Cameron Osborne
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• Recent, selected Publications

The Link between Nuclear Organization of Transcription and Chromosomal Translocation

Chromosomes are distributed non-randomly within the nucleus such that some chromosomes are preferentially positioned next to specific chromosomal neighbours. Preferred neighbouring is cell type-specific and has been suggested to influence gene expression and the frequency of specific chromosomal translocations . For instance, eighty percent of Burkitt’s lymphoma in humans and plasmacytoma in mice contain translocations between the immediate-early proto-oncogenic transcription factor MYC and the Immunoglobulin heavy chain gene locus IGH . Chromosomes 12 and 15, which harbour the Igh and Myc genes, are preferred neighbors in mouse splenic lymphocytes . Similarly in human lymphoid cells MYC and IGH are often found to be proximal. Any process that brings these genes together would obviously be expected to increase the risk of a translocation between them, however little is known about the forces that organize the chromosomes in the nucleus.

Gene transcription does not occur throughout the nucleus, but rather takes place at discrete foci that are a thousand-fold enriched for RNA polymerase II, which have been called transcription factories. Factories have been estimated to contain up to 10 polymerase complexes each, measure approximately 50 nm in diameter and occupy fixed positions within the nucleus, perhaps associating with a nuclear matrix . Using a combination of FISH methods and Chromosome Conformation Capture (3C), our investigations have suggested that genes are obliged to move to transcription factories in order to be transcribed.



Figure 1.
Co-association of genes at a shared transcription factory.
Genes in cis (loops below) and in trans (loop above),
protruding from their chromosome territories to
transcribe in a transcription factory (blue sphere).

We've demonstrated that transcriptionally active genes are not continuously transcribed, but instead oscillate between ‘active’ and ‘temporarily quiescent’ transcription states that correlate strongly with positioning ‘at’ and ‘away’ from transcription factories, respectively. Furthermore, we've shown that there are surprisingly few transcription factories per cell in mouse tissues, numbering a few hundred. In contrast, there are thousands of active genes in these cells suggesting that multiple genes are obliged to share factories. Indeed, we have shown that genes that are separated by tens of megabases are frequently co-associated with a shared transcription factory. Furthermore, our data also showed that genes on separate chromosomes can co-associate at the same factory at significant, albeit reduced, frequencies (Figure 1).

Figure 2. (Click to enlarge)
RNA FISH detection of transcribing Myc (green)
and Igh (red) alleles in stimulated B cells showing
a co-localizing pair. DAPI staining is blue.

Recently, we have searched for evidence of the co-association of genes that are commonly involved in translocations. We have studied the spatial organization of Myc and Igh alleles and have shown that non-transcribing Myc alleles in resting mouse B cells are positioned away from transcription factories. Upon activation of the cells, the Myc alleles are rapidly recruited to preexisting factories, within just five minutes of B cell stimulation. Remarkably, 25% of the newly activated Myc alleles move to a factory that is already occupied by a transcribing Igh allele. (Figure 2). This extraordinarily high frequency of interchromosomal co-association is two to ten-fold higher than co-association frequencies observed for other gene pairs in trans, including other interactions between other gene pairs on chromosomes 12 and 15. This observation is highly suggestive that there may be a specificity underlying the co-association of specific genes at transcription factories. It is conceivable that networks of preferentially co-associating genes could influence the relative positioning of chromosomes in a cell type-specific manner.

Figure 3. (Click to enlarge)
RNA immuno-FISH detection of Myc (green) and Igh (red) transcription and RNA polymerase II foci (blue) showing that co-localizing Myc and Igh transcription is associated with a transcription factory. Separate colour channels of the co-localizing signals are shown on right.

The high frequencies of transcription-dependent co-associations between the Myc and Igh genes provide compelling support for a model whereby specific chromosomal translocations are more likely to occur as a consequence of the spatial organization of transcription. Thus specific transcriptional organization may provide the opportunity for a translocation to occur. We are currently investigating these possibilities.

Recent selected publications

Osborne CS, Chakalova L, Mitchell JA, Horton AM, Wood AL, Bolland DJ, Corcoran AE, Fraser P (2007) Myc dynamically and preferentially relocates to a transcription factory occupied by Igh.
PLoS Biology 5 e192, 1763-1772
http://dx.doi.org/10.1371/journal.pbio.0050192

Krueger C, Osborne CS (2006) Raising the curtains on interchromosomal interactions.
Trends in Genetics 22 637-639
http://dx.doi.org/10.1016/j.tig.2006.09.008

Chakalova L, Debrand E, Mitchell JA, Osborne CS, Fraser P (2005) Replication and transcription: shaping the landscape of the genome.
Nature Reviews Genetics 6 669-677
http://dx.doi.org/10.1038/nrg1673

Chakalova L, Osborne CS, Dai Y-F, Goyenechea B, Metaxotou-Mavromati A, Kattamis A, Kattamis C, Fraser P (2005) The Corfu δβ thalassemia deletion disrupts γ-globin gene silencing and reveals post-transcriptional regulation of HbF expression.
Blood 105 2154-2160
http://dx.doi.org/10.1182/blood-2003-11-4069

Osborne CS, Chakalova L, Brown KE, Carter D, Horton A, Debrand E, Goyenechea B, Mitchell JA, Lopes S, Reik W, Fraser P (2004) Active genes dynamically co-localize to shared sites of ongoing transcription.
Nature Genetics 36 1065-1071
http://dx.doi.org/10.1038/ng1423

Hacein-Bey-Abina S, Von Kalle C, Schmidt M, McCormack MP, Wulffraat N, Leboulch P, Lim A, Osborne CS, Pawliuk R, Morillon E, Sorensen R, Forster A, Fraser P, Cohen JI, De Saint Basile G, Alexander I, Wintergerst U, Frebourg T, Aurias A, Stoppa-Lyonnet D, Romana S, Radford-Weiss I, Gross F, Valensi F, Delabesse E, Macintyre E, Sigaux F, Soulier J, Leiva LE, Wissler M, Prinz C, Rabbitts TH, Le Deist F, Fischer A, Cavazzana-Calvo M (2003) LMO2-associated clonal T cell proliferation in two patients after gene therapy for SCID-X1.
Science 302 415-419
http://dx.doi.org/10.1126/science.1088547

Carter D, Chakalova L, Osborne CS, Dai Y-F, Fraser P (2002) Long-range chromatin regulatory interactions in vivo. Nature Genetics 32 623-626
http://dx.doi.org/10.1038/ng1051