Editing Functional genomics (section)

====Massively Parallel Reporter Assays (MPRAs)====
Massively parallel reporter assays is a technology to test the cis-regulatory activity of DNA sequences.<ref>{{cite journal | vauthors = Kwasnieski JC, Fiore C, Chaudhari HG, Cohen BA | title = High-throughput functional testing of ENCODE segmentation predictions | journal = Genome Research | volume = 24 | issue = 10 | pages = 1595–602 | date = October 2014 | pmid = 25035418 | pmc = 4199366 | doi = 10.1101/gr.173518.114 }}</ref><ref>{{cite journal | vauthors = Patwardhan RP, Hiatt JB, Witten DM, Kim MJ, Smith RP, May D, Lee C, Andrie JM, Lee SI, Cooper GM, Ahituv N, Pennacchio LA, Shendure J | title = Massively parallel functional dissection of mammalian enhancers in vivo | journal = Nature Biotechnology | volume = 30 | issue = 3 | pages = 265–70 | date = February 2012 | pmid = 22371081 | pmc = 3402344 | doi = 10.1038/nbt.2136 }}</ref> MPRAs use a [[plasmid]] with a synthetic cis-regulatory element upstream of a promoter driving a synthetic gene such as Green Fluorescent Protein. A library of cis-regulatory elements is usually tested using MPRAs, a library can contain from hundreds to thousands of cis-regulatory elements. The cis-regulatory activity of the elements is assayed by using the downstream reporter activity. The activity of all the library members is assayed in parallel using barcodes for each cis-regulatory element. One limitation of MPRAs is that the activity is assayed on a plasmid and may not capture all aspects of gene regulation observed in the genome.