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Nucleosomes, transcription, and probability.

Boeger H - Mol. Biol. Cell (2014)

Bottom Line: Speaking of current measurements on single ion channel molecules, David Colquhoun wrote in 2006, "Individual molecules behave randomly, so suddenly we had to learn how to deal with stochastic processes." Here I describe theoretical efforts to understand recent experimental observations on the chromatin structure of single gene molecules, a molecular biologist's path toward probabilistic theories.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064.

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Transition graphs. (A) Strongly connected, branched graph. Nodes are indicated as squares. (B) Not strongly connected, unbranched (deterministic) graph. The darker gray square represents an absorbing state. (C) Cyclical graph. (D) Transition graph for simple process model of PHO5 promoter nucleosome dynamics (Brown et al., 2013). The promoter is represented by a box and occupied nucleosome positions as dots. Black, gray, and dashed arrows indicate assembly, disassembly, and sliding transitions, respectively.
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Figure 1: Transition graphs. (A) Strongly connected, branched graph. Nodes are indicated as squares. (B) Not strongly connected, unbranched (deterministic) graph. The darker gray square represents an absorbing state. (C) Cyclical graph. (D) Transition graph for simple process model of PHO5 promoter nucleosome dynamics (Brown et al., 2013). The promoter is represented by a box and occupied nucleosome positions as dots. Black, gray, and dashed arrows indicate assembly, disassembly, and sliding transitions, respectively.

Mentions: We may think about the underlying nucleosome dynamics in terms of a directed graph; it consists of labeled nodes, representing the eight nucleosome configurations, and directed edges joining pairs of nodes (Figure 1). Edges represent possible transitions between configurations and are thus directed (directed edges may be represented by arrows; Figure 1), An outgoing edge to node i is an edge that points away from i. For our purposes it is suitable to call such graphs transition graphs (however, since no other graphs will be considered, I may occasionally simply say “graph”).


Nucleosomes, transcription, and probability.

Boeger H - Mol. Biol. Cell (2014)

Transition graphs. (A) Strongly connected, branched graph. Nodes are indicated as squares. (B) Not strongly connected, unbranched (deterministic) graph. The darker gray square represents an absorbing state. (C) Cyclical graph. (D) Transition graph for simple process model of PHO5 promoter nucleosome dynamics (Brown et al., 2013). The promoter is represented by a box and occupied nucleosome positions as dots. Black, gray, and dashed arrows indicate assembly, disassembly, and sliding transitions, respectively.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4230601&req=5

Figure 1: Transition graphs. (A) Strongly connected, branched graph. Nodes are indicated as squares. (B) Not strongly connected, unbranched (deterministic) graph. The darker gray square represents an absorbing state. (C) Cyclical graph. (D) Transition graph for simple process model of PHO5 promoter nucleosome dynamics (Brown et al., 2013). The promoter is represented by a box and occupied nucleosome positions as dots. Black, gray, and dashed arrows indicate assembly, disassembly, and sliding transitions, respectively.
Mentions: We may think about the underlying nucleosome dynamics in terms of a directed graph; it consists of labeled nodes, representing the eight nucleosome configurations, and directed edges joining pairs of nodes (Figure 1). Edges represent possible transitions between configurations and are thus directed (directed edges may be represented by arrows; Figure 1), An outgoing edge to node i is an edge that points away from i. For our purposes it is suitable to call such graphs transition graphs (however, since no other graphs will be considered, I may occasionally simply say “graph”).

Bottom Line: Speaking of current measurements on single ion channel molecules, David Colquhoun wrote in 2006, "Individual molecules behave randomly, so suddenly we had to learn how to deal with stochastic processes." Here I describe theoretical efforts to understand recent experimental observations on the chromatin structure of single gene molecules, a molecular biologist's path toward probabilistic theories.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064.

Show MeSH
Related in: MedlinePlus