Chapter 12, Problem 21P

In an experiment published in the journal Cell in 2014, Amnon Koren and Steven McCarroll isolated two populations of growing tissue culture cells from each of two unrelated people from different parts of the world.

One population from each person consisted of millions of cells that were in G of the cell cycle; the other population was a similar number of cells that were in S phase for various amounts of time. The scientists then performed high-throughput DNA sequencing on these cell populations.

The two graphs that follow show the data for the two individuals. In each graph, the x-axis represents positions along a chromosome (here, chromosome 8), and the y-axis represents the ratio between the number of reads obtained for a given region of the genome from the S phase sample divided by the number of reads obtained for the same region from the G sample. Each small purple dot is 2 kb along the chromosome; the black line is the moving average of the purple.

a.	At chromosomal coordinate 33 Mb, the y-axis value is much higher than at coordinate 35 Mb. What does this fact tell you about the timing of DNA replication at these two locations?
b.	Scientists still do not have a good idea about the nature of DNA sequences or chromatin structures that define origins of replication in human cells. If you were trying to locate such origins of replication, where would you look?
c.	Suppose you did a similar experiment using two populations with the same number of cells, one population in G and the other in G . If you graphed the data in a similar fashion, with the y-axis representing the ratio of the number of reads from the G sample divided by the number of reads from the G sample, what would the plot look like?
d.	The patterns for these two people are very nearly the same, even though they are completely unrelated. What does this fact suggest?
e.	These scientists later reasoned that they could obtain the same kind of information from any person whose genome had been sequenced by high-throughput methods, without separating out populations of cells at different cell cycle stages. What would have to be true about the cells analyzed and the kinds of data available? Why would you want to look at this data from many different people?