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Castration resistant prostate cancer (CRPC) is an advanced form of prostate cancer associated with loss of androgen receptor activity and resistance to AR-targeted therapies. CRPC is often associated with higher metastasis, invasion, and proliferation. Thus, there’s a strong need for additional molecular markers in CRPC, and therapies that target them directly. Transcriptomic profiling of prostate cancer patients revealed an upregulated signature specific to high-grade tumors in cell cycle progression, E2F targets, G2M checkpoint, DNA repair, Aurora Kinase B, and FOXM1 pathway. Validation in a separate cohort of neuroendocrine prostate cancer patients, the most resistant and invasive form of CRPC which lacks AR expression, showed CCP signature as a dominant driver gene set for NEPC. Moreover, high expression of mRNA targets in each of these pathways is associated with poor overall survival in NEPC patients. Gene set variation analysis revealed a strong inverse correlation between AR signaling and CCP.31, set of 31 markers associated with high proliferation, and a positive correlation between CCP.31 and NEPC signature. FOXM1, a prioritized candidate in CCP is shown to be upregulated in CRPC cell lines and human clinical sections of Gleason 9 patients. GSNO, a nitric oxide donor, known for its inhibitory effect on cell proliferation and an effective inhibitor of cell cycle checkpoints, was able to reverse CCP signature both in-vitro and in-vivo. GSNO exhibits a dependence on AR signaling in-vitro by showing mild effect on CRPC clones, but successfully inhibits tumor growth of AR-null CRPC xenografts. FOXM1 is also targeted by GSNO in-vivo and in-vitro models of both CRPC and AD prostate cancer. This establishes an important link between androgen receptor status in prostate cancer and proposes nitric oxide donors as therapeutic intervention. GSNO is effective against AR-null castration resistant prostate cancer.SignificanceNitric oxide donor, S-glutathione-transferase inhibits tumor growth of castration resistant prostate cancer, regardless of androgen receptor expression status by targeting FOXM1, a critical regulator of cell cycle progression.

Introduction Adult Leydig cells in the testes are essential for testosterone production. The growth and differentiation of Leydig cells could be affected by paracrine factors released by testicular microenvironment (TME) (Sertoli and peritubular myoid cells). In our recent study, we demonstrated that Leptin, a paracrine factor secreted by TME, is critical for Leydig stem cells (LSCs) differentiation and subsequent testosterone production via its interaction with Leptin receptor on LSCs, followed by downstream regulation of desert hedgehog (DHH) signaling. Although it is well-known that obesity adversely affects male fertility and testosterone production, the endogenous effects of Leptin on Leydig stem cell differentiation and transcription factors genes (TFs) binding to leptin receptor (LEPR) and the mechanism that are specific to patient's BMI (normal, obese and lean men) are understudied. Additionally, the underlying mechanism behind the differential effects of Leptin (if any) is unknown. Therefore, In the present study, we evaluated the impacts and mechanism of Leptin as a paracrine factor on LSC differentiation in patients with different BMI's. Objective To uncover the mechanism of Leptin as a paracrine factor on LSC differentiation in patients with different BMI's. Methods A total of 13 men with testicular failure that were subcategorized as obese (BMI >35), normal (BMI 25-30), and lean (BMI Results Results showed that a strong relationship exists between BMI and leptin levels. Immunostaining, flow cytometry and RNA sequencing results showed that in the men with normal BMI, in the presence of low doses of leptin, there was a shift of the testicular cell population towards adult Leydig cells (increased population of cells staining positive for 3BHSD, LHR) and increased DHH signaling (GLI and SMO). On the contrary, at higher concentrations, the positive effects of leptin on cells from men with normal BMI were neutralized. Furthermore, in cells from lean patients, leptin treatment had a consistent, linear and positive impact on LSC differentiation markers and DHH signaling. Moreover, in cells from obese patients, leptin had a consistent, linear and negative impact on LSC differentiation and markers of DHH signaling. Enrichment analysis identified 50 TFs, of which SOX2, SOX8 and SOX9 were enriched for abnormal pituitary function and therefore for hypothalamic pituitary gonadal axis. The role of these TFs on LSC differentiation remained under-explored. RNA sequencing data from cells exposed to different concentrations of Leptin showed an inducing effect of Leptin on SOX2, SOX8 Sox9 respectively. Consequently, with increasing leptin doses SOX2, SOX8 Sox9 protein and expression has been upregulated. Mechanistically, Leptin-LEPR-TFs induced DHH signaling regulates LSCs differentiation in a different manner which is specific to patient's BMI. Conclusions Our results demonstrate the influence, BMI has on Leptin induced LSC differentiation. These findings suggest the future potential use of Leptin as a personalized therapy for inducing LSC differentiation and overcoming low Testosterone levels. Further studies are necessary to identify potential therapeutic effects of leptin treatment in improving fertility in the setting of leptin resistance and obesity. Financial Support: Supported by the American Urological Association Research Scholar Award to H.A. J.M.H. is supported by NIH grants 1R01 HL137355, 1R01 HL107110, 1R01 HL134558, 5R01 CA136387, 5UM1 HL113460 and Soffer Family Foundation. Disclosure No

