Chromatin Computation

PLoS One

Barbara Bryant¹ 

[1] Bioinformatics Department, Constellation Pharmaceuticals, Cambridge, Massachusetts, United States of America

关键词: Chromatin;    Nucleosomes;    Nucleosome mapping;    Transcription factors;    Computer modeling;    DNA transcription;    Gene expression;    Histones;   

DOI  :  10.1371/journal.pone.0035703

学科分类：医学（综合）

来源: Public Library of Science

【 摘 要 】

In living cells, DNA is packaged along with protein and RNA into chromatin. Chemical modifications to nucleotides and histone proteins are added, removed and recognized by multi-functional molecular complexes. Here I define a new computational model, in which chromatin modifications are information units that can be written onto a one-dimensional string of nucleosomes, analogous to the symbols written onto cells of a Turing machine tape, and chromatin-modifying complexes are modeled as read-write rules that operate on a finite set of adjacent nucleosomes. I illustrate the use of this “chromatin computer” to solve an instance of the Hamiltonian path problem. I prove that chromatin computers are computationally universal – and therefore more powerful than the logic circuits often used to model transcription factor control of gene expression. Features of biological chromatin provide a rich instruction set for efficient computation of nontrivial algorithms in biological time scales. Modeling chromatin as a computer shifts how we think about chromatin function, suggests new approaches to medical intervention, and lays the groundwork for the engineering of a new class of biological computing machines.

【 授权许可】

CC BY