The C. elegans Snail homolog CES-1 can activate gene expression in vivo and share targets with bHLH transcription factors

Extracellular glucose and dysfunctional insulin receptor signaling independently upregulate arterial smooth muscle TMEM16A expression

Diabetes alters the function of ion channels responsible for regulating arterial smooth muscle membrane potential, resulting in vasoconstriction. Our prior research demonstrated an elevation of TMEM16A in diabetic arteries. Here, we explored the mechanisms involved in Transmembrane protein 16A (TMEM16A) gene expression. Our data indicate that a Snail-mediated repressor complex regulates arterial TMEM16A gene transcription. Snail expression was reduced in diabetic arteries while TMEM16A expression was upregulated. The TMEM16A promoter contained three canonical E-box sites. Electrophoretic mobility and super shift assays revealed that the -154 nt E-box was the binding site of the Snail repressor complex and binding of the repressor complex decreased in diabetic arteries. High glucose induced a biphasic contractile response in pressurized nondiabetic mouse hindlimb arteries incubated ex vivo. Hindlimb arteries incubated in high glucose also showed decreased phospho-protein kinase D1 and TMEM16A expression. In hindlimb arteries from nondiabetic mice, administration of a bolus dose of glucose activated protein kinase D1 signaling to induce Snail degradation. In both in vivo and ex vivo conditions, Snail expression exhibited an inverse relationship with the expression of protein kinase D1 and TMEM16A. In diabetic mouse arteries, phospho-protein kinase D1 increased while Akt2 and pGSK3β levels declined. These results indicate that in nondiabetic mice, high glucose triggers a transient deactivation of the Snail repressor complex to increase arterial TMEM16A expression independently of insulin signaling. Conversely, insulin resistance activates GSK3β signaling and enhances arterial TMEM16A channel expression. These data have uncovered the Snail-mediated regulation of arterial TMEM16A expression and its dysfunction during diabetes.NEW & NOTEWORTHY The calcium-activated chloride channel, TMEM16A, is upregulated in the diabetic vasculature to cause increased vasoconstriction. In this paper, we have uncovered that the TMEM16A gene expression is controlled by a Snail-mediated repressor complex that uncouples with both insulin-dependent and -independent pathways to allow for upregulated arterial protein expression thereby causing vasoconstriction. The paper highlights the effect of short- and long-term glucose-induced dysfunction of an ion channel expression as a causative factor in diabetic vascular disease.

GATA zinc finger protein p66β promotes breast cancer cell migration by acting as a co-activator of Snail

The transcriptional repressor Snail induces EMT during embryonic development and tumor metastasis. Growing evidence indicates that Snail functions as a trans-activator to induce gene expression; however, the underlying mechanism remains elusive. Here, we report that Snail cooperates with GATA zinc finger protein p66β to transactivate genes in breast cancer cells. Biologically, depletion of p66β reduces cell migration and lung metastasis in BALB/c mice. Mechanistically, Snail interacts with p66β and cooperatively induces gene transcription. Notably, a group of genes induced by Snail harbor conserved G-rich cis-elements (5'-GGGAGG-3', designated as G-box) in their proximal promoter regions. Snail directly binds to G-box via its zinc fingers and transactivates the G-box-containing promoters. p66β enhances Snail binding affinity to G-box, whereas depletion of p66β results in a decreased binding affinity of Snail to the endogenous promoters and concomitantly reduces the transcription of Snail-induced genes. Taken together, these data demonstrated that p66β is critical for Snail-mediated cell migration by acting as a co-activator of Snail to induce genes containing G-box elements in the promoters.

A coherent FOXO3-SNAI2 feed-forward loop in autophagy

Understanding autophagy regulation is instrumental in developing therapeutic interventions for autophagy-associated disease. Here, we identified SNAI2 as a regulator of autophagy from a genome-wide screen in HeLa cells. Upon energy stress, SNAI2 is transcriptionally activated by FOXO3 and interacts with FOXO3 to form a feed-forward regulatory loop to reinforce the expression of autophagy genes. Of note, SNAI2-increased FOXO3-DNA binding abrogates CRM1-dependent FOXO3 nuclear export, illuminating a pivotal role of DNA in the nuclear retention of nucleocytoplasmic shuttling proteins. Moreover, a dFoxO-Snail feed-forward loop regulates both autophagy and cell size in Drosophila, suggesting this evolutionarily conserved regulatory loop is engaged in more physiological activities.

Autophagy is a highly conserved programmed degradation process that regulates a variety of physiological and pathological activities in health, aging, and disease. To identify additional factors that modulate autophagy, we utilized serum-free starvation or Torin1 to induce autophagy in HeLa cells for unbiased mRNA-sequencing analysis and identified SNAI2, a crucial player in epithelial-to-mesenchymal transition and cancer progression, as a regulator of autophagy. Mechanistically, SNAI2 promotes autophagy by physically interacting with FOXO3 and enhancing FOXO3 binding affinity to its response elements in autophagy-related genes. Intriguingly, binding to the DNA targets appears necessary and sufficient for FOXO3 to antagonize its CRM1-dependent nuclear export, illustrating a critical role of DNA in regulating protein nuclear localization. Moreover, stress-elevated SNAI2 expression is mediated by FOXO3, which activates SNAI2 transcription by directly binding to its promoter. Herein, FOXO3 and SNAI2 form a coherent feed-forward regulatory loop to reinforce autophagy genes induction in response to energy stress. Strikingly, a dFoxO-Snail feed-forward circuit also regulates autophagy in Drosophila, suggesting this mechanism is evolutionarily conserved from fly to human.

