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<p>Abstract</p><p>Transcription factors control numerous vital processes in the cell through their ability to control gene expression. Dysfunctional regulation by transcription factors lead to disorders and disease. Transcription factors regulate gene expression by binding to DNA sequences (motifs) on the genome and altering chromatin. DNase-seq footprinting is a well-established assay for identification of DNA sequences that bind to transcription factors. We developed computational techniques to analyze footprints and predict transcription factor binding. These transcription factor specific predictive models are able to correct for DNase sequence bias and characterize variation in DNA binding sequence. We found that DNase-seq footprints are able to identify cell-type or condition specific transcription factor activity and may offer information about the type of the interaction between DNA and transcription factor. Our DNase-seq footprint model is able to accurately discover high confidence transcription factor binding sites and discover alternative interactions between transcription factors and DNA. DNase-seq footprints can be used with ChIP-seq data to discover true binding sites and better understand transcription regulation.</p> / Dissertation

<p>After finishing a human genome reference sequence in 2002, the genomics community has</p><p>turned to the task of interpreting it. A primary focus is to identify and characterize not only</p><p>protein-coding genes, but all functional elements in the genome. The effort has identified</p><p>millions of regulatory elements across species and in hundreds of human cell-types. Nearly</p><p>all identified regulatory elements are found in non-coding DNA, hypothesizing a function</p><p>for previously unannotated sequence. The ability to identify regulatory DNA genome-wide</p><p>provides a new opportunity to understand gene regulation and to ask fundamental questions</p><p>in diverse areas of biology.</p><p>One such area is the aim to understand the molecular basis for phenotypic differences</p><p>between humans and other primates. These phenotypic differences are partially driven</p><p>by mutations in non-coding regulatory DNA that alter gene expression. This hypothesis</p><p>has been supported by differential gene expression analyses in general, but we have not</p><p>yet identified specific regulatory variants responsible for differences in transcription and</p><p>phenotype. I have worked to identify regulatory differences in the same cell-type isolated</p><p>from human, chimpanzee, and macaque. Most regulatory elements were conserved among</p><p>all three species, as expected based on their central role in regulating transcription. How-</p><p>ever, several hundred regulatory elements were gained or lost on the lineages leading to</p><p>modern human and chimpanzee. Species-specific regulatory elements are enriched near</p><p>differentially expressed genes, are positively correlated with increased transcription, show</p><p>evidence of branch-specific positive selection, and overlap with active chromatin marks.</p><p>ivSpecies-specific sequence differences in transcription factor motifs found within this regu-</p><p>latory DNA are linked with species-specific changes in chromatin accessibility. Together,</p><p>these indicate that species-specific regulatory elements contribute to transcriptional and</p><p>phenotypic differences among primate species.</p><p>Another fundamental function of regulatory elements is to define different cell-types in</p><p>multicellular organisms. Regulatory elements recruit transcription factors that modulate</p><p>gene expression distinctly across cell-types. In a study of 112 human cell-types, I classified</p><p>regulatory elements into clusters based on regulatory signal tissue specificity. I then used</p><p>these to uncover distinct associations between regulatory elements and promoters, CpG-</p><p>islands, conserved elements, and transcription factor motif enrichment. Motif analysis</p><p>identified known and novel transcription factor binding motifs in cell-type-specific and</p><p>ubiquitous regulatory elements. I also developed a classifier that accurately predicts cell-</p><p>type lineage based on only 43 regulatory elements and evaluated the tissue of origin for</p><p>cancer cell-types. By correlating regulatory signal and gene expression, I predicted target</p><p>genes for more than 500k regulatory elements. Finally, I introduced a web resource to</p><p>enable researchers to explore these regulatory patterns and better understand how expression</p><p>is modulated within and across human cell-types.</p><p>Regulation of gene expression is fundamental to life. This dissertation uses identified</p><p>regulatory DNA to better understand regulatory systems. In the context of either evolution-</p><p>ary or developmental biology, understanding how differences in regulatory DNA contribute</p><p>to phenotype will be central to completely understanding human biology.</p> / Dissertation

