Dear Santhi, I guess it depends on what you mean by interactions? If you are looking for methods for measuring when different regions of chromatin touch each other, you will need a chromosome/chromatin conformation capture (3C) type method (http://en.wikipedia.org/wiki/Chromosome_conformation_capture). ChIP-PET would allow you to follow the presence/absence of whatever mark/protein you have antibodies for. As a tangent to the PET idea, we use paired-end sequence reads to map and define the sizes of chromatin species in genomes (doi: 10.1093/nar/gkq1183) - if you are working on higher eukaryotes, this type of approach may be too expensive in terms of sequencing though.Any help? Regards, Nick Kent.

My project is to study different cromatin/chromosomal interactions during differentiation,what you said exactly right just i refereed ChIP-PET and 3C method..any other techniques are there may i know please..may i know how to work with 3C method..thank you Nicholas Sir..

Hi Santhi, best place to go is the Dekker lab site (http://my5c.umassmed.edu/welcome/welcome.php) - Job Dekker invented the technique whilst in Nancy Kleckner's lab. You'll be able to find both practical and computational method resources there. Good luck with your experiments. N

My paper:"Morphogens:Compostion and Function" deals with the chromatin remodelling during differentiation. I can e-mail it to you if you give me your e-address.My is: [email protected]