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Long-TUC-seq is a robust method for quantification of metabolically labeled full-length isoforms

ABSTRACT: The steady state expression of each gene is the result of transcriptional rate, dynamic processing, and degradation of RNA. While regular RNA-seq methods only measure steady state expression levels, RNA-seq of metabolically labeled RNA identifies transcripts that were transcribed during the window of metabolic labeling. Whereas short-read RNA sequencing can identify metabolically labeled RNA at the gene level, long-read sequencing results in dramatically improved resolution of isoform-level transcription. Here we combine thiouridine-to-cytosine conversion (TUC) with PacBio long-read sequencing to study the dynamics of mRNA transcription in the GM12878 cell line. We show that using long-TUC-seq, we can detect metabolically labeled mRNA of distinct isoforms more reliably than using short reads. Long-TUC-seq holds the promise of capturing isoform dynamics robustly and without the need for enrichment.

ORGANISM(S): Homo sapiens

PROVIDER: GSE149551 | GEO | 2020/04/30

REPOSITORIES: GEO

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