling in mouse embryonic stem cells. We find that enhancer-promoter (E-P) interactions are largely insensitive to acute (3-h) depletion of CTCF, cohesin or WAPL. YY1 has been proposed as a structural regulator of E-P loops, but acute YY1 depletion also had minimal effects on E-P loops, transcription and 3D genome folding. Strikingly, live-cell, single-molecule imaging revealed that cohesin depletion reduced transcription factor (TF) binding to chromatin. Thus, although CTCF, cohesin, WAPL or YY1 is not required for the short-term maintenance of most E-P interactions and gene expression, our results suggest that cohesin may facilitate TFs to search for and bind their targets more efficiently.

MYB orchestrates T cell exhaustion and response to checkpoint inhibition

Abstract: Abstract CD8 + T cells that respond to chronic viral infections or cancer are characterized by the expression of inhibitory receptors such as programmed cell death protein 1 (PD-1) and by the impaired production of cytokines. This state of restrained functionality—which is referred to as T cell exhaustion 1,2 —is maintained by precursors of exhausted T (T PEX ) cells that express the transcription factor T cell factor 1 (TCF1), self-renew and give rise to TCF1 − exhausted effector T cells 3–6 . Here we show that the long-term proliferative potential, multipotency and repopulation capacity of exhausted T cells during chronic infection are selectively preserved in a small population of transcriptionally distinct CD62L + T PEX cells. The transcription factor MYB is not only essential for the development of CD62L + T PEX cells and maintenance of the antiviral CD8 + T cell response, but also induces functional exhaustion and thereby prevents lethal immunopathology. Furthermore, the proliferative burst in response to PD-1 checkpoint inhibition originates exclusively from CD62L + T PEX cells and depends on MYB. Our findings identify CD62L + T PEX cells as a stem-like population that is central to the maintenance of long-term antiviral immunity and responsiveness to immunotherapy. Moreover, they show that MYB is a transcriptional orchestrator of two fundamental aspects of exhausted T cell responses: the downregulation of effector function and the long-term preservation of self-renewal capacity.

Fusobacterium nucleatum reduces METTL3-mediated m6A modification and contributes to colorectal cancer metastasis

Abstract: Microbiota-host interactions play critical roles in colorectal cancer (CRC) progression, however, the underlying mechanisms remain elusive. Here, we uncover that Fusobacterium nucleatum (F. nucleatum) induces a dramatic decline of m6A modifications in CRC cells and patient-derived xenograft (PDX) tissues by downregulation of an m6A methyltransferase METTL3, contributing to inducation of CRC aggressiveness. Mechanistically, we characterized forkhead box D3 (FOXD3) as a transcription factor for METTL3. F. nucleatum activates YAP signaling, inhibits FOXD3 expression, and subsequently reduces METTL3 transcription. Downregulation of METTL3 promotes its target kinesin family member 26B (KIF26B) expression by reducing its m6A levels and diminishing YTHDF2-dependent mRNA degradation, which contributes to F. nucleatum-induced CRC metastasis. Moreover, METTL3 expression is negatively correlated with F. nucleatum and KIF26B levels in CRC tissues. A high expression of KIF26B is also significantly correlated with a shorter survival time of CRC patients. Together, our findings provide insights into modulating human m6A epitranscriptome by gut microbiota, and its significance in CRC progression.

MYCN mediates cysteine addiction and sensitizes neuroblastoma to ferroptosis

Abstract: Abstract Aberrant expression of MYC transcription factor family members predicts poor clinical outcome in many human cancers. Oncogenic MYC profoundly alters metabolism and mediates an antioxidant response to maintain redox balance. Here we show that MYCN induces massive lipid peroxidation on depletion of cysteine, the rate-limiting amino acid for glutathione (GSH) biosynthesis, and sensitizes cells to ferroptosis, an oxidative, non-apoptotic and iron-dependent type of cell death. The high cysteine demand of MYCN -amplified childhood neuroblastoma is met by uptake and transsulfuration. When uptake is limited, cysteine usage for protein synthesis is maintained at the expense of GSH triggering ferroptosis and potentially contributing to spontaneous tumor regression in low-risk neuroblastomas. Pharmacological inhibition of both cystine uptake and transsulfuration combined with GPX4 inactivation resulted in tumor remission in an orthotopic MYCN -amplified neuroblastoma model. These findings provide a proof of concept of combining multiple ferroptosis targets as a promising therapeutic strategy for aggressive MYCN -amplified tumors.

Gene regulation by gonadal hormone receptors underlies brain sex differences

Abstract: Abstract Oestradiol establishes neural sex differences in many vertebrates 1–3 and modulates mood, behaviour and energy balance in adulthood 4–8 . In the canonical pathway, oestradiol exerts its effects through the transcription factor oestrogen receptor-α (ERα) 9 . Although ERα has been extensively characterized in breast cancer, the neuronal targets of ERα, and their involvement in brain sex differences, remain largely unknown. Here we generate a comprehensive map of genomic ERα-binding sites in a sexually dimorphic neural circuit that mediates social behaviours. We conclude that ERα orchestrates sexual differentiation of the mouse brain through two mechanisms: establishing two male-biased neuron types and activating a sustained male-biased gene expression program. Collectively, our findings reveal that sex differences in gene expression are defined by hormonal activation of neuronal steroid receptors. The molecular targets we identify may underlie the effects of oestradiol on brain development, behaviour and disease.