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The role of supercoiling in transcriptional control of MYC and its importance in molecular therapeutics

Key Points

  • MYC is a pivotal player in normal cells, not only in proliferation but also in apoptosis and differentiation. MYC is deregulated in most tumour types and stages.

  • MYC expression is sometimes an addictive character of cancer and is therefore an Achilles heel for cancer cells. Initial studies indicate that MYC suppression can lead to apoptosis and cell death in cancer cells, while producing only rapidly reversible effects in normal cells, providing a wide therapeutic window for specific and efficacious anti-tumour treatment.

  • Transcriptionally induced negative supercoiling is crucial for controlling MYC expression. The distance that this negative supercoiling travels upstream from the transcriptional start sites can be large (>1 kb) and is constrained within the boundaries imposed by looping and other features of the chromatin.

  • There are two important elements in the MYC promoter that are dynamically affected by negative supercoiling: far upstream element (FUSE) and NHE III1.

  • FUSE, in concert with the effector proteins FUSE-binding protein (FBP), FBP-interacting repressor (FIR) and TFIIH, constitutes a cruise control system that can precisely control the rate of MYC promoter firing. NHE III1 can exist in three different forms, of which two (duplex and single stranded) constitute an on switch and the third (G-quadruplex and i-motif) constitutes an off switch.

  • There are defined strategies to suppress MYC expression by small-molecule targeting of the FUSE–FBP interface or by small-molecule stabilization of the G-quadruplex or i-motif structure in the on–off switch.

Abstract

MYC is deregulated in most tumour types, but an effective means to selectively target its aberrant expression is not yet available. Supercoiling that is induced by transcription has been demonstrated to have dynamic effects on DNA in the MYC promoter element: it converts duplex DNA to non-duplex DNA structures, even at considerable distances from the transcriptional start site. These non-duplex DNA structures, which control both turning on and off of transcription and the rate of transcription firing, are amenable to small-molecule targeting. This dynamic system provides a unique opportunity for the treatment of tumours in which MYC is an important oncogene.

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Figure 1: The mechanics of torsional stress transmission through the chromatin fibre.
Figure 2: Positions and functions of FUSE and NHE III1.
Figure 3: A possible scheme for a molecular servomechanism for the regulation of MYC transcription.
Figure 4: Models of the different promoter forms in MYC NHE III1.
Figure 5: Building blocks and structures of the G-quadruplex and i-motif located in the NHE III1 MYC promoter element.
Figure 6: NM23-H2, nucleolin and a G-quadruplex-interactive compound can modulate the activity of NHE III1.
Figure 7: Proposed mechanism for inhibiting MYC-mediated cell growth by targeting FBP.
Figure 8: Cancer hallmarks and G-quadruplexes.

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Acknowledgements

This research has been supported by grants from the US National Institutes of Health (CA95060, GM085585 and CA122952) and the Leukemia & Lymphoma Society (6225-08). We are grateful to D. Bishop for help with the manuscript.

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Correspondence to Laurence H. Hurley.

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Laurence H. Hurley was the scientific founder of Cylene Pharmaceutics, which has the first-in-class G-quadruplex drug Quarfloxin in Phase II clinical trials.

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DATABASES

National Cancer Institute Drug Dictionary

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tamoxifen

Glossary

Negative supercoiling

The reduction of twist or unwinding. Because the transcriptional complex associated with RNAP is large, it is unable to rotate around the DNA and instead the DNA rotates to allow forward movement. The DNA twist ahead of the transcriptional complex increases and the twist behind the complex decreases.

B-DNA

DNA with the normal right-handed double helix structure that makes a turn every 3.4 Å.

Bidirectional transcription

Transcription that occurs when there are closely placed divergent promoters in the genome. The dynamic supercoils generated reinforce each other, which increases the likelihood of DNA melting owing to the additive negative supercoiling.

Melting

The process whereby a double helix dissociates into two single strands.

Stress-induced duplex destabilization

The propensity of a duplex site to melt is dependent on the precise sequence and sequence context. Torsional stress induced by negative supercoiling will then open up those sequences that have the lowest energy barrier for melting and this can be calculated using an algorithm.

Slipped mismatched structures

Structures that can occur in regions of DNA with direct repeat symmetry. In the case of the CT element, the repetition of the five repeats of (C/T)C(C/T)TCCCCA allows considerable residual base pairing even when there is an unpaired region. For realignment back to the fully duplex DNA the slipped structure must be melted, which potentially allows the formation of other secondary DNA structures.

Z-DNA element

An element found in DNA molecules with alternating purine and pyrimidine sequences. It is left-handed, with a zigzag pattern of the sugar–phosphate backbone.

Cruise control

The maintenance of an optimum level of promoter firing by using two counter mechanisms to control transcriptional run-off speed.

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Brooks, T., Hurley, L. The role of supercoiling in transcriptional control of MYC and its importance in molecular therapeutics. Nat Rev Cancer 9, 849–861 (2009). https://doi.org/10.1038/nrc2733

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