Nuclear Pore Proteins in Regulation of Chromatin State and Gene Expression

Nuclear Pore Proteins in Regulation of Chromatin State and Gene Expression
Author: Terra Kuhn
Publisher:
Total Pages: 250
Release: 2019
Genre:
ISBN:

Nuclear pore complexes are best known for their regulation of nucleocytoplasmic transport as integral components of the eukaryotic nuclear envelope. Over the years, their importance in regulation of genome function has become apparent. Many of the 30 individual nuclear pore proteins, Nups, have been found to play distinct roles interacting with and regulating various genomic targets, especially in a cell-type specific manner. The mechanism behind this regulation is often unknown. We have developed a method by which to study the roles of Nups on chromatin using an ectopic-tethering system. Drosophila melanogaster provide a powerful tool with which to combine many genetic elements of interest together in individual organisms quickly and efficiently, and additionally has allowed for powerful high-resolution visualization of chromatin structure perturbations through the imaging of their larval salivary gland polytene chromosomes. Using this system we observed that tethering Nups to chromatin was sufficient to induce chromatin decondensation, visualized by robust and reproducible loss of DNA and histone fluorescene signal associated with Nup binding. Additionally we observed recruitment of chromatin-remodeling complex PBAP, and reliance on PBAP for the observed Nup-induced decondensation, suggesting an important functional relationship between these proteins. We then took our findings and hypotheses generated from this ectopic-tethering imaging system to next conduct functional biochemical analysis of these proteins in Drosophila S2 cell culture. We found that nucleoporin Elys has a robust biochemical interaction with components of PBAP in an endogenous context, supporting the recruitment of these proteins we observed via immunofluorescence. Additionally, MNase experiments determined that Elys was critical for facilitating the formation and/or maintenance of open chromatin, both genome-wide and on a local nucleosomal level at Elys target genes. Together these results demonstrate the importance of nucleoporins in regulation of chromatin structure, and provide one mechanism to explain this phenomenon. These findings are of particular interest in the fields of chromatin biology and the study of nuclear pore protein function, demonstrating a possible explanation for not only associations of NPCs with decondensed chromatin at the nuclear periphery, but also regulation of Nup target gene expression, through regulation of chromatin accessibility.

Nuclear Pore Complexes in Genome Organization, Function and Maintenance

Nuclear Pore Complexes in Genome Organization, Function and Maintenance
Author: Maximiliano D’Angelo
Publisher: Springer
Total Pages: 245
Release: 2018-02-02
Genre: Medical
ISBN: 331971614X

The three-dimensional organization of the DNA inside the eukaryotic cell nucleus has emerged a critical regulator of genome integrity and function. Increasing evidence indicates that nuclear pore complexes (NPCs), the large protein channels that connect the nucleus to the cytoplasm, play a critical role in the establishment and maintenance of chromatin organization and in the regulation of gene activity. These findings, which oppose the traditional view of NPCs as channels with only one: the facilitation of nucleocytoplasmic molecule exchange, have completely transformed our understanding of these structures. This book describes our current knowledge of the role of NPCs in genome organization and gene expression regulation. It starts by providing an overview of the different compartments and structures of the nucleus and how they contribute to organizing the genome, then moves to examine the direct roles of NPCs and their components in gene expression regulation in different organisms, and ends by describing the function of nuclear pores in the infection and genome integration of HIV, in DNA repair and telomere maintenance, and in the regulation of chromosome segregation and mitosis. This book provides an intellectual backdrop for anyone interested in understanding how the gatekeepers of the nucleus contribute to safeguarding the integrity and function of the eukaryotic genome.

Nuclear Architecture and Dynamics

Nuclear Architecture and Dynamics
Author: Christophe Lavelle
Publisher: Academic Press
Total Pages: 620
Release: 2017-10-27
Genre: Science
ISBN: 012803503X

Nuclear Architecture and Dynamics provides a definitive resource for (bio)physicists and molecular and cellular biologists whose research involves an understanding of the organization of the genome and the mechanisms of its proper reading, maintenance, and replication by the cell. This book brings together the biochemical and physical characteristics of genome organization, providing a relevant framework in which to interpret the control of gene expression and cell differentiation. It includes work from a group of international experts, including biologists, physicists, mathematicians, and bioinformaticians who have come together for a comprehensive presentation of the current developments in the nuclear dynamics and architecture field. The book provides the uninitiated with an entry point to a highly dynamic, but complex issue, and the expert with an opportunity to have a fresh look at the viewpoints advocated by researchers from different disciplines. Highlights the link between the (bio)chemistry and the (bio)physics of chromatin Deciphers the complex interplay between numerous biochemical factors at task in the nucleus and the physical state of chromatin Provides a collective view of the field by a large, diverse group of authors with both physics and biology backgrounds

