The ability to artificially control transcription is essential both to the study of gene function and to the construction of synthetic gene networks with desired properties. Cas9 is an RNA-guided double-stranded DNA nuclease that participates in the CRISPR-Cas immune defense against prokaryotic viruses. We describe the use of a Cas9 nuclease mutant that retains DNA-binding activity and can be engineered as a programmable transcription repressor by preventing the binding of the RNA polymerase (RNAP) to promoter sequences or as a transcription terminator by blocking the running RNAP. In addition, a fusion between the omega subunit of the RNAP and a Cas9 nuclease mutant directed to bind upstream promoter regions can achieve programmable transcription activation. The simple and efficient modulation of gene expression achieved by this technology is a useful asset for the study of gene networks and for the development of synthetic biology and biotechnological applications.National Institutes of Health (U.S.) (Pioneer Award DP1MH100706)National Institutes of Health (U.S.) (Transformative Research Award)W. M. Keck FoundationMcKnight FoundationBill & Melinda Gates FoundationDamon Runyon Cancer Research FoundationKinship Foundation. Searle Scholars ProgramEsther A. & Joseph Klingenstein Fund, Inc.Simons Foundation