Brian Gebelein - US grants

DESCRIPTION (provided by applicant) Hox transcription factors are expressed in unique patterns along the anterior-posterior axis to regulate diverse morphogenetic processes. Members of this protein family bind DNA and regulate gene expression by forming protein complexes with the Hox cofactors, Extradenticle (Exd) and Homothorax (Hth). This finding has led to the hypothesis that Hox proteins select for distinct developmental pathways by controlling the expression of unique combinations of target genes. Interestingly, however, many of the different Hox protein complexes interact with identical or overlapping DNA sequences. Thus, how Hox transcription factors can bind highly related sequences in vitro, and yet direct different developmental pathways in vivo remains unclear. Recently, we, in collaboration with M. Affolter's laboratory (Basel, Switzerland), have characterized a 48 base pair enhancer element (1ab48/95) within the labial (lab) homeobox gene that contains binding sites for Lab, Exd, and Hth. These three transcription factor proteins form a complex with 1ab48/95 in vitro, and each of these binding sites is required to confer gut-specific gene expression in vivo. However, these factors are not sufficient to drive expression of 1ab48/95, as no activity is detected within regions of the head ectoderm, where all three proteins are also co-expressed. These results suggest that additional cofactors are required for the proper spatial expression pattern of the 1ab48/95 enhancer. In this proposal our goals are to: 1) identify the critical nucleotide sequences within 1ab48/95 required for enhancer activity, 2) identify additional proteins that interact with Lab/Exd/Hth and the 1ab48/95 DNA element, and determine their role in the activation of 1ab48/95, and 3) establish an in vivo system to test the ability of additional Hox transcription factors to regulate sequence elements within the endoderm. Taken together, we are optimistic that the characterization of Hox gene activation within the endoderm will serve as a model for how a developmentally-regulated DNA element achieves specificity in vivo.

DESCRIPTION (provided by applicant): How cells interpret positional information to properly differentiate and form distinct tissues and organs is a fundamental problem in developmental biology. In the nervous system, for example, numerous neuronal subtypes and sensory organs form at precisely defined positions. The long-term goal of this proposal is to understand how anterior- posterior positional information provided by Hox transcription factors is combined with neuronal differentiation pathways to dictate the type, number, and location of different neurons and sensory organs in the body. Using Drosophila as a model organism, we are focused on understanding how a specific Hox factor, Abdominal-A (Abd-A), modulates sensory organ formation by activating rhomboid (rho). rho encodes a protease that processes an epidermal growth factor (EGF) ligand to induce additional neurons and a set of hepatocyte-like cells. Through bioinformatics and transgenic reporter assays, we identified two Hox-regulated rho enhancers expressed in a specific subset of abdominal sensory neurons. The biochemical and genetic characterization of a conserved enhancer region uncovered a novel mechanism used by Hox factors and their conserved co-factors Extradenticle (Exd) and Homothorax (Hth) to stimulate gene expression: Abd- A antagonizes transcriptional repression by Senseless (Sens), a neuronal zinc finger protein, through direct competition for DNA binding sites. Sens and its vertebrate homologues Growth factor independence-1 (Gfi1) are critical regulators of sensory organ development in both the fly and mouse. We hypothesize that Hox-Sens antagonism is a general mechanism of gene regulation. This hypothesis as well as the identification of other Hox-neuronal transcription factor interactions will be tested in the following aims: 1) Determine the mechanisms used by Abd-A to stimulate rho, 2) Test the role of Hox- Sens competition in the regulation of gene expression, and 3) Identify additional neuronal inputs that regulate rho in ch organ SOP cells. These experiments take advantage of genetic tools available in Drosophila, which unlike in the vertebrate, contain a single set of non-redundant Hox factors. In addition to controlling neuronal development, the Hox, Exd, Hth, and Sens vertebrate homologues all regulate blood cell formation and have been implicated in leukemia. Thus, the Hox and Sens/Gfi1 molecular mechanisms uncovered in this grant are relevant to human development and disease. Public Health Relevance: We have identified two factors that regulate nervous and blood system development. This grant is focused on how these factors function to specify sensory organs using the fruit fly as a model system. As both factors have been implicated in leukemia, our studies are likely to shed new insight into both Human development and disease.

