Table 2.

Approaches Used to Investigate the Coding Potential of a Long Noncoding RNA

Methods	Advantages	Disadvantages
Bioinformatic tools (eg, CPC, CPAT, and CNCI)	Rapid and easy-to-use web interface for many	Output considered probability rather than definitive evidence
In vitro transcription and translation assays	Low hands on time	Somewhat artificial overexpression system
Genetic modification, including knockin of a protein tag	Allows for testing of endogenous expression	Time consuming
Ribosome profiling	Allows for genome- wide interrogation and resolution mapping of binding sites	Signal-to-noise ratio and other technical concerns have been questioned
Mass spectrometry	Definitive	Tedious and requires judicious titration of conditions

CNCI indicates Coding-Non-Coding Index; CPAT, coding-potential assessment tool; and CPC, coding-potential calculator.