A Cis-regulatory Lexicon of DNA Motif Combinations Mediating Cell Type-specific Gene Regulation PDF Download

Author: Laura Kaitlin Hill Donohue
Publisher:
ISBN:
Category :
Languages : en
Pages :

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Book Description
The role of the DNA sequence in protein-coding genes has been widely established due to the obvious functional relevance and well-defined relationships between DNA variation and protein sequence. However, most disease-associated variants are not in protein-coding sequences. This has led to much investigation of non-coding variation as it relates to protein-coding gene regulation. Critically, non-coding regulatory elements within DNA are intricately linked to cell type-specific protein-coding gene expression. This dissertation contributes to the goal of uncovering the underlying cis-regulatory logic of non-coding DNA sequences driving cell type-specific gene expression in homeostasis and disease. Cell type-specific non-coding cis-regulatory elements are known to drive important gene expression programs. However, it is still unclear what combinatorial DNA sequences underlie cell type-specific gene regulatory mechanisms. The objective of this dissertation is to progress our understanding of cis-regulatory logic through integration of genome-wide regulatory maps followed by modeling of combinatorial DNA motif logic in cis-regulatory modules regulating cell type-specific gene expression programs and focused identification of functional regulatory DNA motif combinations (DMCs) in homeostasis and complex disease. In Chapter 2, I generate epigenomic and transcriptomic profiles of 15 primary human cell types and perform integrated analysis to define cell type-specific open chromatin peak-long range looped-expressed target gene transcripts (PLTs). I then incorporate disease-associated single nucleotide variants (SNVs) from the NHGRI GWAS catalog and Genotype-Tissue Expression (GTEx) data to link SNVs enriched in cell type-specific PLTs to putative target genes. In Chapter 3, I model the genomic information necessary to derive cis-regulatory modules linked to cell type-specific gene expression programs and nominate transcription factor (TF) DMCs underlying cell type-specific regulatory logic. Finally, in Chapter 4, I validate DMC logic in four primary human cell types and identify cancer-specific regulatory logic in human squamous cell carcinoma and melanoma cells. The findings and approaches described in this dissertation add to the existing annotation of functional combinatorial TF motif logic and help build a framework for future studies of cis-regulatory logic.

Author: Christopher M. Fiore
Publisher:
ISBN:
Category : Electronic dissertations
Languages : en
Pages : 121

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Transcription is regulated through interactions between regulatory proteins, such as transcription factors (TFs), and DNA sequence. It is known that TFs act combinatorially in some cases to regulate transcription, but in which situations and to what degree is unclear. I first studied the contribution of TF binding sites to expression in mouse embryonic stem (ES) cells by using synthetic cis-regulatory elements (CREs). The synthetic CREs were comprised of combinations of binding sites for the pluripotency TFs Oct4, Sox2, Klf4, and Esrrb. A statistical thermodynamic model explained 72% of the variation in expression driven by these CREs. The high predictive power of this model depended on five TF interaction parameters, including favorable heterotypic interactions between Oct4 and Sox2, Klf4 and Sox2, and Klf4 and Esrrb. The model also included two unfavorable homotypic interaction parameters. These homotypic parameters help to explain the fact that synthetic CREs with mixtures of binding sites for various TFs drive much higher expression than multiple binding sites for the same TF. I then found that the expression of these synthetic CREs largely changes as ES cells differentiate down the neural lineage. However, CREs with no repeat binding sites drove similar levels of expression, suggesting that heterotypic interactions may be similar in the two conditions. In a separate set of experiments I interrogated the determinants of expression driven by genomic sequences previously segmented into classes based on chromatin features. A set of these sequences was assayed in K562 cells. As expected, we found that Enhancers and Weak Enhancers drove expression over background, while Repressed elements and Enhancers from another cell type did not. Unexpectedly, we found that Weak Enhancers drove higher expression than Enhancers, possibly based on their lower H3K36me3 and H3K27ac, which we found to be weakly associated with lower expression. Using a logistic regression model, we showed that matches to TF binding motifs were best able to predict active sequences, but chromatin features contributed significantly as well. These results demonstrate that interactions between certain combinations of pluripotency TFs, but not all combinations, are important to transcriptional regulation. Furthermore, chromatin modifications can still contribute to predictions of expression even after accounting for binding site motifs. Better understanding of the process of cis-regulation will allow us to predict which sequences can drive expression and how perturbations affect this expression.

