Author : Nathalia Monique Henry-Headley
Publisher :
Page : 240 pages
File Size : 42,25 MB
Release : 2001
Category :
ISBN :
Author : Arjan Hada
Publisher :
Page : 356 pages
File Size : 28,44 MB
Release : 2017
Category : Adenosine triphosphate
ISBN :
Chromatin is highly regulated nucleoprotein complex facilitating the dynamic balance between genome packaging and accessibility. The central workhorses regulating the dynamic nature of chromatin are ATP-dependent chromatin remodelers- ISWI, SWI/SNF, INO80, and CHD/Mi2. All chromatin remodelers transduce the energy from ATP hydrolysis to translocate on DNA, break histone-DNA contacts, and mobilize nucleosomes. However, the final outcomes of nucleosome remodeling are diverse - nucleosome sliding, dimer exchange, nucleosome disassembly, and nucleosome conformation alteration. This study sheds light on how different chromatin remodelers catalyze various structural transformations. We provide novel insights into the nucleosome dynamics, the role of histone octamer dynamics on nucleosome remodeling by ISW2, mechanism of dimer exchange by INO80 and mechanism of nucleosome disassembly by the coordinated action of RSC and histone chaperone Nap1. We also provide insights on how aberrant SWI/SNF complexes affect fundamental enzymatic properties such as ATPase and processive nucleosome remodeling. ISW2 remodelers sense and respond to the length of linker DNA separating the nucleosome and centers nucleosome. Histone octamers are perceived as a mostly static structure whereas DNA deforms itself to fit nucleosome. We have found change in histone octamer conformation as a novel step in ISW2 mobilizing DNA through the nucleosome. We provide evidence for an induced fit mechanism where histone-histone and histone-DNA interactions change in respond to remodeler, and these changes promote DNA entry into the nucleosome. Our data supports a model in which DNA translocation causes the change in histone octamer conformation, followed by DNA entry into nucleosome and resetting of the histone octamer core. We also move a step ahead and show that SANT domain promotes the entry of DNA into nucleosome and resets the histone octamer core allowing processive nucleosome mobilization. INO80 nucleosome remodeling provides two outcomes- nucleosome centering and dimer exchange. INO80 exchanges H2A.Z-H2B dimer for H2A-H2B. We show that INO80 is incredibly slow at centering nucleosome compared to ISW2. We also provide evidence for a mechanism where INO80 persistently displaces DNA from the dimer interface, unlike ISW2, facilitating dimer exchange. In another instance, we show that kinetic step sizes are modulated by a combination of enzyme and DNA sequence properties, and are not hardwired into the enzyme. ISW2 has been previously shown to translocate DNA with a kinetic step sizes of ~7bp and ~3bp. We show that kinetic step sizes may vary depending on nucleosomal location where we monitor DNA movement. Next, we studied the mechanism of nucleosome disassembly by RSC in the presence of Nap1. We found that Nap1 promotes the disassembly of the distal nucleosome that RSC collides with rather than the proximal nucleosomes it mobilizes. SWI/SNF tops the list of the frequently mutated epigenetic factor in cancer with its subunits mutated in more than 20% of all cancers. Loss of hSnf5 is a driver mutation in pediatric rhabdoid tumors. Our lab has previously identified that the deletion of Snf5 causes yeast SWI/SNF to lose an entire module comprised of Snf5, Swp82, and Taf14. In this study, we establish the properties of aberrant SWI/SNF complex formed in the absence of Snf5 module. The deletion resulted in lower ATP hydrolysis and nucleosome mobilization activities of the mutant SWI/SNF. We found that Snf5 module is necessary to couple ATP hydrolysis with DNA translocation. We studied the role of accessory domain AT-hooks in the ATPase subunit of SWI/SNF and found similar results. Interestingly, AT hook and SnAC domains, and Snf5 subunit were found to communicate with the same region in ATPase domain physically. These studies provide valuable mechanistic insights into chromatin structure and function and highlight how different chromatin remodelers catalyze different chromatin remodeling outcomes. We also provide new insights on how the activity of the core ATPase motor is regulated either by accessory domains on the same subunit or by accessory subunits as a part of the larger complex.
