Nucleosomes

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Author: Paul M. Wassarman
Publisher: Academic Press
ISBN:
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Nucleosomes by Paul M. Wassarman


Original Title: Nucleosomes

The critically acclaimed laboratory standard, Methods in Enzymology, is one of the most highly respected publications in the field of biochemistry. Since 1955, each volume has been eagerly awaited, frequently consulted, and praised by researchers and reviewers alike. The series contains much material still relevant today - truly an essential publication for researchers in all fields of life sciences.

Statistical Mechanics Of Nucleosomes

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Author: Răzvan V. Chereji
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Statistical Mechanics Of Nucleosomes by Răzvan V. Chereji


Original Title: Statistical Mechanics Of Nucleosomes

Eukaryotic cells contain long DNA molecules (about two meters for a human cell) which are tightly packed inside the micrometric nuclei. Nucleosomes are the basic packaging unit of the DNA which allows this millionfold compactification. A longstanding puzzle is to understand the principles which allow cells to both organize their genomes into chromatin fibers in the crowded space of their nuclei, and also to keep the DNA accessible to many factors and enzymes. With the nucleosomes covering about three quarters of the DNA, their positions are essential because these influence which genes can be regulated by the transcription factors and which cannot. We study physical models which predict the genome-wide organization of the nucleosomes and also the relevant energies which dictate this organization. In the last five years, the study of chromatin knew many important advances. In particular, in the field of nucleosome positioning, new techniques of identifying nucleosomes and the competing DNA-binding factors appeared, as chemical mapping with hydroxyl radicals, ChIP-exo, among others, the resolution of the nucleosome maps increased by using paired-end sequencing, and the price of sequencing an entire genome decreased. We present a rigorous statistical mechanics model which is able to explain the recent experimental results by taking into account nucleosome unwrapping, competition between different DNA-binding proteins, and both the interaction between histones and DNA, and between neighboring histones. We show a series of predictions of our new model, all in agreement with the experimental observations.

Nucleosomes Histones Chromatin

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Author: Carl Wu
Publisher: Academic Press
ISBN: 012391938X
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Nucleosomes Histones Chromatin by Carl Wu


Original Title: Nucleosomes Histones Chromatin

This new volume of Methods in Enzymology continues the legacy of this premier serial by containing quality chapters authored by leaders in the field. The volume covers nucleosomes, histones and chromatin and has chapters on dynamic mapping of histone-DNA interactions in nucleosomes by unzipping single molecules of DNA, digital DNase technology, and genome-wide analysis of chromatin transition. Contains quality chapters authored by leaders in the field The volume covers nucleosomes, histones and chromatin Has chapters on dynamic mapping of histone-DNA interactions in nucleosomes by unzipping single molecules of DNA, digital DNase technology, and genome-wide analysis of chromatin transition

Nucleosomes Histones And Chromatin

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Publisher: Academic Press
ISBN: 012391941X
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Nucleosomes Histones And Chromatin by


Original Title: Nucleosomes Histones And Chromatin

This new volume of Methods in Enzymology continues the legacy of this premier serial by containing quality chapters authored by leaders in the field. The first of 2 volumes covering nucleosomes, histones and chromatin, it has chapters on methods applied to the study of protein arginine methylation, high-resolution identification of intra- and interchromosomal DNA interactions by 4C technology, and peptide arrays to interrogate the binding specificity of chromatin-binding proteins. Continues the legacy of this premier serial by containing quality chapters authored by leaders in the field The first of 2 volumes covering nucleosomes, histones and chromatin Chapters on methods applied to the study of protein arginine methylation, high-resolution identification of intra- and interchromosomal DNA interactions by 4C technology, and peptide arrays to interrogate the binding specificity of chromatin-binding proteins

Mobilization Of Nucleosomes In Short Arrays

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Author: Abdellah Sabri
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Mobilization Of Nucleosomes In Short Arrays by Abdellah Sabri


Original Title: Mobilization Of Nucleosomes In Short Arrays

DNA is compacted into chromatin in eukaryotic cells. The histone-modifying enzymes and the enzymatic activity of the ATP-dependent chromatin-remodeling proteins are often involved in the disruption of the chromatin structure to allow access for the molecular machines that use it as a substrate for transcription, replication, recombination and repair. DNA-protein site directed mapping showed that various chromatin remodeling complexes slide nucleosomes within di and tri-nucleosome arrays differently. ISW2 can translocate (slide) nucleosomes within an array up to 30 bp from the adjacent nucleosome. ISW2 slides nucleosomes towards the DNA ends in contrast to INO80 that slides the nucleosomes away from the DNA ends and introduces 30 bp spacing between nucleosomes. SWI/SNF slides nucleosomes apart within a di-nucleosome array. In addition to the sliding, SWI/SNF demonstrates capacity to evict an H2A-H2B dimer as an intermediate step, followed by eviction of one nucleosome.

