. Author manuscript; available in PMC: 2020 Apr 1.

Published in final edited form as: Trends Cancer. 2019 Mar 22;5(4):245–262. doi: 10.1016/j.trecan.2019.02.011

Table 2:

Massively parallel functional assays designed for investigation of the 5’ and 3’UTRs.

UTR	Sequence Length	Sequence Source	Measurement	Experimental Design	Citation
5’UTR	50mer	Randomized + human 5’UTR + ClinVar 5’UTR variants	Translation efficiency	RNA-seq & polysome profiling of mRNA libraries in 293T cells	[163]
5’UTR	11mer	Randomized sequence from −6 to +5 positions around AUG	Translation efficiency	FACS + DNA-seq of retroviral plasmid library infected into mouse lymphocytes	[164]
3’UTR	200mer	Random combinations of known 3’UTR cis- elements	Transcript abundance, translation initiation & efficiency	RNA-seq & polysome profiling of plasmid library in HeLa cells	[165]
3’UTR	110mer	3’UTRs of ~7,000 zebrafish transcripts	mRNA degradation	RNA-seq over time course of mRNA libraries in zebrafish embryos	[166]
3’UTR	8mer	Random sequence inserted into endogenous 3’UTR	Protein expression	FACS + DNA-seq of genomically- integrated dual fluorescent reporters in 293 cells	[167]
3’UTR	34mer	3’UTR sequences conserved across vertebrates	Protein expression	FACS + DNA-seq of genomically- integrated dual fluorescent reporters in 293 cells	[168]
3’UTR	200mer + 160mer	Deep mutational scanning of active 3’UTR ARE + full coverage of CXCL2 + highly conserved sequences	mRNA stability, protein expression	RNA-seq over time course & FACS + DNA-seq of plasmid library transfected into human epithelial cells	[169]