Public Health Relevance

- from Parent Grant The Encyclopedia of DNA Elements (ENCODE) project has made remarkable progress towards identifying all regulatory elements in the human genome, but nearly all of these predictions have not been functionally tested. We plan to use massively parallel reporter assays to characterize at least 100,000 ENCODE-annotated candidate regulatory elements for their function. In addition, we will use CRISPR/Cas9-based multiplex genome editing to generate mutations in thousands of these elements in their endogenous context, followed by genomic assays that will provide further validation while also linking elements to the genes that they regulate.

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Research Project with Complex Structure Cooperative Agreement (UM1)
Project #
3UM1HG009408-04S1
Application #
10238522
Study Section
Program Officer
Pazin, Michael J
Project Start
2017-02-01
Project End
2022-01-31
Budget Start
2021-02-01
Budget End
2022-01-31
Support Year
4
Fiscal Year
2021
Total Cost
Indirect Cost
Name
University of California San Francisco
Department
Pharmacology
Type
Schools of Pharmacy
DUNS #
094878337
City
San Francisco
State
CA
Country
United States
Zip Code
94143
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Sukenik Halevy, Rivka; Chien, Huan-Chieh; Heinz, Bo et al. (2018) Mutations in the fourth ?-propeller domain of LRP4 are associated with isolated syndactyly with fusion of the third and fourth fingers. Hum Mutat 39:811-815
Hill, Andrew J; McFaline-Figueroa, José L; Starita, Lea M et al. (2018) On the design of CRISPR-based single-cell molecular screens. Nat Methods 15:271-274
Jorgenson, Eric; Matharu, Navneet; Palmer, Melody R et al. (2018) Genetic variation in the SIM1 locus is associated with erectile dysfunction. Proc Natl Acad Sci U S A 115:11018-11023
Klein, Jason C; Chen, Wei; Gasperini, Molly et al. (2018) Identifying Novel Enhancer Elements with CRISPR-Based Screens. ACS Chem Biol 13:326-332
Chatterjee, Sumantra; Ahituv, Nadav (2017) Gene Regulatory Elements, Major Drivers of Human Disease. Annu Rev Genomics Hum Genet 18:45-63
Starita, Lea M; Ahituv, Nadav; Dunham, Maitreya J et al. (2017) Variant Interpretation: Functional Assays to the Rescue. Am J Hum Genet 101:315-325