Download or read book Developing Bind n Seq for Identification of C2H2 Zinc Fingers and Other Proteins DNA Binding Properties written by Artem Zykovich and published by . This book was released on 2010 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Transcription factors (TF) play a central role in the regulation of gene expression. Knowledge of TF-DNA binding preferences can significantly improve our understanding of global cellular processes such as differentiation and apoptosis as well as mechanisms that lead to abnormalities in cell fate like cancer. The C2H2 zinc finger is the most common DNA binding domain in the human genome. In addition to being so widespread, there is great interest in studying this domain because it has been successfully employed in targeted genome engineering. Despite years of research on amino acid-nucleotide binding preferences, there is no comprehensive recognition code. Therefore every new zinc finger protein must be tested to empirically determine its DNA binding properties. We developed a new high-throughput method, Bind-n-Seq, for the in vitro analysis of protein-DNA interactions using massively parallel sequencing. The procedure has three steps: (i) binding proteins to randomized oligonucleotide DNA targets, (ii) sequencing the bound oligonucleotides with next-generation technology and (iii) finding motifs among the sequences. There are several key features of Bind-n-Seq that provide advantages over extant methods. Three nucleotide barcodes allow pooling up to 64 binding reactions in a single sequencing run. Extensive library coverage in conjunction with massive sequencing output results in identification of thousands of protein-DNA interactions. The technique is simple and inexpensive. Proteins with long or cooperative binding sites can also be analyzed. We have developed a new motif finding algorithm, Merminator, specifically designed for Bind-n-Seq data. Merminator is based on differential k-mer compositions before and after protein binding. Merminator can be used online at the Bind-n-Seq Source website, where one can process and store data from Bind-n-Seq experiments. The combination of Bind-n-Seq and Merminator allows researchers to investigate protein-DNA interactions in unprecedented depth and breadth.
Download or read book Zinc Finger Proteins written by Shiro Iuchi and published by Springer Science & Business Media. This book was released on 2007-03-06 with total page 291 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the early 1980s, a few scientists started working on a Xenopus transcription factor, TFIIIA. They soon discovered a novel domain associated with zinc, and named this domain "zinc finger. " Th e number of proteins with similar zinc fingers grew quickly and these proteins are now called C2H2, Cys2His2 or classical zinc finger proteins. To date, about 24,000 C2H2 zinc finger proteins have been recognized. Approximately 700 human genes, or more than 2% of the genome, have been estimated to encode C2H2 finger proteins. From the beginning these proteins were thought to be numerous, but no one could have predicted such a huge number. Perhaps thousands of scientists are now working on C2H2 zinc finger proteins fi-om variou s viewpoints. This field is a good example of how a new science begins with the insight of a few scientists and how it develops by efforts of numerous independent scientists, in contrast to a policy-driven scientific project, such as the Human Genome Project, with goals clearly set at its inception and with work performed by a huge collaboration throughout the world. As more zinc finger proteins were discovered, several subfamilies, such as C2C2, CCHC, CCCH, LIM, RING, TAZ, and FYVE emerged, increasing our understanding of zinc fingers. The knowledge was overwhelming. Moreover, scientists began defining the term "zinc finger" differently and using various names for identical zinc fingers. These complications may explain why no single comprehensive resource of zinc finger proteins was available before this publication.
Download or read book The Protein Binding Potential of C2H2 Zinc Finger Domains written by and published by . This book was released on 2008 with total page 372 pages. Available in PDF, EPUB and Kindle. Book excerpt: Cys2-His2 (C2H2) zinc finger domains were originally identified as DNA binding domains, and uncharacterized domains are typically assumed to bind DNA. However, a growing body of evidence suggests an important and widespread role for these domains in protein binding. Over 100 C2H2 zinc finger-protein interactions have been described. This study uses common bioinformatics tools to identify sequence features that predict a DNA- or protein-binding function. Several issues, including uncertainties about the full functional capabilities of the zinc fingers, complicated these efforts. Therefore, an unbiased approach which directly examined the potential for zinc fingers to facilitate DNA or protein interactions was used to determine the full functional capabilities of the C2H2 domains in two model proteins, human OLF-1/EBF associated zinc finger (OAZ) protein and Zif268. OAZ contains 30 zinc fingers in six clusters, some of which have been previously indicated in DNA or protein interactions. Zif268 is a well-known DNA binding protein with three C2H2 domains. DNA binding was assessed using a target site selection (CAST) assay, and protein binding was assessed using a yeast two-hybrid assay. Results indicate that clusters known to bind DNA could facilitate specific protein interactions, but clusters known to bind protein did not facilitate specific DNA interactions, indicating that DNA binding is a more restricted function of zinc fingers than has previously beenrecognized. These results also suggest that the role of C2H2 zinc finger domains in protein interactions has probably been underestimated. The implication of these findings for the prediction of zinc finger function is discussed.
