Comparison of Standard and Novel Chromatin Immunoprecipitation Protocols

Mentors: Robbyn Issner, Holly Jane Whitton, Chuck Epstein

Modifications to histone proteins, such as acetylation and methylation, can promote or repress gene expression by affecting how tightly or loosely DNA is wound around these histone proteins. Chromatin Immunoprecipitation (ChIP) is a method by which DNA can be isolated, based on whether it is bound by a specific protein, such as a modified form of a histone protein. Data from these experiments can used to create genomic maps of all of the DNA sites that are bound by various types of modified histones.

Grace’s research focused on comparing the efficacy of two different ChIP protocols to study the binding sites of methylated histone H3, in human leukemia cells. Grace conducted Nanostring experiments on the DNA libraries produced by each of the two methods, and then submitted the DNA for sequencing. Grace found that the current standard method used at the Broad displayed higher precision and quality control, but the new method was faster and simpler.



Grace, a senior at Lexington High School, compared two methods of the “ChIP” protocol, to study the epigenetic marks present on the chromosomes of human leukemia cells.