Challenging on transcriptome

mRNA translation is one of crucial process in cellular metabolism. Several approaches have been developed by cells to perfectly regulate the translation. microRNAs bind mRNA and determine its half life, while numerous proteins directly bind the mRNA and favor or avoid the interaction with ribosomes. Studying the interaction between proteins and mRNAs is important to well understand whether alteration in these binding sites have any contribution to genetic disease that are caused by a loss of an RNA- binding protein such as fragile X mental retardation or familial amyotrophic lateral sclerosis. Scientists form the Rockefeller University described a method to isolate complexes protein- RNA. They used the UV radiation that are known to form covalent bonds between protein and mRNA. So, live cells are exposed to UV radiation, and an immunoprecipitation against the protein binder allows to identify the sequence involved in the binding. This technique called CLIP (PDF), cross linking and immunoprecipitation, can be applied also to high throughput experiments. To do this some improvement are necessary in order to separate the signal from background. The use of photo- activable ribonucleotides introduces into the RNA some non-toxic and efficient linkers. Indeed, a specific base change during reverse transcription, scoring for thymidine to cytidine in the sequenced cDNA allows to precisely map the interaction site. This is an important step to unravelling the gene regulation.