Genome-Scale Identification of Nucleosome Positions in
            <i>S. cerevisiae</i>

Yuan, Guo‐Cheng; Liu, Yuen-Jong; Dion, Michael F.; Slack, Michael D.; Wu, Lani F.; Altschuler, Steven J.; Rando, Oliver J.

doi:10.1126/science.1112178

Cited by 1,063 publications

(1,399 citation statements)

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“…This chromatin signature was used to identify a novel enhancer element for the SLC22A5 gene [45]. Notably, the enhancer elements also tend to show hypersensitivity to DNase in genomic assays, but lack the nucleosome-free region shown to be a general characteristic of transcription start sites [47,48].…”

Section: Chromatin Signatures Of Functional Genomic Elementsmentioning

confidence: 99%

Chromatin state maps: new technologies, new insights

Mendenhall

Bernstein

2008

Current Opinion in Genetics & Development

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Recent years have seen unprecedented characterization of mammalian chromatin thanks to advances in chromatin assays, antibody development and genomics. Genome-wide maps of chromatin state can now be readily acquired using microarrays or next-generation sequencing technologies. These datasets reveal local and long-range chromatin patterns that offer insight into the locations and functions of underlying regulatory elements and genes. These patterns are dynamic across developmental stages and lineages. Global studies of chromatin in embryonic stem cells have led to intriguing hypotheses regarding Polycomb/trithorax and RNA polymerase roles in 'poising' transcription. Chromatin state maps thus provide a rich resource for understanding chromatin at a 'systems level', and a starting point for mechanistic studies aimed at defining epigenetic controls that underlie development.

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Section: Chromatin Signatures Of Functional Genomic Elementsmentioning

confidence: 99%

Chromatin state maps: new technologies, new insights

Mendenhall

Bernstein

2008

Current Opinion in Genetics & Development

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“…Around the TSS of Saccharomyces cerevisiae (baker's yeast), nucleosomes have been found to be depleted on average, both in vitro and in vivo (12)(13)(14)(15)(16)(17)(18). The persistence of this depletion in vitro, in the absence of active remodeling, identifies the sequence preferences of nucleosomes as the dominant cause.…”

Section: Introductionmentioning

confidence: 99%

Genomes of Multicellular Organisms Have Evolved to Attract Nucleosomes to Promoter Regions

Tompitak

Vaillant

Schiessel

2017

Biophysical Journal

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Sequences that influence nucleosome positioning in promoter regions, and their relation to gene regulation, have been the topic of much research over the last decade. In yeast, significant nucleosome-depleted regions are found, which facilitate transcription. With the arrival of nucleosome positioning maps for the human genome, it was discovered that in our genome, unlike in that of yeast, promoters encode for high nucleosome occupancy. In this work, we look at the genomes of a range of different organisms, to provide a catalog of nucleosome positioning signals in promoters across the tree of life. We utilize a computational model of the nucleosome, based on crystallographic analyses of the structure and elasticity of the nucleosome, to predict the nucleosome positioning signals in promoter regions. To be able to apply our model to large genomic datasets, we introduce an approximative scheme that makes use of the limited range of correlations in nucleosomal sequence preferences to create a computationally efficient approximation of the full biophysical model. Our predictions show that a clear distinction between unicellular and multicellular life is visible in the intrinsically encoded nucleosome affinity. Furthermore, the strength of the nucleosome positioning signals correlates with the complexity of the organism. We conclude that encoding for high nucleosome occupancy, as in the human genome, is in fact a universal feature of multicellular life.

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“…Nucleosome positioning was most extensively studied in the compact yeast genome, and the first genome-wide mapping of nucleosome positions at high resolution showed that the nucleosomes at most genes are generally organized in the same way [40]. Around the beginning of a gene there is a nucleosome free region (NFR) flanked by two well-positioned nucleosomes (the -1 and +1 nucleosomes), which is followed by an array of nucleosomes that package the gene body.…”

Section: Mapping Tsss Of Nascent Transcriptsmentioning

confidence: 99%

Promoter architectures and developmental gene regulation

Haberle

Lenhard

2016

Seminars in Cell & Developmental Biology

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Core promoters are minimal regions sufficient to direct accurate initiation of transcription and are crucial for regulation of gene expression. They are highly diverse in terms of associated core promoter motifs, underlying sequence composition and patterns of transcription initiation.Distinctive features of promoters are also seen at the chromatin level, including nucleosome positioning patterns and presence of specific histone modifications. Recent advances in identifying and characterizing promoters using next-generation sequencing-based technologies have provided the basis for their classification into functional groups and have shed light on their modes of regulation, with important implications for transcriptional regulation in development.This review discusses the methodology and the results of genome-wide studies that provided insight into the diversity of RNA polymerase II promoter architectures in vertebrates and other Metazoa, and the association of these architectures with distinct modes of regulation in embryonic development and differentiation.

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Genome-Scale Identification of Nucleosome Positions in S. cerevisiae

Cited by 1,063 publications

References 29 publications

Chromatin state maps: new technologies, new insights

Chromatin state maps: new technologies, new insights

Genomes of Multicellular Organisms Have Evolved to Attract Nucleosomes to Promoter Regions

Promoter architectures and developmental gene regulation

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