Tuesday, July 22, 2014

Measuring Epigenetic Changes in Individual Cells

There is so much DNA within a cell's genome that it has to be folded and packaged within the cell's nucleus, with the help of various proteins.  When it comes time to express genes, the DNA can be remodeled around the "helper" proteins, or small tags can be added - like a methyl or acetyl group.  This gives the transcription proteins easier or harder access to certain genes, thereby affecting which genes are expressed and which are not (technical term: epigenetics).  Your genome still contains all of its original genes, but doesn't always express them.  The pattern of methylation can also be passed on to offspring.  Typically, the measure of epigenetic modifications within a genome is measured using many cells whose DNA is pooled, but researchers from the UK have developed a new method for investigating these effects on development.  This technique is powerful enough to measure the epigenetic changes within the genome of a single cell.  This method has the potential to increase our understanding of embryonic development, and to enhance cancer, gene, and fertility therapies.  It could also reduce the use of animals in gene and cancer research.

This new technique started with the principle of bisulfite sequencing, which is often used in measuring levels of DNA methylation.  Bisulfite sequencing involves a bisulfite treatment on pre-acquired and fragmented DNA, which replaces the cytosines with uracils, but leaves methylated cytosines alone.  The remaining methylated cytosines are analyzed using a high-throughput sequencing machine.  The authors changed up the bisulfite sequencing method by isolating and breaking up individual cells, then applying the bisulfite treatment to the DNA, rather than fragmenting the DNA first.  This reduced DNA loss, and the bisulfite treatment ended up fragmenting the DNA itself, saving a step in the procedure.

To test their technique, the researchers used egg cells in metaphase and mouse embryonic stem cells.  They found that single-cell bisulfite sequencing (scBS-seq) was more efficient in detecting sites where methylation varied more than the genome average, including those sites where methylation varies from one cell to another.  Data from multiple single-cell analyses can also be integrated to simulated looking at the whole organism.  Dr. Gavin Kelsey, the principle investigator of this study, is confident that this method will facilitate the study of epigenetic changes that control embryonic development.  He suggests that this method could also be used to analyze individual cancer cells, providing options for tailored cancer treatments.

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