Compositions, methods and kits are provided that are useful, for example, fordetermining activities of multiple cis-regulatory sequences, such as promotersand enhancers, and/or multiple trans-acting factors, such as transcriptionfactors, in a cell. In particular, in certain embodiments, compositions areprovided comprising a population of polynucleotide reporter transcriptionunits (RTUs) in which each RTU comprises a reporter sequence, a processing taglocated in the reporter sequence and a cis-regulatory element operably linkedto the reporter sequence, wherein the reporter sequences between any two RTUsin the population, outside of the processing tags, are substantially identicaland wherein the positions of the processing tags within the reporter sequencesdistinguish between any two RTUs differing, for example, in their cis-regulatory elements. The compositions, methods and kits can further be used,for example, to identify a cell type or disease state, for example, in abiological organism.
