The Regulatory Genome

Author: Eric H. Davidson
Editor: Academic Press
ISBN: 9780120885633
File Size: 30,19 MB
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Gene regulatory networks are the most complex, extensive control systems found in nature. The interaction between biology and evolution has been the subject of great interest in recent years. This book beautifully explains animal evolution in terms of gene regulatory networks and includes 42 full-color descriptive figures. An authoritative and easy to read volume, presenting the biological processes during development (and their regulation) within the framework of evolution. This book is written to explain the idea of gene regulation without the reader needing to have a strong background in developmental biology. Eric Davidson has been instrumental in elucidating this relationship and he is a recognized expert in the field of developmental biology. This unique text supersedes anything currently available in the market.

Functionally Dissecting The Regulatory Genome Of Paralogous Cardiac Gene Clusters

Author: Joyce C. K. Man
Editor:
ISBN: 9789464161878
File Size: 26,67 MB
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Exploring The Regulatory Genome And Functional Genetic Variation

Author: William Walter Young Greenwald
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A substantial fraction of SNPs associated with human traits and diseases through genome-wide association studies (GWAS) are likely regulatory variants as they tend to be located within enhancers and associated with differential gene expression. Thus, as a key step in implementing personalized medicine, it is important to identify regulatory variants in the human genome, and characterize their underlying molecular mechanisms. However, identifying and elucidating the functions of regulatory variants is currently challenging as these variants show similar associations with many other neutral variants due to linkage disequilibrium, can be quite far from the gene(s) they regulate, and often have cell type-specific effects. In order to overcome these challenges and interrogate the function of these regulatory variants, it could be possible to examine and integrate epigenetic information in a cell type dependent manner. Here, I present three studies which focus on the functionality of the epigenome--specifically chromatin looping and co-accessibility--in the context of gene regulation, genetics, and disease. I present a tool for computationally working with chromatin loop data, and utilize this tool to show that genetic variation is not associated with large changes in chromatin looping, but rather small modulation in contact propensity which are associated with large changes in gene expression. I then examine chromatin co-accessibility, and show that genetic variants may be able to mediate long range effects on genes and accessible sites hundreds of megabases away--across entire chromosomes--which are associated with cell type relevant genes and diseases.

Tackling The Regulatory Genome

Author: Charles Titus Brown
Editor:
ISBN:
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Regulatory Genomics Proceedings Of The 3rd Annual Recomb Workshop

Author: Hon Wai Leong
Editor: World Scientific
ISBN: 1908978740
File Size: 53,18 MB
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Research in the field of gene regulation is evolving rapidly in the ever-changing scientific environment. Advances in microarray techniques and comparative genomics have enabled more comprehensive studies of regulatory genomics. The study of genomic binding locations of transcription factors has enabled a more comprehensive modeling of regulatory networks. In addition, complete genomic sequences and comparison of numerous related species have demonstrated the conservation of non-coding DNA sequences, which often provide evidence for cis-regulatory binding sites. Systematic methods to decipher the regulatory mechanism are also crucial for corroborating these regulatory networks; key to these methods are motif discovery algorithms that can help predict cis-regulatory elements. These DNA-motif discovery programs are becoming more sophisticated and are beginning to leverage evidence from comparative genomics. These topics and more were discussed at the 3rd Annual RECOMB Workshop on Regulatory Genomics, which brought together more than 90 attendees and included about 22 excellent talks from leading researchers in the field. This proceedings volume contains ten selected, original manuscripts that were presented during the workshop./a

