We propose to systematically investigate and characterize sequence elements that are necessary for genome function in their native context in contrast to existing high- throughput assays of genome function that detect sequence elements that are sufficient for function. We will accomplish this goal with three specific aims. We will develop a novel Multiplexed Editing Regulatory Assay (MERA) to test the effect of thousands of targeted mutations in native regulatory regions in a single experiment (Aim 1). We will use MERA to characterize the regulation of key developmental genes, the function of selected regulatory elements, and the gene expression effects of SNPs that are discovered in GWAS studies (Aim 2). Using these data we will build a model that will allow us to predict the bases that comprise the necessary genome and estimate the effect of non-coding genotype on gene expression (Aim 3). Through our new experimental and computational method we will help lay the groundwork for a novel paradigm in revealing the effect of human variation at base pair resolution.
We will develop a new method to measure in living cells the function of millions of individual letters that comprise the human genome. We will use this method to develop a catalog of the consequences of genomic variation on cellular function and health. As part of our work we will examine the importance of genome differences found in individuals with Type 2 Diabetes.
| Shen, Max W; Arbab, Mandana; Hsu, Jonathan Y et al. (2018) Predictable and precise template-free CRISPR editing of pathogenic variants. Nature 563:646-651 |
| Kang, Daniel; Sherwood, Richard; Barkal, Amira et al. (2017) DNase-capture reveals differential transcription factor binding modalities. PLoS One 12:e0187046 |
| Banerjee, Budhaditya; Sherwood, Richard I (2017) A CRISPR view of gene regulation. Curr Opin Syst Biol 1:1-8 |
| Betancur, Paola A; Abraham, Brian J; Yiu, Ying Y et al. (2017) A CD47-associated super-enhancer links pro-inflammatory signalling to CD47 upregulation in breast cancer. Nat Commun 8:14802 |
| Arbab, Mandana; Sherwood, Richard I (2016) Self-Cloning CRISPR. Curr Protoc Stem Cell Biol 38:5B.5.1-5B.5.16 |
| Barkal, Amira A; Srinivasan, Sharanya; Hashimoto, Tatsunori et al. (2016) Cas9 Functionally Opens Chromatin. PLoS One 11:e0152683 |
| Rajagopal, Nisha; Srinivasan, Sharanya; Kooshesh, Kameron et al. (2016) High-throughput mapping of regulatory DNA. Nat Biotechnol 34:167-74 |
