Integrating telomeres into genome-wide ChIP-seq analyses
Telomeric chromatin organization studies using Chromatin Immunoprecipitation (ChIP) might be challenged by the presence of Interstitial Telomeric Sequences (ITSs). In this protocol we describe a method to study the chromatin structure of telomeres independently of ITSs by analyzing ChIP-seq data. This method has been used successfully in Arabidopsis thaliana and could be applied to other model systems including humans. It could greatly speed the knowledge of telomeres biology and their influence in aging, illness or cancer. The method requires that the mean telomeric lengths of the biological sources to be studied are known as well as the built DNA sequence of their chromosomes. First, the numbers of sequences with four or more perfect tandem telomeric repeats are determined in silico at ITSs. These numbers are normalized to the corresponding numbers of sequences of the same type present at telomeres. Those sequences for which the ITSs/telomeres ratios are lower than 2% can be selected to analyze telomeres in ChIP-seq experiments. The ChIP-seq experiments to be studied should be suitable for telomeric chromatin structure analyses and render reads longer than the telomeric sequences selected. Finally, the levels of telomeric enrichments are determined and represented together with the values corresponding to the rest of the genome. This is the first protocol described to integrate telomeres independently of ITSs into genome-wide studies of chromatin organization.
Figure 1
Figure 2
Figure 3
This is a list of supplementary files associated with this preprint. Click to download.
Table 1 as a Word file Determination of the number of tandem telomeric repeats that could be used to analyze telomeric chromatin structure in different organisms
Posted 08 Apr, 2013
Integrating telomeres into genome-wide ChIP-seq analyses
Posted 08 Apr, 2013
Telomeric chromatin organization studies using Chromatin Immunoprecipitation (ChIP) might be challenged by the presence of Interstitial Telomeric Sequences (ITSs). In this protocol we describe a method to study the chromatin structure of telomeres independently of ITSs by analyzing ChIP-seq data. This method has been used successfully in Arabidopsis thaliana and could be applied to other model systems including humans. It could greatly speed the knowledge of telomeres biology and their influence in aging, illness or cancer. The method requires that the mean telomeric lengths of the biological sources to be studied are known as well as the built DNA sequence of their chromosomes. First, the numbers of sequences with four or more perfect tandem telomeric repeats are determined in silico at ITSs. These numbers are normalized to the corresponding numbers of sequences of the same type present at telomeres. Those sequences for which the ITSs/telomeres ratios are lower than 2% can be selected to analyze telomeres in ChIP-seq experiments. The ChIP-seq experiments to be studied should be suitable for telomeric chromatin structure analyses and render reads longer than the telomeric sequences selected. Finally, the levels of telomeric enrichments are determined and represented together with the values corresponding to the rest of the genome. This is the first protocol described to integrate telomeres independently of ITSs into genome-wide studies of chromatin organization.
Figure 1
Figure 2
Figure 3
© Research Square 2021