Abstract: Methods for the identification of a drug target, wherein the drug target is a component of a signal transduction pathway, are provided. The methods are based, in part, on selection of a gene of therapeutic interest and determination of regulatory DNA sequences which regulate expression of the gene in a cell of interest, followed by reconstruction of signal transduction pathways which act on molecules which bind to the regulatory sequence. Also provided are methods for assessing potential pharmacological effects and/or side effects of an agent, based on the effect of the agent on the distribution and properties of accessible regions in cellular chromatin.

Abstract: Methods and compositions for the identification, isolation and characterization of regulatory DNA sequences in a cell of interest are provided. Also provided are libraries of regulatory sequences obtained according to the methods, and databases comprising collections of regulatory sequences for a particular cell of interest. In addition, various uses for the regulatory sequences so obtained, and uses for the databases of regulatory sequences, are provided. Also disclosed are computer systems and computer program products for utilizing the databases to conduct various genetic analyses, and uses of accessible regulatory sequences in the design of vectors bearing transgenes.

Abstract: Methods and compositions for targeted modification of chromatin structure, within a region of interest in cellular chromatin, are provided. Such methods and compositions are useful for facilitating processes such as, for example, transcription and recombination, that require access of exogenous molecules to chromosomal DNA sequences.

Abstract: Methods for the design of exogenous regulatory molecules, comprising a DNA-binding domain and a functional domain, are provided. The methods rely on the identification, isolation and characterization of regulatory DNA sequences obtained on the basis of their accessibility in cellular chromatin.

Abstract: Methods for the identification of a drug target, wherein the drug target is a component of a signal transduction pathway, are provided. The methods are based, in part, on selection of a gene of therapeutic interest and determination of regulatory DNA sequences which regulate expression of the gene in a cell of interest, followed by reconstruction of signal transduction pathways which act on molecules which bind to the regulatory sequence. Also provided are methods for assessing potential pharmacological effects and/or side effects of an agent, based on the effect of the agent on the distribution and properties of accessible regions in cellular chromatin.

Abstract: Methods and compositions for targeted modification of chromatin structure, within a region of interest in cellular chromatin, are provided. Such methods and compositions are useful for facilitating processes such as, for example, transcription and recombination, that require access of exogenous molecules to chromosomal DNA sequences.

Abstract: Methods and compositions for the identification, isolation and characterization of regulatory DNA sequences in a cell of interest are provided. Also provided are libraries of regulatory sequences obtained according to the methods, and databases comprising collections of regulatory sequences for a particular cell of interest. In addition, various uses for the regulatory sequences so obtained, and uses for the databases of regulatory sequences, are provided. Also disclosed are computer systems and computer program products for utilizing the databases to conduct various genetic analyses, and uses of accessible regulatory sequences in the design of vectors bearing transgenes.

Abstract: Methods for the design of exogenous regulatory molecules, comprising a DNA-binding domain and a functional domain, are provided. The methods rely on the identification, isolation and characterization of regulatory DNA sequences obtained on the basis of their accessibility in cellular chromatin.