Isolation and identification of control sequences and genes modulated by transcription factors

Abstract

One aspect of the present invention is a method for isolating at least one nucleic acid molecule comprising at least a portion of a gene, including: cross-linking at least one transcription factor to a nucleic acid molecule in at least one cell or at least one nucleus, forming at least one transcription factor/nucleic acid molecule complex; fragmenting the nucleic acid molecule to form at least one transcription factor/nucleic acid molecule fragment; and isolating at least one nucleic acid molecule from said at least one transcription factor/nucleic acid molecule fragment to form at least one isolated nucleic acid molecule fragment; wherein said at least one isolated nucleic acid molecule fragment comprises at least a portion of the first exon of a gene whose expression is modulated by said transcription factor; further wherein said at least one isolated nucleic acid molecule fragment comprises at least one transcription factor binding site that is in close proximity to or operably linked to said first exon of a gene. Another aspect of the present invention is a method for isolating at least one nucleic acid molecule that can include at least a portion of a gene operably linked to or in close proximity to a nucleic acid sequence that binds with at least one transcription factor, comprising: cross-inking at least one transcription factor to a nucleic acid molecule in at least one cell or at least one nucleus, forming at least one transcription factor/nucleic acid molecule complex; fragmenting the nucleic acid molecule to form at least one transcription factor/nucleic acid molecule fragment; isolating at least one nucleic acid molecule fragment from said at least one transcription factor/nucleic acid molecule fragment to form at least one isolated nucleic acid molecule fragment; combining the at least one isolated nucleic acid molecule fragment with either: a cDNA library, or a cDNA derived from reverse transcription of a population of RNA molecules, to form a mixture comprising isolated nucleic acid molecule fragment/cDNA complexes; and isolating the cDNA that binds with the isolated nucleic acid molecule fragment to obtain at least one isolated cDNA molecule.

Dependencies are inferred from the claim text.