Introduction Although testosterone deficiency (TD) may be present in 1 out of 5 men 40 years or older, the factors responsible for TD remain largely unknown. Leydig stem cells (LSCs) differentiate into adult Leydig cells (ALC) and produce testosterone in the testes under the pulsatile control of luteinizing hormone (LH) from the pituitary gland. However, our recent studies have suggested that the testicular microenvironment (TME), which is comprised of Sertoli and peritubular myoid cells (PMC), plays an instrumental role in LSC differentiation and testosterone production under the regulation of the desert hedgehog signaling pathway (DHH). In the present study, we hypothesized that testicular TME releases paracrine factors that modulate LSC differentiation. Objective To further examine the TME its see if its release of paracrine factors modulates LSC differentiation. Methods A total of 13 men with testicular failure underwent testis biopsies for sperm retrieval. Using an IRB approved protocol, about 10mg of testicular tissue from each of these men were processed for Leydig stem cell isolation, culture and characterized. Cytokine antibody array was performed to identify the paracrine factors released by TME. The cells were treated with hedgehog signaling agonist and antagonist in the presence or absence of identified paracrine factors from the conditioned media. Two independent biopsies were treated with siRNA against LEPR (25pmol) for 48hrs. This was followed by evaluating the extent of knockdown on LEPR and B3HSD. Further, to evaluate the functional aspects (cell proliferation) modulated by Leptin-DHH signalling by first sorting the Sertoli cells, Peritubular myoid cells, Leydig stem cells and Adult Leydig cells using surface markers. These cells were then treated with Hedgehog agonist (SAG) and antagonist (Vismodigib), in the presence or absence of increasing doses of Leptin (0, 1, 10 ng/ml respectively) 48 hours post treatment, these cells were used for checking the impacts of Leptin-DHH treatments on cell proliferation by MTT assay. GraphPad Prism (GraphPad Software) was used for statistical analysis. All data were presented as the means ± SEM. The statistical significance between two groups was estimated by unpaired two-tailed t-test. Results We successfully isolated and cultured up to 5 × 106million LSC's / biopsy from all 13 human testis biopsies. These cells were characterized for the presence or absence of different cell types in testis such as adult Leydig cells, Leydig stem cells, Sertoli cells, peritublar myoid cells and germ cells. Results showed that, of the cells cultured, up to 70% of the cells were Leydig stem cells and 10% of them were Sertoli-cell in origin on day 14. IF and qPCR data showed as the majority of cell population was undifferentiated (PDGFR-α). Upon stimulation by LH, the expression of 3βHSD (mature Leydig cells) was increased and that of PDGFR-α was decreased. Results from siRNA against LEPR has shown the down-regulated LEPR and B3HSD expression levels. The results from cell proliferation showed that there is minimal to no impact of leptin treatment on upon DHH agonist (SAG) or antagonist (Vismodigib) treatment in either cell types therefore suggesting that Leptin is not involving in the proliferation mechanism. Furthermore, the results demonstrated that TME secretes leptin which induces LSC differentiation and increases T production. Leptin's effects on LSC differentiation and T production, however, are inversely concentration-dependent: positive at low doses and negative at higher doses. Mechanistically, leptin acts on LSCs upstream of DHH; leptin-DHH regulation functions unidirectionally insofar as DHH gain or loss of function has no effects on leptin levels. Conclusions Taken together, results from this study demonstrate the instrumental role of leptin as a paracrine factor secreted by TME on human LSC function and differentiation. Moreover, this study established the molecular events (DHH signaling) that underlie the leptin-modulated effects on LSCs. Further studies are ongoing to validate the implications of these Leptin in terms of its role in LSCs function, differentiation and survival Disclosure No

