A microscopic analysis of Arabidopsis chromatin

A microscopic analysis of Arabidopsis chromatin General Introduction 8 Nuclear DNA of eukaryotic organisms is associated with several proteins, which together fo rm chromatin. The most abundant chromatin proteins are histones. In all eukaryotes DNA is folded around a core of histones (H) by which the so-called nucleosomes are formed. (Kornberg 1974); 146 base pairs of DNA are wrapped around an octamer cont aining two copies of each of the four core histones. During replication DNA is fi rst wrapped around H3-H4 tetram ers before two H2A-H2B dimers assemble into the nucleosome complex (Ridgway and G. 2000). These nucleosomes are positioned every 200bp on a DNA strand, and can be linked together by H1. H1 and other proteins are believed to stabilize this 10 nm fib er and other more compact nucleosome structures involved in the higher order organization of the nucleus. Chromatin is roughly divided in heterochromatin and euchromatin. Euchromatin is less compact ed and gene rich, whereas heterochrom atin is more compact and mainly consists of repetitive DNA (Heitz 1928; Fransz et al. 2003). In many organisms heteroch romatic DNA is hypermethylated and this is used as an additional mechanism to regulate transcription (Finnegan and Kovac 2000). Between 5% and 40% of the cytosines in an organism can be modi fied into 5-methylcytosine by DNA-methyltrans ferases, either after DNA replication during maintenance o f methylation, or through de novo mehylation at speci fic sites. Three classes of cytosine modi fications can be distinguished, CpG, CpNpG, and asymmetric Cytosine methylation respectively. Besides DNA also histones can be cov alently modi fied, by fo r ex ample acetylation, phosphorylation, methylation, and ubiquitination, and this provides signals to which other factors can bind and additionally alters the biochemical properties of chromatin (i.e., 'histone code' (Jenuwein and Allis 2001; Berger 2002; Turner 2002)). In general acetylation o f histones is correlated with active g enes, wh ereas methylation o f histones at different positions result in different effects; methylation of lysine 9 of H3 (H3K9) is associated with heterochromatin formation while H3K4 m ethylation is related to gene activation and positioned in euchromatin (Rice and Allis 2001). In recent years the number of modi fications, both positional as well as structural, that have been identi fied on histones has increas ed. Over 50 di fferent amino acids in the histones (mainly in the histone tails) have the potential to be modified in …