PPA1 Promotes Breast Cancer Proliferation and Metastasis Through PI3K/AKT/GSK3β Signaling Pathway

Breast cancer is the most common malignancy among women. Inorganic pyrophosphatase 1 (PPA1) is a multifunctional protein involved in the development of several tumors. However, the role of PPA1 in breast cancer progression remains unclear. In this study, we found that PPA1 was highly expressed in breast cancer compared to its levels in normal breast tissue and that it was correlated with breast cancer clinicopathological characteristics, as well as poor survival in breast cancer patients. Silencing PPA1 restrained breast cancer proliferation and metastasis by regulating Slug-mediated epithelial-mesenchymal transition (EMT). Opposite results were observed following PPA1 overexpression. In addition, investigation of the underlying mechanism demonstrated that PPA1 ablation led to decrease phosphatidylinositol 3 kinase (PI3K) phosphorylation levels and attenuate phosphorylated AKT and glycogen synthase kinase-3 β (GSK3β), while ectopic PPA1 expression had the opposite effects. Moreover, PI3K inhibitors suppress the signaling pathways mediating the effects of PPA1 on breast cancer, resulting in tumor growth and metastasis suppression in vitro and in vivo. In summary, our results verify that PPA1 can act as an activator of PI3K/AKT/GSK3β/Slug-mediated breast cancer progression and that it is a potential therapeutic target for the inhibition of tumor progression.

The Snail transcription factor CES-1 regulates glutamatergic behavior in C. elegans

Regulation of AMPA-type glutamate receptor (AMPAR) expression and function alters synaptic strength and is a major mechanism underlying synaptic plasticity. Although transcription is required for some forms of synaptic plasticity, the transcription factors that regulate AMPA receptor expression and signaling are incompletely understood. Here, we identify the Snail family transcription factor ces-1 in an RNAi screen for conserved transcription factors that regulate glutamatergic behavior in C. elegans. ces-1 was originally discovered as a selective cell death regulator of neuro-secretory motor neuron (NSM) and I2 interneuron sister cells in C. elegans, and has almost exclusively been studied in the NSM cell lineage. We found that ces-1 loss-of-function mutants have defects in two glutamatergic behaviors dependent on the C. elegans AMPA receptor GLR-1, the mechanosensory nose-touch response and spontaneous locomotion reversals. In contrast, ces-1 gain-of-function mutants exhibit increased spontaneous reversals, and these are dependent on glr-1 consistent with these genes acting in the same pathway. ces-1 mutants have wild type cholinergic neuromuscular junction function, suggesting that they do not have a general defect in synaptic transmission or muscle function. The effect of ces-1 mutation on glutamatergic behaviors is not due to ectopic cell death of ASH sensory neurons or GLR-1-expressing neurons that mediate one or both of these behaviors, nor due to an indirect effect on NSM sister cell deaths. Rescue experiments suggest that ces-1 may act, in part, in GLR-1-expressing neurons to regulate glutamatergic behaviors. Interestingly, ces-1 mutants suppress the increased reversal frequencies stimulated by a constitutively-active form of GLR-1. However, expression of glr-1 mRNA or GFP-tagged GLR-1 was not decreased in ces-1 mutants suggesting that ces-1 likely promotes GLR-1 function. This study identifies a novel role for ces-1 in regulating glutamatergic behavior that appears to be independent of its canonical role in regulating cell death in the NSM cell lineage.

Function, dynamics and evolution of network motif modules in integrated gene regulatory networks of worm and plant

Gene regulatory networks (GRNs) consist of different molecular interactions that closely work together to establish proper gene expression in time and space. Especially in higher eukaryotes, many questions remain on how these interactions collectively coordinate gene regulation. We study high quality GRNs consisting of undirected protein–protein, genetic and homologous interactions, and directed protein–DNA, regulatory and miRNA–mRNA interactions in the worm Caenorhabditis elegans and the plant Arabidopsis thaliana. Our data-integration framework integrates interactions in composite network motifs, clusters these in biologically relevant, higher-order topological network motif modules, overlays these with gene expression profiles and discovers novel connections between modules and regulators. Similar modules exist in the integrated GRNs of worm and plant. We show how experimental or computational methodologies underlying a certain data type impact network topology. Through phylogenetic decomposition, we found that proteins of worm and plant tend to functionally interact with proteins of a similar age, while at the regulatory level TFs favor same age, but also older target genes. Despite some influence of the duplication mode difference, we also observe at the motif and module level for both species a preference for age homogeneity for undirected and age heterogeneity for directed interactions. This leads to a model where novel genes are added together to the GRNs in a specific biological functional context, regulated by one or more TFs that also target older genes in the GRNs. Overall, we detected topological, functional and evolutionary properties of GRNs that are potentially universal in all species.

