<p>Cis-elements govern the key step of transcription to regulate gene expression within a cell. Identification of utilized elements within a particular cell line will help further our understanding of individual and cumulative effects of trans-acting factors. These elements can be identified through an assay leveraging the ability of DNaseI to cut DNA that is in an open and accessible state making it hypersensitive to cleavage. Here we develop and explore computational techniques to measure open chromatin from sequencing and microarray data. We are able to identify 94,925 DNaseI hypersensitive sites genome-wide in CD4+ T cells. Interestingly, only 16%-20% of these sites were found in promoters. We also show that these regions are associated with different chromatin modifications. We found that DNaseI data can also be used to identify precise 'footprints' indicating protein-DNA interaction sites. Footprints for specific transcription factors correlate well with ChIP-seq enrichment, reveal distinct conservation patters, and reveal a cell-type specific arrangement of transcriptional regulation. These footprints can be used in addition to or in lieu of ChIP-seq data to better understand genomic regulatory systems.</p> / Dissertation

Chemistry / Although molecules that bind DNA have the potential to modify gene expression, the reality of targeting DNA in a sequence-specific manner is still a problematic but worthwhile goal. The Iverson lab has been exploring DNA recognition through a motif known as threading polyintercalation based on connecting intercalating naphthalene diimide (NDI) units, which are molecules that insert themselves between DNA base pairs, together with peptide linkers. These polyintercalators interact with both DNA grooves by “threading” or winding through the DNA, like a snake might climb a ladder. Initially, two different bisintercalator modules with altered sequence specificities and different groove binding topologies were discovered and used to inspire the design of a hybrid NDI tetraintercalator. Surprisingly enough, this tetraintercalator bound sequence-specifically with a dissociation half-life of 16 days to its preferred 14 bp site, a record at the time it was reported for a synthetic DNA-binding molecule. The work reported here expands on the capabilities of this modular threading polyintercalation motif. Chapter 2 describes the ability of a new hybrid NDI tetraintercalator, where the bisintercalator modules are connected together in a different way compared to the previously studied tetraintercalator, to subtly discriminate between similar binding sites. Chapter 3 offers a structural understanding, through NMR analysis, for the sequence recognition abilities of this new tetraintercalator. Chapter 4 analyzes the binding abilities of an un-optimized NDI octaintercalator and proposes how to approach the second-generation design of longer polyintercalators. Chapter 5 describes the optimization of the originally designed NDI tetraintercalator by serially lengthening one of the linkers to produce a tetraintercalator with a 57 day dissociation half-life from its 14 bp sequence, a new record for a synthetic DNA-binding molecule. Using the optimized linker in the context of an NDI hexaintercalator allows for binding to a 22 bp designed site, a record for a synthetic non-nucleic acid molecule. Chapter 6 recounts a focused library screening to search for bisintercalators with new sequence specificities. These efforts have laid the groundwork to progress toward studies aimed at understanding how these molecules might function to prevent transcription in a sequence-dependent manner in vivo. / text

Indiana University-Purdue University Indianapolis (IUPUI) / Hydroxyl radical protein footprinting coupled with mass spectrometry has become an invaluable technique for protein structural characterization. In this method, hydroxyl radicals react with solvent exposed amino acid side chains producing stable, covalently attached labels. Although this technique yields beneficial information, the extensive list of known oxidation products produced increases the complexity of identifying and quantifying oxidation products. The current methods available for quantifying the extent of oxidation either involve manual analysis steps, or limit the number of searchable modifications or the size of sequence database. This creates a bottleneck which can result in a long and arduous analysis process, which is further compounded in a complex sample. In addition to the data complexity, the peptides containing the oxidation products of hydroxyl radical-mediated protein footprinting experiments are typically much less abundant than their unoxidized counterparts. This is inherent to the design of the experiment as excessive oxidation may lead to undesired conformational changes or unfolding of the protein, skewing the results. Thus, as the complexity of the systems studied using this method expands, the detection and identification of these oxidized species can be increasingly difficult with the limitations of data-dependent acquisition (DDA) and one-dimensional chromatography. The recently published in cell FPOP method exemplifies where this field is headed - larger and more complex systems. This dissertation describes two new methodologies and one new technology for hydroxyl radical-mediated protein footprinting, expanding the applicability of the method. First is development of a new footprinting analysis method for both peptide and residue level analysis, allowing for faster quantification of results. This method utilizes a customized multilevel search workflow developed for an on-market search platform in conjunction with a quantitation platform developed using a free Excel add-in, expediting the analysis process. Second is the application of multidimensional protein identification technology (MudPIT) in combination with hydroxyl radical footprinting as a method to increase the identification of quantifiable peptides in these experiments. Last is the design and implementation of a flow system for in cell FPOP, which hydrodynamically focuses the cells, and when used yielded a 13-fold increase in oxidized proteins and 2 orders of magnitude increase in the dynamic range of the method.