Download or read book Protein protein and Protein DNA Interactions of the Human C2H2 Zinc Finger Proteins written by Ernest Radovani and published by . This book was released on 2019 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: TFs (transcription factors) bind DNA in a sequence specific manner and regulate transcription. Humans encode ~1600 TFs, which have been identified almost entirely on the basis of a putative DNA-binding domain. Knowledge of the mechanisms by which they regulate transcription is sparse. TFs sometimes contain effector domains, but often utilize uncharacterized regions to recruit various cofactors, including chromatin modifiers, components of the general transcription machinery, and other TFs. This thesis focuses on describing the interactome of C2H2-ZNFs (C2H2 zinc finger proteins) which have been classified as TFs due to their ability to bind DNA and regulate transcription in some studied cases. With ~750 proteins, C2H2-ZNFs have greatly expanded in mammals and are the largest and least well characterized subfamily of DNA-binding proteins in humans. Through AP/MS (affinity purification and mass spectrometry), we have identified PPIs (protein-protein interactions) for 345 C2H2-ZNFs and, through ChIP-seq (chromatin immunoprecipitation followed by next generation sequencing), we have identified genomic binding sites for 217 C2H2-ZNFs. From the AP/MS data it appears that, overall, the C2H2-ZNFs exhibit a diverse set of interactions that may give them the ability to perform dual functions in transcription activation and repression, therefore suggesting that they may act as TFs. However, they also exhibit PPIs suggestive of roles additional to what the conventional definition of a TF entails, such as in AS (alternative splicing), which provides evidence that they are multifunctional proteins. Furthermore, C2H2-ZNFs are enriched for binding to AS exons and 3'-ends of genes, providing additional evidence for involvement in co-transcriptional processes. Strikingly, from the AP/MS data, C2H2-ZNFs extensively associate with each other and, based on their DNA-binding patterns, I show that interacting pairs may co-bind DNA, since they bind in closer proximity to each other in the genome compared to pairs that were not found to interact. Lastly, by integrating the PPI data with ChIP-seq, ChIA-PET (chromatin interaction analysis by paired-end tag sequencing), and HiC data, I show that C2H2-ZNF interacting pairs may mediate long range DNA interactions and thus organize chromatin architecture. Altogether, this work provides a snapshot of the C2H2-ZNF interactome and its potential to regulate gene expression.
Download or read book Engineered Zinc Finger Proteins written by Joel P. Mackay and published by Humana Press. This book was released on 2011-08-24 with total page 440 pages. Available in PDF, EPUB and Kindle. Book excerpt: Among the many types of DNA binding domains, C2H2 zinc finger proteins (ZFPs) have proven to be the most malleable for creating custom DNA-binding proteins. In Engineered Zinc Finger Proteins: Methods and Protocols, expert researchers from some of the most active laboratories in this field present detailed methods, guidance, and perspectives. The volume contains sections covering the engineering of ZFPs, methods for the creation, evaluation, and delivery of artificial transcription factors (ATFs), methods for the creation and evaluation of zinc finger nucleases (ZFNs), and a collection of the several applications and assays beyond ATFs and ZFNs, including zinc finger transposases and ChIP-seq methodology amongst other subjects. Written in the highly successful Methods in Molecular BiologyTM series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Comprehensive and cutting-edge, Engineered Zinc Finger Proteins: Methods and Protocols aims to aid both seasoned practitioners and new investigators with its vital methods and insights as they seek to create the next generation of engineered ZFPs and applications.
Download or read book Identification of DNA binding Domains and Target Genes of the Hindsight Zinc finger Protein written by Liang Ming and published by . This book was released on 2006 with total page 174 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Drosophila hindsight gene encodes a putative transcription factor containing 14 C2H2 zinc fingers and crucial in regulating epithelial morphogenesis. Two HNT DNA binding sequences, designated as HNT site A, YGGWCCA, and HNT site B, GGATGCTG, have been identified in vitro. Biochemical and cytogenetic approaches were conducted to elucidate the molecular pathways regulated by HNT. To identify the functional domains of HNT, the DNA-binding abilities of different HNT zinc-finger clusters were analyzed by gel-shift assay. The three most C-terminal zinc fingers bound HNT site A, and the adjacent two zinc fingers bound HNT site B. To identify HNT's in vivo binding sites and target genes, polytene immunostaining by alpha-HNT was performed and 57 unique HNT binding loci were identified. The strongest band, 60C, was further narrowed to 60C4 & sim;60C7 region, covering & sim;100 kb and seven genes. Collectively, the data demonstrate a DNA binding domain and seven candidate target genes of HNT.