The Regulatory Genome

Author: Eric H. Davidson
Editor: Elsevier
ISBN: 9780080455570
File Size: 67,52 MB
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Gene regulatory networks are the most complex, extensive control systems found in nature. The interaction between biology and evolution has been the subject of great interest in recent years. The author, Eric Davidson, has been instrumental in elucidating this relationship. He is a world renowned scientist and a major contributor to the field of developmental biology. The Regulatory Genome beautifully explains the control of animal development in terms of structure/function relations of inherited regulatory DNA sequence, and the emergent properties of the gene regulatory networks composed of these sequences. New insights into the mechanisms of body plan evolution are derived from considerations of the consequences of change in developmental gene regulatory networks. Examples of crucial evidence underscore each major concept. The clear writing style explains regulatory causality without requiring a sophisticated background in descriptive developmental biology. This unique text supersedes anything currently available in the market. The only book in the market that is solely devoted to the genomic regulatory code for animal development Written at a conceptual level, including many novel synthetic concepts that ultimately simplify understanding Presents a comprehensive treatment of molecular control elements that determine the function of genes Provides a comparative treatment of development, based on principles rather than description of developmental processes Considers the evolutionary processes in terms of the structural properties of gene regulatory networks Includes 42 full-color descriptive figures and diagrams

Mechanisms Of Gene Regulation

Author: Carsten Carlberg
Editor: Springer
ISBN: 9401777411
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This textbook aims to describe the fascinating area of eukaryotic gene regulation for graduate students in all areas of the biomedical sciences. Gene expression is essential in shaping the various phenotypes of cells and tissues and as such, regulation of gene expression is a fundamental aspect of nearly all processes in physiology, both in healthy and in diseased states. This pivotal role for the regulation of gene expression makes this textbook essential reading for students of all the biomedical sciences, in order to be better prepared for their specialized disciplines. A complete understanding of transcription factors and the processes that alter their activity is a major goal of modern life science research. The availability of the whole human genome sequence (and that of other eukaryotic genomes) and the consequent development of next-generation sequencing technologies have significantly changed nearly all areas of the biological sciences. For example, the genome-wide location of histone modifications and transcription factor binding sites, such as provided by the ENCODE consortium, has greatly improved our understanding of gene regulation. Therefore, the focus of this book is the description of the post-genome understanding of gene regulation. The purpose of this book is to provide, in a condensed form, an overview on the present understanding of the mechanisms of gene regulation. The authors are not aiming to compete with comprehensive treatises, but rather focus on the essentials. Therefore, the authors have favored a high figure-to-text ratio following the rule stating that “a picture tells more than thousand words”. The content of the book is based on the lecture course, which is given by Prof. Carlberg since 2001 at the University of Eastern Finland in Kuopio. The book is subdivided into 4 sections and 13 chapters. Following the Introduction there are three sections, which take a view on gene regulation from the perspective of transcription factors, chromatin and non-coding RNA, respectively. Besides its value as a textbook, Mechanisms of Gene Regulation will be a useful reference for individuals working in biomedical laboratories.

Exploring The Regulatory Genome In Melanoma Innate Resistance

Author: Rose Tran-Bussat
Editor:
ISBN:
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Targeted therapy for cancer treatment has been confronted with acquired resistance. In metastatic melanoma, for many years conventional chemotherapy and radiation were the common treatment options. The first generation of targeted therapy against BRAFV600E, a mutation found in about 50% of metastatic melanoma, revolutionized standard treatment. This first generation targeted therapy, Vemurafenib, resulted in > 50% clinical response in the first few months of treatment. Unfortunately, drug resistance to this therapy occurs about six months to a year after treatment. Subsequently, numerous genome sequencing studies on Vemurafenib-resistant melanomas identified extensive acquired DNA mutations that up-regulate components of the MAPK signaling pathway, therefore effectively re-wiring around the initial BRAF inhibition. It is hypothesized that during targeted therapy, cancer cells initially engage an innate resistance program to survive, in order to generate secondary DNA mutations in the same pathway to be resistant to the targeted therapy (acquired resistance). Recent studies have shown that HGF in the tumor microenvironment is important for cell survival on targeted BRAF therapy. This suggest that melanoma cells must have drug response and pro-survival mechanisms, including the MET signaling pathway. Using an integrated genomics approach, we identified a dynamic genomic interaction between the MET TSS and a lineage-specific enhancer 63kb downstream during targeted BRAF inhibition. This dynamic interaction is further mediated by the melanocyte lineage master transcription factor, MITF. MITF pro-differentiation and tumorigenic function can be uncoupled by selective editing of the MET specific enhancer. This initial study showed the importance of looking at distal regulatory elements in dynamic cellular responses such as cellular reprogramming in response to drug treatment. We extended this initial study of the MET locus to look at global dynamic regulatory changes. We assessed the global open chromatin dynamics and transcriptomic changes during acute BRAF inhibition and MITF depletion. Using a statistical framework, we generated a global regulatory network of important transcriptional regulators during targeted BRAF inhibition in melanoma cells treated with vemurafenib (PLX4032). Focusing on the MITF sub-network can help identify putative MITF transcriptional co-regulators and parallel pathways during acute oncogenic signaling inhibition.

