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Linking Stochastic Fluctuations in Chromatin Structure and Gene Expression

https://doi.org/10.1371/journal.pbio.1001621

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Removal of positioned nucleosomes from the yeast PHO5 promoter upon PHO5 induction releases additional upstream activating DNA elements.

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A functional role for nucleosomes in the repression of a yeast promoter.

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Markovian Modeling of Gene-Product Synthesis

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[7] Electron microscopy of chromatin

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Cross-linking of DNA with trimethylpsoralen is a probe for chromatin structure

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Post-replicative nonribosomal transcription units in D. melanogaster embryos

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Binding of transcription factor TFIID to the major late promoter during in vitro nucleosome assembly potentiates subsequent initiation by RNA polymerase II

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Nucleosome loss activates yeast downstream promoters in vivo

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A Chromatin Landmark and Transcription Initiation at Most Promoters in Human Cells

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Nucleosome Retention and the Stochastic Nature of Promoter Chromatin Remodeling for Transcription

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Removal of Promoter Nucleosomes by Disassembly Rather Than Sliding In Vivo

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Transcriptional Activators Are Dispensable for Transcription in the Absence of Spt6-Mediated Chromatin Reassembly of Promoter Regions

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SWI/SNF Has Intrinsic Nucleosome Disassembly Activity that Is Dependent on Adjacent Nucleosomes

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Models of stochastic gene expression

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DNA sequence specificity of 4,5′,8-trimethylpsoralen cross-linking. Effect of neighboring bases on cross-linking the 5′-TA dinucleotide.

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Purification of Defined Chromosomal Domains

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Signaling phosphate starvation

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A Transient Histone Hyperacetylation Signal Marks Nucleosomes for Remodeling at the PHO8 Promoter In Vivo

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Nucleosomes Unfold Completely at a Transcriptionally Active Promoter

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A bacterial repressor protein or a yeast transcriptional terminator can block upstream activation of a yeast gene

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Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast

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Quantitative analysis of the transcription control mechanism

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Dynamics of protein noise can distinguish between alternate sources of gene‐expression variability

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Global landscape of protein complexes in the yeast Saccharomyces cerevisiae

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Genome-wide protein–DNA binding dynamics suggest a molecular clutch for transcription factor function

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The accessible chromatin landscape of the human genome

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RNA polymerase is poised for activation across the genome

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RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo

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Non-genetic heterogeneity from stochastic partitioning at cell division

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General properties of transcriptional time series in Escherichia coli

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Nucleosome positioning and gene regulation: advances through genomics

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A quantitative model of transcription factor–activated gene expression

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Single-RNA counting reveals alternative modes of gene expression in yeast

inferredcites →https://doi.org/10.1038/nsmb1062openalex-snapshot

Active PHO5 chromatin encompasses variable numbers of nucleosomes at individual promoters

inferredcites →https://doi.org/10.1038/nsmb801openalex-snapshot

Nucleosomes facilitate their own invasion

inferredcites →https://doi.org/10.1073/pnas.162041399openalex-snapshot

Intrinsic and extrinsic contributions to stochasticity in gene expression

inferredcites →https://doi.org/10.1074/jbc.m111.289918openalex-snapshot

In Vivo Role for the Chromatin-remodeling Enzyme SWI/SNF in the Removal of Promoter Nucleosomes by Disassembly Rather Than Sliding

inferredcites →https://doi.org/10.1074/jbc.m112.433623openalex-snapshot

Formation and Fate of a Complete 31-Protein RNA Polymerase II Transcription Preinitiation Complex*

inferredcites →https://doi.org/10.1101/gr.149096.112openalex-snapshot

Two DNA-encoded strategies for increasing expression with opposing effects on promoter dynamics and transcriptional noise

inferredcites →https://doi.org/10.1126/science.1070919openalex-snapshot

Stochastic Gene Expression in a Single Cell

inferredcites →https://doi.org/10.1126/science.1087374openalex-snapshot

Transcription Elongation Factors Repress Transcription Initiation from Cryptic Sites

inferredcites →https://doi.org/10.1126/science.1098641openalex-snapshot

Control of Stochasticity in Eukaryotic Gene Expression

inferredcites →https://doi.org/10.1126/science.1134053openalex-snapshot

Dynamics of Replication-Independent Histone Turnover in Budding Yeast

inferredcites →https://doi.org/10.1126/science.1172926openalex-snapshot

Nucleosomal Fluctuations Govern the Transcription Dynamics of RNA Polymerase II

inferredcites →https://doi.org/10.1126/science.1181421openalex-snapshot

Global Analysis of Short RNAs Reveals Widespread Promoter-Proximal Stalling and Arrest of Pol II in Drosophila

inferredcites →https://doi.org/10.1126/science.1216379openalex-snapshot

Using Gene Expression Noise to Understand Gene Regulation

inferredcites →https://doi.org/10.1126/science.1221648openalex-snapshot

The lac Repressor Displays Facilitated Diffusion in Living Cells

inferredcites →https://doi.org/10.1128/mcb.15.3.1405openalex-snapshot

Binding of disparate transcriptional activators to nucleosomal DNA is inherently cooperative

inferredcites →https://doi.org/10.1128/mcb.23.24.9275-9282.2003openalex-snapshot

Affinity Purification of Specific Chromatin Segments from Chromosomal Loci in Yeast

inferredcites →https://doi.org/10.1128/mcb.9.5.2050openalex-snapshot

The two positively acting regulatory proteins PHO2 and PHO4 physically interact with PHO5 upstream activation regions.

inferredcites →https://doi.org/10.1371/journal.pone.0017521openalex-snapshot

Occlusion of Regulatory Sequences by Promoter Nucleosomes In Vivo

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inferred← citeshttps://doi.org/10.70675/38091454z2125z486dz9a33z29c2bfa53a01openalex-snapshot

Stochastic gene expression, phenotypic variability and adaptation of budding yeast to environmental stresses

inferred← citeshttps://doi.org/10.7554/elife.58394openalex-snapshot

Effective dynamics of nucleosome configurations at the yeast PHO5 promoter

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