No description available.

L'objet de cette thèse de bioinformatique est de mieux comprendre l’ensemble des systèmes de régulation génique chez les bactéries. La disponibilité de centaines de génomes complets chez les bactéries ouvre la voie aux approches de génomique comparative et donc à l’étude de l’évolution des réseaux transcriptionnels bactériens. Dans un premier temps, nous avons implémenté et validé plusieurs méthodes de prédiction d’opérons sur base des génomes bactériens séquencés. Suite à cette étude, nous avons décidé d’utiliser un algorithme qui se base simplement sur un seuil sur la distance intergénique, à savoir la distance en paires de bases entre deux gènes adjacents. Notre évaluation sur base d’opérons annotés chez Escherichia coli et Bacillus subtilis nous permet de définir un seuil optimal de 55pb pour lequel nous obtenons respectivement 78 et 79% de précision. Deuxièmement, l’identification des motifs de régulation transcriptionnelle, tels les sites de liaison des facteurs de transcription, donne des indications de l’organisation de la régulation. Nous avons développé une méthode de recherche d’empreintes phylogénétiques qui consiste à découvrir des paires de mots espacés (dyades) statistiquement sur-représentées en amont de gènes orthologues bactériens. Notre méthode est particulièrement adaptée à la recherche de motifs chez les bactéries puisqu’elle profite d’une part des centaines de génomes bactériens séquencés et d’autre part les facteurs de transcription bactériens présentent des domaines Hélice-Tour-Hélice qui reconnaissent spécifiquement des dyades. Une évaluation systématique sur 368 gènes de E.coli a permis d’évaluer les performances de notre méthode et de tester l’influence de plus de 40 combinaisons de paramètres concernant le niveau taxonomique, l’inférence d’opérons, le filtrage des dyades spécifiques de E.coli, le choix des modèles de fond pour le calcul du score de significativité, et enfin un seuil sur ce score. L’analyse détaillée pour un cas d’étude, l’autorégulation du facteur de transcription LexA, a montré que notre approche permet d’étudier l’évolution des sites d’auto-régulation dans plusieurs branches taxonomiques des bactéries. Nous avons ensuite appliqué la détection d’empreintes phylogénétiques à chaque gène de E.coli, et utilisé les motifs détectés comme significatifs afin de prédire les gènes co-régulés. Au centre de cette dernière stratégie, est définie une matrice de scores de significativité pour chaque mot détecté par gène chez l’organisme de référence. Plusieurs métriques ont été définies pour la comparaison de paires de profils de scores de sorte que des paires de gènes ayant des motifs détectés significativement en commun peuvent être regroupées. Ainsi, l’ensemble des nos méthodes nous permet de reconstruire des réseaux de co-régulation uniquement à partir de séquences génomiques, et nous ouvre la voie à l’étude de l’organisation et de l’évolution de la régulation transcriptionnelle pour des génomes dont on ne connaît rien. The purpose of my thesis is to study the evolution of regulation within bacterial genomes by using a cross-genomic comparative approach. Nowadays, numerous genomes have been sequenced facilitating in silico analysis in order to detect groups of functionally related genes and to predict the mechanism of their relative regulation. In this project, we combined prediction of operons and regulons in order to reconstruct the transcriptional regulatory network for a bacterial genome. We have implemented three methods in order to predict operons from a bacterial genome and evaluated them on hundreds of annotated operons of Escherichia coli and Bacillus subtilis. It turns out that a simple distance-based threshold method gives good results with about 80% of accuracy. The principle of this method is to classify pairs of adjacent genes as “within operon” or “transcription unit border”, respectively, by using a threshold on their intergenic distance: two adjacent genes are predicted to be within an operon if their intergenic distance is smaller than 55bp. In the second part of my thesis, I evaluated the performances of a phylogenetic footprinting approach based on the detection of over-represented spaced motifs. This method is particularly suitable for (but not restricted to) Bacteria, since such motifs are typically bound by factors containing a Helix-Turn-Helix domain. We evaluated footprint discovery in 368 E.coli K12 genes with annotated sites, under 40 different combinations of parameters (taxonomical level, background model, organism-specific filtering, operon inference, significance threshold). Motifs are assessed both at the level of correctness and significance. The footprint discovery method proposed here shows excellent results with E. coli and can readily be extended to predict cis-acting regulatory signals and propose testable hypotheses in bacterial genomes for which nothing is known about regulation. Moreover, the predictive power of the strategy, and its capability to track the evolutionary divergence of cis-regulatory motifs was illustrated with the example of LexA auto-regulation, for which our predictions are remarkably consistent with the binding sites characterized in different taxonomical groups. A next challenge was to identify groups of co-regulated genes (regulons), by regrouping genes with similar motifs, in order to address the challenging domain of the evolution of transcriptional regulatory networks. We tested different metrics to detect putative pairs of co-regulated genes. The comparison between predicted and annotated co-regulation networks shows a high positive predictive value, since a good fraction of the predicted associations correspond to annotated co-regulations, and a low sensitivity, which may be due to the consequence of highly connected transcription factors (global regulator). A regulon-per-regulon analysis indeed shows that the sensitivity is very weak for these transcription factors, but can be quite good for specific transcription factors. The originality of this global strategy is to be able to infer a potential network from the sole analysis of genome sequences, and without any prior knowledge about the regulation in the considered organism.

