Submitted to the faculty of the Bioinformatics Graduate Program in partial fulfillment of the requirements for the degree Master of Science in the School of Informatics, Indiana University September 2005 / Study of the transcriptional regulation of lymphocyte development has advanced greatly in the past 15 years. Owing to improved techniques and intense interest in the topic, a great many interactions between transcription factors and their target genes have been described. For these B and T cells, a more clear picture is beginning to emerge of how they start with a common progenitor cell, and progressively restrict potential to give many different types of terminally differentiated cells. As B and T cells develop they both follow a roughly similar path that involves early stepwise progression to later stages where multiple developmental options are available. To progress in the developmental regime they share requirements for proper anatomical location and successful rearrangements of the germ line DNA to give the plethora of antibodies and T cell receptors seen in the immune system. Because the amount of information is quickly becoming more than can be assimilated by researchers, a knowledge gap has opened between what is known about the transcription factor activities during this process and what any one individual can recall. To help fill this gap, we have created the LymphTF Database. This database holds interactions between individual transcription factors and their specific targets at a given developmental time. It is our hope that storing the interactions in developmental time will allow for elucidation of regulatory networks which guide the process. Work for this project also included construction of a custom data entry web page that automates many tasks associated with populating the database tables. These tables have also been related in multiple ways to allow for storage of incomplete information on transcription factor activity. This is done without having to replace existing records as details become available. The LymphTF DB is a relational MySQL database which can be accessed freely on the web at http://www.iupui.edu/~tfinterx/.

Notch signals are required to promote T lineage commitment and development and suppress alternative cell fates in the thymus. Although the Notch activating ligand(s) in the thymus is(are) not known, studies have shown that hematopoietic progenitors are sensitive to Delta-like (DL), but not Jagged (Jag)-type ligands. In Chapter 3, I show that DL-expressing bone marrow stromal cell lines exhibit Notch ligand-independent functional heterogeneity in their capacity to support T cell development in vitro. These findings thus suggest the existence of stromal cell-derived signals that work with Notch to support T cell development. In Chapters 4 and 5, I investigated the ability of Fringe proteins to modulate Notch ligand-receptor interactions and the developmental consequences of these interactions for hematopoetic progenitors. Fringe proteins are glycosyl-transferases that enhance Notch activation by DL ligands and inhibit Notch activation by Jag ligands. In Chapter 4 I show that Lunatic Fringe (Lfng) enhances the strength of DL-mediated Notch activation to drive proliferation and expansion of early thymocytes and that DL4 and DL1 display different potencies to induce Notch-dependent outcomes. In Chapter 5, I demonstrate for the first time in a mammalian system that Lfng and Manic Fringe (Mfng) co-operate to enhance DL-Notch interactions and inhibit Jag-Notch interactions in hematopoietic stem cells. Thus, Lfng and Mfng function together to induce T cell development and inhibit B cell, myeloid and NK cell development. Collectively, these data highlight the importance of Fringe proteins in modulating the strength and specificity of Notch signaling levels during hematopoieisis.

Notch signals are required to promote T lineage commitment and development and suppress alternative cell fates in the thymus. Although the Notch activating ligand(s) in the thymus is(are) not known, studies have shown that hematopoietic progenitors are sensitive to Delta-like (DL), but not Jagged (Jag)-type ligands. In Chapter 3, I show that DL-expressing bone marrow stromal cell lines exhibit Notch ligand-independent functional heterogeneity in their capacity to support T cell development in vitro. These findings thus suggest the existence of stromal cell-derived signals that work with Notch to support T cell development. In Chapters 4 and 5, I investigated the ability of Fringe proteins to modulate Notch ligand-receptor interactions and the developmental consequences of these interactions for hematopoetic progenitors. Fringe proteins are glycosyl-transferases that enhance Notch activation by DL ligands and inhibit Notch activation by Jag ligands. In Chapter 4 I show that Lunatic Fringe (Lfng) enhances the strength of DL-mediated Notch activation to drive proliferation and expansion of early thymocytes and that DL4 and DL1 display different potencies to induce Notch-dependent outcomes. In Chapter 5, I demonstrate for the first time in a mammalian system that Lfng and Manic Fringe (Mfng) co-operate to enhance DL-Notch interactions and inhibit Jag-Notch interactions in hematopoietic stem cells. Thus, Lfng and Mfng function together to induce T cell development and inhibit B cell, myeloid and NK cell development. Collectively, these data highlight the importance of Fringe proteins in modulating the strength and specificity of Notch signaling levels during hematopoieisis.

