The chromatin structure of eukaryotic telomeres plays an essential role in

The chromatin structure of eukaryotic telomeres plays an essential role in telomere functions. exhibit high levels of H3K27Me3, a repressive mark that associates with many euchromatic genes. The epigenetic profile of Arabidopsis telomeres is usually closely related to the previously defined chromatin state 2. This chromatin state is found in 23% of Arabidopsis genes, many of which are repressed or lowly expressed. At least, in part, this scenario is similar in rice. INTRODUCTION Telomeres prevent chromosome fusions and degradation by exonucleases and are implicated in DNA repair, homologous recombination, chromosome pairing and segregation. Telomeric DNA usually contains tandem repeats of a buy CHIR-98014 short GC-rich motif, which can also be found at interstitial chromosomal loci (1C5). These interstitial telomeric sequences (ITSs) have a widespread distribution in different model systems, including Arabidopsis, and have been related to chromosomal aberrations, fragile sites, warm spots for recombination and diseases caused by genomic instability, although their functions remain unknown (5C8). Two major chromatin businesses can be found inside the cell nucleus: heterochromatin and euchromatin. Heterochromatic regions are highly condensed in interphase nuclei giving rise to buy CHIR-98014 the so-called chromocenters and usually associate with repetitive and silent DNA, although certain level of transcription is required for their establishment and maintenance. By contrast, euchromatic regions have an open conformation and are often related to the capacity to be transcribed. Both kinds of chromatin businesses exhibit defined epigenetic modifications that influence their biochemical behavior. In Arabidopsis, chromocenters contain pericentromeric heterochromatin, which associates with the 178-bp satellite buy CHIR-98014 repeats (also known as 180-bp repeats) and with other repetitive DNA sequences including mobile elements and ITSs (9C15). Capn1 Arabidopsis heterochromatin is usually characterized by high levels of cytosine methylation, which can be targeted at CpG, CpNpG or CpNpN residues (where N is usually any nucleotide), and by H3K9Me1,2, H3K27Me1,2 and H4K20Me1. In turn, Arabidopsis euchromatin is usually characterized by H3K4Me1,2,3, H3K36Me1,2,3, H4K20Me2,3 and by histones acetylation (16). In addition, many genes that localize in Arabidopsis euchromatin are labeled with H3K27Me3, a repressive mark that is thought to regulate tissue-specific gene expression (17C19). The analysis of telomeric chromatin structure from ChIP, ChIP-on-chip or ChIP-seq experiments might be challenged by the presence of ITSs (20). This problem might also be extensive to other repetitive sequences. Here, we have developed an approach to study the epigenetic modifications of Arabidopsis telomeres independently of ITSs by analyzing genome-wide ChIP-seq data. The ChIP-seq experiments revealed that Arabidopsis telomeres have higher density of histone H3 than centromeres. These experiments also revealed that Arabidopsis telomeres have lower levels of heterochromatic marks than centromeres (H3K9Me2 and H3K27Me), higher levels of some euchromatic marks (H3K4Me2 and H3K9Ac) and comparable or lower levels of other euchromatic marks (H3K4Me3, H3K36Me2, H3K36Me3 and H3K18Ac). Interestingly, the ChIP-seq data also revealed that Arabidopsis telomeres exhibit higher levels of H3K27Me3 than centromeres. At least, in part, this scenario is buy CHIR-98014 similar in rice. MATERIALS AND METHODS Determination of the relative amounts of (CCCTAAA)4 sequences at telomeres and ITSs To analyze the chromatin structure of Arabidopsis telomeres using genome-wide ChIP-seq experiments, we had to define a specific DNA sequence that revealed telomeres but not ITSs. For that purpose, we estimated the number of times that this sequence (CCCTAAA)4 appears at internal chromosomal loci and at telomeres in the (Col-0) genome. First, we performed Blast analyses at the Map Viewer web site in National Center for Biotechnology Information (NCBI) to determine the number of times that the sequence (CCCTAAA)4 appears at internal chromosomal loci (