Transcriptional enhancers are a predominant category of functional elements in the non-coding portion of the human genome, far outnumbering the ~20,000 protein-coding genes. Mutations affecting enhancers have been implicated in human disease, and comprehensively understanding the genome-wide architecture and function of enhancers remains a major unsolved challenge arising from The Human Genome Project. Despite substantial progress in mapping of these elements (e.g., by the ENCODE consortium), the in vivo target genes of enhancers are generally unknown, and the mechanisms of their long range regulation during development are not well explored. Recently, I developed a novel method that allows manipulation of enhancers at their endogenous genomic location in mice using CRISPR/Cas9 genome editing (Kvon et al., Cell, 2016). In this application, I propose to better understand the mechanisms of gene regulation by distant-acting enhancers through in vivo mouse studies, exploiting this highly efficient CRISPR/Cas9 genome editing technology to create enhancer knock-out and knock-in mice and employing novel methods to map enhancer-promoter interactions. I will address the following questions regarding distal enhancer function in the genome: 1) Which genes do different classes of enhancers regulate? 2) Is there enhancer-promoter specificity for distant-acting enhancers? and 3) What are the consequences of enhancer loss or replacement on an organism's function? Mentored phase: First, I propose to adapt CRISPR/Cas9 genome editing for studying long-range enhancer- gene interactions in vivo using mouse embryonic limb as a model system. I will create a series of enhancer knock-outs to identify their target gene(s) and a series of enhancer knock-ins to study enhancer-promoter specificity. Second, I will adopt and optimize the Capture-C technology to identify interaction partners of enhancers directly in mouse tissues. Independent phase: I will use methods developed in the mentored phase to systematically map target genes for important developmental enhancers in vivo and to gain a detailed understanding of the mechanisms governing long-range enhancer-promoter interactions on a genomic scale. I will also use elucidated enhancer-promoter interactions to study basic principles of long-range enhancer regulation in the mammalian genome using CRISPR/Cas9 technology. This will enable me to develop several long-term research directions, focused on the role of enhancer-gene interactions in human evolution, disease, and development. The main areas of research training will include: 1) Further advancing the use of CRISPR/Cas9 in mice, 2) Capture-C technology development in mouse tissues, and 3) computational genome analysis. My mentor (Dr. Len Pennacchio) and co-mentor (Dr. Axel Visel) are leaders in these fields. My career development activities will focus on skills in key areas of my research, attending courses and workshops, developing leadership and mentorship skills, and securing a faculty position. To ensure progress in my goals I have also established a scientific advisory board consisting of my mentors, and Drs. D. Dickel, and E. Rubin.
The human genome contains millions of enhancers that play important roles in organismal development and human disease, yet we know little about their target genes and mechanisms of their long-range regulation. I propose to use as series of novel genomic methods to identify target genes of enhancers and study the mechanisms by which they influence the activity of these target genes. Through this work, I expect to gain significant insights into the in vivo function of enhancers during development, with particular emphasis on enhancer-gene interactions.