<p>The E-protein transcription factors E2A and HEB regulate various cell processes during the development of B and T lymphocytes, including cell differentiation, lineage commitment, recombination of immune receptor genes, proliferation, and survival. B cell development is dependent on E2A from the earliest stages whereas T cell development relies on the cooperative efforts of both E2A and HEB. Established work demonstrates that the timing and dosage of E-protein expression is critical for mediating these diverse functions. The goal of this dissertation is to develop and utilize new genetic tools to manipulate the timing and dosage of E2A and HEB expression in order to enhance our understanding of E-protein function. Here we develop two new mouse models to identify novel lineage and stage specific roles of E-proteins during B lineage commitment and thymocyte selection.</p><p>First, we have generated an E2A inducible mouse model to allow reversible regulation of E2A function and precise timing of induction at the protein level. This system was created by inserting a tamoxifen responsive region of the estrogen receptor ligand binding domain (ER) at the carboxyl end of the <italic>tcfe2a</italic> gene, encoding E2A, to generate E2AER fusion proteins. To our knowledge, the ER fusion system has not yet been tested from an endogenous locus in live animals. Using the E2AER system, we have demonstrated rapidly induced E2AER activity upon tamoxifen treatment that is capable of supporting B cell development in an <italic>ex vivo</italic> culture system. In addition to characterizing the kinetics and reversibility of this inducible system, we have utilized tamoxifen treatment of E2AER B cell progenitors to identify potential novel E2A target genes driving B lineage commitment.</p><p>Second, we have analyzed E-protein function during the double positive (DP) stage of alpha beta T cell development by using a Cre-loxp conditional deletion system. Here, E-protein dosage was manipulated by removal of both E2A and HEB, and the timing of deletion was controlled by using a CD4Cre transgene. During development, survival through the DP stage and initiation of differentiation to the subsequent single positive (SP) stage for generation mature alpha beta T cells is dependent on the production of a functional alpha beta T cell receptor (TCR). The mechanism that maintains cells at the DP stage prior to expression of a mature TCR remains unclear. In this study, we have shown that E2A and HEB together are required to maintain DP fate and regulate the transition to the SP stage. Loss of E2A and HEB in DP thymocytes was sufficient to trigger DP to SP differentiation, even in the absence of a TCR. Deletion of E2A and HEB allowed cells to bypass the requirement for a TCR-mediated positive selection signal. These findings identify E2A and HEB as key regulators enforcing thymocyte positive selection to ensure maturing T cells express a functional receptor.</p> / Dissertation