<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

<p>Deciphering the molecular mechanisms driving the phenotypic differences between humans and primates remains a daunting challenge. Mutations found in protein coding DNA alone has not been able to explain these phenotypic differences. The hypothesis that mutations in non-coding regulatory DNA are responsible for altered gene expression leading to these phenotypic changes has now been widely supported by differential gene expression experiments. Yet, comprehensive identification of all regulatory DNA elements across different species has not been performed. To identify the genetic source of regulatory change, genome-wide DNaseI hypersensitivity assays, marking all types of active gene regulatory element sites, were performed in human, chimpanzee, macaque, orangutan, and mouse. Many DNaseI hypersensitive (DHS) sites were conserved among all 5 species, but we also identified hundreds of novel human- and chimpanzee-specific DHS gains and losses that showed signatures of positive selection. Species-specific DHS gains were enriched in distal non-coding regions, associated with active histone modifications, and positively correlated with increased expression - indicating that these are likely to be functioning as enhancers. Comparison to mouse DHS data indicate that human or chimpanzee DHS gains are likely to have been a result of single events that occurred primarily on the human- or chimpanzee-specific branch, respectively. In contrast, DHS losses are associated with events that occurred on multiple branches. At least one mechanism contributing to DHS gains and losses are species-specific variants that lead to sequence changes at transcription factor binding motifs, affecting the binding of TFs such as AP1. These variants were functionally verified by DNase footprinting and ChIP-qPCR analyses.</p> / Dissertation

Sex differences in mammalian gene expression result from differences in genotypic sex as well as in hormonal regulators between males and females. In rat, mouse and human liver, ~1000 genes are expressed in a sex-dependent manner, and contribute to sex differences in metabolism of drugs, steroids and lipids, and in liver and cardiovascular disease risk. In rats and mice, sex-biased liver gene expression is primarily dictated by the sexually dimorphic pattern of pituitary growth hormone (GH) release and its STAT5-dependent transcriptional activities. Studies presented in this thesis include the following. (1) A computational approach based on DNA sequence and phylogenetic conservation was developed and used to identify novel functional STAT5 binding sites - both consensus and non-consensus STAT5 sequences - near prototypic GH-responsive genes. (2) Global gene expression analysis of livers from pituitary-ablated male and female mice identified four major classes of sex-biased genes differing in their profiles of GH dependence. (3) Sex-differences in DNase-hypersensitive sites (DHS, corresponding to open chromatin regions) were identified genome-wide in mouse liver. These sex-differential DHSs were enriched for association with sex-biased genes, but a majority was distant from sex-biased genes. Furthermore, many were responsive to GH treatment, demonstrating that GH-mediated regulation involves chromatin remodeling. Analysis of sequence motifs enriched at sex-biased DHSs implicated STAT5 and novel transcription factors such as PBX1 and TAL1 in sex-biased gene regulation. (4) Genome-wide mapping of histone modifications revealed distinct mechanisms of sex-biased gene regulation in male and female liver: sex-dependent K27me3-mediated repression is an important mechanism of repression of female-biased, but not of male-biased, genes, and a sex-dependent K4me1 distribution, suggesting nucleosome repositioning by pioneer factors, is observed at male-biased, but not female-biased, regulatory sites. STAT5-mediated activation was most strongly associated with sex-biased chromatin modifications, while BCL6-mediated repression primarily occurs in association with sex-independent chromatin modifications, both at binding sites and at target genes. The relationships between sex-dependent chromatin accessibility, chromatin modifications and transcription-factor binding uncovered by these studies help elucidate the molecular mechanisms governing sex-differential gene expression, and underscore the utility of functional genomic and epigenetic studies as tools for elucidating transcriptional regulation in complex mammalian systems.