Options and Considerations When Using a Yeast One-Hybrid System

Comprehensive mapping of protein-DNA interactions is essential to uncover the mechanisms involved in gene regulation. However, the data generated has been sparse given the number of regulatory elements and transcription factors (TFs) encoded in the genomes of metazoan organisms. Yeast one-hybrid (Y1H) assays provide a powerful "DNA-centered" method, complementary to "TF-centered" methods such as chromatin immunoprecipitation, to identify the TFs that can bind a DNA sequence of interest. Here, we present different technical variations that should be considered when using a Y1H system, including the type of DNA sequence to test, source of TF clones, as well as types of vectors and screening format. Finally, we discuss limitations of the assay and future challenges.

Identifying Interactors from an Activation Domain Prey Library

In yeast hybrid assays, the process of identifying preys that interact with the bait of interest involves several steps. First, in this protocol, the bait yeast strain is transformed with a library of activation domain (AD)-prey clones and plated on selective media containing 3-aminotriazole (3AT). This selects transformants containing an AD-prey clone that induces HIS3 reporter expression. Second, these "HIS-positive" colonies are analyzed for LacZ induction (and, optionally, URA3 induction in yeast two-hybrid (Y2H) assays). Third, yeast PCR is used on these "double-positive" colonies to amplify the insert from the AD-prey plasmid. Fourth, some of this PCR product is used to perform a gap-repair retest to confirm the interaction in fresh bait-strain yeast, and the remainder is used for DNA sequencing to determine prey identity for those that successfully retest. Finally, interactions are carefully examined to filter out likely false-positive interactions. This protocol takes 20-43 d plus sequence confirmation to complete.

Gateway-Compatible Yeast One-Hybrid and Two-Hybrid Assays

In the first section of this introduction, we provide background information for yeast two-hybrid (Y2H) assays that provide a genetic method for the identification and analysis of binary protein-protein interactions and that are complementary to biochemical methods such as immunoprecipitation. In the second section, we discuss yeast one-hybrid (Y1H) assays that provide a "gene-centered" (DNA-to-protein) genetic method to identify and study protein-DNA interactions between cis-regulatory elements and transcription factors (TFs). This method is complementary to "TF-centered" (protein-to-DNA) biochemical methods such as chromatin immunoprecipitation.

Caenorhabditis elegans CES-1 Snail Represses pig-1 MELK Expression To Control Asymmetric Cell Division

Snail-like transcription factors affect stem cell function through mechanisms that are incompletely understood. In the Caenorhabditis elegans neurosecretory motor neuron (NSM) neuroblast lineage, CES-1 Snail coordinates cell cycle progression and cell polarity to ensure the asymmetric division of the NSM neuroblast and the generation of two daughter cells of different sizes and fates. We have previously shown that CES-1 Snail controls cell cycle progression by repressing the expression of cdc-25.2 CDC25. However, the mechanism through which CES-1 Snail affects cell polarity has been elusive. Here, we systematically searched for direct targets of CES-1 Snail by genome-wide profiling of CES-1 Snail binding sites and identified >3000 potential CES-1 Snail target genes, including pig-1, the ortholog of the oncogene maternal embryonic leucine zipper kinase (MELK). Furthermore, we show that CES-1 Snail represses pig-1 MELK transcription in the NSM neuroblast lineage and that pig-1 MELK acts downstream of ces-1 Snail to cause the NSM neuroblast to divide asymmetrically by size and along the correct cell division axis. Based on our results we propose that by regulating the expression of the MELK gene, Snail-like transcription factors affect the ability of stem cells to divide asymmetrically and, hence, to self-renew. Furthermore, we speculate that the deregulation of MELK contributes to tumorigenesis by causing cells that normally divide asymmetrically to divide symmetrically instead.

Lamprey neural crest migration is Snail-dependent and occurs without a differential shift in cadherin expression

The acquisition of neural crest cells was a key step in the origin of the vertebrate body plan. An outstanding question is how neural crest cells acquired their ability to undergo an epithelial-mesenchymal transition (EMT) and migrate extensively throughout the vertebrate embryo. We tested if differential regulation of classical cadherins-a highly conserved feature of neural crest EMT and migration in jawed vertebrates-mediates these cellular behaviors in lamprey, a basal jawless vertebrate. Lamprey has single copies of the type I and type II classical cadherins (CadIA and CadIIA). CadIIA is expressed in premigratory neural crest, and requires the transcription factor Snail for proper expression, yet CadIA is never expressed in the neural tube during neural crest development, suggesting that differential regulation of classical cadherin expression is not required to initiate neural crest migration in basal vertebrates. We hypothesize that neural crest cells evolved by retention of regulatory programs linking distinct mesenchymal and multipotency properties, and emigrated from the neural tube without differentially regulating type I/type II cadherins. Our results point to the coupling of mesenchymal state and multipotency as a key event facilitating the origin of migratory neural crest cells.

Gene-Centered Yeast One-Hybrid Assays

An important question when studying gene regulation is which transcription factors (TFs) interact with which cis-regulatory elements, such as promoters and enhancers. Addressing this issue in complex multicellular organisms is challenging as several hundreds of TFs and thousands of regulatory elements must be considered in the context of different tissues and physiological conditions. Yeast one-hybrid (Y1H) assays provide a powerful "gene-centered" method to identify the TFs that can bind a DNA sequence of interest. In this introduction, we describe the basic principles of the Y1H assay and its advantages and disadvantages and briefly discuss how it is complementary to "TF-centered" methods that identify protein-DNA interactions for a known protein of interest.

