The Costello Lab at UCSF is another of the four Reference Epigenome Mapping Centers (REMCs, not to be confused with REM although I’m sure Michael Stipe would be very proud of the work going on at the REMCs). According to Dr. Joseph Costello, his lab will be rolling up their sleeves with scientists at UC Davis, UCSC and the British Columbia and producing epigenomic profiles from blood, brain, breast, and human embryonic stem cells.
“Our group is focused on primary human cells which can be isolated without culturing, and which have relevance to complex disease. For example, our initial efforts will focus on three subtypes of Adult Primary Human Breast Cells, including cells from two different ethnic groups. We will also include four different types of human blood cells with relevance to immunity and autoimmunity. We are considering many other primary cell types, depending on how sequencing costs change over time.”
This unique effort will be looking at epigenetic, miRNA, and gene expression profiles in concert. More specifically, the teams will be taking a close look at six histone modifications selected for their ying/yang roles in regulating active and inactive chromatin, DNA methylation patterns, miRNA and gene expression patterns. The data will be pulled together with advanced informatics to get at the fundamental roles of epigenetics in differentiation, maintenance of cell-type identity and gene expression.
Seqing miRNA, DNA Methylation, and Histone Profiles
What methods will the crew use? “Chip-seq, miRNA-seq and RNA-seq. For DNA methylation we will use two or three methods, including bisulfite, MeDIP and methylation-sensitivive restriction enzymes, followed by next-gen sequencing,” according to Costello.
There will, without a doubt, some very interesting data generated with these experiments, but who’s responsible for handling the mounds of data coming out of the labs?
Reference Epigenome Data Management
According to Dr. Costello, “The REMCs will certainly be responsible for some of the data management and analysis, though each REMC works closely with the EDACC, the primary data “center”. Our REMC informatics team is led by Dr. David Haussler and Ting Wang at UCSC, and Dr. Steve Jones at the British Columbia Cancer Agency, Genome Sciences Centre.”