The cancer tissue exists not as a single entity, but as a combination of different cellular phenotypes which, taken together, dramatically contribute to the entirety of their ecosystem, collectively termed as the tumor microenvironment (TME). The TME is composed of both immune and nonimmune cell types, stromal components, and vasculature-all of which cooperate to promote cancer progression. Not all immune cells, however, are immune-suppressive; some of them can promote the immune microenvironment to fight the invading and uncontrollably dividing cell populations at the initial stages of tumor growth. Yet, many of these processes and cellular phenotypes fall short, and the immune ecosystem more often than not ends up stabilizing in favor of the "resistant" resident cells that begin clonal expansion and may progress to metastatic forms. Stromal components, making up the extracellular matrix and basement membrane, are also not the most innocuous: CAFs embedded throughout secrete proteases that allow the onset of one of the most invasive processes-angiogenesis-through destruction of the ECM and the basement membrane. Vasculature formation, because of angiogenesis, is the largest invader of the TME and the reason metastasis happens. Vasculature is so sporadic and omnipresent in the TME that most drug therapies are mainly focused on stopping this uncontrollable process. As the tumor continues to grow, different processes are constantly supplying it with the ingredients favorable for tumor progression and eventual metastasis. For example, angiogenesis promotes blood vessel formation that will allow the bona fide escape of tumor cells to take place. Another process like hypoxia will present itself in several forms throughout the tumor (mild or acute, cycling or permanent), starting mechanisms such as epithelial to mesenchymal transitions (EMT) of resident cells and inadvertently placing the cells in such a stressful condition that production of ROS and DNA damage is unavoidable. DNA damage can induce mutagenicity while allowing resistant cells to survive. This is where drugs and treatments can subsequently suffer in effectiveness. Finally, another molecule has just surfaced as being a very important player in the TME: nitric oxide. Often overlooked and equated with ROS and initially assigned in the category of pathogenic molecules, nitric oxide can definitely do some damage by causing metabolic reprogramming and promotion of immunosuppressive phenotypes at low concentrations. However, its actions seem to be extremely dose-dependent, and this issue has become a hot target of current treatment goals. Shockingly, nitric oxide, although omnipresent in the TME, can have a positive effect on targeting the TME broadly. Thus, while the TME is a myriad of cellular phenotypes and a combination of different tumor-promoting processes, each process is interconnected into one whole: the tumor microenvironment.

The cancer tissue exists not as a single entity, but as a combination of different cellular phenotypes which, taken together, dramatically contribute to the entirety of their ecosystem, collectively termed as the tumor microenvironment (TME). The TME is composed of both immune and nonimmune cell types, stromal components, and vasculature-all of which cooperate to promote cancer progression. Not all immune cells, however, are immune-suppressive; some of them can promote the immune microenvironment to fight the invading and uncontrollably dividing cell populations at the initial stages of tumor growth. Yet, many of these processes and cellular phenotypes fall short, and the immune ecosystem more often than not ends up stabilizing in favor of the "resistant" resident cells that begin clonal expansion and may progress to metastatic forms. Stromal components, making up the extracellular matrix and basement membrane, are also not the most innocuous: CAFs embedded throughout secrete proteases that allow the onset of one of the most invasive processes-angiogenesis-through destruction of the ECM and the basement membrane. Vasculature formation, because of angiogenesis, is the largest invader of the TME and the reason metastasis happens. Vasculature is so sporadic and omnipresent in the TME that most drug therapies are mainly focused on stopping this uncontrollable process. As the tumor continues to grow, different processes are constantly supplying it with the ingredients favorable for tumor progression and eventual metastasis. For example, angiogenesis promotes blood vessel formation that will allow the bona fide escape of tumor cells to take place. Another process like hypoxia will present itself in several forms throughout the tumor (mild or acute, cycling or permanent), starting mechanisms such as epithelial to mesenchymal transitions (EMT) of resident cells and inadvertently placing the cells in such a stressful condition that production of ROS and DNA damage is unavoidable. DNA damage can induce mutagenicity while allowing resistant cells to survive. This is where drugs and treatments can subsequently suffer in effectiveness. Finally, another molecule has just surfaced as being a very important player in the TME: nitric oxide. Often overlooked and equated with ROS and initially assigned in the category of pathogenic molecules, nitric oxide can definitely do some damage by causing metabolic reprogramming and promotion of immunosuppressive phenotypes at low concentrations. However, its actions seem to be extremely dose-dependent, and this issue has become a hot target of current treatment goals. Shockingly, nitric oxide, although omnipresent in the TME, can have a positive effect on targeting the TME broadly. Thus, while the TME is a myriad of cellular phenotypes and a combination of different tumor-promoting processes, each process is interconnected into one whole: the tumor microenvironment.