The Nucleolus

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Author: Mark O. J. Olson
Publisher: Springer Science & Business Media
ISBN: 9780306478734
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The Nucleolus by Mark O. J. Olson


Original Title: The Nucleolus

As the first comprehensive overview of the nucleolus since 1985, The Nucleolus covers our current understanding of the cell nucleolus, including its role in ribosome assembly and its additional newly-discovered activities. The eighteen chapters have been written by experts who are actively engaged in research on the nucleolus and have an in depth review of the following topics: - nucleolar ultrastructure and dynamics, - behavior during mitosis, - ribosomal DNA gene and chromatin structure, - pre-ribosomal RNA transcription, - processing and modification, - ribosome assembly, - small nucleolar RNAs, - proteomics and non-traditional functions of the nucleolus. Separate chapters are also provided for yeast and higher eukaryotes on many topics. The Nucleolus will appeal not only to scientists directly engaged in nucleolar research, but also those working in related areas such as gene expression, protein biosynthesis, ribosome structure, transcription, chromatin structure, molecular genetics and the structure and functions of the cell nucleus in general.

Swi Snf Nucleosome Interactions And Disassembly Of Nucleosomes

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Author: Mekonnen Lemma Dechassa
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Swi Snf Nucleosome Interactions And Disassembly Of Nucleosomes by Mekonnen Lemma Dechassa


Original Title: Swi Snf Nucleosome Interactions And Disassembly Of Nucleosomes

The SWI/SNF complex disrupts and mobilizes chromatin in an ATP-dependent manner. A site-directed photoaffinity crosslinking approach in which photoreactive moieties attached at specific sites within histone octamer was developed and used to map the interactions of SWI/SNF with the histone octamer face of the nucleosome. The data shows that the presence of adjacent nucleosomes promotes nucleosome eviction and the recruitment of SWI/SNF by Gal4-VP16 to dinucleosomes restricted the nucleosome mobilization in one direction.

The Nucleosome

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Author: A.P. Wolffe
Publisher: Elsevier
ISBN: 9780080537849
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The Nucleosome by A.P. Wolffe


Original Title: The Nucleosome

This is the first in a series of volumes concerning the properties of the eukaryotic nucleus. Contributions from several of the most active laboratories are brought together to present a focused overview of a selected aspect of nuclear structure and function.

Dissecting The Role Of Nucleosomes In Transcription And The Application Of Crispr Cas9 Technology

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Author: Lea Bengtson Witkowsky
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Dissecting The Role Of Nucleosomes In Transcription And The Application Of Crispr Cas9 Technology by Lea Bengtson Witkowsky


Original Title: Dissecting The Role Of Nucleosomes In Transcription And The Application Of Crispr Cas9 Technology

In the 43 years since the first observation of nucleosome core particles as beads on a string, our understanding of the relationship between nucleosome structure and its function in living cells has made giant strides. Despite this progress, many questions remain unanswered regarding the role of nucleosomes in transcription initiation, and their interaction with the core transcriptional machinery. Here, I present my progress on addressing the role of TAF1 recognition of acetylated histone H4 tails, and its effect on transcription initiation and start site selection. Preliminary results suggest that H4 acetylation may play a role in start site selection. One remarkable advancement in technology that will undoubtedly help answer remaining questions in chromatin biology is the repurposing of the prokaryotic CRISPR-Cas system to edit eukaryotic genomes with exquisite precision. Ironically, a tool that may shed light on complex eukaryotic chromatin interactions was evolved in a prokaryotic environment. My work with in vitro nucleosomes positioned me to address whether Cas9 is capable of engaging nucleosomal DNA. Both in vitro and in vivo analyses done in collaboration with Max Horlbeck and Jonathan Weissman at UCSF suggest that nucleosomes pose a strong barrier to Cas9.

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