We study the dependence of a cluster algebra on the choice of coefficients. We write general formulas expressing the cluster variables in any cluster algebra in terms of the initial data; these formulas involve a family of polynomials associated with a particular choice of ‘principal’ coefficients. We show that the exchange graph of a cluster algebra with principal coefficients covers the exchange graph of any cluster algebra with the same exchange matrix. We investigate two families of parameterizations of cluster monomials by lattice points, determined, respectively, by the denominators of their Laurent expansions and by certain multi-gradings in cluster algebras with principal coefficients. The properties of these parameterizations, some proven and some conjectural, suggest links to duality conjectures of Fock and Goncharov. The coefficient dynamics leads to a natural generalization of Zamolodchikov's $Y$-systems. We establish a Laurent phenomenon for such $Y$-systems, previously known in finite type only, and sharpen the periodicity result from an earlier paper. For cluster algebras of finite type, we identify a canonical ‘universal’ choice of coefficients such that an arbitrary cluster algebra can be obtained from the universal one (of the same type) by an appropriate specialization of coefficients.
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