Chromatin Structure and Human Genome Evolution

Colin AM Semple, MRC Human Genetics Unit, Edinburgh, UK

Published online: May 2008

DOI: 10.1002/9780470015902.a0020999

Functional and comparative genomics have provided data on the evolution and function of the human genome, but we still know relatively little about its spatial organization. What is the three-dimensional structure of the genome? How and when does this structure vary? It has long been suspected that the structural organization of the genome might impose constraints on its evolution. Recent genome-wide data on chromatin structure have revealed the complex physical landscape of the human genome, and have yielded unexpected insights into the evolution of chromosome architecture, gene order and patterns of mutation and selection.

Keywords: evolution; chromatin structure; human; epigenetics

Figure 1. Increased mutation rates in closed chromatin at non-CpG sites. (a+b) Mean intergenic and ancient repeat divergence observed across chromatin categories (Intergenic r2:=0.87, p=9.1e-05; Intergenic repeats only r2:=0.93, p=7.3e-06; Ancient repeats only r2:=0.93, p=6.1e-06). (c) Intergenic divergence of each 1 Mb clone from chromosome 1 against their corresponding chromatin score (10 clones containing less than 10 000 intergenic bases were excluded). (d) Mean human SNP densities (SNPs/bp) observed across chromatin categories (All SNPs r2:=0.89, p=0.016; randomly assayed TSCM0019 SNPs only r2:=0.93, p=0.008). Reproduced from Prendergast et al. (2007).
Figure 2. Human–mouse divergence across chromatin categories. Mean dN (a), dN/dS (b) and dS (c) in human/mouse coding sequence alignments. (All protein coding genes dS r2:=0.99, p=0.001; dN r2:=0.92, p=0.01; dN/dS r2:=0.92, p=0.009. Genes associated with a CpG island dS r2:=0.72, p=0.07; dN r2:=0.17, p=0.5; dN/dS r2:=0.64, p=0.1. Genes not associated with a CpG island only dS r2:=0.84, p=0.03; dN r2:=0.95, p=0.005; dN/dS r2:=0.92, p=0.01). Reproduced from Prendergast et al. (2007).
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 Further Reading
    Bernstein BE, Meissner A and Lander ES (2007) The mammalian epigenome. Cell 128: 669–681.
    Fraser P and Bickmore W (2007) Nuclear organization of the genome and the potential for gene regulation. Nature 447: 413–417.
    Misteli T (2007) Beyond the sequence: cellular organization of genome function. Cell 128: 787–800.
    Prendergast JG, Campbell H, Gilbert N et al. (2007) Chromatin structure and evolution in the human genome. BMC Evolutionary Biology 7: 72.
    Sproul D, Gilbert N and Bickmore WA (2005) The role of chromatin structure in regulating the expression of clustered genes. Nature Reviews. Genetics 6: 775–781.

Related Sub-Topics:

Nucleic Acid Structure | Evolutionary Genomics | Molecular Evolution | Human Evolution | Chromosomes and Chromatin Modifications | Evolution of Coding and Functional Modules
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Article Title: Chromatin Structure and Human Genome Evolution
 
How to Cite close
Semple, Colin AM(May 2008) Chromatin Structure and Human Genome Evolution. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0020999]