Legionella pneumophila, an intracellular pathogen of protozoa, is well known for its dimorphic life cycle that alternates between the vegetative replicative form (RF) and highly infectious cyst-like form (CLF). To this date several virulence factors including LpRpoS, LpIHF, and the Dot/Icm secretion system have been found to be required for the survival of L. pneumophila in macrophage and protozoa. Here we have identified and characterised Lpg1967, an orthologue of Pseudomonas PsrA in L. pneumophila. PsrA (Lpg1967) was found to regulate the expression of previously known virulence factors such non-coding RNAs, RsmY/Z, RpoS, LpIHF, flagella and Dot/Icm Type IV secretion system. In addition, the ΔpsrA mutant strain was unable to establish Legionella-containing vacuole and thus displayed a severe growth defect in the U937 derived macrophage cell line. Thus, PsrA was found to play an important role in controlling the regulatory cascade governing virulence in L. pneumophila. / October 2014

Les télomères sont les extrémités des chromosomes linéaires des eucaryotes.Ils sont constitués de répétitions en tandem d'un motif court riche enguanine, et liés par des protéines spécifiques. Chez les vertébrés cesprotéines forment un complexe appelé le shelterin et dont l'intégrité estcritique pour assurer la réplication correcte des extrémités deschromosomes, et pour les protéger contre une prise en charge illicite parles voies de réparation des cassures double-brin de l'ADN. Des dysfonctionsdes télomères engendrent une instabilité du génome qui peut conduire à lasénescence ou au cancer. Les télomères représentent une région subnucléaireoù les protéines du shelterin sont fortement enrichies, ce qui permetl'implication dans les fonctions biologiques d'interactions de basseaffinité. Parmi les protéines du shelterin, la protéine de liaison auxrépétitions télomériques TRF2 et son partenaire constitutif RAP1 sont lesfacteurs majeurs responsables de la protection des extrémités. Nous avonsétudié en détails l'assemblage du complexe TRF2/RAP1 par des approchesintégrées de biologie structurale, de biophysique et de biochimie.Nous avons montré que cet assemblage s'accompagne d'importants ajustementsde conformation des deux protéines, et implique une interaction de basseaffinité qui engage de grandes régions des deux protéines et affecte leurspropriétés d'interactions. / Telomeres are the ends of eukaryotic linear chromosomes. They are made oftandem repeats of a short guanine-rich motif and bound by specific proteins.In vertebrates, these proteins form a complex called shelterin, theintegrity of which is critical to ensure proper replication of chromosomeends and to protect them against illicit targeting by DNA double-strandbreak repair pathways. Telomere dysfunctions lead to genome instability,which can ultimately cause senescence or cancer. Telomeres are a subnuclearregion in which shelterin proteins are highly enriched, enhancing lowaffinity interactions of important biological function. Among shelterinproteins, telomeric repeat-binding protein TRF2 and its constitutive partnerRAP1 are the main factors responsible for end protection. We studied indetails the assembly of TRF2/RAP1 complex by means of integrated structural,biophysical and biochemical approaches. We showed that this assemblydisplays important conformational adjustments of both proteins, and involvesa low affinity interaction engaging large regions in both proteins whichaffects their interaction properties.

