Distal regulatory elements are increasingly implicated as an integral part in the transcriptional networks that regulate normal and aberrant cellular development. A growing body of evidence suggests that these regulatory elements exert their function through direct physical interactions mediated by chromatin looping. As interactions between regulatory elements cannot be readily predicted their functions remain minimally explored. The proposed project aims to bridge this gap between genomic localization and function by experimentally determining interactions between regulatory elements. This will allow us to begin unraveling their function and impact of distal regulatory elements on transcriptional regulation and cellular development.
For a range of hierarchically related hematopoietic developmental stages, this proposal aims to:
1) Map genomic interactions on a genome-wide level using a chromatin conformation capture coupled to massive high throughput sequencing.
2) Identify regulatory elements genome-wide using chromatin immunoprecipitation and combine this with genomic interaction data to create comprehensive maps of interactions between regulatory elements and target loci.
3) Determine gene expression profiles of assessed stages of development to identify commonly and differentially expressed genes.
4) Build integrated models for stage and lineage specific transcriptional regulation based on determined interactions between regulatory elements and target loci
5) Validate models for transcriptional regulation by direct comparison to stage specific transcriptional profiles and further to gene expression profiles and changes in expression/interaction profiles observed in genetically modified mice.
Together this will further our understanding of distal gene regulatory elements and their impact and function in the transcriptional regulatory networks that govern hematopoietic development.