Download or read book Zinc Finger Interactions with Nucleic Acids written by Micah David Gearhart and published by . This book was released on 2001 with total page 364 pages. Available in PDF, EPUB and Kindle. Book excerpt: To investigate protein-DNA interactions, particularly the mechanism of DNA binding by Type III monomeric nuclear receptors, this work focuses on the human estrogen related receptor 2 (hERR2) in association with its consensus recognition element. The structure of hERR2 bound to an extended half-site was determined in solution by high resolution NMR methods. The structure explains how Type III monomeric nuclear receptors extend the specificity beyond the single half-site and overcome the requirement to bind cooperatively as dimers. The C-Terminal Extension (CTE) flanking the core DBD uses a modified adenine-thymine binding motif to accommodate the exocyclic amino group on a guanine nucleotide in the minor groove. Residues in the CTE then stabilize the complex by packing against a region of the core DBD normally reserved for dimerization. Mutation of residues involved in DNA-induced intramolecular packing significantly reduces the affinity of hERR2 for DNA. The importance of the interactions in the minor groove are examined by an investigation of the relative binding properties of hERR2 and small synthetic ligands, polyamides, which interact site-specifically in the minor groove. Polyamides designed to bind to the same region of the minor groove as the CTE of hERR2 were shown to inhibit hERR2 binding. These studies identified a novel mechanism for extending the specificity outside of the half-site and stabilizing the monomer through DNA-induced intramolecular interactions. A preliminary study was carried out using C2H2 zinc fingers from TFIIIA and p43 that associate with 5S RNA. Differences in the thermodynamic properties of the full length proteins with 5S RNA were localized to interactions between three finger constructs and a truncated version of the 5S RNA. A disruption in the hydrophobic core of the sixth finger in p43 was identified as the probable origin of the observed thermodynamic differences. A software package, NvAsn, was written to assist in the assignment of NOEs in the spectra of the hERR2 DNA complex. The program incorporates recently developed automatic NOESY assignment algorithms into the visualization package NMRView. NvAsn provides powerful bookkeeping and model-based NOE filtering tools for spectra based, high-throughput structure determination.
Download or read book RNA protein Interactions written by Kiyoshi Nagai and published by Oxford University Press, USA. This book was released on 1994 with total page 302 pages. Available in PDF, EPUB and Kindle. Book excerpt: The study of RNA-protein interactions is crucial to understanding the mechanisms and control of gene expression and protein synthesis. The realization that RNAs are often far more biologically active than was previously appreciated has stimulated a great deal of new research in this field. Uniquely, in this book, the world's leading researchers have collaborated to produce a comprehensive and current review of RNA-protein interactions for all scientists working in this area. Timely, comprehensive, and authoritative, this new Frontiers title will be invaluable for all researchers in molecular biology, biochemistry and structural biology.
Download or read book Abiotic Stress Response in Plants written by Narendra Tuteja and published by John Wiley & Sons. This book was released on 2016-01-08 with total page 456 pages. Available in PDF, EPUB and Kindle. Book excerpt: Understanding abiotic stress responses in plants is critical for the development of new varieties of crops, which are better adapted to harsh climate conditions. The new book by the well-known editor team Narendra Tuteja and Sarvajeet Gill provides a comprehensive overview on the molecular basis of plant responses to external stress like drought or heavy metals, to aid in the engineering of stress resistant crops. After a general introduction into the topic, the following sections deal with specific signaling pathways mediating plant stress response. The last part covers translational plant physiology, describing several examples of the development of more stress-resistant crop varieties.
Download or read book Transcription factors in blood cell development written by Tilman Borggrefe and published by Springer Nature. This book was released on with total page 457 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Cumulated Index Medicus written by and published by . This book was released on 1997 with total page 1860 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book The Hormonal Control of Gene Transcription written by P. Cohen and published by Elsevier. This book was released on 2012-12-02 with total page 517 pages. Available in PDF, EPUB and Kindle. Book excerpt: Over the past few years there have been considerable advances in our understanding of cellular control mechanisms, and current research is now linking areas of biology that were previously thought of as being quite separate. Molecular Aspects of Cellular Regulation is a series of occasional books on multidisciplinary topics which illustrate general principles of cellular regulation. Previous volumes described Recently Discovered Systems of Enzyme Regulation by Reversible Phosphorylation (Volumes 1 and 3), The Molecular Actions of Toxins and Viruses (Volume 2), Molecular Mechanisms of Transmembrane Signalling (Volume 4) and Calmodulin (Volume 5). This sixth volume, The Hormonal Control of Gene Transcription, has now been published to highlight recent important advances in our understanding of this topic which is linking two of the most active areas of current biochemical and molecular biological research (hormone action and gene transcription) and leading to the emergence of unifying concepts.
