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Genome Wide Analysis Of Transcriptional Expression Programs Regulatory Networks And Cis Regulatory Sequences In Saccharomyces Cerevisiae
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Book Synopsis Genome-wide Analysis of Transcriptional Expression Programs, Regulatory Networks and Cis-regulatory Sequences in Saccharomyces Cerevisiae by : Christopher T. Harbison
Download or read book Genome-wide Analysis of Transcriptional Expression Programs, Regulatory Networks and Cis-regulatory Sequences in Saccharomyces Cerevisiae written by Christopher T. Harbison and published by . This book was released on 2005 with total page 456 pages. Available in PDF, EPUB and Kindle. Book excerpt: Historically, knowledge of gene-specific transcription has been accumulated by the study of the individual genetic and physical interactions between transcriptional regulators and the genes they regulate, often requiring considerable time and effort. Microarray technology now enables investigation of gene expression at the level of the entire genome, allowing researchers access to rich datasets and promising new levels of depth in the understanding of transcriptional regulation. Our lab has made use of these technologies both to measure the levels of all mRNA transcripts within a population of cells, as well as to locate the regions within the genome that are bound by transcriptional regulators. Such studies not only allow for the functional annotation of both genes and regulators, but can also provide clues about the identity of the regulatory regions within DNA, the structure of global regulatory networks and the regulation of DNA-binding proteins. These and other insights are presented here based on our genome-wide studies of transcriptional regulation in the yeast Saccharomyces cerevisiae.
Book Synopsis Genome-wide Expression and Location Profiling in Saccharomyces Cerevisiae by : Ezra Gray Jennings
Download or read book Genome-wide Expression and Location Profiling in Saccharomyces Cerevisiae written by Ezra Gray Jennings and published by . This book was released on 2002 with total page 500 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Bacterial Regulatory Networks by : Alain Filloux
Download or read book Bacterial Regulatory Networks written by Alain Filloux and published by Caister Academic Press Limited. This book was released on 2012 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Regulatory networks enable bacteria to adapt to almost every environmental niche on earth. Regulation is achieved by a network of interactions among diverse types of molecules including DNA, RNA, proteins and metabolites. The primary role of regulatory networks in bacteria is to control the response to environmental changes, such as nutritional status and environmental stress. A complex organization of networks allows the organism to coordinate and integrate multiple environmental signals. Renowned authors under the expert guidance of the editor Alain A.M. Filloux, have contributed authoritative, up-to-date reviews of the current research and theories on regulatory networks in bacteria. The volume contains critical reviews written by the leading research scientists in this topical field. The authors fully explore various regulatory networks, discuss variations of common themes and provide fresh insights into bacterial regulatory mechanisms. Topics include: the sigma network in Escherichia coli, control of bacterial virulence, ECF sigma factors, quorum sensing, cyclic di-GMP, RNA-mediated regulation, the H-NS regulator, two-component regulatory systems, bacterial chemotaxis, regulation of iron homeostasis, anaerobic regulatory networks, bacterial bistable regulatory networks, and evolution of transcription factors and regulatory networks. This book is essential reading for everyone interested in gene expression and regulation in bacteria and is a recommended text for all microbiology libraries.
