Improving the study of RNA dynamics through advances in RNA-seq with metabolic labeling and nucleotide-recoding chemistry.

ABSTRACT: RNA metabolic labeling using 4-thiouridine (s⁴U) captures the dynamics of RNA synthesis and decay. The power of this approach is dependent on appropriate quantification of labeled and unlabeled sequencing reads, which can be compromised by the apparent loss of s⁴U-labeled reads in a process we refer to as dropout. Here we show that s⁴U-containing transcripts can be selectively lost when RNA samples are handled under sub-optimal conditions, but that this loss can be minimized using an optimized protocol. We demonstrate a second cause of dropout in nucleotide recoding and RNA sequencing (NR-seq) experiments that is computational and downstream of library preparation. NR-seq experiments involve chemically converting s⁴U from a uridine analog to a cy

SUBMITTER: Zimmer JT 

PROVIDER: S-EPMC10245837 | biostudies-literature | 2023 May

REPOSITORIES: biostudies-literature