Say, I get a DNA sequence from a bacteria genome. I can get the RNA transcript in the bacteria. I want to know whether the DNA is responsible for coding a non-coding RNA. What should I do to test the hypothesis?
If its a coding RNA it should contain a ribosome binding sequence to iniate translation.
There are both computational and experimental procedures to detect the presence of nc RNAs in the bacterial genome. SIPHT is an online tool that can predict computationally the presence of ncRNAs based on several criteria such as presence of a promoter sequence upstream of the ncRNA, terminator sequence downstream, absence of RBS and the overall location in the interoperonic region. Experimental validation can be performed using Northerns or strand-specific RNAseq. For more details refer to my work on ncRNAs in clostridia.
http://www.biomedcentral.com/1471-2164/14/849
Latest papers on ribosome footprinting and ribosome profiling have shown that several RNAs which were thought to be non-coding actually bound to 80S ribosomes and produced polypeptides.
So the best strategy would be to perform ribosome profilng - where ribosome bound RNA is treated with RNAse and ribosome protected sequences are then sequenced to identify all translated RNAs.
http://arxiv.org/abs/1405.4174
However, other groups have identified that several long noncoding RNAs bind to ribosomes without any translation events happening.
http://www.cell.com/cell/pdf/S0092-8674(13)00711-3.pdf.
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