Book Synopsis Advances in CRISPR-Cas9 Genome Engineering Technologies in Saccharomyces Cerevisiae and Tests for Cis-regulatory Evolution by : Justin Daniel Smith
Download or read book Advances in CRISPR-Cas9 Genome Engineering Technologies in Saccharomyces Cerevisiae and Tests for Cis-regulatory Evolution written by Justin Daniel Smith and published by . This book was released on 2016 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: This thesis is organized into two primary areas of research: cis-regulatory evolution and genome engineering. It is now known that noncoding regions comprise the vast majority of genomic regions under selective constraint in mammals. Despite this, the ability to detect natural selection on noncoding regions has lagged behind the ability to detect selection on coding regions. In Chapter 1, we introduce a new test to detect selection on cis-regulatory elements, and demonstrate its utility on three mammalian transcriptional enhancers. In Chapter 2, we investigate the evolution of resistance to the mycotoxin citrinin by comparing two closely related species of budding yeast, Saccharomyces paradoxus and Saccharomyces cerevisiae. Applying a genome-wide test for selection on cis-regulation, we identified five genes involved in resistance in S paradoxus, four of which are necessary for resistance and increase resistance in S cerevisiae when over-expressed. In the second half of this dissertation, I discuss my work with genome engineering and CRISPR-Cas9. In Chapter 2, we build an improved CRISPR activator (CRISPRa) to simultaneously induce overexpression (in S cerevisiae) of the four genes identified to confirm their role in citrinin resistance. In Chapter 3, we build an inducible CRISPR interference (CRISPRi) system and and designed gRNA libraries to determine design rules for CRISPRi gRNA design in S cerevisiae. We determined that gRNAs targeted to a region with low nucleosome occupancy and high chromatin accessibility within a window of 0 to 200bp upstream of the transcription start site (TSS) are most likely to be effective. In Chapter 4 we confirm and refine these rules in a much larger library consisting of ~9000 unique strains. Additionally, we present a novel method for parsing complex oligonucleotide libraries into single, sequence verified DNA sequences using high throughput sequencing and yeast synthetic biology. We utilize this technology to create and characterize a collection of ~9000 individual inducible CRISPRi strains to the vast majority of essential and respiratory essential genes in S cerevisiae. In Chapter 5, we compare mismatch tolerance for Cas9 in vitro and in vivo (in S cerevisiae) and test a variety of truncated and full-length gRNAs (with 17, 18, and 20 nucleotides of complementarity sequence). We observed notable differences between in vitro and in vivo Cas9 cleavage specificity profiles, with in vivo cleavage being more sensitive/less tolerant to mismatches.
Book Synopsis Microarrays and Transcription Networks by : M. Francis Shannon
Download or read book Microarrays and Transcription Networks written by M. Francis Shannon and published by CRC Press. This book was released on 2006-09 with total page 156 pages. Available in PDF, EPUB and Kindle. Book excerpt: While every cell of an organism has an identical genomic content, extremely complex networks exist to tailor the genomic output to the needs of that cell. This program of gene expression is different for every cell type and stage of development. In addition, the cell can respond to its environment by modulating its gene expression program in a fairly dramatic manner. For many decades gene transcription has been investigated in systems from bacteria to mammalian cells and along the way many landmark findings have set new paradigms that often apply across wide evolutionary distances. Studying individual genes, however, especially in mammalian systems has been a painstaking business and although we know the transcription activators and other complexes that control specific genes in minute detail, generalizing these findings has often proven to be difficult. It has become clear that transcription factors do not operate alone but form complex networks in the cell. If one component of this complexity is disturbed then there are repercussions across the entire network, but it has been impossible to study these networks until very recently. The advent of microarray technology within the last decade has revolutionized how we study gene transcription. There are several types of array technology that essentially screen for relative mRNA levels for many thousands of genes at once. We do not focus here on the technology as this has become routine and is available to many researchers. Microarray technology has given us the ability to measure the entire gene expression program of a cell in a single experiment and compare it to other cells thus allowing a global view of cell behaviour at the level of gene transcription. Expression profiling, as this endeavour has become known, is now a relatively simple undertaking and hundreds, probably thousands of papers have been published demonstrating the power of this technology. Expression profiling has been applied to many diverse biological problems and is also being developed as a method for disease diagnosis especially in the cancer classification field. There are constant improvements or modified uses of the technology that are allowing more and more high throughput experiments to be carried out.
