Science and Reason: Embryonic stem cell differentiaton

A typical mammal, like a human, has over 200 different cell types in its body, corresponding to tissue types such as liver, heart, brain, muscle, etc. Obviously, for each specialized type of cell to perform its function, rather different sets of genes have to be expressed. Yet the DNA of each cell type contains all the genes, whether they're needed or not. One may reasonably wonder what kind of mechanisms are used to keep unneeded (and unwanted) genes "out of the way" in fully differentiated cells.

Further, a multipotent stem cell, and especially a pluripotent stem cell, might be expected to manage its supply of genes somewhat differently than does a fully differentiated cell. If it does, the question of how is especially interesting with respect to "induced pluripotent stem cells" that are obtained by a relatively, and surprisingly, simple "reprogramming" of fully differentiated cells such as skin cells.

Some new research has begun to address these questions:

Unlocking Stem Cell, DNA Secrets To Speed Therapies (10/10/08)

In a groundbreaking study led by a molecular biologist at Florida State University, researchers have discovered that as embryonic stem cells turn into different cell types, there are dramatic corresponding changes to the order in which DNA is replicated and reorganized.

The findings bridge a critical knowledge gap for stem cell biologists, enabling them to better understand the enormously complex process by which DNA is repackaged during differentiation -- when embryonic stem cells, jacks of all cellular trades, lose their anything-goes attitude and become masters of specialized functions. ...

"Understanding how replication works during embryonic stem cell differentiation gives us a molecular handle on how information is packaged in different types of cells in manners characteristic to each cell type," said David M. Gilbert, the study's principal investigator. "That handle will help us reverse the process in order to engineer different types of cells for use in disease therapies."

"We know that all the information (DNA) required to take on the identity of any tissue type is present in every cell.... We must learn how cells lose pluripotency in the first place so we can do a better job of reversing the process without risks to patients.

"The challenge is, adult cells are highly specialized and over the course of their family history over many generations they've made decisions to be certain cell types rather than others," he said. "In doing so, they have tucked away the information they no longer need on how to become other cell types. Hence, all cells contain the same genetic information in their DNA, but during differentiation they package it with proteins into 'chromatin' in characteristic ways that define each cell type. The rules that determine how cells package DNA are complicated and have been difficult for scientists to decipher."

But, Gilbert noted, one time that the cell "shows its cards" is during DNA replication.

"During this process, which was the focus of our FSU research, it's not just the DNA that replicates," he said. "All the packaging must be replicated as well in each cell division cycle."

He explained that embryonic stem cells have many more, smaller "domains" of organization than differentiated cells, and it is during differentiation that they consolidate information.

"In fact, 'domain consolidation' is what we call the novel concept we discovered," he said.

The open access paper is available here:

Global Reorganization of Replication Domains During Embryonic Stem Cell Differentiation

Author Summary

Microscopy studies have suggested that chromosomal DNA is composed of multiple, megabase-sized segments, each replicated at different times during S-phase of the cell cycle. However, a molecular definition of these coordinately replicated sequences and the stability of the boundaries between them has not been established. We constructed genome-wide replication-timing maps in mouse embryonic stem cells, identifying multimegabase coordinately replicated chromosome segments—“replication domains”—separated by remarkably distinct temporal boundaries. These domain boundaries were shared between several unrelated embryonic stem cell lines, including somatic cells reprogrammed to pluripotency (so-called induced pluripotent stem cells). However, upon differentiation to neural precursor cells, domains encompassing approximately 20% of the genome changed their replication timing, temporally consolidating into fewer, larger replication domains that were conserved between different neural precursor cell lines. Domains that changed replication timing showed a unique sequence composition, a strongly biased directionality for changes in resident gene expression, and altered radial positioning within the three-dimensional space in the cell nucleus, suggesting that changes in replication timing are related to the reorganization of higher-order chromosome structure and function during differentiation. Moreover, the property of smaller discordantly replicating domains may define a novel characteristic of pluripotency.