Redundant ERF-VII Transcription Factors Bind to an Evolutionarily Conserved cis-Motif to Regulate Hypoxia-Responsive Gene Expression in Arabidopsis

The response of Arabidopsis thaliana to low-oxygen stress (hypoxia), such as during shoot submergence or root waterlogging, includes increasing the levels of ∼50 hypoxia-responsive gene transcripts, many of which encode enzymes associated with anaerobic metabolism. Upregulation of over half of these mRNAs involves stabilization of five group VII ethylene response factor (ERF-VII) transcription factors, which are routinely degraded via the N-end rule pathway of proteolysis in an oxygen- and nitric oxide-dependent manner. Despite their importance, neither the quantitative contribution of individual ERF-VIIs nor the cis-regulatory elements they govern are well understood. Here, using single- and double-null mutants, the constitutively synthesized ERF-VIIs RELATED TO APETALA2.2 (RAP2.2) and RAP2.12 are shown to act redundantly as principle activators of hypoxia-responsive genes; constitutively expressed RAP2.3 contributes to this redundancy, whereas the hypoxia-induced HYPOXIA RESPONSIVE ERF1 (HRE1) and HRE2 play minor roles. An evolutionarily conserved 12-bp cis-regulatory motif that binds to and is sufficient for activation by RAP2.2 and RAP2.12 is identified through a comparative phylogenetic motif search, promoter dissection, yeast one-hybrid assays, and chromatin immunopurification. This motif, designated the hypoxia-responsive promoter element, is enriched in promoters of hypoxia-responsive genes in multiple species.

Snail mediates medial-lateral patterning of the ascidian neural plate

The ascidian neural plate exhibits a regular, grid-like arrangement of cells. Patterning of the neural plate across the medial-lateral axis is initiated by bilateral sources of Nodal signalling, such that Nodal signalling induces expression of lateral neural plate genes and represses expression of medial neural plate genes. One of the earliest lateral neural plate genes induced by Nodal signals encodes the transcription factor Snail. Here, we show that Snail is a critical downstream factor mediating this Nodal-dependent patterning. Using gain and loss of function approaches, we show that Snail is required to repress medial neural plate gene expression at neural plate stages and to maintain the lateral neural tube genetic programme at later stages. A comparison of these results to those obtained following Nodal gain and loss of function indicates that Snail mediates a subset of Nodal functions. Consistently, overexpression of Snail can partially rescue a Nodal inhibition phenotype. We conclude that Snail is an early component of the gene regulatory network, initiated by Nodal signals, that patterns the ascidian neural plate.

Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities

Caenorhabditis elegans is a powerful model for studying gene regulation, as it has a compact genome and a wealth of genomic tools. However, identification of regulatory elements has been limited, as DNA-binding motifs are known for only 71 of the estimated 763 sequence-specific transcription factors (TFs). To address this problem, we performed protein binding microarray experiments on representatives of canonical TF families in C. elegans, obtaining motifs for 129 TFs. Additionally, we predict motifs for many TFs that have DNA-binding domains similar to those already characterized, increasing coverage of binding specificities to 292 C. elegans TFs (∼40%). These data highlight the diversification of binding motifs for the nuclear hormone receptor and C2H2 zinc finger families and reveal unexpected diversity of motifs for T-box and DM families. Motif enrichment in promoters of functionally related genes is consistent with known biology and also identifies putative regulatory roles for unstudied TFs.

DOI:http://dx.doi.org/10.7554/eLife.06967.001

Many scientists use ‘model’ species—such as the fruit fly or a nematode worm called Caenorhabditis elegans—in their research because these organisms have useful features that make it easier to carry out many experiments. For example, C. elegans has a smaller genome compared to many other animals, which is useful for studying the roles of individual genes or stretches of DNA.

Transcription factors are a type of protein that can bind to specific stretches of DNA and help to switch certain genes on or off. These ‘motifs’ may be close to the gene or further away in the genome, and therefore, must stand out amongst the rest of the DNA, like lights on a landing strip. However, the motifs for only 10% of the estimated 763 transcription factors in C. elegans have been identified so far.

In this study, Narasimhan, Lambert, Yang et al. used a technique called a ‘protein binding microarray’ to identify the motifs for many more of the C. elegans transcription factors. These findings were then used to predict motifs for other transcription factors. Together, these methods increased the proportion of C. elegans transcription factors with known DNA-binding motifs from 10% to around 40%.

Now that more DNA motifs have been identified, it is possible to look for similarities and differences between them. For example, Narasimhan, Lambert, Yang et al. found that transcription factors with similar sequences can bind to very varied motifs. On the other hand, some transcription factors that are very different are able to recognize very similar motifs. The experiments also indicate that motifs found very close to genes—in sequences known as ‘promoters’—may be able to interact with many proteins to influence the activity of genes.

Narasimhan, Lambert, Yang et al.'s findings increase the number of C. elegans transcription factors with a motif, bringing the knowledge of these proteins more in line with the better-studied transcription factors of humans and fruit flies. The next challenge is to identify DNA motifs for the remaining 60% of transcription factors.