Author : Ralph A. Bradshaw
Publisher : Academic Press
Page : 3188 pages
File Size : 32,75 MB
Release : 2009-11-03
Category : Science
ISBN : 0080920918
Handbook of Cell Signaling, Three-Volume Set, 2e, is a comprehensive work covering all aspects of intracellular signal processing, including extra/intracellular membrane receptors, signal transduction, gene expression/translation, and cellular/organotypic signal responses. The second edition is an up-to-date, expanded reference with each section edited by a recognized expert in the field. Tabular and well illustrated, the Handbook will serve as an in-depth reference for this complex and evolving field. Handbook of Cell Signaling, 2/e will appeal to a broad, cross-disciplinary audience interested in the structure, biochemistry, molecular biology and pathology of cellular effectors. Contains over 350 chapters of comprehensive coverage on cell signaling Includes discussion on topics from ligand/receptor interactions to organ/organism responses Provides user-friendly, well-illustrated, reputable content by experts in the field
Author : Weiwei Dang
Publisher :
Page : 318 pages
File Size : 47,88 MB
Release : 2006
Category :
ISBN :
The mechanism of ATP-dependent chromatin remodeling was explored using the Saccharomyces cerevisiae ISW2 complex, a member of the ISWI subfamily of chromatin remodeling factors. Site-specific DNA photoaffinity labeling and peptide mapping were utilized to study the specific interactions between ISW2 and nucleosomes. The subunits of ISW2 that contact particular sites on nucleosomal and extranucleosomal DNA were identified. In an extensive scan, three DNA regions on the end-positioned nucleosome were shown to be the major contact sites of ISW2. The extranucleosomal DNA region was bound by the largest subunit Itc1 and one of the small histone fold subunits (Dpb4). The region around the DNA entry/exit site or the edge of the nucleosome was contacted by both Itc1 and the catalytic subunit Isw2. The internal site 2 helical turns from the dyad axis of the nucleosome, which has been shown to be critical for chromatin remodeling, was associated with the two large subunits Itc1 and Isw2. The contacts of specific Isw2 domains were determined by peptide mapping of photoaffinity labeled Isw2. The SLIDE domain was found to interact with extranucleosomal DNA 20 bp from the entry/exit site and the novel HAND domain contacts the DNA just 10 bp inside the nucleosome. The helicase domain containing the ATP binding pocket is bound at the critical internal site two helical turns from the dyad. Determination of the spatial arrangement of ISW2 with nucleosomes illustrates, for the first time, the interaction of a chromatin remodeling factor with the nucleosome and key structural information for understanding how ISW2 repositions mononucleosomes and generates regularly spaced nucleosome arrays. The interaction of ISW2 with the nucleosome was found to be affected by the length of the extranucleosomal DNA with an optimal length of ~70 bp and by the histone H4 tail in parallel pathways to direct ISW2 to the critical internal site of the nucleosome. The domains of Ume6 that binds to ISW2 was determined and to be sufficient to recruit ISW2 under limiting conditions. Finally, studies on the histone fold dimer of ISW2 have suggested roles in facilitating ISW2 interacting with extranucleosomal DNA, as well as nucleosome mobilization.