Genomic Control Process

Author: Eric H. Davidson
Editor: Academic Press
ISBN: 9780124047297
File Size: 54,52 MB
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Genomic Control Process explores the biological phenomena around genomic regulatory systems that control and shape animal development processes, and which determine the nature of evolutionary processes that affect body plan. Unifying and simplifying the descriptions of development and evolution by focusing on the causality in these processes, it provides a comprehensive method of considering genomic control across diverse biological processes. This book is essential for graduate researchers in genomics, systems biology and molecular biology seeking to understand deep biological processes which regulate the structure of animals during development. Covers a vast area of current biological research to produce a genome oriented regulatory bioscience of animal life Places gene regulation, embryonic and postembryonic development, and evolution of the body plan in a unified conceptual framework Provides the conceptual keys to interpret a broad developmental and evolutionary landscape with precise experimental illustrations drawn from contemporary literature Includes a range of material, from developmental phenomenology to quantitative and logic models, from phylogenetics to the molecular biology of gene regulation, from animal models of all kinds to evidence of every relevant type Demonstrates the causal power of system-level understanding of genomic control process Conceptually organizes a constellation of complex and diverse biological phenomena Investigates fundamental developmental control system logic in diverse circumstances and expresses these in conceptual models Explores mechanistic evolutionary processes, illuminating the evolutionary consequences of developmental control systems as they are encoded in the genome

Regulation Of Genome Editing In Plant Biotechnology

Author: Hans-Georg Dederer
Editor: Springer
ISBN: 3030171191
File Size: 59,75 MB
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This book provides in-depth insights into the regulatory frameworks of five countries and the EU concerning the regulation of genome edited plants. The country reports form the basis for a comparative analysis of the various national regulations governing genetically modified organisms (GMOs) in general and genome edited plants in particular, as well as the underlying regulatory approaches.The reports, which focus on the regulatory status quo of genome edited plants in Argentina, Australia, Canada, the EU, Japan and the USA, were written by distinguished experts following a uniform structure. On this basis, the legal frameworks are compared in order to foster a rational assessment of which approaches could be drawn upon to adjust, or to completely realign, the current EU regime for GMOs. In addition, a separate chapter identifies potential best practices for the regulation of plants derived from genome editing.