DOI:http://dx.doi.org/10.7554/eLife.06967.002

FBXO11 promotes ubiquitination of the Snail family of transcription factors in cancer progression and epidermal development

The Snail family of transcription factors are core inducers of epithelial-to-mesenchymal transition (EMT). Here we show that the F-box protein FBXO11 recognizes and promotes ubiquitin-mediated degradation of multiple Snail family members including Scratch. The association between FBXO11 and Snai1 in vitro is independent of Snai1 phosphorylation. Overexpression of FBXO11 in mesenchymal cells reduces Snail protein abundance and cellular invasiveness. Conversely, depletion of endogenous FBXO11 in epithelial cancer cells causes Snail protein accumulation, EMT, and tumor invasion, as well as loss of estrogen receptor expression in breast cancer cells. Expression of FBXO11 is downregulated by EMT-inducing signals TGFβ and nickel. In human cancer, high FBXO11 levels correlate with expression of epithelial markers and favorable prognosis. The results suggest that FBXO11 sustains the epithelial state and inhibits cancer progression. Inactivation of FBXO11 in mice leads to neonatal lethality, epidermal thickening, and increased Snail protein levels in epidermis, validating that FBXO11 is a physiological ubiquitin ligase of Snail. Moreover, in C. elegans, the FBXO11 mutant phenotype is attributed to the Snail factors as it is suppressed by inactivation/depletion of Snail homologs. Collectively, these findings suggest that the FBXO11-Snail regulatory axis is evolutionarily conserved and critically governs carcinoma progression and mammalian epidermal development.

A conserved role for Snail as a potentiator of active transcription

The transcription factors of the Snail family are key regulators of epithelial-mesenchymal transitions, cell morphogenesis, and tumor metastasis. Since its discovery in Drosophila ∼25 years ago, Snail has been extensively studied for its role as a transcriptional repressor. Here we demonstrate that Drosophila Snail can positively modulate transcriptional activation. By combining information on in vivo occupancy with expression profiling of hand-selected, staged snail mutant embryos, we identified 106 genes that are potentially directly regulated by Snail during mesoderm development. In addition to the expected Snail-repressed genes, almost 50% of Snail targets showed an unanticipated activation. The majority of "Snail-activated" genes have enhancer elements cobound by Twist and are expressed in the mesoderm at the stages of Snail occupancy. Snail can potentiate Twist-mediated enhancer activation in vitro and is essential for enhancer activity in vivo. Using a machine learning approach, we show that differentially enriched motifs are sufficient to predict Snail's regulatory response. In silico mutagenesis revealed a likely causative motif, which we demonstrate is essential for enhancer activation. Taken together, these data indicate that Snail can potentiate enhancer activation by collaborating with different activators, providing a new mechanism by which Snail regulates development.

Transcription factor binding to Caenorhabditis elegans first introns reveals lack of redundancy with gene promoters

Gene expression is controlled through the binding of transcription factors (TFs) to regulatory genomic regions. First introns are longer than other introns in multiple eukaryotic species and are under selective constraint. Here we explore the importance of first introns in TF binding in the nematode Caenorhabditis elegans by combining computational predictions and experimentally derived TF–DNA interaction data. We found that first introns of C. elegans genes, particularly those for families enriched in long first introns, are more conserved in length, have more conserved predicted TF interactions and are bound by more TFs than other introns. We detected a significant positive correlation between first intron size and the number of TF interactions obtained from chromatin immunoprecipitation assays or determined by yeast one-hybrid assays. TFs that bind first introns are largely different from those binding promoters, suggesting that the different interactions are complementary rather than redundant. By combining first intron and promoter interactions, we found that genes that share a large fraction of TF interactions are more likely to be co-expressed than when only TF interactions with promoters are considered. Altogether, our data suggest that C. elegans gene regulation may be additive through the combined effects of multiple regulatory regions.

Transcriptional regulation of gene expression in C. elegans

Protein coding gene sequences are converted to mRNA by the highly regulated process of transcription. The precise temporal and spatial control of transcription for many genes is an essential part of development in metazoans. Thus, understanding the molecular mechanisms underlying transcriptional control is essential to understanding cell fate determination during embryogenesis, post-embryonic development, many environmental interactions, and disease-related processes. Studies of transcriptional regulation in C. elegans exploit its genomic simplicity and physical characteristics to define regulatory events with single-cell and minute-time-scale resolution. When combined with the genetics of the system, C. elegans offers a unique and powerful vantage point from which to study how chromatin-associated proteins and their modifications interact with transcription factors and their binding sites to yield precise control of gene expression through transcriptional regulation.

The transcription factor chicken Scratch2 is expressed in a subset of early postmitotic neural progenitors

Scratch proteins are members of the Snail superfamily which have been shown to regulate invertebrate neural development. However, in vertebrates, little is known about the function of Scratch or its relationship to other neural transcription factors. We report the cloning of chicken Scratch2 (cScrt2) and describe its expression pattern in the chick embryo from HH15 through HH29. cScrt2 was detected in cranial ganglia, the nasal placode and neural tube. At all stages examined, cScrt2 expression is only detected within a subregion of the intermediate zone of the neural tube. cScrt2 is also expressed in the developing dorsal root ganglia from HH22-23 onwards and becomes limited to its dorsal medial domain at HH29. phospho-Histone H3 and BrdU-labeling revealed that the cScrt2 expression domain is located immediately external to the proliferative region. In contrast, cScrt2 domain overlapped almost completely with that of the postmitotic neural transcription factor NeuroM/Ath3/NEUROD4. Together, these data define cScrt2-positive cells as a subset of immediately postmitotic neural progenitors. Previous data has shown that Scrt2 is a repressor of E-box-driven transcription whereas NeuroM is an E-box-transactivator. In light of these data, the co-localization detected here suggests that Scrt2 and NeuroM may have opposing roles during definition of neural subtypes.

