Spatial Organisation of the Human Genome

 

Summary

Despite its immense length, the linear sequence map of the human genome is an incomplete description of our genetic information. This is because information on genome function and gene regulation is also encoded in the way that the DNA sequence is folded up with proteins within chromosomes and within the nucleus. Our work tries to understand the three-dimensional folding of the genome, and how this controls how our genome functions in normal development and how this may be perturbed in disease.

 

 

Purpose

Our work is aimed at understanding the genome at a level beyond that of the DNA sequence alone. We are investigating how the genome is organised within the nuclear space, both within normal, and diseased, cells and also how this organisation changes during development.

 

 

Approach, Progress and Future Work

We take a multidisciplinary approach, using cytological, genetic and biochemical methods to understand genome spatial organisation. However, a main feature of our work is the use of visual assays to investigate how the genome is folded up. To do this we combine fluorescence in situ hybridisation (FISH) and digital microscopy with the use of automated image analysis software.

 

Key Publications

1. Boyle S, Rodesch MJ, Halvensleben HA, Jeddeloh JA, Bickmore WA: Fluorescence in situ hybridization with high-complexity repeat-free oligonucleotide probes generated by massively parallel synthesis Chromosome Res 19:901-909, 2011. PubMed Abstract
2. Eskeland R, Leeb M, Grimes GR, Kress C, Boyle S, Sproul D, Gilbert N, Fan Y, Skoultchi AI, Wutz A, Bickmore WA: Ring1B compacts chromatin structure and represses gene expression independent of histone ubiquitination. Mol Cell 38:452-464, 2010. PubMed Abstract
3. Finlan, L.E.; Sproul, D.; Thomson, I.; Boyle, S.; Kerr, E.; Perry, P.; Ylstra, B.; Chubb, J.R. and Bickmore, W.A. Recruitment to the nuclear periphery can alter expression of genes in human cells. PLoS Genet 4(3):e1000039, 2008 PubMed Abstract
4. Morey, C.; Da Silva, N.R.; Kmita, M.; Duboule, D. and Bickmore, W.A. Ectopic nuclear reorganisation driven by a Hoxb1 transgene transposed into Hoxd. J Cell Sci 121(Pt 5):571-577, 2008 PubMed Abstract
5. Morey C, Da Silva NR, Perry P and Bickmore WA Nuclear re-organisation and chromatin decondensation are conserved, but distinct, mechanisms linked to Hox gene activation. Develop. 134:909-919, 2007 PubMed Abstract
6. Chambeyron, S. and Bickmore, W.A. Chromatin decondensation and nuclear reorganization of the HoxB locus upon induction of transcription. Genes Dev 18:1119-1130, 2004 PubMed Abstract
7. Gilbert, N.; Boyle, S.; Fiegler, H.; Woodfine, K.; Carter, N.P. and Bickmore, W.A. Chromatin architecture of the human genome; gene-rich domains are enriched in open chromatin fibers.
   Cell 118:555-566, 2004 PubMed Abstract

Collaborations and Funding

Our work is funded by: Medical Research Council, and the European Union FP6 and Wellcome Trust.

 

 

 

Lab Members

Current lab members involved in this work are:

• Shelagh Boyle
• Elizabeth Kerr
• Pradeepa Madapura-Marulasiddappa
• Pierre Therizols
• Robert Illingworth
• Leisha Nolen
• Iain Williamson
• Betul Hemikoglu-Balkan
• Celine Courilleau
• Andrew Wood
• Gillian Taylor
• Sehrish Rafique
• Michael Moffat
• Jessica Woodward
  

 

Wendy Bickmore's Home Page

 

 

 

 

Chromatin Folding

Nuclear Organisation

 

Chromatin Folding

We examine the spatial organisation of human and mouse chromosomes and genes in the nucleus and how this organisation is changed, for example, during development and in certain genetic diseases. We use microscopy to follow the folding path of specific gene loci as they are activated or switched off, and to identify the proteins that bring about this folding (Fig. 1). A particular interest is whether regulatory elements (enhancers) control their target genes – which may be located a million base pairs away -by chromatin looping (Fig 2) .

 

 

 

 

 

 

Figure 1. Nuclei (blue) hybridised with probes for two loci (red and green) that are 100kb apart. The chromatin is normally so compact that the red and green spots are coincident. On the right, loss of a particular protein complex results in the unfolding of chromatin so that the red and green probes are now separated.

Figure 2. Model of chromatin folding that may underlie enhancer-promoter communication. A chromatin loop formed by factors bound to the enhancer (blue) and gene promoter (green) juxtaposes the distal enhancer and gene promoter.

 

 

Nuclear Organisation

Chromatin is not randomly organised in the nucleus. Gene-poor and some silenced loci are found preferentially at the periphery of the nucleus.  Structural rearrangements of the human genome e.g. translocations can disrupt this organisation. Within individual chromosomes, the gene-rich parts can be seen looping out of the rest of the chromosome territory and away from the nuclear periphery (Fig 3).

 

 

 

 

 

 

 

 

 

Figure 3. A nucleus hybridized with a ‘paint’ for a chromosome (green) and with a probe that only contains the genes from that same chromosome (red). DNA is stained with DAPI (blue). This illustrates en masse the ‘looping-out’ of gene-rich areas from the chromosome territory and away from the nuclear periphery.

 

 

We have also developed a searchable Nuclear Protein Database that contains information on protein structure, function and sub-cellular localisation for >2500 mammalian proteins.