Author: Candace Britton
Publisher:
ISBN: 9781392048436
Category :
Languages : en
Pages : 127

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Life often diversifies through changes in gene expression patterns. These patterns evolve via changes in transcriptional regulatory circuits that are determined by transcriptional regulatory proteins and the cis-regulatory sequences they bind in the genome. While it has long been known that changes in cis-regulatory sequences can affect the evolution of gene expression patterns and that transcriptional regulatory proteins can themselves evolve, we know little of how these two types of regulatory changes occur together to generate new circuits. I discerned a stepwise order of evolutionary events in which both regulator protein-coding and cis-regulatory changes were necessary to evolve a new transcriptional regulatory circuit (repression of the a-specific genes by Matalpha2 in yeast). The two changes evolved at separate points in time, millions of years apart. First to evolve were coding-sequence changes in the regulator that formed new protein-protein interaction regions. In one lineage, these new protein-protein interactions became necessary for Matalpha2's ancestral gene regulatory function (repression of the haploid-specific genes with Mata1). In another lineage, millions of years after the coding-sequence changes to Matalpha2, cis-regulatory changes occurred in the a-specific genes, thereby co-opting Matalpha2 for regulation of this new set of target genes. We propose that this evolutionary trajectory is an example of constructive neutral evolution in that Matalpha2's new protein-protein interactions initially had no consequence to the logic of cell-type specific gene regulation, but eventually allowed for the creation of a novel circuit (Chapter 2). In the course of these investigations, I also observed additional coding-sequence changes in the DNA-binding domain of Matalpha2 (Chapter 3), and evolutionary changes in the identities of some of the yeast cell-type specific genes (Chapter 4). The results presented here add to our understanding of the ways in which transcriptional regulatory circuits diversify.

Author: David Murphy
Publisher: John Wiley & Sons
ISBN: 1119162181
Category : Science
Languages : en
Pages : 682

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Book Description
Molecular Neuroendocrinology: From Genome to Physiology, provides researchers and students with a critical examination of the steps being taken to decipher genome complexity in the context of the expression, regulation and physiological functions of genes in neuroendocrine systems. The 19 chapters are divided into four sectors: A) describes and explores the genome, its evolution, expression and the mechanisms that contribute to protein, and hence biological, diversity. B) discusses the mechanisms that enhance peptide and protein diversity beyond what is encoded in the genome through post-translational modification. C) considers the molecular tools that today’s neuroendocrinologists can use to study the regulation and function of neuroendocrine genes within the context of the intact organism. D) presents a range of case studies that exemplify the state-of-the-art application of genomic technologies in physiological and behavioural experiments that seek to better understand complex biological processes. • Written by a team of internationally renowned researchers • Both print and enhanced e-book versions are available • Illustrated in full colour throughout This is the third volume in a new Series ‘Masterclass in Neuroendocrinology’ , a co- publication between Wiley and the INF (International Neuroendocrine Federation) that aims to illustrate highest standards and encourage the use of the latest technologies in basic and clinical research and hopes to provide inspiration for further exploration into the exciting field of neuroendocrinology. Series Editors: John A. Russell, University of Edinburgh, UK and William E. Armstrong, The University of Tennessee, USA

Author: Hau-Hsuan Hwang
Publisher: Frontiers Media SA
ISBN: 2889195740
Category : Botany
Languages : en
Pages : 167

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Book Description
The broad host range pathogenic bacterium Agrobacterium tumefaciens has been widely studied as a model system to understand horizontal gene flow, secretion of effector proteins into host cells, and plant-pathogen interactions. Agrobacterium-mediated plant transformation also is the major method for generating transgenic plants for research and biotechnology purposes. Agrobacterium species have the natural ability to conduct interkingdom genetic transfer from bacteria to eukaryotes, including most plant species, yeast, fungi, and even animal cells. In nature, A. tumefaciens causes crown gall disease resulting from expression in plants of auxin and cytokinin biosynthesis genes encoded by the transferred (T-) DNA. Gene transfer from A. tumefaciens to host cells requires virulence (vir) genes that reside on the resident tumor-inducing (Ti) plasmid. In addition to T-DNA, several Virulence (Vir) effector proteins are also translocated to host cells through a bacterial type IV secretion system. These proteins aid in T-DNA trafficking through the host cell cytoplasm, nuclear targeting, and T-DNA integration. Genes within native T-DNAs can be replaced by any gene of interest, making Agrobacterium species important tools for plant research and genetic engineering. In this research topic, we provided updated information on several important areas of Agrobacterium biology and its use for biotechnology purposes.

Author: Heinrich Klefenz
Publisher: Wiley-VCH
ISBN:
Category : Medical
Languages : de
Pages : 328

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Book Description
This volume focuses on pharmaceutical biotechnology as a key area of life sciences. The complete range of concepts, processes and technologies of biotechnology is applied in modern industrial pharmaceutical research, development and production. The results of genome sequencing and studies of biological-genetic function are combined with chemical, micro-electronic and microsystem technology to produce medical devices and diagnostic biochips. A multitude of biologically active molecules is expanded by additional novel structures created with newly arranged gene clusters and bio-catalytic chemical processes. New organisational structures in the co-operation of institutes, companies and networks enable faster knowledge and product development and immediate application of the results of research and process development. This book is the ideal source of information for scientists and engineers in research and development, for decision-makers in biotech, pharma and chemical corporations, as well as for research institutes, but also for founders of biotech companies and people working for venture capital corporations.