DESCRIPTION (provided by applicant): Complex animals use hundreds of transcription factors (TFs) to accurately control cell-specific gene expression during the differentiation of specialized cell types within each organ. While genomic approaches have shown that many TFs bind thousands of overlapping regions, deciphering which DNA binding events and TF interactions are biologically meaningful remains a major challenge. The long-term goal of this application is to obtain a high-resolution understanding of the TFs, transcriptional mechanisms, and cis-regulatory logic used to ensure robust cell-specific EGF signaling during Drosophila development. Our experimental system is the transcriptional activation of the rhomboid (rho) protease that triggers EGF secretion from specific abdominal sensory organ precursor cells (SOPs) to induce metabolic cells (oenocytes) needed for animal growth and viability. Since only a subset of abdominal but not thoracic SOPs activate rho and the transcriptional levels of rho dictate the number of oenocytes specified, the regulation of rho serves as a great model to understand how regional- and tissue-restricted transcription factors are integrated to control robust cell-specific gene expression and phenotypic outcomes. Our findings during the first funding cycle of this grant revealed that: A) rho contains multiple cis-regulatory modules (CRMs) that activate abdominal SOP gene expression; B) A rho CRM contains numerous overlapping TF binding sites that directly integrate five TFs including an Abdominal-A (Abd-A) Hox complex containing the Extradenticle and Homothorax Hox cofactors and two neuronal transcription factors (Senseless and Pax2); C) AbdA-Senseless antagonism is a novel conserved Hox transcriptional mechanism that controls both EGF signaling in flies and blood cell proliferation and leukemia progression in mice. Building on these findings, this application has three aims: 1) Determine how the regional Abd-A Hox factor is integrated with the neural-restricted Pax2 factor to activate rho and assess which other Hox factors use Pax2 as a cofactor. 2) Define the role of additional neuronal transcriptional inputs that regulate rho in a specific subset of SOPs. 3) Use the underlying cis-regulatory logic to develop a bioinformatics algorithm to predict additional rho CRMs that ensure robust expression levels and phenotypes. Our approach combines the advantages of Drosophila genetics, non-biased mutagenesis reporter assays, and BAC genomic rescue assays with the speed of cell culture, biochemistry and bioinformatics. The successful completion of these aims has a high potential to uncover novel TF interactions that will open up new avenues of research. In addition, by coupling high-resolution mutagenesis studies with genomic rescue assays that provide a biologically meaningful readout, we will obtain new insights into how CRMs and transcription factors control robust cell-specific gene expression within a complex animal. Since the TFs and biological processes studied are highly conserved between flies and mammals, we are optimistic our mechanistic studies will continue to uncover new gene regulatory mechanisms relevant to human health and development.

DESCRIPTION (provided by applicant): Normal brain function relies on the correct assembly of neural circuits during development. This process starts with the patterning of neural progenitors along the dorsal-ventral and anterior-posterior axes to give rise to distinct subtypes of neurons. A number of key transcription factors have been shown to control the process of neuronal subtype specification. Of these, the homeobox genes Gsx1 and Gsx2 play essential roles in the patterning and differentiation of neuronal cell types that arise from the lateral ganglionic eminence (LGE) progenitors of the mouse telencephalon including striatal projection neurons and olfactory bulb interneurons. Not only is the correct specification of neuronal subtypes crucial for neural circuit formation but also the generation of appropriate numbers of each subtype. Less is known about the mechanisms that control this balance during brain development. In our previous funding period for this grant, we showed that while both Gsx1 and Gsx2 can ultimately specify the same subtypes of neurons, they regulate LGE progenitor maturation differently. Specifically, Gsx2 appears to maintain LGE progenitors in an immature (i.e. stem cell) state while Gsx1 promotes progenitor maturation and transition from the ventricular zone (VZ) to the subventricular zone (SVZ). Accordingly, these results correlate well with the expression of these genes; Gsx2 is largely restricted to VZ progenitors whereas Gsx1 is found enriched in progenitors positioned at the VZ/SVZ boundary. With this application, we plan to combine the mouse genetic expertise of the Campbell lab with the molecular and biochemical expertise of the Gebelein lab to uncover the mechanisms underlying some of the genetic phenotypes our group and others have described for the Gsx mouse mutants. Thus, the studies outlined in this proposal will test the general hypothesis that differential regulation of Gsx2 gen expression and unique protein modifications/interactions underlie the distinct roles that Gsx1 and Gsx2 play in LGE progenitor development. We will test this hypothesis in 3 independent specific aims: 1) To understand the cis-regulatory mechanisms that control Gsx2 expression in LGE progenitors. 2) To determine whether selective MAPK phosphorylation of Gsx1, but not Gsx2, underlies its unique role in regulating LGE progenitor maturation. 3) To study the role of physical interactions between Ascl1 (Mash1) and Gsx2 in the control of LGE progenitor maturation. Our approach will combine the use of mouse, frog and fly genetics with molecular and biochemical approaches to study transcriptional control of neuronal specification in the ventral telencephalon. The unique makeup of our Division of Developmental Biology allows us to take this broad approach and as a result increases our chances of success to both, gain a deeper understanding of how Gsx factors control telencephalic development as well as uncover new gene regulatory mechanisms that may underlie aspects of dysfunction in certain childhood neurological disorders.

