this study in human K562 cells ~50min: previous study in mice immune dendritic cells (DCs) ~139min min
||Schwalb B et al., TT-seq maps the human transient transcriptome. Science. 2016 Jun 3 352(6290):1225-8. doi: 10.1126/science.aad9841. p.1226 middle column bottom paragraphPubMed ID27257258
|| Rabani M et al., High-resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies. Cell. 2014 Dec 18 159(7):1698-710. doi: 10.1016/j.cell.2014.11.015. Supplemental information p.S22 footnote (I) beneath figure S6PubMed ID25497548
||Abstract: "[Investigators] developed transient transcriptome sequencing (TT-seq), a protocol that uniformly maps the entire range of RNA-producing units and estimates rates of RNA synthesis and degradation. Application of TT-seq to human K562 cells recovers stable messenger RNAs and long intergenic noncoding RNAs and additionally maps transient enhancer, antisense, and promoter-associated RNAs." Primary source abstract: "Here, [investigators] combine RNA metabolic labeling, rRNA-depleted RNA-seq, and DRiLL, a novel computational framework, to quantify the level editing sites and transcription, processing, and degradation rates of each transcript at a splice junction resolution during the LPS [lipopolysaccharide] response of mouse dendritic cells."
||P.1226 middle column bottom paragraph: "Kinetic modeling of TT-seq and RNA-seq data enabled [investigators] to estimate rates of RNA synthesis and degradation (Fig. 3 and fig. S7A) (ref 4). [They] estimated rates of phosphodiester bond formation or breakage at each transcribed position and averaged these within TUs [transcriptional units], thus obtaining estimates of relative transcription rates and RNA
stabilities (ref 4).[They] found that mRNAs and lincRNAs [long intergenic noncoding RNAs] had the highest synthesis rates and longest halflives.
[They] determined a median mRNA half-life of ~50 min, compared with a previous estimate of ~139 min (primary source). Other transcript classes had
low synthesis rates and short half-lives, explaining why short ncRNAs [noncoding RNAs] are difficult to detect. eRNAs [enhancer RNAs] had half-lives of a few minutes, consistent
with prior data (primary source). Short RNA half-lives correlated with a lack of secondary structure (fig. S7B). The folding energy of eRNAs was comparable to the genomic background level (fig. S7C), and only 10% of their sequence was predicted to be structured, compared with 52% in
mRNAs (fig. S7D)."