INTRODUÇÃO: A síndrome de Sjögren primária (SSp) é uma doença autoimune inflamatória crônica que afeta principalmente as glândulas exócrinas, levando aos sintomas de síndrome sicca. O olho seco é uma das características mais importantes dessa síndrome e um estudo recente relatou redução da atividade da DNase I em lágrimas de pacientes com olho seco de várias etiologias. Portanto, postulamos que pacientes com SSp possam ter anticorpos direcionados à DNase I. MÉTODOS: Avaliamos em um estudo de corte transversal 85 pacientes com SSp (conforme os critérios de classificação do American European Consensus Group Criteria, 2002), 50 pacientes com artrite reumatoide (AR) (American College of Rheumatology Criteria/ 1987) sem sintomas de síndrome sicca e 88 voluntários saudáveis. A reatividade IgG anti-DNase I foi detectada por ELISA utilizando a enzima de pâncreas bovino como antígeno e confirmada por Imunoblotting. RESULTADOS: A idade e sexo foram comparáveis nos três grupos (p > 0,05). A anti-DNase I foi detectada em 43,5% dos pacientes com SSp, conforme determinado por ELISA. Em contraste, essa reatividade estava ausente em todos os pacientes com AR (p= 0,0001). Comparações adicionais dos pacientes com SSp com (n= 37) e sem (n= 48) anti-DNase I revelaram que o primeiro grupo tinha níveis séricos de IgG mais altos (2293,2 ± 666,2 vs. 1483,9 ± 384,6 mg/dL, p= 0,0001) e uma frequência maior de leucopenia não induzida por drogas (43% vs. 19%, p= 0,02). A análise de regressão logística multivariada mostrou que apenas os níveis de IgG foram independentemente associados com o anti-DNase I. CONCLUSÃO: Descrevemos uma alta frequência de anticorpos anti-DNase I em pacientes com SSp associados a níveis séricos de IgG mais elevados. A falta dessa reatividade em pacientes com AR sem sintomas de sicca sugere que esse anticorpo pode ser útil no diagnóstico diferencial dessas doenças / INTRODUCTION: Primary Sjögren\'s syndrome (pSS) is a chronic inflammatory autoimmune disease that mainly affects exocrine glands. Dry eye is one of the most important features of this syndrome and a recent study reported reduced DNase I activity in tears of patients with dry eye of various etiologies. We therefore postulated that patients with pSS may have antibodies targeting DNase I. METHODS: We have evaluated in a cross-sectional study 85 pSS patients (American European Consensus Group Criteria/ 2002), 50 rheumatoid arthritis (RA) patients (American College of Rheumatology Criteria/ 1987) without sicca symptoms and 88 healthy volunteers. The IgG anti-DNase I reactivity was detected by ELISA using bovine pancreas enzyme as antigen and confirmed by Immunoblotting. RESULTS: Age/ gender were comparable in the three groups (p > 0.05). Anti-DNase I was detected in 43.5% of the pSS patients as determined by ELISA. In contrast, this reactivity was absent in all RA patients (p= 0.0001). Further comparison of pSS patients with (n= 37) and without (n= 48) anti-DNase I revealed that the former group had higher IgG serum levels (2293.2 ± 666.2 vs. 1483.9 ± 384.6 mg/dL, p= 0.0001) and a higher frequency of non-drug induced leukopenia (43% vs. 19%, p= 0.02). A multivariate logistic regression analysis identified that only IgG levels were independently associated with anti-DNase I. CONCLUSION: We describe a high frequency of anti-DNase I antibodies in pSS patients associated with higher serum IgG levels. The lack of this reactivity in RA patients without sicca symptoms suggests that this antibody may be helpful in the differential diagnosis of these diseases

Bnip3 is a BH3-only member of the Bcl-2 family of apoptotic proteins. Our laboratory has previously shown that Bnip3 induces a unique pathway of cardiac myocyte cell death, characterized by mitochondrial dysfunction, cytochrome c release and DNA fragmentation. Bnip3 is induced by hypoxia and the death pathway is activated by concurrent acidosis. We have shown that hypoxia-acidosis creates an environment that is permissive to calpain but not caspase activation and is characterized by enhanced DNase(s) activity as evidenced by genomic DNA fragmentation. This dissertation describes the nuclear consequences of Bnip3 activation by hypoxia-acidosis. Chapter 3 presents my evidence that hypoxia with progressive acidosis in cardiac myocytes results in a biphasic activation of DNases. In phase 1, [pH]o 6.9-6.7, apoptosis-inducing factor (AIF) is released from the mitochondria and translocates to the nucleus. AIF release coincided with the loss of mitochondrial membrane potential and with the release of cytochrome c from the mitochondria. In Phase II, [pH]o 6.3-6.0, DNase II translocates from the cytoplasm to the nuclear compartment. Nuclear localization of DNase II was associated with the collapse of endosomal pH gradients, indicated by diffuse Lysotracker Red staining and with single strand DNA nicks. Both phases of DNase release were independent of Bnip3, the mPTP and calpains. Neither phase involved activation of caspase-dependent DNases. Chapter 4 describes a unique role for Bnip3 in the modulation of histone acetylation. I found that hypoxia with acidosis in cardiac myocytes but not hypoxia alone stimulated a global increase in the acetylation of histones H3 and H4. Acetylation was initiated at [pH]o ~ 6.8 and increased as the pH declined. Histone hyperacetylation was associated with an increase in histone acetyltransferase (HAT) activity but no change in deacetylase (HDAC) activity. Knockdown of Bnip3 protein expression with siRNA dramatically reduced both histone H3 and H4 acetylation levels and HAT activity indicating an essential role for Bnip3 in this process. Components of the hypoxia-acidosis death pathway including the mPTP and calpains are not required for Bnip3-mediated histone hyperacetylation. These results reveal a novel role for Bnip3 in regulating HAT activity and histone acetylation which may lead to altered cardiac gene expression.