How an animal develops complex tissue types during its lifetime is an important and fundamental question. Many cell signals are required to work together so this process works flawlessly. This project will systematically build a theoretical understanding of a cell signaling pathway in developing fruit fly embryos. Like many genetic pathways required for animal development, this signaling pathway was initially discovered using fruit flies and later shown to be essential for normal human development and health. This project will foster scientific collaborations between the U.S and Israel. Students from biology, engineering, and physics will examine how an external signal is converted into specific outputs using experimental and computational approaches. Both graduate and undergraduate students will be trained by a multidisciplinary research team that has wide-ranging expertise in laboratory and theoretical methods. Undergraduate students in Biomedical and Computer engineering will gain hands-on laboratory experiences and work with advanced students as a team, to achieve a common goal. This will help them to communicate ideas and results to fellow students and will promote interdisciplinary training.

The central aim of this collaborative research project is to understand how different cell types convert the same cell signaling pathway into distinct responses during animal development. Defining how a signal invokes appropriate cell responses is of fundamental importance because signaling pathways ensure essential cell types are generated throughout an organism's lifespan. The Notch signaling pathway in Drosophila is iteratively used to invoke distinct responses in different cell types throughout animal development. The specific goals of this project are to develop a systematic, quantitative understanding of how the Notch signal is converted into cell-specific outputs using an in vivo synthetic biology approach and mathematical modeling. Drosophila carrying a set of reporters that systematically vary in number and architecture of Notch-regulated DNA binding sites will be created. Quantitative expression analysis and transcription factor occupancy data will be obtained using high resolution imaging of fixed and live tissues. Experimental data will be used to build mathematical models and computational simulations. Models will be based on a statistical mechanics description of transcription to describe how key parameters (DNA binding sites, ratios of effector proteins, binding affinities, and protein degradation) alter Notch output. Predictions from these models will be tested experimentally and will be used to improve the mathematical models. A quantitative description for the core Notch transcription module will provide a framework to systematically explore the role of additional biological factors on Notch-mediated transcription.

This collaborative US/Israel project is supported by the US National Science Foundation and the Israeli Binational Science Foundation.

PROJECT ABSTRACT Homeodomain (HD) proteins comprise a large family of transcription factors (TFs) that regulate numerous aspects of animal development. For example, members of the Hox-like (HoxL) and Nkx-like (NKL) HD proteins regulate processes ranging from patterning of the anterior-posterior axis (A-P) of the embryo to specifying individual cell fates within different organ systems. Intriguingly, the HoxL and NKL proteins have highly similar HDs that bind largely overlapping AT-rich DNA sequences in vitro. These findings provide a classic TF specificity paradox: How do TFs with highly similar in vitro DNA binding activities achieve sufficient in vivo specificity to ensure the accurate regulation of genetic programs in different cell types? To address this paradox, my lab is focused on defining how HD TFs achieve in vivo specificity by forming cooperative TF complexes on cis-regulatory modules. Our preliminary and published data reveal that members of the HoxL and NKL TFs differ in their ability to form homo- and heterodimer TF complexes on DNA. For instance, we unexpectedly found that the Gsx/Ind TFs, which specify neuronal cell fates in animals from flies to mammals, differentially regulate gene expression when bound to DNA as monomers versus homodimers. In contrast, the Abdominal-A (Abd-A) Hox TF, which specifies distinct cell fates in the Drosophila abdomen, does not bind DNA as a homodimer, but instead cooperatively binds DNA with three other HD proteins: Extradenticle (Exd), Homothorax (Hth), and Engrailed (En). These data support the hypothesis that HD TFs achieve target and regulatory specificity by binding distinct combinations of AT-rich DNA sites as monomers, cooperative homodimers, or cooperative heterodimers. To test this hypothesis, we propose two aims: In Aim1, we propose to determine how HD monomer versus homodimer binding impacts target gene binding and regulation. To achieve this goal, we will (1) systematically define which HoxL and NKL HDs cooperatively bind DNA as homodimers; (2) assess the regulatory potential of each HD on monomer vs dimer sites in cell culture assays; and (3) define the mechanism and function of Ind homodimer formation on Drosophila neuroblast gene expression using structural biology and transgenic reporter, CUT&RUN, and RNA-seq assays. In Aim2, we propose to define how the choice of Hox heterodimer partner impacts the DNA binding and regulatory specificity of the Abd-A Hox TF. To achieve this goal, we will (1) define the DNA motifs and molecular domains required for cooperative Abd-A/Hth and Abd-A/En complexes; (2) test the role of Abd-A heterodimerization domains in gene activation and repression assays in the Drosophila embryo; (3) define the in vivo binding motifs and target genes regulated by Abd-A with a focus on identifying heterodimer binding events using CUT&RUN and RNA-seq assays. Since the TFs and biological processes studied are highly conserved between flies and mammals, we are optimistic our studies will uncover gene regulatory mechanisms relevant to human health and development.