Twist1 controls a cell-specification switch governing cell fate decisions within the cardiac neural crest

Neural crest cells are multipotent progenitor cells that can generate both ectodermal cell types, such as neurons, and mesodermal cell types, such as smooth muscle. The mechanisms controlling this cell fate choice are not known. The basic Helix-loop-Helix (bHLH) transcription factor Twist1 is expressed throughout the migratory and post-migratory cardiac neural crest. Twist1 ablation or mutation of the Twist-box causes differentiation of ectopic neuronal cells, which molecularly resemble sympathetic ganglia, in the cardiac outflow tract. Twist1 interacts with the pro-neural factor Sox10 via its Twist-box domain and binds to the Phox2b promoter to repress transcriptional activity. Mesodermal cardiac neural crest trans-differentiation into ectodermal sympathetic ganglia-like neurons is dependent upon Phox2b function. Ectopic Twist1 expression in neural crest precursors disrupts sympathetic neurogenesis. These data demonstrate that Twist1 functions in post-migratory neural crest cells to repress pro-neural factors and thereby regulate cell fate determination between ectodermal and mesodermal lineages.

During vertebrate development, a unique population of cells, termed neural crest cells, migrates throughout the developing embryo, generating various cell types, for example, the smooth muscle that divides the aorta and pulmonary artery where they connect to the heart, and the autonomic neurons, which coordinate organ function. The distinctions between neural crest cells that will form smooth muscle and those that will become neurons are thought to occur prior to migration. Here, we show that, in mice with mutations of the transcription factor Twist1, a subpopulation of presumptive smooth muscle cells, following migration to the heart, instead mis-specify to resemble autonomic neurons. Twist1 represses transcription of the pro-neural factor Phox2b both through antagonism of its upstream effector, Sox10, and through direct binding to its promoter. Phox2b is absolutely required for autonomic neuron development, and indeed, the aberrant neurons in Twist1 mutants disappear when Phox2b is also mutated. Ectopic Twist1 expression within all neural crest cells disrupts the specification of normal autonomic neurons. Collectively, these data reveal that neural crest cells can alter their cell fate from mesoderm to ectoderm after they have migrated and that Twist1 functions to maintain neural crest cell potency during embryonic development.

Global analysis of Drosophila Cys₂-His₂ zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants

Cys₂-His₂ zinc finger proteins (ZFPs) are the largest group of transcription factors in higher metazoans. A complete characterization of these ZFPs and their associated target sequences is pivotal to fully annotate transcriptional regulatory networks in metazoan genomes. As a first step in this process, we have characterized the DNA-binding specificities of 129 zinc finger sets from Drosophila using a bacterial one-hybrid system. This data set contains the DNA-binding specificities for at least one encoded ZFP from 70 unique genes and 23 alternate splice isoforms representing the largest set of characterized ZFPs from any organism described to date. These recognition motifs can be used to predict genomic binding sites for these factors within the fruit fly genome. Subsets of fingers from these ZFPs were characterized to define their orientation and register on their recognition sequences, thereby allowing us to define the recognition diversity within this finger set. We find that the characterized fingers can specify 47 of the 64 possible DNA triplets. To confirm the utility of our finger recognition models, we employed subsets of Drosophila fingers in combination with an existing archive of artificial zinc finger modules to create ZFPs with novel DNA-binding specificity. These hybrids of natural and artificial fingers can be used to create functional zinc finger nucleases for editing vertebrate genomes.

Yeast one-hybrid assays: a historical and technical perspective

Since its development about two decades ago, the yeast one-hybrid (Y1H) assay has become an important technique for detecting physical interactions between sequence-specific regulatory transcription factor proteins (TFs) and their DNA target sites. Multiple versions of the Y1H methodology have been developed, each with technical differences and unique advantages. We will discuss several of these technical variations in detail, and also provide some ideas for how Y1H assays can be further improved.

Enhanced yeast one-hybrid assays for high-throughput gene-centered regulatory network mapping

A major challenge in systems biology is to understand the gene regulatory networks that drive development, physiology and pathology. Interactions between transcription factors and regulatory genomic regions provide the first level of gene control. Gateway-compatible yeast one-hybrid (Y1H) assays present a convenient method to identify and characterize the repertoire of transcription factors that can bind a DNA sequence of interest. To delineate genome-scale regulatory networks, however, large sets of DNA fragments need to be processed at high throughput and high coverage. Here we present enhanced Y1H (eY1H) assays that use a robotic mating platform with a set of improved Y1H reagents and automated readout quantification. We demonstrate that eY1H assays provide excellent coverage and identify interacting transcription factors for multiple DNA fragments in a short time. eY1H assays will be an important tool for mapping gene regulatory networks in Caenorhabditis elegans and other model organisms as well as in humans.

