RNA polymerase control by chromatin structure

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This is an outline of an example mechanism of yeast cells by which chromatin structure and histone posttranslational modification help regulate and record the transcription of genes by RNA polymerase II.

This pathway gives examples of regulation at these points of transcription:

  • Pre-initiation (promotion by Bre1, histone modification)
  • Initiation (promotion by TFIIH, PolII modification AND promotion by COMPASS, histone modification)
  • Elongation (promotion by Set2, Histone Modification)

This is intended as an extension and example for RNA polymerase II, it is fairly involved and the following articles are strongly recommended to aid understanding:

Please note that this refers to various stages of the process as regulatory steps. It has not been proven that they are used for regulation, but is very likely they are.

RNA PolII elongation promoters can be summarised in 3 classes.

  1. Drug/sequence-dependent arrest affected factors (Various interfering proteins).
  2. Chromatin structure oriented factors (Histone posttranscriptional modifiers, eg HMTs).
  3. RNA PolII catalysis improving factors (Various interfering proteins and PolIII cofactors, see RNA polymerase II).

Protein Complexes Involved

We are mostly concerned with chromatin structure oriented factors, although there are other factors that become involved in the pathway:

RNA PolII cofactors:
TFIIH - Phosphorylates C terminal domain (CTD) of the largest RNA PolII subunit - serine 5. Acts to switch the RNA PolII into elongation from initiation.
Ctk1 - Phosphorylates C terminal domain (CTD) of the largest RNA PolII subunit - serine 2. Acts in compliment to phosphorylation of serine 5 and is thus seen in middle to late elongation.

Chromatin structure oriented factors:
(HMTs (Histone MethylTransferases)):
COMPASS§† - (COMplex of Proteins ASsociated with Set1) - Methylates lysine 4 of histone H3.
Set2 - Methylates lysine 36 of histone H3.
(interesting irrelevant example: Dot1*‡ - Methylates lysine 79 of histone H3.)

Bre1 - Ubiquinates (adds ubiquitin to) lysine 123 of histone H2B. Associated with pre-initiation and allowing RNA PolII binding.


  1. Bre1, Recruited by Rad6, ubiquinates lysine 123 of histone H2B near a promoter. This is pre-initiation regulation control, initiation cannot occur until the chromatin structure around the promoter is loosened by this process.
  2. RNA PolII and its associated cofactors (TFIIA-D and TFIIH) bind to the now revealed promoter.
  3. (Not shown on diagram) TFIIH phosphorylates serine 5 of the C terminal region of the RNA PolII. This switches the polymerase to 'elongation mode'. This is initiation regulation control, the initiation phase cannot be left until PolII is phosphorylated in this way, however elongation is currently further inhibited by the chromatin structure.
  4. An additional 'bridge' factor, Paf1, binds to the polymerase. This has no direct regulatory effect.
  5. COMPASS binds to Paf1. COMPASS methylates lysine 4 of histone H3, loosening the chromatin structure sufficiently to allow transcription. This is initiation regulation control, the initiation phase cannot be left until the chromatin structure is loosened in this way.
  6. As The polymerase advances COMPASS works to continually methylate ahead of the polymerase, allowing continued transcription, up to a point. Midway through elongation Ctk1 (a kinase) moves the point of polymerase phosphorylation to serine 2 on the C terminal region.
  7. This causes dissociation of COMPASS and allows the binding of Set2 to the complex. Set2 methylates lysine 36 of histone H3, replacing the lost loosening effect of COMPASS. This is elongation regulation control, elongation cannot continue until the chromatin structure is loosened in this replacement way.

Note how the action of the two HMTs is (semi)permanent - later transcription will not need either COMPASS or Set2 assistance. There is much speculation about the function of this, and it seems likely it is involved in memory of when the gene was last transcribed, another potential level of regulation.