Median transcription speed in five cell lines

Range HF1, CS-B, and K562 ~1.25 kb/min: TM and MCF-7 ~1.75 kb/min kb/min
Organism Human Homo sapiens
Reference Veloso A. et al., Rate of elongation by RNA polymerase II is associated with specific gene features and epigenetic modifications. Genome Res. 2014 Jun24(6):896-905. doi: 10.1101/gr.171405.113. p.899 left column top paragraph & p.901 right column top paragraphPubMed ID24714810
Method "Here [researchers] utilize BruDRB-seq to assess transcription elongation rates genome-wide. This technique involves the transient inhibition of initiated RNAPII prior to elongation using 5,6-dichlorobenzimidazole1-ß-D-ribofuranoside (DRB) (Singh and Padgett 2009). Following drug removal, RNA polymerases enter the elongation phase in a synchronized manner, and nascent RNA is labeled with bromouridine (Bru), isolated with anti-BrdU antibodies, and subjected to deep sequencing. By measuring the width of the transcription “wave” generated during the labeling period, the transcription elongation rates of all expressed genes longer than 40 kb were assessed."
Comments "In this study, [researchers] used five cell lines and BruDRB-seq to assess transcription elongation rates genome-wide. Three of these cell lines are human fibroblasts, and two cell lines, K562 [human immortalised myelogenous leukemia line] and MCF-7 [breast cancer cell line], are cancer-derived. HF1 and TM cells are normal human fibroblasts, while Cockayne syndrome B cells (CS-B) have a genetic defect in the ERCC6 gene, which encodes the CSB protein, resulting in a defect in transcription coupled DNA repair...The median elongation rate was found to be similar across the five cell lines, with HF1, CS-B, and K562 being nearly identical (~1.25 kb/min), and TM and MCF-7 rates slightly higher than the other cell lines (~1.75 kb/min) (Fig. 3A)."
Entered by Uri M
ID 111271