Epigenetics
Figure 4 Regions of transcriptionally
active euchromatin (blue bar) and inactive heterochromatin (red bar) are indicated below the schematic of the locus. Shown graphically at the bottom of the figure, histone
H3 lysine 4 methylation (blue) and H3 lysine 9 methylation (red) are associated with
discrete regions of this locus, as determined by chromatin
immunoprecipitation. Lysine 4 methylation is limited to the
active regions of euchromatin, whereas high levels of lysine 9 methylation are detected only in transcriptionally silent heterochromatin. Figure
courtesy of Shiv Grewal, NCI
that allows cells to package their DNA, provides scaffolding for cell division and enables control of gene expression. The fundamental unit of chro- matin is the nucleosome, in which DNA wraps around an octamer of four core histone proteins, two molecules each of histone H2A, H2B, H3 and H4 (Figure 2). Histone H1 associates with chro- matin outside the nucleosome and regulates chro- matin structure. Histones are subject to a variety of post-translational modifications, including acetyla- tion of lysine, methylation of arginine and lysine, phosphorylation of serine, ubiquitinylation of lysine, and citrullination of arginine (Figure 3). Histone modifications, which occur primarily with- in the amino-terminal tails, are highly correlated with active DNA processes, including transcription, repair, and replication and it is becoming increas- ingly clear that these modifications represent regu- latory events that govern the accessibility and func- tion of the genome. In S. pombe, for example, lysine 4 methylation is limited to the transcriptionally active regions of euchromatin (lightly packed form of chromatin), whereas high levels of lysine 9 methylation are detected only in transcriptionally silent heterochromatin (Figure 4). The mechanism of maintaining chromatin modifications during cell division is not well understood.
There are two proposed mechanisms by which histone modifications are believed to mediate tran- scriptional activity12. The first mechanism propos- es that these modifications alter the electrostatic charge of the histone, affecting the affinity between the histone and DNA. For example, histone acety- lation relaxes the chromatin, allowing easier access for RNA polymerase and transcription factors. The second mechanism proposes that these modifi- cations create protein binding sites, such as bro- modomains and chromodomains, which recruit other proteins that recognise acetylated and methy- lated lysines, respectively, and these recruited pro- teins then promote transcription.
30
In addition to post-translational modifications, each histone protein (except H4) has a range of vari- ants that differ in their amino acid sequence mainly in the N-terminal region. These variants are typical- ly expressed at very low levels and are believed to provide novel structural and functional properties of the nucleosome. Although the exact role of these variants remains unclear, it is believed that their presence contributes to epigenetic memory. Studies in models of Huntington Disease (HD) have shown that mutant Huntington affects his- tone acetyltransferase activity, suggesting that aberrant epigenetic activity may play a role in the development of this disease13. Furthermore, stud- ies are showing a potential therapeutic role for his- tone deacetylase inhibitors in HD14. Further advances are being made in our understanding of the role of chromatin modification in disease through the use of various tools and technologies that provide a powerful means to explore these markers, including genome-wide profiling of DNA-protein interactions by chromatin immuno- precipitation (ChIP) coupled with high throughput sequencing (ChIP-Seq) (Figure 5) and histone mod- ification-specific antibodies. ChIP is proving to be a powerful technique for studying protein-DNA complexes and analysing histone modifications. Antibodies specific to the modification under study enrich for regions of chromatin that contain the modification, which is then detected using quanti- tative PCR or microarray technology.
Non-coding RNA
Eukaryotic genomes transcribe up to 90% of their genomic DNA, however, only 1-2% of these tran- scripts encode for proteins. The vast majority is therefore transcribed as non-coding RNAs (ncRNAs) which display tissue-specific expression patterns and sub-cellular locations. On an evolu- tionary scale, the amount of non-coding RNA markedly increases along with the complexity of
Drug Discovery World Fall 2011
Page 1 |
Page 2 |
Page 3 |
Page 4 |
Page 5 |
Page 6 |
Page 7 |
Page 8 |
Page 9 |
Page 10 |
Page 11 |
Page 12 |
Page 13 |
Page 14 |
Page 15 |
Page 16 |
Page 17 |
Page 18 |
Page 19 |
Page 20 |
Page 21 |
Page 22 |
Page 23 |
Page 24 |
Page 25 |
Page 26 |
Page 27 |
Page 28 |
Page 29 |
Page 30 |
Page 31 |
Page 32 |
Page 33 |
Page 34 |
Page 35 |
Page 36 |
Page 37 |
Page 38 |
Page 39 |
Page 40 |
Page 41 |
Page 42 |
Page 43 |
Page 44 |
Page 45 |
Page 46 |
Page 47 |
Page 48 |
Page 49 |
Page 50 |
Page 51 |
Page 52 |
Page 53 |
Page 54 |
Page 55 |
Page 56 |
Page 57 |
Page 58 |
Page 59 |
Page 60 |
Page 61 |
Page 62 |
Page 63 |
Page 64 |
Page 65 |
Page 66 |
Page 67 |
Page 68 |
Page 69 |
Page 70 |
Page 71 |
Page 72 |
Page 73 |
Page 74 |
Page 75 |
Page 76 |
Page 77 |
Page 78 |
Page 79 |
Page 80 |
Page 81 |
Page 82 |
Page 83 |
Page 84 |
Page 85 |
Page 86 |
Page 87 |
Page 88 |
Page 89 |
Page 90 |
Page 91 |
Page 92