title: Chromatin computation.
abstract: 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.
authors.affiliation: Bioinformatics Department, Constellation Pharmaceuticals, Cambridge, Massachusetts, United States of America. barbara.bryant@constellationpharma.com
authors.forename: Barbara
authors.initials: B
authors.lastname: Bryant
mesh_terms: D002843:Chromatin / Q000378:metabolism*; D003198:Computer Simulation; D006801:Humans; D009707:Nucleosomes / Q000378:metabolism*
chemical_list: D002843:Chromatin; D009707:Nucleosomes