Analysis of the epigenetic status of telomeres by using ChIP-seq data

Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, IBVF (CSIC-USE), c/ Américo Vespucio n° 49, 41092 Seville, Spain and Department of Plant Biology and Pathology, Rutgers University, New Brunswick, NJ, USA.
Nucleic Acids Research (Impact Factor: 9.11). 08/2012; 40(21). DOI: 10.1093/nar/gks730
Source: PubMed


The chromatin structure of eukaryotic telomeres plays an essential role in telomere functions. However, their study might be impaired by the presence of interstitial telomeric sequences (ITSs), which have a widespread distribution in different model systems. We have developed a simple approach to study the chromatin structure of Arabidopsis telomeres independently of ITSs by analyzing ChIP-seq data. This approach could be used to study the chromatin structure of telomeres in some other eukaryotes. The analysis of ChIP-seq experiments revealed that Arabidopsis telomeres have higher density of histone H3 than centromeres, which might reflects their short nucleosomal organization. These experiments also revealed that Arabidopsis telomeres have lower levels of heterochromatic marks than centromeres (H3K9(Me2) and H3K27(Me)), higher levels of some euchromatic marks (H3K4(Me2) and H3K9Ac) and similar or lower levels of other euchromatic marks (H3K4(Me3), H3K36(Me2), H3K36(Me3) and H3K18Ac). Interestingly, the ChIP-seq experiments also revealed that Arabidopsis telomeres exhibit high levels of H3K27(Me3), a repressive mark that associates with many euchromatic genes. The epigenetic profile of Arabidopsis telomeres is 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.

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Available from: Miguel A Vega-Palas, Feb 13, 2015
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    • "Therefore, these primer dimers are not expected to amplify themselves. Primers TelA and TelB were designed with more than 4 degenerated telomeric repeats because we have previously found that the sequence (CCCTAAA)4 is fundamentally present at Arabidopsis telomeres (in 98% of the cases), whereas it is very infrequent at ITSs (only in 2% of the cases)24. Therefore, primers TelA and TelB should amplify telomeres more efficiently than perfect ITSs. "
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    ABSTRACT: In humans, telomere length studies have acquired great relevance because the length of telomeres has been related to natural processes like disease, aging and cancer. However, very little is known about the influence of telomere length on the biology of wild type plants. The length of plant telomeres has been usually studied by Terminal Restriction Fragment (TRF) analyses. This technique requires high amounts of tissue, including multiple cell types, which might be the reason why very little is known about the influence of telomere length on plant natural processes. In contrast, many of the human telomere length studies have focused on homogenous cell populations. Most of these studies have been performed by PCR, using telomeric degenerated primers, which allow the determination of telomere length from small amounts of human cells. Here, we have adapted the human PCR procedure to analyze the length of Arabidopsis thaliana telomeres. This PCR approach will facilitate the analysis of telomere length from low amounts of tissue. We have used it to determine that CG and non CG DNA methylation positively regulates Arabidopsis telomere length.
    Scientific Reports 07/2014; 4:5540. DOI:10.1038/srep05540 · 5.58 Impact Factor
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    • "Although telomeres were originally thought to consist of heterochromatin, a recent molecular analysis of epigenetic marks in A. thaliana telomeres revealed that telomeric chromatin has some unexpected and unique features that are characteristic of intermediate heterochromatin [Vrbsky et al., 2010] or even euchromatin [Vaquero-Sedas and Vega-Palas, 2013]. Indeed, Arabidopsis telomeres are enriched in H3K9me2 and H3K27me1 heterochromatic marks but still retain the euchromatic H3K4me3 mark [Vrbsky et al., 2010; Vaquero-Sedas et al., 2012]. Furthermore, the A. thaliana telomeres are also relatively enriched in the H3.3 histone variant (which is usually associated with transcriptionally active regions) in comparison to centromeres that are enriched in H3.1 in comparison to telomeres [Vaquero-Sedas and Vega-Palas, 2013]. "
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    ABSTRACT: The interphase cell nucleus is extraordinarily complex, ordered, and dynamic. In the last decade, remarkable progress has been made in deciphering the functional organisation of the cell nucleus, and intricate relationships between genome functions (transcription, DNA repair, or replication) and various nuclear compartments have been revealed. In this review, we describe the architecture of the Arabidopsis thaliana interphase cell nucleus and discuss the dynamic nature of its organisation. We underline the need for further developments in quantitative and modelling approaches to nuclear organization. © 2014 S. Karger AG, Basel.
    Cytogenetic and Genome Research 06/2014; 143(1-3). DOI:10.1159/000363724 · 1.56 Impact Factor
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    • "However, this is not the case in all organisms. Studies in A. thaliana by ChIP-seq, recently revealed histone marks that more closely resemble those found on repressed or lowly expressed euchromatic genes (Vaquero-Sedas et al., 2011, 2012). With the same technique, the most significant modifications found in the telomeres of human CD4+ T cells were H2BK36me1 and H3K4me3 (more euchromatic) while H3K9me3 and H4K36me3 marks (more heterochromatic) were less represented (Rosenfeld et al., 2009). "
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    ABSTRACT: A major issue in telomere research is to understand how the integrity of chromosome ends is controlled. The fact that different types of nucleoprotein complexes have been described at the telomeres of different organisms raises the question of whether they have in common a structural identity that explains their role in chromosome protection. We will review here how telomeric nucleoprotein complexes are structured, comparing different organisms and trying to link these structures to telomere biology. It emerges that telomeres are formed by a complex and specific network of interactions between DNA, RNA, and proteins. The fact that these interactions and associated activities are reinforcing each other might help to guarantee the robustness of telomeric functions across the cell cycle and in the event of cellular perturbations. We will also discuss the recent notion that telomeres have evolved specific systems to overcome the DNA topological stress generated during their replication and transcription. This will lead to revisit the way we envisage the functioning of telomeric complexes since the regulation of topology is central to DNA stability, replication, recombination, and transcription as well as to chromosome higher-order organization.
    Frontiers in Oncology 03/2013; 3:48. DOI:10.3389/fonc.2013.00048
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