Author: Rainer Renkawitz
Publisher: John Wiley & Sons
ISBN: 9783527278756
Category : Gene expression
Languages : en
Pages : 221

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Book Description
This collection of review articles is a valuable contribution to current research in one of the most important areas of molecular biology. It summarizes the exciting results of research on regulatory mechanisms of a selected number of model genes (for example, immunoglobulin genes, human growth hormone gene, albumin gene). Written by international experts, it concentrates on * regulatory proteins * regulatory sequences * chromatin structure * tissue specific splicing By focusing on a few representative model genes, the book enables the reader to draw both detailed and general conclusions about the mechanisms of tissue specific gene regulation. Geneticists in research and medicine can thus acquire vital information without having to consider an otherwise overwhelming number of systems.

Author: Durdica Ugarkovic
Publisher: Springer Science & Business Media
ISBN: 3642001823
Category : Science
Languages : en
Pages : 191

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Book Description
The centromere is a chromosomal region that enables the accurate segregation of chromosomes during mitosis and meiosis. It holds sister chromatids together, and through its centromere DNA–protein complex known as the kinetochore binds spindle microtubules to bring about accurate chromosome movements. Despite this conserved function, centromeres exhibit dramatic difference in structure, size, and complexity. Extensive studies on centromeric DNA revealed its rapid evolution resulting often in significant difference even among closely related species. Such a plasticity of centromeric DNA could be explained by epigenetic c- trol of centromere function, which does not depend absolutely on primary DNA sequence. According to epigenetic centromere concept, which is thoroughly d- cussed by Tanya Panchenko and Ben Black in Chap. 1 of this book, centromere activation or inactivation might be caused by modifications of chromatin. Such acquired chromatin epigenetic modifications are then inherited from one cell di- sion to the next. Concerning centromere-specific chromatin modification, it is now evident that all centromeres contain a centromere specific histone H3 variant, CenH3, which replaces histone H3 in centromeric nucleosomes and provides a structural basis that epigenetically defines centromere and differentiates it from the surrounding chromatin. Recent insights into the CenH3 presented in this chapter add important mechanistic understanding of how centromere identity is initially established and subsequently maintained in every cell cycle.

Author: Conrad Hal Waddington
Publisher:
ISBN:
Category : Embryology
Languages : en
Pages : 182

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Book Description
Conrad Hal Waddington's Organisers and Genes, published in 1940, is a summary of available research and theoretical framework for many concepts related to tissue differentiation in the developing embryo. The book is composed of two main conceptual sections. The first section explores the action and nature of the organizer, while the second section delves into genes and their influence on development. In this book Waddington explored organizers in terms of their capacity and method of induction. First he examined the nature of induction, discussing crucial experiments concerning the organizer, including Hans Spemann's discovery of the organizer, and his own research into organizers in higher birds and mammals. Waddington separated the action of the organizer into two distinct categories, evocation and individuation, discussed below. The main experimental approach discussed in this book involved grafting organizing tissue from one embryo or region of an embryo to another. Waddington described evocation as non-assimilative induction, or a one-way inducing signal. He presented this as a chemical signal and illustrated evocation with the dead organizer experiment. The dead organizer was shown to be capable of inducing differentiation of neural tissue in the ectoderm. He also included chemical induction by estrogens and steroids as other evocative signals. An important aspect of any signal of evocation, as presented by Waddington, is that the signal is specific to the differentiation of a certain tissue type.

Author: Julie D. Thompson
Publisher: Humana Press
ISBN: 9781588299710
Category : Science
Languages : en
Pages : 0

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Book Description
As the emerging field of proteomics continues to expand at an extremely rapid rate, the relative quantification of proteins, targeted by their function, becomes its greatest challenge. Complex analytical strategies have been designed that allow comparative analysis of large proteomes, as well as in depth detection of the core proteome or the interaction network of a given protein of interest. In Functional Proteomics: Methods and Protocols, expert researchers describe the latest protocols being developed to address the problems encountered in high-throughput proteomics projects, with emphasis on the factors governing the technical choices for given applications. The case studies within the volume focus on the following three crucial aspects of the experimental design: 1) the strategy used for the selection, purification and preparation of the sample to be analyzed by mass spectrometry, 2) the type of mass spectrometer used and the type of data to be obtained from it, and 3) the method used for the interpretation of the mass spectrometry data and the search engine used for the identification of the proteins in the different types of sequence data banks available. As a part of the highly successful Methods in Molecular BiologyTM series, the chapters compile step-by-step, readily reproducible laboratory protocols, lists of the necessary materials and reagents, and tips on troubleshooting and avoiding known pitfalls. Comprehensive and cutting-edge, Functional Proteomics: Methods and Protocols is an ideal resource for all scientists pursuing this developing field and its multitudinous data.