Biologically-active DNA-binding sites and related methods
AssigneeWhitehead Institute for Biomedical Research
InventorsChristopher T. Harbison, Richard A. Young, David B. Gordon, Ernest Fraenkel
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Abstract
The invention relates to the identification of biologically-active DNA-binding sites to which a protein of interest binds in a cell. The invention also relates to the identification of agents and conditions which alter the biologically-active DNA-binding sites to which a protein binds. One aspect of the invention also provides methods for identifying pathways that are regulated by transcriptional regulators and for modulating the activity of the pathways.
Claims17
A method of identifying a set of biologically-active DNA-binding sites for a protein of interest in the genome of a cell, the method comprising
- (i) identifying a set of regions of genomic DNA to which the protein of interest is bound in the cell;
- (ii) identifying candidate DNA-binding sites in the identified regions of genomic DNA, wherein a candidate DNA-binding site comprises a sequence corresponding to a DNA-sequence motif for the protein of interest, and wherein said DNA sequence motif is enriched in said identified regions by a statistically significant amount relative to a set of genomic regions which are bound by a mutant form of the protein of interest in the cell;
- (iii) determining if the candidate DNA-binding sites are conserved in an equivalent genomic region in one or more species different from the species from which the cell is obtained, wherein a candidate DNA-binding site that is conserved in at least one of the different species is a biologically-active DNA-binding site.
A method of identifying an agent which alters the set of biologically-active DNA-binding sites for a protein of interest in the genome of a cell, the method comprising
- (i) contacting an experimental cell with a candidate agent;
- (ii) identifying a set of biologically-active DNA-binding sites for a protein of interest in the genome of the cell of step (i) by:
- (a) identifying a set of regions of genomic DNA to which the protein of interest is bound in the cell;
- (b) identifying candidate DNA-binding sites in the identified regions of genomic DNA, wherein a candidate DNA-binding site comprises a sequence corresponding to a DNA-sequence motif for the protein of interest, wherein the DNA sequence motif is enriched by a statistically significant amount relative to a suitable control;
- (c) determining if the candidate DNA-binding sites are conserved in an equivalent genomic region in one or more species different from the species from which the cell is obtained, wherein a candidate DNA-binding site that is conserved in at least one of the different species is a biologically-active DNA-binding site;
- thereby generating an experimental set of biologically-active DNA-binding sites;
- (iii) comparing
- (1) the experimental set of biologically-active DNA-binding sites to
- (2) a control set of biologically-active DNA-binding sites for the protein of interest;
- wherein a candidate agent is identified if the experimental set and the control set differ.
A method of identifying two cell genotypes in which a protein of interest differentially binds to the genome, the method comprising:
- (i) identifying a first set of biologically-active DNA-binding sites for the protein of interest in the genome of a cell of a first genotype;
- (ii) identifying a second set of biologically-active DNA-binding sites for the protein of interest in the genome of a cell of a second genotype;
- (iii) comparing the first set of biologically-active DNA-binding sites to the second set of biologically-active DNA-binding sites and determining if the two sets differ, thereby identifying two cell genotypes in which said protein of interest differentially binds to the genome.
Dependencies are inferred from the claim text.