Author : Stanley Maloy
Publisher : Academic Press
Page : 4360 pages
File Size : 47,98 MB
Release : 2013-03-03
Category : Science
ISBN : 0080961568
The explosion of the field of genetics over the last decade, with the new technologies that have stimulated research, suggests that a new sort of reference work is needed to keep pace with such a fast-moving and interdisciplinary field. Brenner's Encyclopedia of Genetics, Second Edition, Seven Volume Set, builds on the foundation of the first edition by addressing many of the key subfields of genetics that were just in their infancy when the first edition was published. The currency and accessibility of this foundational content will be unrivalled, making this work useful for scientists and non-scientists alike. Featuring relatively short entries on genetics topics written by experts in that topic, Brenner's Encyclopedia of Genetics, Second Edition, Seven Volume Set provides an effective way to quickly learn about any aspect of genetics, from Abortive Transduction to Zygotes. Adding to its utility, the work provides short entries that briefly define key terms, and a guide to additional reading and relevant websites for further study. Many of the entries include figures to explain difficult concepts. Key terms in related areas such as biochemistry, cell, and molecular biology are also included, and there are entries that describe historical figures in genetics, providing insights into their careers and discoveries. This 7-volume set represents a 25% expansion from the first edition, with over 1600 articles encompassing this burgeoning field Thoroughly up-to-date, with many new topics and subfields covered that were in their infancy or not inexistence at the time of the first edition. Timely coverage of emergent areas such as epigenetics, personalized genomic medicine, pharmacogenetics, and genetic enhancement technologies Interdisciplinary and global in its outlook, as befits the field of genetics Brief articles, written by experts in the field, which not only discuss, define, and explain key elements of the field, but also provide definition of key terms, suggestions for further reading, and biographical sketches of the key people in the history of genetics
Author : Nathan Gamarra
Publisher :
Page : pages
File Size : 37,98 MB
Release : 2020
Category :
ISBN :
Eukaryotic genomes are packaged into chromatin: a highly heterogeneous structure composed of nucleic acids and proteins. This packaging controls access to the underlying DNA sequences and, as a result plays a critical role in nearly all genomic processes. The primary molecular structure of chromatin is the nucleosome: ~147 bp of DNA wrapped around a core of histone proteins. Both the location and status of nucleosomes in the genome are critical for the proper packaging of chromatin. As a result, cells have evolved several sophisticated molecular machines to disrupt or modify nucleosomes to achieve specific packaging states. A critical member of these machines are the SWI2/SNF2 superfamily of ATP-dependent chromatin remodeling enzymes, which are DNA translocases that harness the energy of ATP hydrolysis to physically disrupt nucleosomes. Because of their central role in control nucleosome structure throughout the genome, remodelers play roles in virtually all DNA-dependent process, but the precise mechanisms of how remodelers disrupt nucleosomes and how this disruption is coupled to other molecular events remains very poorly understood. In this thesis we focus on understanding the remodeling mechanisms of two subfamilies of SWI2/SNF2 remodelers that slide nucleosomes: INO80 and ISWI. To understand how these and other SWI2/SNF2 ATP-dependent remodelers might cooperate with nuclear machinery to enable biological processes, we first review our broad understanding of remodeling mechanism as it compares to another molecular motor that disrupts nucleosomes: RNA polymerase. We then speculate on how these two distinct families cooperate to accomplish transcription on chromatin templates. After this, we set out to uncover elements of nucleosome that control remodeler activity and identify a conserved surface of the nucleosome known as the acidic patch that is required to activate both ISWI and INO80 family remodelers. Using a combination of biochemical and biophysical assays, we show that this surface activates remodeling by these two families after they bind the nucleosome. For the ISWI remodeler SNF2h, the acidic patch activates remodeling by serving as a landing pad for the binding of autoinhibitory domains while INO80 uses a separate mechanism. We then solve the near-atomic CryoEM structure of SNF2h bound to the nucleosome. Unexpectedly, we find that SNF2h binding in an activated state asymmetrically distorts the histone core of the nucleosome and that this may be important in regulating the activity of the enzyme. Finally, we test the hypothesis that by measuring remodeling activity of nucleosomes with site-specific restraints in the histone core. We find that specifically restraining histone dynamics in locations across all 4 histone proteins inhibits SNF2h-mediated nucleosome sliding. Taken together, these results suggest that remodelers rely on the structure and dynamics of both the DNA and protein components of the nucleosome to accomplish their activities.
