XXXX -sensitive ribosome profiling reveals the scope of translation in @entity19 embryonic stem cells.

@entity5808 @entity72730 @entity2828 @entity1 @entity72732 @entity19 @entity3173 @entity33387 @entity72731
BACKGROUND: Open reading frames are common in long noncoding RNAs (lncRNAs) and 5'UTRs of protein coding transcripts (uORFs). The question of whether those ORFs are translated was recently addressed by several groups using ribosome profiling. Most of those studies concluded that certain lncRNAs and uORFs are translated, essentially based on computational analysis of ribosome footprints. However, @entity3173 remain on the scope of translation and the translational status of individual ORFs. In consequence, further criteria are required to reliably identify translated ORFs from ribosome profiling data. RESULTS: We examined the effect of the translation inhibitors @entity72730 , @entity72731 and @entity5808 on @entity19 @entity2828 cell ribosome footprints. We found that @entity72730 , a drug that targets eIF4A, allows a far more accurate identification of translated sequences than previously used drugs and computational scoring schemes. Our data show that at least one third but less than two thirds of @entity2828 cell lncRNAs are translated. We also identified translated uORFs in hundreds of annotated coding transcripts including key pluripotency transcripts, such as dicer, @entity33387 , @entity72732 , and ctcf. CONCLUSION: @entity72730 inhibition data clearly increase the precision of the detection of translated ORFs in ribosome profiling experiments. Our data show that translation of lncRNAs and uORFs in @entity19 @entity2828 cells is rather common although less pervasive than previously suggested. The observation of translated uORFs in several key pluripotency transcripts suggests that translational regulation by uORFs might be part of the network that defines @entity1 stem cell identity.
