Gene regulation is fundamental to every aspect of life. The onset of tissue-specific gene expression depends
on the function of genomic elements called enhancers. Enhancers activate gene expression by interacting with
gene promoters, often located at great genomic distances through long-range chromosomal interactions.
Misregulation of enhancer-promoter interactions contributes to developmental disorders and cancer. Distinct
cancer subtypes often display different 3D genomic organization, which can influence disease progression and
prognosis. Genomic methods based on chromosome conformation capture (3C) techniques such as 4C and Hi-C,
can be used to study these interactions and identify therapeutic targets, but they require large amounts of input
material, limiting their application in disease research.
Here, we propose to develop a novel technique, LI-4C (Low Input Chromatin Conformation Capture), to
study genomic interactions with reduced input requirements. The adapter-tailed linear enrichment used in LI-4C
simplifies 4C library preparation and provide a quantitative, high-resolution view of the spatial organization of
selected loci using minimal starting material.
We will adapt LI-4C to mammalian systems by applying it to breast cancer cells, generating interaction
maps for the promoters of 20 oncogenes that are overexpressed in these cells. The proposed experiments may
reveal regulatory linkages that contribute to malignancy and that can be used as targets for the development of
diagnostic kits. Establishing this method in a breast cancer cell line will pave the way for its application in
clinical samples, potentially leading to advances in cancer diagnosis and treatment.