SUMMARY Combinatorial interactions among transcription factors (TFs) play essential roles in generating gene expression specificity and diversity in metazoans. Using yeast 2-hybrid (Y2H) assays on nearly all sequence-specific Drosophila TFs, we identified 1,983 protein-protein interactions (PPIs), more than doubling the number of currently known PPIs among Drosophila TFs. For quality assessment, we validated a subset of our interactions using MITOMI and bimolecular fluorescence complementation assays. We combined our interactome with prior PPI data to generate an integrated Drosophila TF-TF binary interaction network. Our analysis of ChIP-seq data, integrating PPI and gene expression information, uncovered different modes by which interacting TFs are recruited to DNA. We further demonstrate the utility of our Drosophila interactome in shedding light on human TF-TF interactions. This study reveals how TFs interact to bind regulatory elements in vivo and serves as a resource of Drosophila TF-TF binary PPIs for understanding tissue-specific gene regulation., Graphical Abstract, In Brief Combinatorial regulation by transcription factors (TFs) is one mechanism for achieving condition and tissue-specific gene regulation. Shokri et al. mapped TF-TF interactions between most Drosophila TFs, reporting a comprehensive TF-TF network integrated with previously known interactions. They used this network to discern distinct TF-DNA binding modes.

Sequencing of exomes and genomes has revealed abundant genetic variation affecting the coding sequences of human transcription factors (TFs), but the consequences of such variation remain largely unexplored. We developed a computational, structure-based approach to evaluate TF variants for their impact on DNA binding activity and used universal protein-binding microarrays to assay sequence-specific DNA binding activity across 41 reference and 117 variant alleles found in individuals of diverse ancestries and families with Mendelian diseases. We found 77 variants in 28 genes that affect DNA binding affinity or specificity and identified thousands of rare alleles likely to alter the DNA binding activity of human sequence-specific TFs. Our results suggest that most individuals have unique repertoires of TF DNA binding activities, which may contribute to phenotypic variation., National Human Genome Research Institute (U.S.) (Grant R01 HG003985)

Cardiac cell therapy (CCT) holds great promise as a regenerative medicine approach for the treatment of cardiovascular diseases (CVDs).1 The first generation of CCTs tested various adult cell types, including skeletal myoblasts, bone marrow (BM)–derived mesenchymal stem cells (MSCs), and cardiac progenitor cells (CPCs). More recently, the advent of induced pluripotent stem cells (PSCs) led to the much-anticipated second generation of CCTs with bona fide, PSC-derived CPCs and cardiomyocytes.1 The bad news is that, to date, both adult and PSC-based CCTs have failed to meet their promise of directly remuscularizing and repairing the heart to a therapeutically meaningful extent.2,3 The good news is that some cell types clearly demonstrate encouraging results in terms of efficacy and safety and, more importantly, reveal a previously underestimated key role of CCT, to indirectly promote repair by regulating mechanisms of endogenous cardiac regeneration in the host.1,4 Article, see p 113 The increasingly high burden of CVDs, coupled with the limited efficacy seen in both adult and PSC-based CCTs, and incomplete mechanistic understanding of adult human heart regeneration, have fueled disappointment, skepticism, and polarized the field.5 This schism has been particularly apparent in the area of adult CCTs, which also faces a current crisis of scientific distrust.5 However, the interpretation that a possible stumble in research progress is proof that CCT is broken would be unscientific. As Daniel Wegner noted, “…tipping the balance toward skepticism can eradicate ideas faster than we can generate them. Eventually, we arrive at a vacuous chasm, with no theory standing and no idea left without serious wounds.”6 Under this prism, it is worth exploring how the field of adult CCTs fares, compared with other regenerative medicine approaches. PSC-based CCTs offer perhaps the …

