Rho-dependent termination is not fully understood but there’s a brief description in almost every concerned book about it.

In Snustard and Instant notes-Molecular Biology it is written that, the rho protein binds a stretch of 72 nucleotides at the 3' end of the nascent RNA, which could be a recognition site and then moves along 5' -> 3' direction separating the DNA-RNA hybrid.

But how's it possible, rho binding to 3' end (which is not free) and moving in 5'-> 3' (if so it is sure to fall off!)?

Diagram from Berg showing something opposite, i.e. it has attached to the 5' end and is moving in 5' -> 3' direction.

enter image description here

What is the right thing?


There is no dichotomy in the two sources you have described. The text book you linked to says, exactly (emphasis added):

Rho appears to bind to a stretch of 72 nucleotides near the 3'-end of the nascent RNA...

It doesn't say at the 3'-end, which is obviously impossible since the 3'-end forms a double-stranded hybrid within the transcription bubble. Rho is not loaded at the 5'-end of RNA, either, but rather binds internally at cytidine-rich Rho utilization (rut) sites, which will be somewhere 5' of the actual point of transcription termination. As you mentioned, there is a lot of uncertainty in the process and, while a lot is known about rut sites, as far as I can tell there is no consensus sequence, thus making it difficult to systematically identify rut sites throughout the genome. I have found papers which identify rut sites in the 5'-UTR (1) as well as within the 3'-UTR, intercistronic regions and coding sequences (2, 3, 4).

Mechanism of internal Rho loading:

enter image description here

Koslover DJ, Fazal FM, Mooney RA, Landick R, Block SM. 2012. Binding and Translocation of Termination Factor Rho Studied at the Single-Molecule Level. J Mol Biol 423:664-676


Your diagram is correct. Rho protein binds at the 5' end and "chases" RNA Polymerase. It's not possible for Rho protein to bind at the 3' end, as this hasn't been transcribed by RNA Polymerase yet.


Some of the information contained in this post requires additional references. Please edit to add citations to reliable sources that support the assertions made here. Unsourced material may be disputed or deleted.

  • 4
    $\begingroup$ can you add some references to your answer? $\endgroup$ – Vance L Albaugh Feb 23 '17 at 1:31

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