Book Synopsis Reconstruction and Systems Analysis of Genome-scale Metabolic and Regulatory Networks in Saccharomyces Cerevisiae by : Markus Juhana Herrgard
Download or read book Reconstruction and Systems Analysis of Genome-scale Metabolic and Regulatory Networks in Saccharomyces Cerevisiae written by Markus Juhana Herrgard and published by . This book was released on 2004 with total page 736 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Genomewide Analysis of RNA Processing in Saccharomyces Cerevisiae by : Tyson A. Clark
Download or read book Genomewide Analysis of RNA Processing in Saccharomyces Cerevisiae written by Tyson A. Clark and published by . This book was released on 2002 with total page 422 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Genome-wide Analysis of Transcription Factors and Chromatin in Saccharomyces Cerevisiae by : John Jason Wyrick
Download or read book Genome-wide Analysis of Transcription Factors and Chromatin in Saccharomyces Cerevisiae written by John Jason Wyrick and published by . This book was released on 2002 with total page 496 pages. Available in PDF, EPUB and Kindle. Book excerpt: (Cont.) Telomere-proximal genes were derepressed over regions extending 20 kb from telomere ends, well beyond the extent of Sir protein binding and the effects resulting from loss of Sir function. These results indicate that histones make Sir-independent contributions to telomeric silencing, and that the role of histones located elsewhere in chromosomes is gene specific To map the in vivo binding sites of transcription factors, a new technique-genome-wide location analysis-was developed. Genome-wide location and expression analysis was used to identify the target genes of the yeast activator proteins Gal4 and Ste 12. All of the known targets for these two activators were confirmed, and new target genes in multiple functional pathways were identified.
Book Synopsis Transcriptional Regulation by Non-coding RNAs in Saccharomyces Cerevisiae by : Ana Serra Barros
Download or read book Transcriptional Regulation by Non-coding RNAs in Saccharomyces Cerevisiae written by Ana Serra Barros and published by . This book was released on 2012 with total page 442 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Extracellular and Intracellular Signaling by : James D. Adams
Download or read book Extracellular and Intracellular Signaling written by James D. Adams and published by Royal Society of Chemistry. This book was released on 2011 with total page 319 pages. Available in PDF, EPUB and Kindle. Book excerpt: Intracellular cell signaling is a well understood process. However, extracellular signals such as hormones, adipokines, cytokines and neurotransmitters are just as important but have been largely ignored in other works. Aimed at medical professionals and pharmaceutical specialists, this book integrates extracellular and intracellular signalling processes and offers a fresh perspective on new drug targets.
Book Synopsis Genetics and Biotechnology by : Ulrich Kück
Download or read book Genetics and Biotechnology written by Ulrich Kück and published by Springer Science & Business Media. This book was released on 2013-03-09 with total page 372 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mycology, the study of fungi, originated as a subdiscipline of botany and was a descriptive discipline, largely neglected as an experimental science until the early years of this century. A seminal paper by Blakeslee in 1904 provided evidence for self incompatibility, termed "heterothallism", and stimulated interest in studies related to the control of sexual reproduction in fungi by mating-type specificities. Soon to follow was the demonstration that sexually reproducing fungi exhibit Mendelian inheritance and that it was possible to conduct formal genetic analysis with fungi. The names Burgeff, Kniep and Lindegren are all associated with this early period of fungal genetics research. These studies and the discovery of penicillin by Fleming, who shared a Nobel Prize in 1945, provided further impetus for experimental research with fungi. Thus began a period of interest in mutation induction and analysis of mutants for bio chemical traits. Such fundamental research, conducted largely with Neurospora crassa, led to the one gene: one enzyme hypothesis and to a second Nobel Prize for fungal research awarded to Beadle and Tatum in 1958. Fundamental research in biochemical genetics was extended to other fungi, especially to Saccharomyces cere visiae, and by the mid-1960s fungal systems were much favored for studies in eukaryotic molecular biology and were soon able to compete with bacterial systems in the molecular arena.
