More on ChIP to identify DNA-protein interactions

Progress:

Our current focus is to identify a role for sICD (the small intracellular protein fragment formed by the cleavage of FGFR3 receptor) using chromatin immunoprecipitation (ChIP). We would like to find out whether sICD protein could interact with DNA to change the genetic environment of the cell and alter the outcome of FGFR3 signaling. We have conducted preliminary experiments to establish the ChIP method to look at DNA-protein interactions in cartilage cells. These ChIP experiments will be combined with ChIP-sequencing analysis to recognize a functional role for sICD protein.

ChIP-sequencing is a powerful tool that gives information on DNA-protein interaction sites on a genome-wide (in the whole organism) level. Briefly, ChIP isolates pieces of DNA that are occupied (or bound) by a transcription factor (typically a protein) within the whole genome. The isolated pieces of DNA represent various sites within the whole genome that the protein binds. Loosely speaking, if a protein occupies or binds to a certain region (or site) of a DNA, it is probable that it may participate in regulating expression of that gene. The information encoded by these pieces of DNA is determined by sequencing simply by determining the arrangement of the nucleotide bases adenine (A), thymine (T), guanine (G), and cytosine(C) within that DNA. ChIP-sequencing will provide valuable information and lead to better understanding of the system. More on ChIP-sequencing can be found here:

http://en.wikipedia.org/wiki/Chip-sequencing.

In our next blog update, we will present a second research that is being conducted in the lab using transgenic mice to help characterize the role of FGFR3 signaling in achondroplasia