e17537 Background: A significant proportion of men with Prostate Cancer (PCa) develop castration resistant prostate cancer (CRPC) and do not respond to hormonal agents that decrease androgens. In trying to understand the causes of androgen resistance that develop in CRPC, it is considered most relevant to study the role of Androgen receptor (AR) in the development and progression of PCa from androgen dependent to androgen independent state. Recent studies have highlighted the significance of tumor microenvironment (TME) in regulation of PCa progression in addition to AR. A key molecule in the regulation of TME interactions is nitric oxide (NO). We have shown in our recent study, the critical association of NO with the TME in CRPC. However, the effects of NO to modulate the progression of PCa to CRPC with respect to AR still remains largely unexplored. Methods: 22RV1, LNCaP, LNCaPAPIPC(cells expressing no AR), and LNCaPshAR/pATK (cells expressing low AR), cells were used for the study. Cell proliferation was first assessed by MTT assay. The castrated SCID mice were grafted with 22RV1 cells and were treated with GSNO at the dosage of 10mg/kg/day IP. After treatment, animals were humanely sacrificing. Tumor RNA and proteins were analysed for markers that are important for PCa progression using qPCR, western blot and cytokine antibody array. Animal experiments were carried out in compliance with the IACUC of University of Miami. GraphPad Prism (GraphPad Software) was used for statistical analysis. Results: In addition to reducing the tumor burden, the expression of anti-inflammatory (M2) macrophages (CD206 and Arginase1) is decreased and that of the pro-inflammatory (M1) macrophage (iNOS) is increased in mice which received increased NO levels. Furthermore, to study the effects of NO on progression of PCa from androgen dependent to androgen independent stage, we characterized the LNCAP cell models with differential extent of AR knockdown (LNCaP, LNCaPshAR/pATK and LNCaPAPIPC) for the effects of increased NO levels. Results showed that NO had significant impact on cell proliferation on androgen dependent PCa cells however the effects were negligible in cells expressing low or no AR, suggesting that effects of NO on PCa cell proliferation are AR dependent. Conclusions: Our results suggest that during PCa progression, NO suppresses TAMs to target the TME in an AR dependent manner. Further studies are undergoing to establish the impacts of NO in PCa progression.

Transcription factors (TFs) control cellular processes by binding specific DNA motifs to modulate gene expression. Motif enrichment analysis of regulatory regions can identify direct and indirect TF binding sites. Here, we created a glossary of 108 non-redundant TF-8mer "modules" of shared specificity for 671 metazoan TFs from publicly available and new universal protein binding microarray data. Analysis of 239 ENCODE TF chromatin immunoprecipitation sequencing datasets and associated RNA sequencing profiles suggest the 8mer modules are more precise than position weight matrices in identifying indirect binding motifs and their associated tethering TFs. We also developed GENRE (genomically equivalent negative regions), a tunable tool for construction of matched genomic background sequences for analysis of regulatory regions. GENRE outperformed four state-of-the-art approaches to background sequence construction. We used our TF-8mer glossary and GENRE in the analysis of the indirect binding motifs for the co-occurrence of tethering factors, suggesting novel TF-TF interactions. We anticipate that these tools will aid in elucidating tissue-specific gene-regulatory programs.

