Ribo-ITP expands the translatome of limited input samples

Abstract In the last decade, an unexpectedly large number of translated regions (translons) have been discovered using ribosome profiling and proteomics. Translons can act as regulatory elements or encode functional micropeptides. However, identification of translons has been limited to cell lines or large organs due to high input requirements for conventional ribosome profiling and mass spectrometry. Here, we address this input limitation using Ribo-ITP on difficult-to-collect samples such as microdissected hippocampal tissues and single preimplantation embryos to identify thousands of translons. To test the translational capacity of the identified translons, we engineered a translon-dependent GFP reporter system and detected expression of translons initiating at ATG and near-cognate start codons in mouse embryonic stem cells (mESCs). Mutating the translons in mESCs identified a small proportion that may negatively impact growth. We identified distinct expression patterns of translons using a comparative analysis of more than a thousand ribosome profiling datasets across a wide range of cell types. Further, using a machine learning model we predict that specific upstream translons in synaptically enriched mRNAs regulate translation efficiency of the annotated coding region. Taken together, we present a proof-of-concept study to identify non-canonical translation events from low input samples which can be applied to cell and tissue types inaccessible to conventional methods. Competing Interest Statement The authors have declared no competing interest. Footnotes Figure4 and Figure5 are updated with new data. Data Availability All ribosome profiling raw data sets and the processed .ribo files generated in this study have been submitted to the Gene Expression Omnibus GSE300869, GSE300832, GSE318608. All custom scripts used to perform bioinformatics analyses are available at GitHub (https://github.com/up114/translons) and as Supplemental Code.