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Pros and cons of methylation-based enrichment methods for ancient DNA.

Seguin-Orlando A, Gamba C, Der Sarkissian C, Ermini L, Louvel G, Boulygina E, Sokolov A, Nedoluzhko A, Lorenzen ED, Lopez P, McDonald HG, Scott E, Tikhonov A, Stafford TW, Alfarhan AH, Alquraishi SA, Al-Rasheid KA, Shapiro B, Willerslev E, Prokhortchouk E, Orlando L - Sci Rep (2015)

Bottom Line: The recent discovery that DNA methylation survives in fossil material provides an opportunity for novel molecular approaches in palaeogenomics.MBD enrichment, however, appears principally biased towards the recovery of CpG-rich and long DNA templates and is limited by the fast post-mortem cytosine deamination rates of methylated epialleles.This work represents an essential step toward the characterization of ancient methylation signatures, which will help understanding the role of epigenetic changes in past environmental and cultural transitions.

View Article: PubMed Central - PubMed

Affiliation: 1] Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark [2] National High-throughput DNA Sequencing Centre, Øster Farimagsgade 2D, 1353K Copenhagen, Denmark.

ABSTRACT
The recent discovery that DNA methylation survives in fossil material provides an opportunity for novel molecular approaches in palaeogenomics. Here, we apply to ancient DNA extracts the probe-independent Methylated Binding Domains (MBD)-based enrichment method, which targets DNA molecules containing methylated CpGs. Using remains of a Palaeo-Eskimo Saqqaq individual, woolly mammoths, polar bears and two equine species, we confirm that DNA methylation survives in a variety of tissues, environmental contexts and over a large temporal range (4,000 to over 45,000 years before present). MBD enrichment, however, appears principally biased towards the recovery of CpG-rich and long DNA templates and is limited by the fast post-mortem cytosine deamination rates of methylated epialleles. This method, thus, appears only appropriate for the analysis of ancient methylomes from very well preserved samples, where both DNA fragmentation and deamination have been limited. This work represents an essential step toward the characterization of ancient methylation signatures, which will help understanding the role of epigenetic changes in past environmental and cultural transitions.

No MeSH data available.


Related in: MedlinePlus

Relative amount of CpGs to TpGs transitions over all other kind of possible C->T mutations in CpN contexts.A minimum threshold of 2,000 reads was applied.
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f4: Relative amount of CpGs to TpGs transitions over all other kind of possible C->T mutations in CpN contexts.A minimum threshold of 2,000 reads was applied.

Mentions: We next evaluated whether cytosine deamination occurs at faster rates when CpG dinucleotides are methylated, as expected from genetic assay based on reversion of mutations in single-stranded28 and double-stranded29 DNA contexts and as previously observed in archeological barley material from Qasr-Ibrim, Egypt22. For this, we used C→T mutation rates to calculate the relative proportion of cytosine deaminations detected at CpG sites and other CpN dinucleotide contexts (MQ25 filter; Fig. 4). We observed that this proportion was up to 8.3-fold higher in endogenous sequences from the MBD+ fractions relative to MBD− fractions (Supplementary Table S3.6), except for two samples showing minimal sequence data (MKm_2 and MZm_1). This adds to the body of empirical evidence supporting faster cytosine deamination rates at methylated epialleles2229. This fast decay of mCpGs also participates to reducing the molecular complexity of MBD+ libraries.


Pros and cons of methylation-based enrichment methods for ancient DNA.

Seguin-Orlando A, Gamba C, Der Sarkissian C, Ermini L, Louvel G, Boulygina E, Sokolov A, Nedoluzhko A, Lorenzen ED, Lopez P, McDonald HG, Scott E, Tikhonov A, Stafford TW, Alfarhan AH, Alquraishi SA, Al-Rasheid KA, Shapiro B, Willerslev E, Prokhortchouk E, Orlando L - Sci Rep (2015)

Relative amount of CpGs to TpGs transitions over all other kind of possible C->T mutations in CpN contexts.A minimum threshold of 2,000 reads was applied.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4488743&req=5

f4: Relative amount of CpGs to TpGs transitions over all other kind of possible C->T mutations in CpN contexts.A minimum threshold of 2,000 reads was applied.
Mentions: We next evaluated whether cytosine deamination occurs at faster rates when CpG dinucleotides are methylated, as expected from genetic assay based on reversion of mutations in single-stranded28 and double-stranded29 DNA contexts and as previously observed in archeological barley material from Qasr-Ibrim, Egypt22. For this, we used C→T mutation rates to calculate the relative proportion of cytosine deaminations detected at CpG sites and other CpN dinucleotide contexts (MQ25 filter; Fig. 4). We observed that this proportion was up to 8.3-fold higher in endogenous sequences from the MBD+ fractions relative to MBD− fractions (Supplementary Table S3.6), except for two samples showing minimal sequence data (MKm_2 and MZm_1). This adds to the body of empirical evidence supporting faster cytosine deamination rates at methylated epialleles2229. This fast decay of mCpGs also participates to reducing the molecular complexity of MBD+ libraries.

Bottom Line: The recent discovery that DNA methylation survives in fossil material provides an opportunity for novel molecular approaches in palaeogenomics.MBD enrichment, however, appears principally biased towards the recovery of CpG-rich and long DNA templates and is limited by the fast post-mortem cytosine deamination rates of methylated epialleles.This work represents an essential step toward the characterization of ancient methylation signatures, which will help understanding the role of epigenetic changes in past environmental and cultural transitions.

View Article: PubMed Central - PubMed

Affiliation: 1] Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark [2] National High-throughput DNA Sequencing Centre, Øster Farimagsgade 2D, 1353K Copenhagen, Denmark.

ABSTRACT
The recent discovery that DNA methylation survives in fossil material provides an opportunity for novel molecular approaches in palaeogenomics. Here, we apply to ancient DNA extracts the probe-independent Methylated Binding Domains (MBD)-based enrichment method, which targets DNA molecules containing methylated CpGs. Using remains of a Palaeo-Eskimo Saqqaq individual, woolly mammoths, polar bears and two equine species, we confirm that DNA methylation survives in a variety of tissues, environmental contexts and over a large temporal range (4,000 to over 45,000 years before present). MBD enrichment, however, appears principally biased towards the recovery of CpG-rich and long DNA templates and is limited by the fast post-mortem cytosine deamination rates of methylated epialleles. This method, thus, appears only appropriate for the analysis of ancient methylomes from very well preserved samples, where both DNA fragmentation and deamination have been limited. This work represents an essential step toward the characterization of ancient methylation signatures, which will help understanding the role of epigenetic changes in past environmental and cultural transitions.

No MeSH data available.


Related in: MedlinePlus