Les interactions protéine–protéine jouent un rôle essentiel dans le fonctionnement cellulaire et sont impliquées dans diverses pathologies. L'étude de ces interactions est donc primordiale. Nous avons entrepris de développer une méthode de « footprinting » basée sur la différence d'accessibilité à l'eau des acides aminés d'une protéine selon qu'elle est seule ou en interaction. Le principe de cette méthode de caractérisation des zones d'interactions protéine–ligand, est basé sur une étape de génération de radicaux carbo-centrés sur les chaînes latérales des acides aminés de la protéine, et sur une étape de réparation de ces radicaux par un atome de tritium.<br /> <br />La première étape a été de déterminer la réactivité des 20 acides aminés communs vis-à-vis de notre méthode : <br />Lys>Leu>Arg>Ile>Trp>Phe>Val>Cys>Met>His>Tyr>Glu>Thr>Asp><br />Gln>Pro>Ala>Asn> Ser>Gly. Notre méthode ensuite appliquée à l'étude du complexe entre la protéine hAsf11-156 et un fragment de l'histone H3 a permis de caractériser sans ambiguïté les trois résidus principaux de H3 (L126, R129 et I130) impliqués dans cette interaction. De plus, nous avons mis en évidence que notre méthode de caractérisation des interactions protéique est à la fois sensible aux phénomènes d'interaction et de repliement.

<p>Ribosomes stalled on problematic mRNAs can be rescued by a mechanism called <i>trans</i>-translation. This mechanism employs a dual transfer-messenger RNA molecule (tmRNA) together with a helper protein (SmpB). </p><p>In this work we have used an <i>in vitro</i> translation system with pure components to further clarify the roles of tmRNA and SmpB in <i>trans-</i>translation. </p><p>We found that SmpB binds ribosomes <i>in vivo</i> and <i>in vitro</i> independently of tmRNA presence and is essential for tmRNA binding and <i>trans-</i>peptidation. We show that two SmpB molecules can bind per ribosome, that SmpB does not leave the ribosome after <i>trans-</i>peptidation and that SmpB pre-bound to the ribosome can trigger <i>trans-</i>translation. </p><p>We demonstrated that the rate of <i>trans-</i>transfer of a peptide from the P-site tRNA to Ala-tmRNA and the efficiency by which Ala-tmRNA competes with peptide release factors decrease with increasing the mRNA length downstream from the P site of the ribosome. We showed that <i>trans-</i>translation is strongly stimulated by RelE cleavage of A-site mRNA. We concluded that tmRNA action<i> in vivo</i> must always be preceded by mRNA truncation.</p><p>We showed that rapid release of truncated mRNAs from the ribosome requires translocation of the peptidyl-tmRNA into the ribosomal P site, which is strictly EF-G dependent. mRNA release is slowed down by strong Shine and Dalgarno like sequences upstream the A site and by long 3’-extensions downstream from the P-site codon. </p><p>Footprinting was used to monitor SmpB binding to tmRNA, ribosomes and subunits and to study tmRNA interactions with the ribosome at distinct <i>trans-</i>translation stages. We confirmed that two SmpB molecules bind per ribosome and interact with nucleotides below the L7/L12-stalk on the 50S subunit and near the subunit interface on the 30S. We showed that tmRNA is mostly in complex with SmpB <i>in vivo</i> and during <i>trans-</i>translation. Specific cleavage patterns of tmRNA were observed at different stages of <i>trans-</i>translation, but the overall tmRNA conformation seems to be maintained during the whole process.</p>

Ribosomes stalled on problematic mRNAs can be rescued by a mechanism called trans-translation. This mechanism employs a dual transfer-messenger RNA molecule (tmRNA) together with a helper protein (SmpB). In this work we have used an in vitro translation system with pure components to further clarify the roles of tmRNA and SmpB in trans-translation. We found that SmpB binds ribosomes in vivo and in vitro independently of tmRNA presence and is essential for tmRNA binding and trans-peptidation. We show that two SmpB molecules can bind per ribosome, that SmpB does not leave the ribosome after trans-peptidation and that SmpB pre-bound to the ribosome can trigger trans-translation. We demonstrated that the rate of trans-transfer of a peptide from the P-site tRNA to Ala-tmRNA and the efficiency by which Ala-tmRNA competes with peptide release factors decrease with increasing the mRNA length downstream from the P site of the ribosome. We showed that trans-translation is strongly stimulated by RelE cleavage of A-site mRNA. We concluded that tmRNA action in vivo must always be preceded by mRNA truncation. We showed that rapid release of truncated mRNAs from the ribosome requires translocation of the peptidyl-tmRNA into the ribosomal P site, which is strictly EF-G dependent. mRNA release is slowed down by strong Shine and Dalgarno like sequences upstream the A site and by long 3’-extensions downstream from the P-site codon. Footprinting was used to monitor SmpB binding to tmRNA, ribosomes and subunits and to study tmRNA interactions with the ribosome at distinct trans-translation stages. We confirmed that two SmpB molecules bind per ribosome and interact with nucleotides below the L7/L12-stalk on the 50S subunit and near the subunit interface on the 30S. We showed that tmRNA is mostly in complex with SmpB in vivo and during trans-translation. Specific cleavage patterns of tmRNA were observed at different stages of trans-translation, but the overall tmRNA conformation seems to be maintained during the whole process.