This is a preprint, a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Method Article
Integrating telomeres into genome-wide ChIP-seq analyses
Miguel Vega-Palas
Instituto de Bioquímica Vegetal y Fotosíntesis (CSIC - U. of Seville), Avda. Américo Vespucio nº 49, 41092 Seville, Spain
Corresponding Author
License:
This work is licensed under a CC BY-NC 3.0 License. Read Full License
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.
Keywords
telomeres, epigenetics, chromatin, ChIP-seq, genome-wide analyses
Figure 1
Figure 2
Figure 3
This is a list of supplementary files associated with this preprint. Click to download.
- supplement0.doc
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
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
History
CURRENT STATUS: Posted
Version 1
Posted 08 Apr, 2013
No community comments so far
Metrics
Comments: 0
HTML Views: ...
Associated Publications
Analysis of the epigenetic status of telomeres by using ChIP-seq data
by M. I. Vaquero-Sedas, C. Luo, and M. A. Vega-Palas
Nucleic Acids Research (02 April, 2013)
Differential association of Arabidopsis telomeres and centromeres with Histone H3 variants
by María I. Vaquero-Sedas and Miguel A. Vega-Palas
Scientific Reports (02 April, 2013)
Learn more about our company.
This is a preprint. It has not completed peer review.
Method Article
Integrating telomeres into genome-wide ChIP-seq analyses
Miguel Vega-Palas
Instituto de Bioquímica Vegetal y Fotosíntesis (CSIC - U. of Seville), Avda. Américo Vespucio nº 49, 41092 Seville, Spain
Corresponding Author
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
History
CURRENT STATUS: Posted
Version 1
Posted 08 Apr, 2013
No community comments so far
Metrics
Comments: 0
HTML Views: ...
License:
This work is licensed under a CC BY-NC 3.0 License. Read Full License
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
Associated Publications
Analysis of the epigenetic status of telomeres by using ChIP-seq data
by M. I. Vaquero-Sedas, C. Luo, and M. A. Vega-Palas
Nucleic Acids Research (02 April, 2013)
Differential association of Arabidopsis telomeres and centromeres with Histone H3 variants
by María I. Vaquero-Sedas and Miguel A. Vega-Palas
Scientific Reports (02 April, 2013)