Transcription factors that mediate epithelial-mesenchymal transition lead to multidrug resistance by upregulating ABC transporters

Development of multidrug resistance (MDR) is a major deterrent in the effective treatment of metastatic cancers by chemotherapy. Even though MDR and cancer invasiveness have been correlated, the molecular basis of this link remains obscure. We show here that treatment with chemotherapeutic drugs increases the expression of several ATP binding cassette transporters (ABC transporters) associated with MDR, as well as epithelial–mesenchymal transition (EMT) markers, selectively in invasive breast cancer cells, but not in immortalized or non-invasive cells. Interestingly, the mere induction of an EMT in immortalized and non-invasive cell lines increased their expression of ABC transporters, migration, invasion, and drug resistance. Conversely, reversal of EMT in invasive cells by downregulating EMT-inducing transcription factors reduced their expression of ABC transporters, invasion, and rendered them more chemosensitive. Mechanistically, we demonstrate that the promoters of ABC transporters carry several binding sites for EMT-inducing transcription factors, and overexpression of Twist, Snail, and FOXC2 increases the promoter activity of ABC transporters. Furthermore, chromatin immunoprecipitation studies revealed that Twist binds directly to the E-box elements of ABC transporters. Thus, our study identifies EMT inducers as novel regulators of ABC transporters, thereby providing molecular insights into the long-standing association between invasiveness and MDR. Targeting EMT transcription factors could hence serve as novel strategies to curb both metastasis and the associated drug resistance.

Systematic characterization of protein-DNA interactions

Sequence-specific protein-DNA interactions (PDIs) are critical for regulating many cellular processes, including transcription, DNA replication, repair, and rearrangement. We review recent experimental advances in high-throughput technologies designed to characterize PDIs and discuss recent studies that use these tools, including ChIP-chip/seq, SELEX-based approaches, yeast one-hybrid, bacterial one-hybrid, protein binding microarray, and protein microarray. The results of these studies have challenged some long-standing concepts of PDI and provide valuable insights into the complex transcriptional regulatory networks.

What does biologically meaningful mean? A perspective on gene regulatory network validation

Gene regulatory networks (GRNs) are rapidly being delineated, but their quality and biological meaning are often questioned. Here, I argue that biological meaning is challenging to define and discuss reasons why GRN validation should be interpreted cautiously.

Gene-centered regulatory network mapping

The Caenorhabditis elegans hermaphrodite is a complex multicellular animal that is composed of 959 somatic cells. The C. elegans genome contains ∼20,000 protein-coding genes, 940 of which encode regulatory transcription factors (TFs). In addition, the worm genome encodes more than 100 microRNAs and many other regulatory RNA and protein molecules. Most C. elegans genes are subject to regulatory control, most likely by multiple regulators, and combined, this dictates the activation or repression of the gene and corresponding protein in the relevant cells and under the appropriate conditions. A major goal in C. elegans research is to determine the spatiotemporal expression pattern of each gene throughout development and in response to different signals, and to determine how this expression pattern is accomplished. Gene regulatory networks describe physical and/or functional interactions between genes and their regulators that result in specific spatiotemporal gene expression. Such regulators can act at transcriptional or post-transcriptional levels. Here, I will discuss the methods that can be used to delineate gene regulatory networks in C. elegans. I will mostly focus on gene-centered yeast one-hybrid (Y1H) assays that are used to map interactions between non-coding genic regions, such as promoters, and regulatory TFs. The approaches discussed here are not only relevant to C. elegans biology, but can also be applied to other model organisms and humans.

A model to die for: signaling to apoptotic cell removal in worm, fly and mouse

Programmed cell death is used during developmental morphogenesis to eliminate superfluous cells or cells with inappropriate developmental potential (e.g., self-reactive immune cells, tumorigenic cells). Recent work in genetic models has led to a number of key observations, revealing signal transduction pathways and identifying new roles for genes previously studied in corpse removal (e.g., removal of broken synapses in the nervous system). Further, studies using mouse models have suggested a role for removal of apoptotic cells in the establishment or maintenance of immune tolerance. In this review, we survey current knowledge of phagocytic pathways derived from studies in the nematode (Caenorhabditis elegans), the fly (Drosophila melanogaster), and mouse (Mus musculus) model systems.

Functional modularity of nuclear hormone receptors in a Caenorhabditis elegans metabolic gene regulatory network

We present the first gene regulatory network (GRN) that pertains to post-developmental gene expression. Specifically, we mapped a transcription regulatory network of Caenorhabditis elegans metabolic gene promoters using gene-centered yeast one-hybrid assays. We found that the metabolic GRN is enriched for nuclear hormone receptors (NHRs) compared with other gene-centered regulatory networks, and that these NHRs organize into functional network modules.

The NHR family has greatly expanded in nematodes; C. elegans has 284 NHRs, whereas humans have only 48. We show that the NHRs in the metabolic GRN have metabolic phenotypes, suggesting that they do not simply function redundantly.

The mediator subunit MDT-15 preferentially interacts with NHRs that occur in the metabolic GRN.

We describe an NHR circuit that responds to nutrient availability and propose a model for the evolution and organization of NHRs in C. elegans metabolic regulatory networks.

Physical and/or regulatory interactions between transcription factors (TFs) and their target genes are essential to establish body plans of multicellular organisms during development, and these interactions have been studied extensively in the context of GRNs. The precise control of differential gene expression is also of critical importance to maintain physiological homeostasis, and many metabolic disorders such as obesity and diabetes coincide with substantial changes in gene expression. Much work has focused on the GRNs that control metazoan development; however, the design principles and organization of the GRNs that control systems physiology remain largely unexplored.

