Monthly Archives: March 2012

The spatial arrangement of chromatin matters – now that is a deep insight!

Pardon the awful title. The objective of this post is to discuss how there are distinctive patterns to the arrangement of chromosomes in three dimensional space and how this may be of significance in gene function. Now, while there are extremely organised-looking chromosomes in mitosis, the chromatin (DNA wrapped around nucleosomes) in the interphase nucleus looks very different; messy, tangled up, disorganised…like a ball of wool after a kitten’s played with it and an irate owner has tried to wind it all up back into a ball (vaguely). The question is if there is a definite structure to interphase chromatin as well.

Chromatin is postulated to contain DNA wrapped around nucleosomes, which are octamers made of two units each of Histones H2A, H2B, H3 and H4l, which themselves fold into and form loops and fibers that eventually show up as the distinct, organised chromosomes seen during mitosis. Now the architecture of loops does matter; in a previous post, I discussed how histone modification and condensation may lock genes into a conformation where transcription is not possible, furthermore, there is evidence from work that used Chromosome Conformation Capture to show that loop formation mediated by transcription factors such as gata1 is associated with transcriptional activation. (See here for a reference).

A map of the nucleus, for your journey through this post.

Already, one begins to see how the conformation of chromatin may play a role in gene expression. Another question surrounding the organisation of chromatin involves its distribution in the nucleus; some people proposed an equilibrium model where everything was pretty much tangled up, and others proposed a fractal globule model where physical constraints prevented one chain from crossing another.

Recently, Erez Lieberman-Aiden and coworkers went some way towards figuring out which model was a better description; They used a method called Hi-C, which combined elements of chromosome conformation capture with massively parallel sequencing and their results confirmed the proximity of gene clusters (previously known) and chromosome territories (which I’ll describe in a bit) and most importantly, they deduced the probability of two of the sequenced genomic regions being in contact as predicted by both models and found that the fractal globule model’s predictions closely fitted observed data.

Hi-C reveals DNA organisation consistent with a fractal globule.

You can savour reading the full paper here http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2858594/?tool=pubmed.

Now, onto chromosome territories, which are the areas that chromosomes consistently occupy in the nucleus for given tissue types. Generally speaking, observed patterns include the relegation of gene poor chromosomes to the periphery while gene rich chromosomes are situated towards the center. Even more remarkable is the fact that homologous chromosomes also occupy distinct territories.

Mid-plane light optical section through a chicken fibroblast nucleus shows mutually exclusive chromosome territories (CTs) with homologous chromosomes seen in separate locations. (Note that only one of the two CTs for each of 4 and 6 is displayed in this section.)

Three-dimensional reconstructions of chromosome 18 (red; gene-poor) and 19 (green; gene-rich) territories painted in the nucleus of a non-stimulated human lymphocyte. (Image courtesy of Marion Cremer and Irina Solovei.) Chromosome 18 territories were typically found at the nuclear periphery, whereas chromosome 19 territories were located in the nuclear interior42. a | X,Y view: a mid-plane section of the nucleus is shown as a grey shade. Only the parts of the territories below this section can be seen. b | X,Z view: the arrow marks the side from which the section in part a is viewed.

This is quite interesting because the spatial arrangement of chromosomes also happens to be conserved across evolutionarily related species. (See here for a reference) and this implies there may be a functional reason for conservation of general spatial architecture; the authors note that chromosomal locations of isochores (gene rich clusters) appear to be conserved despite differences in karyotype (chromosomal numbers) in a radial fashion.

Evolutionary conservation of chromosome territories.

Chromosome territories do tend to have strong phenotypic consequences in terms of gene expression, too. Silent genes have been known to be situated in the nuclear periphery ( See http://cshperspectives.cshlp.org/content/2/6/a000588.full ) and the misexpression of genes has consequently been associated in certain disease models with altered chromosome territories, brought about by mutant Lamin proteins, which are thought to govern chromosomal location of genes (Reference here).

Questions still remain; how does chromosomal location vary with changes in methylation? Can chromosomal location be used as a diagnostic tool for aberrantly expressed genes? What defines where particular chromosomes go? What is the nature of gene expression in terms of its spatial orientation? Can spatial location conversely mark out which genes are subjected to epigenetic silencing? The possibilities are immense and exciting.

Additional Recommended Reading

[ 1 ] A Scitable article on Chromosome Territories.
[ 2 ] Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions, Nature Reviews Genetics.
[ 3 ] Another seminal paper on Chromosome territories, again by the Cremers.

That’s all from me this time round.

Cheers,
Ankur.