Book Synopsis Genetic Basis of Thermal Divergence in Saccharomyces Species by : Xueying C. Li
Download or read book Genetic Basis of Thermal Divergence in Saccharomyces Species written by Xueying C. Li and published by . This book was released on 2018 with total page 186 pages. Available in PDF, EPUB and Kindle. Book excerpt: The genetic architecture of phenotypic divergence is a central question in evolutionary biology. Genetic architecture is impacted by whether evolution occurs through accumulation of many small-effect or a few large-effect changes, the relative contribution of coding and cis-regulatory changes, and the prevalence of epistatic effects. Our empirical understanding of the genetic basis of evolutionary change remains incomplete, largely because reproductive barriers limit genetic analysis to those phenotypes that distinguish closely related species. In this dissertation, I use hybrid genetic analysis to examine the basis of thermal divergence between two post-zygotically isolated species, Saccharomyces cerevisiae and S. uvarum. S. cerevisiae is relatively heat tolerant, whereas S. uvarum is heat sensitive but outperforms S. cerevisiae at 4°C. Gene expression analysis with an S. cerevisiae and S. uvarum hybrid revealed a small set of 136 genes with temperature-dependent cis-acting differences, suggesting that the temperature divergence has not caused widespread cis-regulatory divergence. Using a genome-wide non-complementation screen, I found a single nuclear-encoded gene with a modest contribution to heat tolerance, and a large effect of the species' mitochondrial DNA (mitotype). Recombinant mitotypes and allele replacements indicate multiple mitochondria-encoded genes contribute to thermal divergence, with the coding sequence of COX1 showing a moderate effect on both heat and cold tolerance. The non-complementation approach also identified allele differences of CUP2, a copper-binding transcription factor, in copper resistance of S. cerevisiae and S. uvarum. Chimeric alleles showed that multiple changes underlie the resistance of S. cerevisiae CUP2, with cis-regulatory changes having a larger effect than coding changes. Taken together, my findings suggest that evolution of interspecific phenotypic differences often involves accumulation of small-to-medium effect changes, such as those in mitochondrial DNA and CUP2, and can occur through both coding and cis-regulatory changes.
Book Synopsis The Maize Genome by : Jeffrey Bennetzen
Download or read book The Maize Genome written by Jeffrey Bennetzen and published by Springer. This book was released on 2018-11-24 with total page 390 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book discusses advances in our understanding of the structure and function of the maize genome since publication of the original B73 reference genome in 2009, and the progress in translating this knowledge into basic biology and trait improvement. Maize is an extremely important crop, providing a large proportion of the world’s human caloric intake and animal feed, and serving as a model species for basic and applied research. The exceptionally high level of genetic diversity within maize presents opportunities and challenges in all aspects of maize genetics, from sequencing and genotyping to linking genotypes to phenotypes. Topics covered in this timely book range from (i) genome sequencing and genotyping techniques, (ii) genome features such as centromeres and epigenetic regulation, (iii) tools and resources available for trait genomics, to (iv) applications of allele mining and genomics-assisted breeding. This book is a valuable resource for researchers and students interested in maize genetics and genomics.