Introduction: A major roadblock for generating human pluripotent stem cell (hPSCs) derivatives highly enriched in cardiomyogenic precursors (CPCs), has been the lack of CPC-specific cell surface markers. Hypothesis: Based on observations that adult CPCs are responsive to growth hormone-releasing hormone (GHRH) signaling, we hypothesized that the GHRH receptor (GHRHR) is a specific cell-surface marker for hPSC-derived CPCs. Methods: We performed temporal analysis of GHRHR expression in an in-vitro model of human cardiogenesis using induced hPSCs (hiPSCs) and SOX10::GFP embryonic hPSCs (hESCs) ; and mouse ( in-vivo ) cardiogenesis in wild-type (WT), MEF2c-AHF-Cre, Wnt1-Cre2 and cKit-CreERT2/+ reporter mice. Results: Gene expression and confocal immunofluorescence analyses during chemically-defined, stage-specific, cardiac lineage differentiation indicated that GHRHR is not expressed in undifferentiated hiPSCs or during specification into primitive streak-like Brachyury + or Mesp1 + precardiac cells; but is induced in cardiogenic mesoderm-like cells, at the stage of commitment into NKX2.5 + and/or ISL1 + CPCs ( p =0.001) and persists in Troponin-T + cardiomyocytes. Similarly, experiments modeling cardiac neural crest (CNC) with SOX10::GFP hESCs indicated that GHRHR is not expressed by GFP + CNCs but is induced following differentiation into NKX2.5 + and/or ISL1 + derivatives. Importantly, stimulation with 1μm recombinant GHRH during days 5-7 of hiPSCs differentiation increased NKX2.5 expression 2.5-fold, an effect that was abolished by exposure to 1μM Somatostatin, a GHRH antagonist ( p =0.0009). Last, in vivo analyses in WT , MEF2c-AHF-Cre, Wnt1-Cre2 and cKit-CreERT2/+ reporter embryonic and postnatal hearts corroborated that GHRHR specifically marks NKX2.5 + mesoderm- and CNC-lineage descendants in vivo, whereas GHRHR is not expressed by Wnt1-Cre2 and cKit-CreERT2/+ CNCs descendants that are Nkx2.5 – . Conclusions: Together these findings indicate that GHRHR is universally expressed by NKX2.5 + /ISL1 + CPCs and cardiomyocytes of both mesoderm and CNC origin. Therefore, GHRHR appears to be a valuable cell-surface marker for the selection and enrichment of CPCs from hPSCs for biomedical and regenerative medicine applications.

Genomic analyses often involve scanning for potential transcription factor (TF) binding sites using models of the sequence specificity of DNA binding proteins. Many approaches have been developed to model and learn a protein's DNA-binding specificity, but these methods have not been systematically compared. Here we applied 26 such approaches to in vitro protein binding microarray data for 66 mouse TFs belonging to various families. For nine TFs, we also scored the resulting motif models on in vivo data, and found that the best in vitro-derived motifs performed similarly to motifs derived from the in vivo data. Our results indicate that simple models based on mononucleotide position weight matrices trained by the best methods perform similarly to more complex models for most TFs examined, but fall short in specific cases (

In the vertebrate neural tube, regional Sonic hedgehog (Shh) signaling invokes a time- and concentration-dependent induction of six different cell populations mediated through Gli transcriptional regulators. Elsewhere in the embryo, Shh/Gli responses invoke different tissue-appropriate regulatory programs. A genome-scale analysis of DNA binding by Gli1 and Sox2, a pan-neural determinant, identified a set of shared regulatory regions associated with key factors central to cell fate determination and neural tube patterning. Functional analysis in transgenic mice validates core enhancers for each of these factors and demonstrates the dual requirement for Gli1 and Sox2 inputs for neural enhancer activity. Furthermore, through an unbiased determination of Gli-binding site preferences and analysis of binding site variants in the developing mammalian CNS, we demonstrate that differential Gli-binding affinity underlies threshold-level activator responses to Shh input. In summary, our results highlight Sox2 input as a context-specific determinant of the neural-specific Shh response and differential Gli-binding site affinity as an important cis-regulatory property critical for interpreting Shh morphogen action in the mammalian neural tube.