Download or read book A Handbook of Transcription Factors written by Timothy R. Hughes and published by Springer Science & Business Media. This book was released on 2011-05-10 with total page 310 pages. Available in PDF, EPUB and Kindle. Book excerpt: Transcription factors are the molecules that the cell uses to interpret the genome: they possess sequence-specific DNA-binding activity, and either directly or indirectly influence the transcription of genes. In aggregate, transcription factors control gene expression and genome organization, and play a pivotal role in many aspects of physiology and evolution. This book provides a reference for major aspects of transcription factor function, encompassing a general catalogue of known transcription factor classes, origins and evolution of specific transcription factor types, methods for studying transcription factor binding sites in vitro, in vivo, and in silico, and mechanisms of interaction with chromatin and RNA polymerase.
Download or read book Gene Regulation in Eukaryotes written by Edgar Wingender and published by Wiley-Blackwell. This book was released on 1993 with total page 452 pages. Available in PDF, EPUB and Kindle. Book excerpt: A much-needed guide through the overwhelming amount of literature in the field. Comprehensive and detailed, this book combines background information with the most recentinsights. It introduces current concepts, emphasizing the transcriptional control of genetic information. Moreover, it links data on the structure of regulatory proteins with basic cellular processes. Both advanced students and experts will find answers to such intriguing questions as: - How are programs of specific gene repertoires activated and controlled? - Which genes drive and control morphogenesis? - Which genes govern tissue-specific tasks? - How do hormones control gene expression in coordinating the activities of different tissues? An abundant number of clearly presented glossary terms facilitates understanding of the biological background. Speacial feature: over 2200 (!) literature references.
Download or read book Handbook of Epigenetics written by Trygve O Tollefsbol and published by Academic Press. This book was released on 2017-07-10 with total page 684 pages. Available in PDF, EPUB and Kindle. Book excerpt: Handbook of Epigenetics: The New Molecular and Medical Genetics, Second Edition, provides a comprehensive analysis of epigenetics, from basic biology, to clinical application. Epigenetics is considered by many to be the new genetics in that many biological phenomena are controlled, not through gene mutations, but rather through reversible and heritable epigenetic processes. These epigenetic processes range from DNA methylation to prions. The biological processes impacted by epigenetics are vast and encompass effects in lower organisms and humans that include tissue and organ regeneration, X-chromosome inactivation, stem cell differentiation, genomic imprinting, and aging. The first edition of this important work received excellent reviews; the second edition continues its comprehensive coverage adding more current research and new topics based on customer and reader reviews, including new discoveries, approved therapeutics, and clinical trials. From molecular mechanisms and epigenetic technology, to discoveries in human disease and clinical epigenetics, the nature and applications of the science is presented for those with interests ranging from the fundamental basis of epigenetics, to therapeutic interventions for epigenetic-based disorders. Timely and comprehensive collection of fully up-to-date reviews on epigenetics that are organized into one volume and written by leading figures in the field Covers the latest advances in many different areas of epigenetics, ranging from basic aspects, to technologies, to clinical medicine Written at a verbal and technical level that can be understood by scientists and college students Updated to include new epigenetic discoveries, newly approved therapeutics, and clinical trials
Download or read book Comprehensive Toxicology written by and published by Elsevier. This book was released on 2010-06-01 with total page 6448 pages. Available in PDF, EPUB and Kindle. Book excerpt: An explosive increase in the knowledge of the effects of chemical and physical agents on biological systems has led to an increased understanding of normal cellular functions and the consequences of their perturbations. The 14-volume Second Edition of Comprehensive Toxicology has been revised and updated to reflect new advances in toxicology research, including content by some of the leading researchers in the field. It remains the premier resource for toxicologists in academia, medicine, and corporations. Comprehensive Toxicology Second Edition provides a unique organ-systems structure that allows the user to explore the toxic effects of various substances on each human system, aiding in providing diagnoses and proving essential in situations where the toxic substance is unknown but its effects on a system are obvious. Comprehensive Toxicology Second Edition is the most complete and valuable toxicology work available to researchers today. Contents updated and revised to reflect developments in toxicology research Organized with a unique organ-system approach Features full color throughout Available electronically on sciencedirect.com, as well as in a limited-edition print version
Download or read book Tissue Specific Gene Expression written by Rainer Renkawitz and published by John Wiley & Sons. This book was released on 1989 with total page 221 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
