Patent ID: 6410233
Filing Date: 2002-06-25
Classification: C12N

Abstract:
A method for identifying one or more cDNA molecules that correspond to one or more genes regulated by a transcription factor, comprising:a) cross-linking at least one transcription factor to at least one nucleic acid molecule in at least one cell or at least one nucleus, forming one or more transcription factor-nucleic acid molecule complexes; b) fragmenting said at least one nucleic acid molecule to form one or more transcription factor-nucleic acid molecule fragment complexes; c) isolating one or more nucleic acid molecule fragments from said one or more transcription factor-nucleic acid molecule fragment complexes to form one or more isolated nucleic acid molecule fragments; d) combining said one or more isolated nucleic acid molecule fragments with either: 1) a nucleic acid sequence in a cDNA library of sequences known to be complementary to previously identified nucleic acid molecules, or 2) cDNA obtained by reverse transcription of a population of RNA molecules, to form a mixture comprising isolated nucleic acid molecule fragment/cDNA complexes; e) amplifying one or more cDNAs in said isolated nucleic acid fragment/cDNA complexes using said one or more nucleic acid molecule fragments in said isolated nucleic acid fragment/cDNA complexes as primers to obtain one or more isolated cDNA molecules that correspond to one or more genes regulated by a transcription factor; and f) identifying said one or more cDNA molecules that correspond to one or more genes regulated by a trascription factor by either: 1) sequencing said one or more cDNA molecules that correspond to one or more genes regulated by a transcription factor to obtain a sequence or sequences and comparing said sequence or sequences to the sequences of DNA molecules of known sequence to determine whether said one or more cDNA molecules has homology of greater than 70% with any of said sequences of DNA molecules of known sequence, or 2) hybridizing said one or more cDNA molecules that correspond to one or more genes regulated by a transcription factor to one or more nucleic acid molecules corresponding to known genes or nucleic acid sequences; wherein the presence of a sequence or sequences having homology of greater than 70% or a hybridization results in the identification of said one or more cDNA molecules that correspond to one or more genes regulated by a transcription factor.