How complex organisms with diverse tissue and cell types can arise from the same genome is one of the most enduring and fascinating questions in biology. We study enhancers, which are cis-acting DNA sequences that increase the transcriptional output of genes and, in so doing, orchestrate the cell specific transcriptomes that underlie development and differentiation. We are interested in the mechanisms that underlie formation of long range interactions between distant enhancers and target genes, how they influence and are influenced by overall chromosome folding and how enhancers change gene expression programs. Our studies focus on the family of β-globin genes, and erythroid genes more broadly, as a model system.
We are defining a complex of proteins including Ldb1/Lmo2/Tal1/Gata1 that mediates long range enhancer activation of essentially all erythroid genes. We are investigating the proteins the Ldb1 complex partners with to function in chromatin looping. We are also interested in the functional impact on gene expression of overall chromosome folding in the nucleus, which is thought to depend on architectural factors such as CTCF and cohesin.
To study long range enhancer-gene interactions, epigenetic histone modification and transcription regulation in mammalian cells, we use biochemistry, molecular biology, genetics and genomics. We deploy ChIP, ChIP-seq, RNA-seq and Chromosome Conformation Capture (3C)-related approaches and bioinformatic analysis, as well as RNA and DNA fluorescent in situ hybridization. Our experimental systems include (1) human and mouse erythroid cell lines, primary cells and mouse ES cells, (2) human β-globin YAC transgenic mice, and (3) mice with alterations in endogenous loci that we have targeted through homologous recombination or CRISPR/Cas9 genome editing.