Numerous efforts are underway to determine gene regulatory networks that describe physical relationships between transcription factors (TFs) and their target DNA sequences. Members of paralogous TF families typically recognize similar DNA sequences. Knowledge of the molecular determinants of protein–DNA recognition by paralogous TFs is of central importance for understanding how small differences in DNA specificities can dictate target gene selection. Previously, we determined the in vitro DNA binding specificities of 19 Caenorhabditis elegans basic helix-loop-helix (bHLH) dimers using protein binding microarrays. These TFs bind E-box (CANNTG) and E-box-like sequences. Here, we combine these data with logics, bHLH–DNA co-crystal structures and computational modeling to infer which bHLH monomer can interact with which CAN E-box half-site and we identify a critical residue in the protein that dictates this specificity. Validation experiments using mutant bHLH proteins provide support for our inferences. Our study provides insights into the mechanisms of DNA recognition by bHLH dimers as well as a blueprint for system-level studies of the DNA binding determinants of other TF families in different model organisms and humans., National Institute of General Medical Sciences (U.S.) (DK068429), National Institute of General Medical Sciences (U.S.) (HG003985), European Union (PROSPECTS HEALTH-F4-2008-201648)

Sonic hedgehog (Shh) signaling patterns the vertebrate spinal cord by activating a group of transcriptional repressors in distinct neural progenitors of somatic motor neuron and interneuron subtypes. To identify the action of this network, we performed a genome-wide analysis of the regulatory actions of three key ventral determinants in mammalian neural tube patterning: Nkx2.2, Nkx6.1 and Olig2. Previous studies have demonstrated that each factor acts predominantly as a transcriptional repressor, at least in part, to inhibit alternative progenitor fate choices. Here, we reveal broad and direct repression of multiple alternative fates as a general mechanism of repressor action. Additionally, the repressor network targets multiple Shh signaling components providing negative feedback to ongoing Shh signaling. Analysis of chromatin organization around Nkx2.2-, Nkx6.1- and Olig2-bound regions, together with co-analysis of engagement of the transcriptional activator Sox2, indicate that repressors bind to, and probably modulate the action of, neural enhancers. Together, the data suggest a model for neural progenitor specification downstream of Shh signaling, in which Nkx2.2 and Olig2 direct repression of alternative neural progenitor fate determinants, an action augmented by the overlapping activity of Nkx6.1 in each cell type. Integration of repressor and activator inputs, notably activator inputs mediated by Sox2, is probably a key mechanism in achieving cell type-specific transcriptional outcomes in mammalian neural progenitor fate specification.

Sonic hedgehog (Shh) signaling patterns the vertebrate spinal cord by activating a group of transcriptional repressors in distinct neural progenitors of somatic motor neuron and interneuron subtypes. To identify the action of this network, we performed a genome-wide analysis of the regulatory actions of three key ventral determinants in mammalian neural tube patterning: Nkx2.2, Nkx6.1 and Olig2. Previous studies have demonstrated that each factor acts predominantly as a transcriptional repressor, at least in part, to inhibit alternative progenitor fate choices. Here, we reveal broad and direct repression of multiple alternative fates as a general mechanism of repressor action. Additionally, the repressor network targets multiple Shh signaling components providing negative feedback to ongoing Shh signaling. Analysis of chromatin organization around Nkx2.2, Nkx6.1 and Olig2 bound regions, together with co-analysis of engagement of the transcriptional activator Sox2, indicate that repressors bind to, and likely modulate the action of, neural enhancers. Together, the data suggest a model for neural progenitor specification downstream of Shh signaling wherein Nkx2.2 and Olig2 direct repression of alternative neural progenitor fate determinants, an action augmented by the overlapping activity of Nkx6.1 in each cell type. Integration of repressor and activator inputs, notably activator inputs mediated by Sox2, is likely a key mechanism in achieving cell type-specific transcriptional outcomes in mammalian neural progenitor fate specification.

