Transcription traffic jams

Selth et al Elongation Review: polII collisions yield backtracking, pol II collisions yield reactivation / push through of paused leaders.  Longer genes have more traffic jams (Swinburne 2008 G&D, see below).

Saeki and Svejstrup 2009 Mol Cell Collisions can push through pause zones.

single molecule force experiments indicate that force is unable to terminate most pauses (Neuman et al Cell 2003, and Dala et al Mol Cell 2006).

Swinburne and Silver 2008 Dev Cell commentary (traffic can yield bursting).

Swinburn and Silver 2008 Genes and Development: longer genes experience more traffic jams.  more ‘bursty type’ expression on longer genes, believed to stem from more traffic jams on longer genes (genes have everything the same except variable length intron).

Epshtein and Nudler 2003: pol II cooperativity.  Also use partially repressed vs. fully active IPTG inducible T7 lacZ in E coli, measure elongation rate by comparing appearance of 5′ and 3′ hybridization probes.

  • Report more backtracking and pausing on less heavily transcribed genes / fewer pol IIs.
  • Report much faster (62 nt/s vs 25 nt/s) in more strongly induced.
  • > I think this is completely a detection efficiency thing.
  • cites Foe 1978, Hamming 1981 and Hirayoshi 1999 to say hsp gene and rRNA genes positioned almost without spacing, and cites Condon & Squires 1995 and Giardina & Lis 1993 to say these are rapidly elongating (say rather highly expressed.  I don’t think hsp elongates substantially faster than other genes, it initiates faster).
  • rRNA transcription is precisely the case that Klumpp and Hwa analyze in deriving their effects of traffic.


Adelman 2002 (cited by Swinburne under polymerases accumulate behind a slow leading polymerase, but appears to me to be all single polII with tweezers, no multi-polII experiments. )

Tolic-Norrelykke 2004 cited with above– more evidence on existence of ‘slow polymerases’. Though Adelman concludes all pol IIs are homogenous, just stochastic pausing leads to variable kinetics.

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