Interpretable Machine Learning Methods For Regulatory And Disease Genomics

Author: Peyton Greis Greenside
Editor:
ISBN:
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It is an incredible feat of nature that the same genome contains the code to every cell in each living organism. From this same genome, each unique cell type gains a different program of gene expression that enables the development and function of an organism throughout its lifespan. The non-coding genome - the ~98 of the genome that does not code directly for proteins - serves an important role in generating the diverse programs of gene expression turned on in each unique cell state. A complex network of proteins bind specific regulatory elements in the non-coding genome to regulate the expression of nearby genes. While basic principles of gene regulation are understood, the regulatory code of which factors bind together at which genomic elements to turn on which genes remains to be revealed. Further, we do not understand how disruptions in gene regulation, such as from mutations that fall in non-coding regions, ultimately lead to disease or other changes in cell state. In this work we present several methods developed and applied to learn the regulatory code or the rules that govern non-coding regions of the genome and how they regulate nearby genes. We first formulate the problem as one of learning pairs of sequence motifs and expressed regulator proteins that jointly predict the state of the cell, such as the cell type specific gene expression or chromatin accessibility. Using pre-engineered sequence features and known expression, we use a paired-feature boosting approach to build an interpretable model of how the non-coding genome contributes to cell state. We also demonstrate a novel improvement to this method that takes into account similarities between closely related cell types by using a hierarchy imposed on all of the predicted cell states. We apply this method to discover validated regulators of tadpole tail regeneration and to predict protein-ligand binding interactions. Recognizing the need for improved sequence features and stronger predictive performance, we then move to a deep learning modeling framework to predict epigenomic phenotypes such as chromatin accessibility from just underlying DNA sequence. We use deep learning models, specifically multi-task convolutional neural networks, to learn a featurization of sequences over several kilobases long and their mapping to a functional phenotype. We develop novel architectures that encode principles of genomics in models typically designed for computer vision, such as incorporating reverse complementation and the 3D structure of the genome. We also develop methods to interpret traditionally ``black box" neural networks by 1) assigning importance scores to each input sequence to the model, 2) summarizing non-redundant patterns learned by the model that are predictive in each cell type, and 3) discovering interactions learned by the model that provide indications as to how different non-coding sequence features depend on each other. We apply these methods in the system of hematopoiesis to interpret chromatin dynamics across differentiation of blood cell types, to understand immune stimulation, and to interpret immune disease-associated variants that fall in non-coding regions. We demonstrate strong performance of our boosting and deep learning models and demonstrate improved performance of these machine learning frameworks when taking into account existing knowledge about the biological system being modeled. We benchmark our interpretation methods using gold standard systems and existing experimental data where available. We confirm existing knowledge surrounding essential factors in hematopoiesis, and also generate novel hypotheses surrounding how factors interact to regulate differentiation. Ultimately our work provides a set of tools for researchers to probe and understand the non-coding genome and its role in controlling gene expression as well as a set of novel insights surrounding how hematopoiesis is controlled on many scales from global quantification of regulatory sequence to interpretation of individual variants.

Integrative Modeling For Genome Wide Regulation Of Gene Expression

Author:
Editor: Stanford University
ISBN:
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High-throughput genomics has been increasingly generating the massive amount of genome-wide data. With proper modeling methodologies, we can expect to archive a more comprehensive understanding of the regulatory mechanisms of biological systems. This work presents integrative approaches for the modeling and analysis of gene regulatory systems. In mammals, gene expression regulation is combinatorial in nature, with diverse roles of regulators on target genes. Microarrays (such as Exon Arrays) and RNA-Seq can be used to quantify the whole spectrum of RNA transcripts. ChIP-Seq is being used for the identification of transcription factor (TF) binding sites and histone modification marks. RNA interference (RNAi), coupled with gene expression profiles, allow perturbations of gene regulatory systems. Our approaches extract useful information from those genome-wide measurements for effectively modeling the logic of gene expression regulation. We present a predictive model for the prediction of gene expression from ChIP-Seq signals, based on quantitative modeling of regulator-gene association strength, principal component analysis, and regression-based model selection. We demonstrate the combinatorial regulation of TFs, and their power for explaining genome-wide gene expression variation. We also illustrate the roles of covalent histone modification marks on predicting gene expression and their regulation by TFs. We present a dynamical model of gene expression profiling, and derive the perturbed behaviors of the ordinary differential equation (ODE) system. Based on that, we present a regularized multivariate regression method for inferring the gene regulatory network of a stable cell type. We model the sparsity and stability of the network by a regularization approach. We applied the approaches to both a simulation data set and the RNAi perturbation data in mouse embryonic stem cells.

