Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay (EMSA) and DNA-affinity Precipitation Assay (DAPA)

Daniel E. Miller; Zubin H. Patel; Xiaoming Lu; Arthur T. Lynch; Matthew T. Weirauch; Leah C. Kottyan

doi:10.3791/54093

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Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay (EMSA) and DNA-affinity Precipitation Assay (DAPA)

JoVE Journal
Biology

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JoVE Journal Biology

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay (EMSA) and DNA-affinity Precipitation Assay (DAPA)

12,927 Views

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11:35 min

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August 21, 2016

DOI:

10.3791/54093-v

DOI:

10.3791/54093-v

•

11:35 min

August 21, 2016

•

12920 Views

Daniel E. Miller¹, Zubin H. Patel^1,2,3, Xiaoming Lu^1,3, Arthur T. Lynch¹, Matthew T. Weirauch*^1,4, Leah C. Kottyan*¹

¹Center for Autoimmune Genomics and Etiology,Cincinnati Children’s Hospital ²Medical Scientist Training Program,University of Cincinnati ³Immunology Graduate Program,University of Cincinnati ⁴Divisions of Biomedical Informatics and Developmental Biology,Cincinnati Children’s Hospital

Summary

We present a strategic plan and protocol for identifying non-coding genetic variants affecting transcription factor (TF) DNA binding. A detailed experimental protocol is provided for electrophoretic mobility shift assay (EMSA) and DNA affinity precipitation assay (DAPA) analysis of genotype-dependent TF DNA binding.