La régulation transcriptionnelle des eucaryotes supérieurs est un processus hautement contrôlé du point de vue spatial et temporel lors du développement, ou en réaction à l’environnement. La transcription ciblée des gènes codant requiert l’assemblage d’un complexe de pré-initiation (PIC) aux promoteurs comprenant l’ARN Polymérase (Pol) II et les facteurs généraux de transcription (GTFs) et dépend de la médiation d’un signal par les facteurs activateurs de transcription (TFs). Les années récentes ont montré que la transition de l’initiation vers l’élongation productive de la transcription représente une étape clé de la régulation de l’expression des gènes. Ce processus est également contrôlé par la structure de la chromatine, les modifications d’histones et par la présence d’éléments cis-régulateurs tels que les ‘enhancers’ ou les ‘silencers’. Au cours de ma thèse, nous avons entrepris de décrypter les mécanismes de régulation transcriptionnelle impliqués dans les étapes du développement lymphocytaire. Nous avons essentiellement travaillé sur des thymocytes primaires murins isolés au stade de différenciation double positif (DP, CD4+/CD8+) pour lequel de nombreuses séquences de type ‘enhancers’ ont été caractérisées dans la littérature scientifique. Nous avons également utilisé des lymphocytes B humains (Raji) immortalisés pour certaines des expériences impliquant des manipulation génétiques complexes permettant l’étude de mutants du domaine carboxy-terminal (CTD) de Pol II. En couplant des approches d’analyse à l’échelle du génome au séquençage à haut-débit, nous avons établi des cartographies fines de la localisation de Pol II, des GTFs, des TFs,de modifications d’histones (ChIP-Seq) et de nucléosomes (MNase-seq) ainsi que la caractérisation de populations variées d’ARN par RNA-seq. Nos principaux résultats ont révélé (i) l’assemblage du PIC et la transcription des enhancers tissus-spécifiques, (ii) l’existence de plateforme d’initiation de la transcription (TIPs) aux enhancers et aux promoteurs tissus-spécifique, (ii) que le contenu en GC représente l’un des principaux éléments promoteurs mammifères en permettant une ouverture transcription-indépendante de la chromatine, (iv) l’importance d’une nouvelle modification post-traductionnelle du domaine CTD de Pol II pour la progression de l’enzyme en élongation et finalement (v) que la modification de l’histone H3 sur le résidu K36 methylé corrèle avec l’épissage des transcrits Pol II. Globalement, les résultats les plus important de ce manuscrit consistent dans la mise en évidence de la transcription des enhancers comme caractérisant l’expression des gènes tissus-spécifiques et dans l’importance des ilots CpG comme éléments promoteurs mammifères permettant la formation d’une structure ouverte de la chromatine. / Transcriptional regulation in higher eukaryotes resembles a tightly controlled temporal and spatial process, as exemplified during development or an organism’s response to environmental stimuli. Directed transcription requires the assembly of the preinitiation complex (PIC) at the promoter of protein-coding genes, including RNA Polymerase (Pol) II and the general transcription factors (GTFs), mediated by activating transcription factors (TFs). Several rate-limiting steps further control the progression of Pol II initiation to productive elongation of the gene. This process is further controlled by chromatin structure, histone modifications as well as cis-regulatory elements, such as enhancers or silencers. We set out to decipher some of these regulatory mechanisms during the tightly controlled process of lymphocyte development. Our work primarily made use of primary mouse thymocytes in CD4+/CD8+ double positive (DP, CD4+/CD8+) stage during T-cell development. To our advantage, many developmentally important cis-regulatory regions are well characterized in this cell population. For genetic manipulations, we made use of the Raji B-cell lymphoma cell-line. Using high throughput genome-wide approaches based on next generation sequencing (NGS), we performed both localization studies of Pol II, GTFs, TFs, histone modifying enzymes, histone modifications and nucleosomes as well as deep-sequencing of different RNA transcript populations. In summary, we find that (i) PICs assemble at tissue-specific enhancers leading to local transcription, (ii) large transcription initiation platforms (TIPs) at tissue-specific promoters and enhancers exist, which correlate with high CG-content of the DNA and transcription factor binding sites (TFBS), (iii) GC-content regulates the nucleosomal structure and initiation, including directionality, at promoters, (iv) Pol II is phosphorylated at a new residue of it C-terminal domain (CTD) in the 3’ regions of genes and (v) splicing events can influence the chromatin structure. Altogether, these results show that PIC formation at and transcription of enhancers are important for the regulation of T-cell target genes, that CpG islands represent important if not the major regulatory promoter element in mammals guiding tissue-specific gene expression and nucleosome structure, as well as novel mechanisms of Pol II elongation and the effect on chromatin structure.

No description available.

Lymphocytes are essential for the generation of specific immunity. Development of B cells in the bone marrow and T cells in the thymus have several analogous features, and are tightly regulated processes. Even though there is an increasing amount of information concerning lymphopoiesis, a lot of questions remain. The aim of this thesis has been to understand some of the molecular events that contribute to the control of lymphocyte development. Expression of the B cell receptor is an important checkpoint in B lymphocyte development. The Dµ protein is a truncated B cell receptor that can induce some of the signals elicited by full length µ, but cannot promote further B cell differentiation. In order to determine if this could stem from an impaired survival signal, we introduced Bcl-2 into RAG2 deficient Dµ transgenic mice. Analysis of these mice showed that Dµ could not support pre-B cell maturation despite extended survival of B cell precursors by Bcl-2. In addition, data from recombination competent Dµ transgenic mice demonstrated that the Dµ induced partial block is permissive for marginal zone B cell development, whereas the formation of follicular B cells is severely reduced. The bHLH family of transcription factors is known to be involved in the regulation of lymphocyte development. Whereas the roles of E2A and HEB have been well documented in both B- and T-lymphocytes, detailed knowledge concerning E2-2 is lacking. To address the role of E2-2 in B cell development, we have reconstituted mice, using E2-2 deficient fetal liver cells, and analysed the B cell compartments. We also measured mRNA expression patterns for the three E-proteins in wildtype mice. Resulting data show that, in addition to a role in B cell lineage entry, E2-2 is required for efficient expansion of pro-B cells, and also influences the follicular versus marginal zone decision. While focusing on assigning a role for E2-2 in T-cell development, we analyzed the expression of the E-proteins during this process and performed functional studies in fetal thymic organ cultures. E2-2 deficient mouse embryos were shown to display a partial block at the DN3 stage, which was not due to proliferation or apoptosis defects. In addition, analysis of expression levels of the pre-Talpha chain suggests that E2-2 may play a role in the regulation of transcription of pre-Talpha, and therefore in the assembly of the pre-T cell receptor.