Journal: Science (New York, N.Y.)

Article Title: mRNA initiation and termination are spatially coordinated

doi: 10.1126/science.ado8279

Figure Lengend Snippet: (A) Heatmaps of Pearson’s r values for the pairwise correlations between the relative usage (Ψ) of a gene’s AFEs and ALEs based on their genomic order in HEK293T-A2 cells expressing for WT RNAPII ( left , n = 49), fast elongating RNAPII ( middle , R749H mutation, n= 69) and slowly elongating RNAPII ( right , E1126C mutation, n= 62). All heatmaps show pairwise correlations for genes expressing exactly 3 AFEs and 3 AFEs. ( B ) Schematic of the 4sU-DRB-LRS protocol, which involves transcription blockage and then synchronization with DRB, followed by labeling of nascent RNA with 4sU for 10 minutes, then long-read library preparation using polyI tailing to facilitate direct RNA long-read sequencing. The bottom right schematic shows the estimation of genomic distances the reads map to, which reflects the distance that RNAPII traveled from each TSS in the labeling period. ( C ) Direct RNA-seq for HNRNPL from 4sU-DRB-LRS data in K562 cells. Shown are annotated isoforms ( top , black ) and LRS reads ( middle , introns in thin grey lines ) colored by whether they start in the first expressed AFE ( blue ) or the second expressed AFE ( yellow ). Inset shows the distributions of genomic distances across reads for each AFE. ( D ) Distribution of mean genomic distances for each gene, conditioned on reads starting in AFEs with increasing ordinal positions for no PITA ( grey ) and PITA genes ( blue ). Boxes show the median and 5–95% confidence intervals for each distribution. ( E ) Distribution of elongation velocities around upstream and downstream TSSs ( left ) and PASs ( right ) for no PITA ( grey ) and PITA ( blue ) genes. Elongation velocities are calculated using 50nt bins across +/− 5kb windows around each site and smoothed with a sliding window approach for visualization ( Methods ). Background density represents the confidence intervals across genes.

Article Snippet: During the last 5 minutes of DRB treatment, 4-thio-uridine (4sU; ThermoFisher #J60679.MD) was added to a final concentration of 1mM (as described in ( 61 )).

Techniques: Expressing, Mutagenesis, Labeling, Sequencing, RNA Sequencing

Journal: Molecules

Article Title: Synthesis and Antiviral Activity of a Series of 2′- C -Methyl-4′-thionucleoside Monophosphate Prodrugs

doi: 10.3390/molecules25215165

Figure Lengend Snippet: Examples of early modified nucleoside drugs ( a – c ) and the aryloxy phosphoramidate monophosphate prodrug sofosbuvir ( d ).

Article Snippet: In 2014 Idenix filed a patent claiming the triphosphates of 4′-thioguanosine, 4′-thiouridine, and 2′-β-methyl-4′-thiouridine, as well as monophosphate prodrugs of the latter two, for the treatment of HCV [ ]; they were acquired by Merck that same year, purportedly for their anti-HCV portfolio.

Techniques: Modification