In this study, we present the first gene-centered GRN that includes ∼70 genes involved in C. elegans metabolism and physiology, 100 TFs and more than 500 protein–DNA interactions between them. The resulting metabolic GRN is enriched for NHRs, compared with other gene-centered regulatory networks. NHRs are well-known regulators of lipid meta-qj;bolism in mammals. The transcriptional activity of NHRs can be modified by diffusible ligands, which allows these TFs to function as molecular sensors and rapidly alter the expression of their target genes. Interestingly, NHRs comprise the largest family of TFs in nematodes; the C. elegans genome encodes 284 NHRs, most of which are uncharacterized. Furthermore, their organization in GRNs has not yet been investigated. In our study, we show that the C. elegans NHRs that we retrieved in the metabolic GRN organize into network modules, and that most of these NHRs function to maintain lipid homeostasis in the nematode. Interestingly, network modularity has been proposed to facilitate rapid and robust changes in gene expression. Our results suggest that the C. elegans metabolic GRN may have evolved by combining NHR family expansion with the specific modular wiring of NHRs to enable the rapid adaptation of the animal to different environmental cues.

NHRs can interact with transcriptional cofactors such as chromatin remodeling complexes and Mediator components. For instance, the C. elegans Mediator subunit, MDT-15, can interact with NHR-49 to regulate the expression of its target genes. To find all the TFs that MDT-15 can interact with, we performed systematic yeast two-hybrid assays with MDT-15 versus 755 full-length TFs. We found that MDT-15 preferentially associates with NHRs, and specifically with those NHRs that confer a metabolic phenotype and that occur in the metabolic GRN. This illustrates the central role of MDT-15 in the regulation of metabolic gene expression.

Using a variety of genetic and biochemical approaches, we characterized NHR-86 in more detail. NHR-86 participates in one of the two NHR modules, and has a high-flux capacity; that is it has both a high incoming and a high outgoing degree. We obtained an nhr-86 mutant and generated an NHR-86 antibody, and showed that NHR-86 functions as an auto-repressor in vivo and that nhr-86 mutant animals store abnormally high levels of body fat.

Finally, we discovered a novel NHR circuit that responds to nutrient availability. In this circuit NHR-45 regulates the activity of nhr-178 promoter in two distinct physiologically important tissues: the intestine and the hypodermis. Both of these NHRs are required to maintain lipid homeostasis in C. elegans. The expression of nhr-178 is responsive to the nutritional status of the animal, which switches between ON and OFF states in the hypodermis. We found that NHR-45 activity is necessary to control this switch in the hypodermis. Interestingly, NHR-45 has opposite effects on the activity of the nhr-178 promoter in these tissues: NHR-45 activates this promoter in the intestine, but represses it in the hypodermis.

Altogether our study leads to a model in which the expansion of the NHR family, TFs that have the capacity to act as fast molecular sensors, is combined with a modular network organization to enable rapid and robust responses to various environmental cues.

Gene regulatory networks (GRNs) provide insights into the mechanisms of differential gene expression at a systems level. GRNs that relate to metazoan development have been studied extensively. However, little is still known about the design principles, organization and functionality of GRNs that control physiological processes such as metabolism, homeostasis and responses to environmental cues. In this study, we report the first experimentally mapped metazoan GRN of Caenorhabditis elegans metabolic genes. This network is enriched for nuclear hormone receptors (NHRs). The NHR family has greatly expanded in nematodes: humans have 48 NHRs, but C. elegans has 284, most of which are uncharacterized. We find that the C. elegans metabolic GRN is highly modular and that two GRN modules predominantly consist of NHRs. Network modularity has been proposed to facilitate a rapid response to different cues. As NHRs are metabolic sensors that are poised to respond to ligands, this suggests that C. elegans GRNs evolved to enable rapid and adaptive responses to different cues by a concurrence of NHR family expansion and modular GRN wiring.

Gene-centered regulatory networks

Differential gene expression plays a critical role in the development and physiology of multicellular organisms. At a 'systems level' (e.g. at the level of a tissue, organ or whole organism), this process can be studied using gene regulatory network (GRN) models that capture physical and regulatory interactions between genes and their regulators. In the past years, significant progress has been made toward the mapping of GRNs using a variety of experimental and computational approaches. Here, we will discuss gene-centered approaches that we employed to characterize GRNs and describe insights that we have obtained into the global design principles of gene regulation in complex metazoan systems.

DNA-centered approaches to characterize regulatory protein-DNA interaction complexes

Gene regulation is mediated by site-specific DNA-binding proteins or transcription factors (TFs), which form protein complexes at regulatory loci either to activate or repress the expression of a target gene. The study of the dynamic properties of these regulatory DNA-binding complexes has so far been dominated by protein-centered methodologies, aiming to characterize the DNA-binding behavior of one specific protein at a time. With the emerging evidence for a role of DNA in allosterically influencing DNA-binding protein complex formation, there is renewed interest in DNA-centered approaches to capture protein complexes on defined regulatory loci and to correlate changes in their composition with alterations in target gene expression. In this review, we present the current state-of-the-art in such DNA-centered approaches and evaluate recent technological improvements in the purification as well as in the identification of regulatory DNA-binding protein complexes within or outside their biological context. Finally, we suggest possible areas of improvement and assess the putative impact of DNA-centered methodologies on the gene regulation field for the forthcoming years.