Nuclear Structure and Gene Expression

Nuclear Structure and Gene Expression
Author: R. Curtis Bird
Publisher: Elsevier
Total Pages: 317
Release: 1996-11-28
Genre: Science
ISBN: 0080537812

Nuclear Structure and Gene Expression assimilates the contributions of genome organization and of the components of the nuclear matrix to the control of DNA and RNA synthesis. Nuclear domains which accommodate DNA replication and gene expression are considered in relation to short-term developmental and homeostatic requirements as well as to long-term commitments to phenotypic gene expression in differentiated cells. Consideration is given to the involvement of nuclear structure in gene localization as well as to the targeting and concentration of transcription factors. Aberrations in nuclear architecture associated with and potentially functionally related to pathologies are evaluated. Tumor cells are described from the perspective of the striking modifications in both the composition and organization of nuclear components. Nuclear Structure and Gene Expression presents concepts as well as experimental approaches, which define functionality of nuclear morphology. * Mechanisms of interaction between nuclear structure and genes * Gene expression regulation by elements of the nuclear matrix * How nuclear structure exerts a regulatory effect on other aspects of cell function/physiology

Chromatin Structure and Gene Expression

Chromatin Structure and Gene Expression
Author: Sarah C. R. Elgin
Publisher: Frontiers in Molecular Biology
Total Pages: 372
Release: 2000
Genre: Chromatin
ISBN: 9780199638901

Since publication of the first edition in 1995, there have been significant advances and understanding of chromatin structure and its relation to gene expression. These include a high-resolution structure of the nucleosome core, discovery of the enzymes and complexes that mediate histone acetylation and deacetylation, discovery of novel ATP-dependent chromatin remodeling complexes, new insights into nuclear organization and epigenetic silencing mechanisms. In light of these advances, Chromatin Structure and Gene Expression (2ed.) includes updated chapters and additional material that introduce new concepts in the process of gene regulation in chromatin.

Gene Expression Control by Nuclear Phosphoinositides and Chromatin

Gene Expression Control by Nuclear Phosphoinositides and Chromatin
Author: Dennis Jacob Bua
Publisher:
Total Pages:
Release: 2012
Genre:
ISBN:

The physiological state of the genome is chromatin. Chromatin is a dynamic polymer composed of genomic DNA, histone proteins, and other factors. Dysregulation of chromatin homeostasis can lead to diverse human pathologies including cancer. This work focuses on chromatin-based mechanisms of gene regulation; more specifically the (1) targeting and (2) stabilization of gene-regulatory proteins on the chromatin template. In regard to chromatin targeting, not much is known about how gene-regulatory proteins selectively associate with their targets. Herein we detail the discovery of a new targeting factor, the nuclear phospholipid phosphatidylinositol-5-phosphate (PtdIns(5)P). PtdIns(5)P directly interacts with the tumor suppressor ING2 (inhibitor of growth family member 2) in the nucleus to coordinate gene expression of select ING2 targets. In regard to chromatin stabilization, lysine methylation is a principle mechanism for retaining chromatin-effector modules at discrete chromatin zones. Numerous lysine methylation events have been discovered on the major protein component of chromatin, histones, but relatively few specific modules have been characterized to sense these modifications. We screened through a library of putative methyl-lysine binding domains, which resulted in the identification of three novel chromatin binding modules. Taken together these data shed insight into the molecular modes of action of gene regulation by chromatin and phosphoinositide pathways.

Nuclear Mechanics and Genome Regulation

Nuclear Mechanics and Genome Regulation
Author:
Publisher: Academic Press
Total Pages: 393
Release: 2010-10-12
Genre: Science
ISBN: 0123810108

In recent years new discoveries have made this an exciting and important field of research. This exhaustive volume presents comprehensive chapters and detailed background information for researchers working with in the field of nuclear mechanics and genome regulation. Both classic and state-of-the-art methods readily adaptable and designed to last the test of time Relevant to clinicians and scientists working in a wide range of fields

Introduction to Epigenetics

Introduction to Epigenetics
Author: Renato Paro
Publisher: Springer Nature
Total Pages: 215
Release: 2021-03-23
Genre: 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