Reconstruction Of The Regulatory Network For Bacillus Subtilis And Reconciliation With Gene Expression Data

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Here, we introduce a manually constructed and curated regulatory network model that describes the current state of knowledge of transcriptional regulation of B. subtilis. The model corresponds to an updated and enlarged version of the regulatory model of central metabolism originally proposed in 2008. We extended the original network to the whole genome by integration of information from DBTBS, a compendium of regulatory data that includes promoters, transcription factors (TFs), binding sites, motifs and regulated operons. Additionally, we consolidated our network with all the information on regulation included in the SporeWeb and Subtiwiki community-curated resources on B. subtilis. Finally, we reconciled our network with data from RegPrecise, which recently released their own less comprehensive reconstruction of the regulatory network for B. subtilis. Our model describes 275 regulators and their target genes, representing 30 different mechanisms of regulation such as TFs, RNA switches, Riboswitches and small regulatory RNAs. Overall, regulatory information is included in the model for approximately 2500 of the ~4200 genes in B. subtilis 168. In an effort to further expand our knowledge of B. subtilis regulation, we reconciled our model with expression data. For this process, we reconstructed the Atomic Regulons (ARs) for B. subtilis, which are the sets of genes that share the same "ON" and "OFF" gene expression profiles across multiple samples of experimental data. We show how atomic regulons for B. subtilis are able to capture many sets of genes corresponding to regulated operons in our manually curated network. Additionally, we demonstrate how atomic regulons can be used to help expand or validate the knowledge of the regulatory networks by looking at highly correlated genes in the ARs for which regulatory information is lacking. During this process, we were also able to infer novel stimuli for hypothetical genes by exploring the genome expression metadata relating to experimental conditions, gaining insights into novel biology.

Systems Biology And Regulatory Genomics

Author: Eleazar Eskin
Editor: Springer Science & Business Media
ISBN: 3540482938
File Size: 59,61 MB
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This book constitutes the thoroughly refereed post-proceedings of two joint RECOMB 2005 satellite events: the First Annual Workshop on Systems Biology, RSB 2005 and the Second Annual Workshop on Regulatory Genomics, RRG 2005, held in San Diego, CA, USA in December 2005. It contains 21 revised full papers that address a broad variety of topics in systems biology and regulatory genomics.

Identifying The Regulatory Role Of Transposable Elements In Mammalian Genomes

Author: Vasavi Sundaram
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ISBN:
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Transposable elements (TEs) constitute a large portion of mammalian genomes, including almost half of the human genome. Yet, TEs have been largely ignored from many genomic studies. The reasons for the lack of focus on TEs in most genomic studies are twofold. Firstly TEs were thought to be 'junk' DNA originating from 'selfish' elements that do not provide any benefit to the cell. Secondly, algorithms for the alignment of next-generation sequencing reads often discard non-uniquely mapping reads that mostly enrich for repetitive sequences such as TEs. However, over the past decade, several studies have shown that TEs harbor transcription factor (TF) binding sites for certain TFs. Although these studies have changed the 'junk' paradigm of TE-research, the functional role of the vast number of TEs in our genome and their contribution to genetic pathways still remains to be understood. The aim of this thesis is to understand the regulatory potential of mammalian transposable elements (TEs). A systems-level approach was taken to understand the impact and contribution of TEs to mammalian transcriptional regulatory networks. Three questions are addressed in this thesis. First, using data for twenty-six transcription factors (TFs) in various human and mouse cell types, the extent to which TEs contribute binding sites for TFs was determined. This finding showed that 2-40% of TFs' binding sites are derived from TEs, and this percentage varies by TF and by the cell type. Second, the presence of cis-regulatory modules in TEs was investigated. A cis-regulatory module of binding sites for pluripotency TFs in mouse embryonic stem (ES) cells was identified in mouse-specific TE subfamilies. TEs from these subfamilies were capable of enhancing gene expression and are associated with genes that exhibit mouse-ES specific expression patterns. Finally, the evolution of the regulatory potential in TEs was investigated to understand when and how TEs acquire the ability to regulate gene expression. Towards this, a computational and experimental framework to study the evolution of the regulatory potential in TEs is described and outlined, with preliminary results. Together, the three questions addressed in this thesis aims to comprehensively understand the regulatory potential of TEs. With the knowledge of the regulatory potential encoded in TE subfamilies, the effect of TEs on transcriptional regulatory networks can be deciphered to gain a better understanding of the various gene expression programs or phenotypes that they can impact.

