Long-read Ribo-STAMP simultaneously measures transcription and translation at full length isoform resolution
Transcription and translation are intertwined processes where mRNA isoforms are crucial intermediaries. However, methodological limitations in analyzing translation at the mRNA isoform level have impaired our ability to comprehensively establish links between the full-length transcripts and the translatome. This has left gaps in our understanding of critical biological processes, regulatory mechanisms, and disease progression. To address this, we develop an integrated computational and experimental framework called long-read Ribo-STAMP (LR-Ribo-STAMP). LR-Ribo-STAMP capitalizes on advancements in long-read sequencing and RNA-base editing-mediated technologies to simultaneously and scalably profile translation and transcription at both gene and mRNA isoform levels for the first time. In this report, we show agreement between gene-level translation profiles obtained with LR-Ribo-STAMP and those from previously validated short-read Ribo-STAMP data in unperturbed cells. At the mRNA isoform level, we show that LR-Ribo-STAMP successfully profiles translation in unperturbed cells and links mRNA isoforms and regulatory features, such as upstream ORFs (uORFs) and regulatory sequences, to translation measurements. We further demonstrate the method's effectiveness in profiling disease models by profiling translation at gene and isoform levels in a triple-negative breast cancer cell line under normoxia and hypoxia. Here, we find that LR-Ribo-STAMP effectively delineates orthogonal transcriptional and translation shifts between conditions at gene and isoform levels. At the isoform level, LR-Ribo-STAMP uniquely identifies key regulatory elements and shifts in mRNA isoform transcription that correlate with changes in translational, providing an example of insight that can inform the development of novel therapeutics. Overall, LR-Ribo-STAMP is a significant advancement in translation methods and can have profound implications for basic research and clinical applications. Overall design: Three replicates each of unperturbed HEK293T cells expressing dox-inducible APOBEC1-only or Ribo-STAMP expression vectors to benchmark long-read Ribo-STAMP and profile translation at gene and mRNA isoform level in unperturbed cell state context. Two replicates each of MDA-MB-231 (triple-negative breast cancer cell line) expressing the Ribo-STAMP expression vector with and without 48h cobalt (II) chrolide treatment to induce hypoxia to apply long-read Ribo-STAMP for profiling disease models.