Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization

A. Tsankov; Y. Yanagisawa; N. Rhind; A. Regev; O. J. Rando

doi:10.1101/gr.122267.111

Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization

Genome Research ◽

10.1101/gr.122267.111 ◽

2011 ◽

Vol 21 (11) ◽

pp. 1851-1862 ◽

Cited By ~ 60

Author(s):

A. Tsankov ◽

Y. Yanagisawa ◽

N. Rhind ◽

A. Regev ◽

O. J. Rando

Keyword(s):

Nucleosome Positioning ◽

Chromatin Organization ◽

Evolutionary Divergence

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Sophisticated Conversations between Chromatin and Chromatin Remodelers, and Dissonances in Cancer

International Journal of Molecular Sciences ◽

10.3390/ijms22115578 ◽

2021 ◽

Vol 22 (11) ◽

pp. 5578

Author(s):

Cedric R. Clapier

Keyword(s):

Gene Expression ◽

Regulation Of Gene Expression ◽

Structural Diversity ◽

Nucleosome Positioning ◽

Basic Mechanism ◽

Progressive Increase ◽

Chromatin Organization ◽

Dna Translocation ◽

Dynamic Regulation ◽

Cooperative Action

The establishment and maintenance of genome packaging into chromatin contribute to define specific cellular identity and function. Dynamic regulation of chromatin organization and nucleosome positioning are critical to all DNA transactions—in particular, the regulation of gene expression—and involve the cooperative action of sequence-specific DNA-binding factors, histone modifying enzymes, and remodelers. Remodelers are molecular machines that generate various chromatin landscapes, adjust nucleosome positioning, and alter DNA accessibility by using ATP binding and hydrolysis to perform DNA translocation, which is highly regulated through sophisticated structural and functional conversations with nucleosomes. In this review, I first present the functional and structural diversity of remodelers, while emphasizing the basic mechanism of DNA translocation, the common regulatory aspects, and the hand-in-hand progressive increase in complexity of the regulatory conversations between remodelers and nucleosomes that accompanies the increase in challenges of remodeling processes. Next, I examine how, through nucleosome positioning, remodelers guide the regulation of gene expression. Finally, I explore various aspects of how alterations/mutations in remodelers introduce dissonance into the conversations between remodelers and nucleosomes, modify chromatin organization, and contribute to oncogenesis.

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The histone variant H2A.Z and chromatin remodeler BRAHMA act coordinately and antagonistically to regulate transcription and nucleosome dynamics in Arabidopsis

10.1101/243790 ◽

2018 ◽

Author(s):

E. Shannon Torres ◽

Roger B. Deal

Keyword(s):

Transcriptional Regulation ◽

Transcription Factors ◽

Binding Sites ◽

Transcriptional Repression ◽

Nucleosome Positioning ◽

Chromatin Organization ◽

Histone H2a ◽

Nucleosome Dynamics ◽

Environmentally Responsive ◽

Context Specific

ABSTRACTPlants adapt to changes in their environment by regulating transcription and chromatin organization. The histone H2A variant H2A.Z and the SWI2/SNF2 ATPase BRAHMA have overlapping roles in positively and negatively regulating environmentally responsive genes in Arabidopsis, but the extent of this overlap was uncharacterized. Both have been associated with various changes in nucleosome positioning and stability in different contexts, but their specific roles in transcriptional regulation and chromatin organization need further characterization. We show that H2A.Z and BRM act both cooperatively and antagonistically to contribute directly to transcriptional repression and activation of genes involved in development and response to environmental stimuli. We identified 8 classes of genes that show distinct relationships between H2A.Z and BRM and their roles in transcription. We found that H2A.Z contributes to a range of different nucleosome properties, while BRM stabilizes nucleosomes where it binds and destabilizes and/or repositions flanking nucleosomes. H2A.Z and BRM contribute to +1 nucleosome destabilization, especially where they coordinately regulate transcription. We also found that at genes regulated by both BRM and H2A.Z, both factors overlap with the binding sites of light-regulated transcription factors PIF4, PIF5, and FRS9, and that some of the FRS9 binding sites are dependent on H2A.Z and BRM for accessibility. Collectively, we comprehensively characterized the antagonistic and cooperative contributions of H2A.Z and BRM to transcriptional regulation, and illuminated their interrelated roles in chromatin organization. The variability observed in their individual functions implies that both BRM and H2A.Z have more context-specific roles within diverse chromatin environments than previously assumed.

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DNA structure, nucleosome placement and chromatin remodelling: a perspective

Biochemical Society Transactions ◽

10.1042/bst20110757 ◽

2012 ◽

Vol 40 (2) ◽

pp. 335-340 ◽

Cited By ~ 28

Author(s):

Andrew A. Travers ◽

Cédric Vaillant ◽

Alain Arneodo ◽

Georgi Muskhelishvili

Keyword(s):

Dna Sequence ◽

Thermodynamic Stability ◽

Budding Yeast ◽

Nucleosome Positioning ◽

Chromatin Remodelling ◽

Chromatin Organization ◽

Eukaryotic Genome ◽

Major Question ◽

Chromatin Biology

A major question in chromatin biology is to what extent the sequence of DNA directly determines the genetic and chromatin organization of a eukaryotic genome? We consider two aspects to this question: the DNA sequence-specified positioning of nucleosomes and the determination of NDRs (nucleosome-depleted regions) or barriers. We argue that, in budding yeast, while DNA sequence-specified nucleosome positioning may contribute to positions flanking the regions lacking nucleosomes, DNA thermodynamic stability is a major component determinant of the genetic organization of this organism.

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