Peter Cook

Transcription factories; genome organization and gene regulation.

Human chromosomes are arguably the largest and most important biomolecules, but many aspects of their structure – and how structure affects function – remain unresolved. Our ultimate goal is to elucidate how the genome is folded, and how folding determines function. To this end, we apply a multi-disciplinary approach, combining molecular analyses, high-resolution imaging, and mathematical modeling.

A Transcription cycle.

Nascent Br-RNA in transcription factories.

Our current focus is on the validation of our model for all genomes, which is based on two heterodox concepts: (i) active polymerases are locally concentrated in discrete sites called ‘transcription factories’, and (ii) these molecular machines are immobilized when active. In other words, instead of tracking like locomotives down their templates, polymerases attached to factories reel in their templates as they extrude their transcripts. Then, these factories are both the active sites of transcription, and major organizers of the chromatin fibre (as active polymerases and associated transcription factors tether templates to the factories).

The nucleolus provides the prototypic example of a factory – a place where many rRNA genes are efficiently co-transcribed by local concentrations of RNA polymerase I. We have also shown that different protein-coding genes are co-transcribed in different nucleoplasmic factories containing RNA polymerase II (e.g., TNFalpha-responsive genes in ‘NFkappaB’ factories, and TFGb-responsive ones in ‘SMAD’ factories). Similarly, small nuclear RNAs like 7SK RNA are made in distinct ‘polymerase III’ factories.

We imagine that a promoter out in a loop initiates by binding to a factory containing the appropriate machinery, and that the frequency of initiation is determined by how closely that promoter is tethered to an appropriate factory. Then, regulatory motifs like enhancers (and silencers) act by tethering their target promoters close to (or distant from) suitable factories rich in the appropriate polymerases and factors. [See YouTube movie.]

Relevant Publications

Baboo, S., Bhushan, B., Jiang, H., Grovenor, C.R.M., Pierre, P., Davis, B.G., and Cook, P.R
2014

PLoS One 9: e99346.

Papantonis, A., and Cook, P.R
2013

Chem. Rev. 113: 8683-8705.

Papantonis, A., Kohro, T., Baboo, S., Larkin, J., Deng, B., Short, P., Tsutsumi, T., Taylor, S., Kanki, Y., Kobayashi, M., Li, G., Poh, H.-M., Ruan, X., Aburatani, H., Ruan, Y., Kodama, T., Wada, Y., and Cook, P.R
2012

EMBO J. 31: 4404-4414.

Melnik, S., Deng, B., Papantonis, A., Baboo, S., Carr, I.M., and Cook, P.R
2011

Nat. Methods 8: 962-968.

Papantonis, A., Larkin, J.D., Wada, Y., Ohta, Y., Ihara, S., Kodama, T., and Cook, P.R
2010

PLoS Biol. 8: e1000419.