PROJECT ABSTRACT Homeodomain (HD) proteins comprise a large family of transcription factors (TFs) that regulate numerous aspects of animal development. For example, members of the Hox-like (HoxL) and Nkx-like (NKL) HD proteins regulate processes ranging from patterning of the anterior-posterior axis (A-P) of the embryo to specifying individual cell fates within different organ systems. Intriguingly, the HoxL and NKL proteins have highly similar HDs that bind largely overlapping AT-rich DNA sequences in vitro. These findings provide a classic TF specificity paradox: How do TFs with highly similar in vitro DNA binding activities achieve sufficient in vivo specificity to ensure the accurate regulation of genetic programs in different cell types? To address this paradox, my lab is focused on defining how HD TFs achieve in vivo specificity by forming cooperative TF complexes on cis- regulatory modules. Our preliminary and published data reveal that members of the HoxL and NKL TFs differ in their ability to form homo- and heterodimer TF complexes on DNA. For instance, we unexpectedly found that the Gsx/Ind TFs, which specify neuronal cell fates in animals from flies to mammals, differentially regulate gene expression when bound to DNA as monomers versus homodimers. In contrast, the Abdominal-A (Abd-A) Hox TF, which specifies distinct cell fates in the Drosophila abdomen, does not bind DNA as a homodimer, but instead cooperatively binds DNA with three other HD proteins: Extradenticle (Exd), Homothorax (Hth), and Engrailed (En). These data support the hypothesis that HD TFs achieve target and regulatory specificity by binding distinct combinations of AT-rich DNA sites as monomers, cooperative homodimers, or cooperative heterodimers. To test this hypothesis, we propose two aims: In Aim1, we propose to determine how HD monomer versus homodimer binding impacts target gene binding and regulation. To achieve this goal, we will (1) systematically define which HoxL and NKL HDs cooperatively bind DNA as homodimers; (2) assess the regulatory potential of each HD on monomer vs dimer sites in cell culture assays; and (3) define the mechanism and function of Ind homodimer formation on Drosophila neuroblast gene expression using structural biology and transgenic reporter, CUT&RUN, and RNA-seq assays. In Aim2, we propose to define how the choice of Hox heterodimer partner impacts the DNA binding and regulatory specificity of the Abd-A Hox TF. To achieve this goal, we will (1) define the DNA motifs and molecular domains required for cooperative Abd-A/Hth and Abd-A/En complexes; (2) test the role of Abd-A heterodimerization domains in gene activation and repression assays in the Drosophila embryo; (3) define the in vivo binding motifs and target genes regulated by Abd-A with a focus on identifying heterodimer binding events using CUT&RUN and RNA-seq assays. Since the TFs and biological processes studied are highly conserved between flies and mammals, we are optimistic our studies will uncover gene regulatory mechanisms relevant to human health and development.

The many different cell types within an animal body use signals to communicate, and such signals are required to instruct cells to form complex tissues and organs during embryonic development. Determining how cells convert specific signals into accurate cellular responses is therefore fundamental to understanding both animal and human development. The goal of this project is to systematically build a theoretical model for how a conserved signaling pathway, called Notch, is converted into accurate cellular responses in both developing fruit fly tissues and mammalian cells. Through a scientific collaboration between the U.S and Israel, undergraduate and graduate students from biology, engineering, mathematics, and physics will examine how the Notch signal is converted into specific outputs using experimental and computational approaches. The multidisciplinary research team will also incorporate under-represented high school students, and collectively students will work towards a common goal as a team by combining hands-on laboratory experiences with theoretical computational methods. This approach will help them to communicate ideas and results to fellow students and will promote interdisciplinary training.

Signaling pathways provide a means of cell-to-cell communication to regulate cell-specific responses during development. Cell signaling is typically activated via receptor-ligand interactions at the membrane and relayed into the nucleus via a cascade that converges on an effector transcription factor (TF) that activates and/or represses target genes. How the same core pathway induces reproducible cell-specific outcomes in different tissues remains a major question in biology. The central goal of this project is to build and test predictive models for how the Notch signal is converted into specific transcription responses using an in-vivo synthetic biology approach that incorporates quantitative data with mathematical modeling. Synthetic Notch reporters containing distinct types of DNA binding sites are used to decipher the rules of the Notch transcriptional response. Drosophila genetics, genome engineering, and biochemistry are used to assess how changes in protein stability and gene dose impact cell-specific outputs. Cell culture is used to develop new imaging tools to assess Notch signaling dynamics in real time, and computational simulations are developed to describe how key parameters (DNA binding site composition, ratios of effector proteins, protein binding dynamics, and protein degradation) alter TF complex concentration, enhancer occupancy, and transcriptional output. Collectively, these models will be used to develop a thorough quantitative understanding of Notch signaling using both cell based and whole organism assays.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.