Genome Organization And Coordinate Regulation Of Gene Expression

Author: Kevin Anthony Peterson
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Drosophila Regulatory Genomics

Author: Qianqian Zhu
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For all biological organisms, when, where and how much a gene is expressed is under sophisticated regulation through cis- and trans-acting factors. Using Drosophila as a model system, I investigated the regulation of gene expression by cis-acting factors including cis-regulatory modules (CRMs) and promoters, and the profiling of gene expression by whole-genome microarrays. CRMs, including enhancers, silencers, insulators, refer to the DNA regulatory elements that are responsible for modulating gene expression relative to the basal transcription level. In chapter 2, I incorporate conservation information into genome-wide CRM prediction and successfully identify three truly functional CRMs, while using another approach of selecting CRMs whose flanking genes share high protein sequence similarity does not work well.^In chapter 3, I show the widely used Stinger series of vectors alone can drive reporter gene expression in vivo. In chapter 4, I summarize the findings from a systematic investigation of CRM features. Experimentally verified CRMs are found to be more GC-rich, more conserved across evolution, and more likely to be transcribed than random non-coding sequences.

Applying Super Resolution Microscopy To Investigate The Regulatory Structure Of The Genome

Author: Leslie Johanna Mateo
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ISBN:
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The three-dimensional (3D) organization of the genome is important for cellular function, such as gene expression and differentiation throughout development. Both the spatial and temporal expression of a gene are largely regulated by non-coding sequences in the genome. The genome is folded into compartments, topological associated domains (TADs), and loops, as determined by sequencing-based technology such as Hi-C. Many of the differences in cell type arise from specific interactions between distal enhancers and their target promoters, which are typically located thousands to hundreds of thousands of basepairs apart. Long-range enhancer and promoter activity and the specific of enhancer-promoter interactions are believed to arise from the cell-type specific genome folding. How this genome organization is established and regulated during development is not well understood. Hi-C and other sequencing-based assays lack information pertaining to the spatial organization of cells in tissues, and largely provide population-level information, not single cell, which makes it challenging to understand how genome folding might contribute to differences among cell types. Thus, there is a great need for approaches that provide a view of the chromatin organization and transcriptional activity in single cells. Here, I present my work developing and using a super-resolution technique to gain such an unprecedented view. Our novel super-resolution microscopy approached termed Optical Reconstruction of Chromatin Architecture (ORCA) to trace the DNA path in steps from 30 kb to 2 kb at the single-cell level. We discovered that single cells do have TAD-like structures that are heterogeneous across cells. However, the boundary positions of these single cell TADs do preferentially lie at insulator boundary protein CTCF and cohesin binding sites. Although depletion of cohesin is crucial for the presence of TADs at the population-level, we found that the TAD-like domains in single cells are not dependent on cohesin. Thus, my findings using ORCA in cultured cells (Chapter 2) shed important new light to genome organization in single cells. My interest in gene regulation led me to expand our microscopy approach by making ORCA compatible with multiplex RNA imaging to enable direct correlation between chromatin structure and gene expression on a cell-by-cell basis. Furthermore, I expanded our experimental system by applying ORCA to cryosectioned Drosophila embryos to investigate the role of 3D genome structure in loci, such as in the bithorax complex (BX-C), with well-studied enhancers. I discovered that cell-type specific 3D DNA folding of the BX-C correlates with BX-C expression patterns in different embryonic body segments. Using embryos with genetic perturbations allowed me to determine that the genetic elements at TAD boundaries drive proper cell-type specific enhancer-promoter contacts and gene expression. My results (Chapter 3) suggest that architectural proteins, such as CTCF and cohesin, at TAD boundaries are responsible for the establishment of 3D organization during development. Additionally, my results emphasize the need to study cell-type specific chromatin structures on a cell-by-cell and cell type basis, an area that is still largely unexplored. To facilitate such exploration, I worked towards making our approach accessible to other researchers that are interested in 3D genome architecture and transcriptional activity (Chapter 4). To determine the role of architectural proteins in genome organization (Chapter 5), I took advantage of Drosophila genetics and obtained null allele mutant embryos that lacked zygotic expression of architectural proteins such as Rad21, Wapl, CTCF, and CP190. Using ORCA, I found that these mutants have BX-C TADs that are similar to that of WT in mid to late staged embryos. However, as the maternal transcripts for these architectural proteins were present throughout embryogenesis, the maternally encoded proteins appeared to be sufficient to retain genome structure in the zygotic null mutants. I also observed BX-C TAD structure that looks similar to that of wild-type in the central nervous system (CNS) of mutant CTCF L3 larvae where maternal gene products were fully absent. My results raise the probability that other Drosophila insulator binding proteins, such as CP190, may play a redundant insulation function. To examine the role of various cis-acting insulator elements, I have begun preliminary studies in investigating how inserting insulators into the genome affects long-range cis-regulatory interactions (Chapter 6). Overall, the development of ORCA has enabled us to begin understanding the mechanisms underlying genome organization and their role in regulating transcription in a complex tissue. As our techniques improve and becomes more accessible to other researchers in the field, we are certain that the methods we have developed will play a role in un-covering the function of various chromatin components, such as transcription factors and epigenetic state, in establishing the 3D genome organization during development.

