In the past year, we have presented epigenetic insights that are made possible by several new approaches
Hairpin-bisulfite PCR: analyzing DNA methylation on both strands of individual DNA molecules.
With this approach, we can overcome the limitations of single strand PCR and determine methylation patterns on both strands of individual DNA molecules. We have been successful in applying hairpin-bisulfite PCR to both the single copy gene, FMR1, and to repeated L1 (LINE-1) elements.
Please read more about the processing of hairpin-bisulfite PCR data.
For more general information on hairpin-bisulfite PCR see, current lab research in epigenetics.
Barcoding: a method to determine the authenticity of PCR products by molecular barcodes and batch-stamps.
We use molecular barcodes and batch-stamps to label each genomic DNA template with an individual sequence tag prior to PCR amplification. This highly sensitive method identifies redundant and contaminant sequences, a problem often associated with PCR amplification of limited amounts of DNA template.
Modeling: allows us to calculate site-specific rates of maintenance and de novo methylation using our new double-strand DNA methylation data.
To understand how methylated and unmethylated states of cytosine residues are transmitted during DNA replication, a population-epigenetic model of DNA methylation dynamics has been developed.
The figure at right, from Genereux et al., 2005, indicates the transition from a methylated or unmethylated CpG before DNA replication (t-1), to a methylated, hemimethylated, or unmethylated CpG/CpG dyad after DNA replication (t). Probabilites of maintenance methylation ( µ ) and de novo methylation of the parent strand (delta p) or the daughter strand (delta d) determine the transition probabilites.
The Laird Lab has also published Methods in molecular biology, cell biology, and cytogenetics.