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Integrative analyses of gene regulation via long-range chromatin interactions
Throughout development, gene expression is regulated in part by interactions between gene promoters and distal enhancers that can be tens or hundreds of kilobases away. Our recent work has identified novel mechanisms of such long-range regulation in fly and mouse models. In Drosophila, Argonaute2 is canonically part of the post-transcriptional siRNA silencing machinery. We show it also plays a role in transcription regulation via chromatin topology and RNA PolII phosphorylation though integrative analysis of RNA-seq, ChIP-seq, ChRIP-seq, and 4C-seq assays. In mouse, the erythroid transcription factor LDB1 is known to homodimerize to facilitate enhancer-promoter interactions, but by combining new data with published work we show that it can also interact with the architectural protein CTCF to promote the erythroid gene program in mouse. The software infrastructure that makes such integrative analyses possible -- and reproducible -- will also be highlighted.