Author : Adam Nicholas Yadon
Publisher :
Page : 0 pages
File Size : 26,86 MB
Release : 2012
Category :
ISBN :
The efficient three-dimensional packaging of DNA into eukaryotic nuclei is accomplished through spatially organizing and compacting DNA into chromatin. Maintaining proper access to DNA, by modulation of either the location of DNA within the nucleus or the positions of nucleosomes, is essential for regulating DNA-dependent processes. The work in this dissertation focuses on elucidating the functions and molecular mechanisms by which the three-dimensional packaging of eukaryotic DNA affects DNA-dependent processes. Here I show that the ATP-dependent chromatin remodeling enzyme Isw2 is a global repressor of non-coding RNA (ncRNA) transcription that initiates from the edges of nucleosome free regions (NFRs) genome-wide. Isw2-dependent chromatin remodeling activity is required to reduce accessibility to DNA by sliding nucleosomes toward NFRs and occluding transcription start sites. This work establishes Isw2 as the first factor that functions to reduce the size of NFRs in vivo. My evidence also suggests that proper repression of ncRNA by Isw2 prevents transcriptional interference of mRNA, providing an important biological role for Isw2-dependent chromatin remodeling. Analysis of the targeting mechanisms of Isw2 to NFRs uncovered the sequence-specific transcription factors (TFs) Ume6, Nrg1, Cin5, and Sok2 as globally required for Isw2 recruitment to many target loci genome-wide. This establishes the first comprehensive genome-wide map for TF-dependent targeting of a chromatin remodeling enzyme. The observation that Isw2 is targeted in a TF-dependent fashion to a large number of loci not containing an annotated TF binding site led to the discovery that Isw2 can also be targeted to specific loci via Ume6- and TFIIB-dependent DNA looping. Both Ume6 and TFIIB-dependent DNA looping are required to maintain transcriptional repression at target loci. I have thus identified DNA looping as a previously unknown mechanism to target a chromatin remodeling enzyme and uncovered a novel physiological role for DNA looping. My work has led to a better understanding of how the three dimensional packaging of DNA into eukaryotic nuclei affects a DNA-dependent process in which transcriptional repression is facilitated by DNA-looping mediated TF-dependent targeting of a chromatin remodeling enzyme.
Author :
Publisher :
Page : 788 pages
File Size : 37,94 MB
Release : 2004
Category : Dissertations, Academic
ISBN :
Author : P. Michael Conn
Publisher : Academic Press
Page : 272 pages
File Size : 26,61 MB
Release : 2011-09-06
Category : Science
ISBN : 0080923275
Nucleic acids are the fundamental building blocks of DNA and RNA and are found in virtually every living cell. Molecular biology is a branch of science that studies the physicochemical properties of molecules in a cell, including nucleic acids, proteins, and enzymes. Increased understanding of nucleic acids and their role in molecular biology will further many of the biological sciences, including genetics, biochemistry, and cell biology. Progress in Nucleic Acid Research and Molecular Biology is intended to bring to light the most recent advances in these overlapping disciplines with a timely compilation of reviews comprising each volume. This series provides a forum for discussion of new discoveries, approaches, and ideas Contributions from leading scholars and industry experts Reference guide for researchers involved in molecular biology and related fields
Author : Renato Paro
Publisher : Springer Nature
Page : 215 pages
File Size : 26,50 MB
Release : 2021-03-23
Category : Science
ISBN : 3030686701
This open access textbook leads the reader from basic concepts of chromatin structure and function and RNA mechanisms to the understanding of epigenetics, imprinting, regeneration and reprogramming. The textbook treats epigenetic phenomena in animals, as well as plants. Written by four internationally known experts and senior lecturers in this field, it provides a valuable tool for Master- and PhD- students who need to comprehend the principles of epigenetics, or wish to gain a deeper knowledge in this field. After reading this book, the student will: Have an understanding of the basic toolbox of epigenetic regulation Know how genetic and epigenetic information layers are interconnected Be able to explain complex epigenetic phenomena by understanding the structures and principles of the underlying molecular mechanisms Understand how misregulated epigenetic mechanisms can lead to disease
