Preferential associations between co-regulated genes at transcription factories

While the transcriptional machinery has been studied in great detail, much less is known about the organization of transcription in the three-dimensional space of the nucleus. Transcription in higher eukaryotes takes place in dedicated nuclear sub-compartments known as transcription factories.

Transcription factories are sites highly enriched in the hyperphosphorylated form of RNA polymerase II, the enzyme that transcribes genes into messenger RNA (Osborne et al., Nature Genetics 2004). We have shown that genes rapidly migrate to pre-assembled transcription factories upon activation (Osborne et al., PLoS Biology 2007).

Transcriptional machineryThe number of transcription factories per cell is severely limited compared to the number of expressed genes, compelling multiple genes to share the same factory.

Genes undergo dynamic long-range associations with other genes located on the same chromosome, or on other chromosomes at transcription factories (Mitchell and Fraser Genes & Dev 2008; Eskiw and Fraser J. Cell Sci. 2011).

However, it was unknown how widespread chromosomal associations are, or what the underlying molecular mechanisms are. To address these questions, we have developed e4C, a novel assay to map chromosomal associations on a genome-wide basis.

Using the mouse Hba and Hbb globin genes in erythroid cells as a model system, we found that chromosomal associations between distal genes are widespread. The globin genes associate with hundreds of other active genes, located on all chromosomes, at transcription factories.

Remarkably, these associations are non-random, meaning that the globin genes have preferred interaction partners. Among the genes interacting with the globin genes, we found that genes regulated by the transcription factor Klf1 (Kruppel like factor 1) were overrepresented. In cells lacking Klf1, interaction frequencies between the globin genes and other Klf1-regulated genes were dramatically reduced.

Thus, our results show that the transcription factor Klf1is not only required for the efficient transcription of target genes, but also for their three-dimensional clustering in nuclear space. The interactions between Klf1-regulated genes take place at a subset of transcription factories, which appear to be specialized for the optimal expression of Klf1-regulated genes. These results indicate that the organization of the transcribed genome is inherently plastic and flexible, resulting in multiple different genome conformations.

For more information see: Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells (2010) Stefan Schoenfelder, Tom Sexton, Lyubomira Chakalova, Nathan F Cope, Alice Horton, Simon Andrews, Sreenivasulu Kurukuti, Jennifer A Mitchell, David Umlauf, Daniela S Dimitrova, Christopher H Eskiw, Yanquan Luo, Chia-Lin Wei, Yijun Ruan, James J Bieker & Peter Fraser
Nature genetics 42 (1), 53-61.

Active genes dynamically colocalize to shared sites of ongoing transcription (2004) Cameron S Osborne, Lyubomira Chakalova, Karen E Brown, David Carter, Alice Horton, Emmanuel Debrand, Beatriz Goyenechea, Jennifer A Mitchell, Susana Lopes, Wolf Reik & Peter Fraser
Nature genetics 36 (10), 1065-1071

Peter Fraser diagram 1

In summary, our data uncover a transcriptional “interactome” of the mouse globin genes in erythroid cells. We predict that the three-dimensional organization of active genes in the nucleus will have a major impact on tissue-specific gene expression programs.