Sequencing The Complex And The Regulatory Regions Of The Human Genome

Author: Yuling Liu
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ISBN:
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While huge technological and scientific advances in human genomics have been made in the recent decade, critical questions still remain. In this dissertation, we focus on two problems: Determining variants within highly homologous regions of the human genome; Sequencing and quantification of differences in human regulatory regions. Core to the first problem is the lack of a scalable sequencing technology with sufficiently long read length and accuracy to enable truly unique mapping. Here we present our novel method, RFA, to confidently align short reads in highly homologous regions and enable accurate variant discovery in a cost-effective fashion by exploiting, via a Markov Random Field, the dependency among the short reads generated by a long read in read cloud technology. We test our method through both extensive simulations and experimental validation. We demonstrate that our method accurately recovers variation in 155Mbp of the human genome, including 94% of 67Mbp of segmental duplication sequence and 96% of 11Mbp of transcribed sequence that are currently hidden from short read technologies. To shed light on the second question, we study differences in chromatin state across 19 diverse individuals using six histone modifications, cohesin, Pol2 and CTCF in lymphoblastoid lines. We find extensive regulatory region differences in both activity (strong vs. weak vs. poised) and identity (enhancers vs. promoters vs. repressed regions). Enhancer activity is particularly diverse among individuals, and is divergent across populations in regions associated with signals of positive selection. Differences in modifications are inherited in trios and correlate with gene expression differences, indicating that they have functional consequences. Finally, differences in regulatory elements often reside in the same large chromosomal topological domains. Overall, our results provide fundamental insights into genetic and epigenetic differences of humans and how regulatory elements might evolve within a species.

Mapping Cis Regulatory Domains In The Human Genome Usingmulti Species Conservation Of Synteny

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Our inability to associate distant regulatory elements with the genes that they regulate has largely precluded their examination for sequence alterations contributing to human disease. One major obstacle is the large genomic space surrounding targeted genes in which such elements could potentially reside. In order to delineate gene regulatory boundaries we used whole-genome human-mouse-chicken (HMC) and human-mouse-frog (HMF) multiple alignments to compile conserved blocks of synteny (CBS), under the hypothesis that these blocks have been kept intact throughout evolution at least in part by the requirement of regulatory elements to stay linked to the genes that they regulate. A total of 2,116 and 1,942 CBS>200 kb were assembled for HMC and HMF respectively, encompassing 1.53 and 0.86 Gb of human sequence. To support the existence of complex long-range regulatory domains within these CBS we analyzed the prevalence and distribution of chromosomal aberrations leading to position effects (disruption of a genes regulatory environment), observing a clear bias not only for mapping onto CBS but also for longer CBS size. Our results provide a genome wide data set characterizing the regulatory domains of genes and the conserved regulatory elements within them.