Gene regulatory networks (GRNs) describe the progression of transcriptional states that take a single-celled zygote to a multicellular organism. It is well documented that GRNs can evolve extensively through mutations to cis-regulatory modules (CRMs). Transcription factor proteins that bind these CRMs may also evolve to produce novelty. Coding changes are considered to be rarer, however, because transcription factors are multifunctional and hence are more constrained to evolve in ways that will not produce widespread detrimental effects. Recent technological advances have unearthed a surprising variation in DNA-binding abilities, such that individual transcription factors may recognize both a preferred primary motif and an additional secondary motif. This provides a source of modularity in function. Here, we demonstrate that orthologous transcription factors can also evolve a changed preference for a secondary binding motif, thereby offering an unexplored mechanism for GRN evolution. Using protein-binding microarray, surface plasmon resonance, and in vivo reporter assays, we demonstrate an important difference in DNA-binding preference between Tbrain protein orthologs in two species of echinoderms, the sea star, Patiria miniata ,a nd the sea urchin,Strongylocentrotus purpuratus. Although both orthologs recognize the same primary motif, only the sea star Tbr also has a secondary binding motif. Our in vivo assays demonstrate that this difference may allow for greater evolutionary change in timing of regulatory control. This uncovers a layer of transcription factor binding divergence that could exist for many pairs of orthologs. We hypothesize that this divergence provides modularity that allows orthologous transcription factors to evolve novel roles in GRNs through modification of binding to secondary sites.

The Drosophila male-specific lethal (MSL) dosage compensation complex increases transcript levels on the single male X chromosome to equal the transcript levels in XX females. However, it is not known how the MSL complex is linked to its DNA recognition elements, the critical first step in dosage compensation. Here, we demonstrate that a previously uncharacterized zinc finger protein, CLAMP (chromatin-linked adaptor for MSL proteins), functions as the first link between the MSL complex and the X chromosome. CLAMP directly binds to the MSL complex DNA recognition elements and is required for the recruitment of the MSL complex. The discovery of CLAMP identifies a key factor required for the chromosome-specific targeting of dosage compensation, providing new insights into how subnuclear domains of coordinate gene regulation are formed within metazoan genomes.

Transcriptional enhancers are a primary mechanism by which tissue-specific gene expression is achieved. Despite the importance of these regulatory elements in development, responses to environmental stresses and disease, testing enhancer activity in animals remains tedious, with a minority of enhancers having been characterized. Here we describe 'enhancer-FACS-seq' (eFS) for highly parallel identification of active, tissue-specific enhancers in Drosophila melanogaster embryos. Analysis of enhancers identified by eFS as being active in mesodermal tissues revealed enriched DNA binding site motifs of known and putative, previously uncharacterized mesodermal transcription factors. Naive Bayes classifiers using transcription factor binding site motifs accurately predicted mesodermal enhancer activity. Application of eFS to other cell types and organisms should accelerate the cataloging of enhancers and understanding how transcriptional regulation is encoded in them.

Background: Transcription factors (TFs) play a central role in regulating gene expression by interacting with cis-regulatory DNA elements associated with their target genes. Recent surveys have examined the DNA binding specificities of most Saccharomyces cerevisiae TFs, but a comprehensive evaluation of their data has been lacking. Results: We analyzed in vitro and in vivo TF-DNA binding data reported in previous large-scale studies to generate a comprehensive, curated resource of DNA binding specificity data for all characterized S. cerevisiae TFs. Our collection comprises DNA binding site motifs and comprehensive in vitro DNA binding specificity data for all possible 8-bp sequences. Investigation of the DNA binding specificities within the basic leucine zipper (bZIP) and VHT1 regulator (VHR) TF families revealed unexpected plasticity in TF-DNA recognition: intriguingly, the VHR TFs, newly characterized by protein binding microarrays in this study, recognize bZIP-like DNA motifs, while the bZIP TF Hac1 recognizes a motif highly similar to the canonical E-box motif of basic helix-loop-helix (bHLH) TFs. We identified several TFs with distinct primary and secondary motifs, which might be associated with different regulatory functions. Finally, integrated analysis of in vivo TF binding data with protein binding microarray data lends further support for indirect DNA binding in vivo by sequence-specific TFs. Conclusions: The comprehensive data in this curated collection allow for more accurate analyses of regulatory TF-DNA interactions, in-depth structural studies of TF-DNA specificity determinants, and future experimental investigations of the TFs' predicted target genes and regulatory roles., National Human Genome Research Institute (U.S.) (grant R01 HG003420), National Human Genome Research Institute (U.S.) (grant R01 HG003985), American Heart Association (postdoctoral fellowship 10POST3650060)