Book Synopsis Investigation of Combinatorial Gene Regulation in Saccharomyces Species by : Aaron Taras Spivak
Download or read book Investigation of Combinatorial Gene Regulation in Saccharomyces Species written by Aaron Taras Spivak and published by . This book was released on 2012 with total page 174 pages. Available in PDF, EPUB and Kindle. Book excerpt: Transcriptional control of gene expression is a result of complex interactions between the cis -regulatory elements (CRE) at gene promoters. To understand the regulatory logic of a cell, we need to identify the CRE combinations that regulate gene expression. This dissertation describes a sensitive computational method to identify phylogenetically conserved CRE combinations for any species of interest. In contrast to previous methods, I do not need to align genomes to identify these combinations. I applied the method in 7 sensu stricto and sensu lato Saccharomyces species. 80% of the predictions displayed some evidence of combinatorial transcriptional behavior in several existing datasets including (1) ChIP-chip data for co-localization of transcription factors, (2) gene expression data for co-expression of predicted regulatory targets, and (3) gene ontology databases for common pathway membership of predicted regulatory targets. To establish definitive evidence that these CRE interactions influence TF occupancy, I performed ChIP-Seq experiments on transcription factors in a wild-type strain and strains in which a predicted cofactor was deleted. These experiments showed that TF occupancy at the promoters of the CRE combination target genes depends on the predicted cofactor while occupancy of other promoters is independent of the predicted cofactor. In addition to identifying phylogenetically conserved CRE combinations, the method can annotate potential regulatory differences between species. Previous studies of cis -regulatory rewiring between species assume that CREs act independently and have found that promoter divergence does not necessarily explain expression divergence. By analyzing the S. cerevisiae and S. bayanus genomes, I identified differences in combinatorial cis -regulation between the species and showed that the predicted changes in gene regulation explain several of the species-specific differences seen in gene expression datasets. In some instances, the same CRE combinations appear to regulate genes involved in distinct biological processes in the two different species. The results of this research demonstrate (1) that combinatorial cis -regulation can be inferred from similarities between species and (2) that combinatorial cis -regulation can explain differences between species.
Book Synopsis Mapping RNA Protein Interactions in Saccharomyces Cerevisiae by : Daniel Michael Klass
Download or read book Mapping RNA Protein Interactions in Saccharomyces Cerevisiae written by Daniel Michael Klass and published by . This book was released on 2013 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: We are on the threshold of a new era in our understanding of that fantastic feat of regulation at the core of life itself--gene expression. The rapid pace of new developments in genome-wide, high-throughput technologies has allowed us unprecedented access to observe multiple stages of the gene expression program for nearly the entire genome. This has revealed a widespread discordance between mRNA abundance and protein abundance for many genes whose expression changes in response to environmental stimuli, and a significant coordination of post-transcriptional regulation for specific sets of related mRNAs at the levels localization, translation, decay, and the noise in gene expression. Despite this evidence suggesting the existence of a coordinated regulatory framework that potentially affects the fate of every mRNA in the cell, our efforts to discern the underlying structure and regulatory themes are hindered by an incomplete understanding of RNA-protein interactions. To advance our comprehension of post-transcriptional regulation, we developed new tools to identify which proteins bind to RNA, which of those bind concurrently, which RNAs are bound by a given protein, and where each protein binds on each RNA. Using our proteomic tools we discovered hundreds unexpected RNA binding proteins, uncovered new RNA binding domains, identified widespread, concurrent binding with several RNA binding proteins, and inferred functional information from the simultaneous binding partners of several RNA binding proteins. We used our genomic, sequencing-based tools to systematically interrogate a large set of diverse RNA binding proteins and we discerned new themes from the resulting data. This revealed significant differences in function, localization, and regulation among the proteins encoded by the targets of a given RNA binding protein based on binding position. These results suggest that the functional consequences of the RBP-RNA interaction are determined not only by whether an mRNA is bound by an RBP but also by the position of the binding site within the mRNA and its relation to the other RBPs that bind the same mRNA. Overall, we found evidence of an extensive regulatory framework involving hundreds of RNA binding proteins, encompassing nearly the entire transcriptome, and extending our understanding of the RNA-protein interactions at the heart of post-transcriptional regulation.
Book Synopsis Genomic Control Process by : Isabelle S. Peter
Download or read book Genomic Control Process written by Isabelle S. Peter and published by Academic Press. This book was released on 2015-01-21 with total page 461 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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
Book Synopsis Coordinate Regulation of Glycolytic Gene Expression in Saccharomyces Cerevisiae by : Chang Seo Park
Download or read book Coordinate Regulation of Glycolytic Gene Expression in Saccharomyces Cerevisiae written by Chang Seo Park and published by . This book was released on 1994 with total page 384 pages. Available in PDF, EPUB and Kindle. Book excerpt:
