Study suggests similar pairings may characterize other genetic interactions
By Melissa Lee Phillips (email@example.com) | January 20, 2006
In this week's Science, Na Xu and her colleagues at Harvard Medical School report that mouse X chromosomes transiently pair with each other during early cell differentiation, revealing a key step in X inactivation, in which only one X remains active in females. The authors suggest that interchromosomal interactions may be a common way of regulating gene expression.
"For monoallelically expressed genes, (pairing) may be a more common thing than we think," said Christine Disteche of the University of Washington in Seattle, who was not involved in the study. "Maybe we haven't looked hard enough."
A stretch of DNA on the mammalian X chromosome called the X-inactivation center (Xic) contains several RNA-coding genes crucial for normal X inactivation, including Xist, its antisense transcript Tsix, and Xite. Tsix and Xite mediate two key processes in the beginning of X inactivation: "counting," in which a cell determines the number of X chromosomes present, and "choice," when the cell chooses which chromosome will remain active and which will be silenced. After this decision, Tsix and Xite regulate Xist, which ensures that genes on the inactive X remain suppressed.
Although only cis interactions have been discovered at the Xic, scientists have felt a trans mechanism must exist, senior author Jeannie Lee told The Scientist, because the two X chromosomes must adopt opposite fates. "When one chromosome is chosen to be the inactive one, the other one has to automatically know it's going to be the active one," Lee said.
Physical pairing between X chromosomes has been hypothesized as a way to allow this trans communication, noted Dietsche, but data were lacking.
Lee and her co-workers imaged X chromosome movement in differentiating mouse embryonic stem cells using fluorescuence in situ hybridization (FISH). Although the X chromosomes began at random positions, most of them moved close together after two to four days of differentiation ? the same time that X inactivation begins. By day six of differentiation, the chromosomes were no longer paired.
When the researchers treated the cells with a variety of probes, they found that only the X-inactivation centers aligned with each other; positions of other regions on the X chromosome were unconstrained.
To confirm that the X-inactivation centers were physically interacting, Lee and her colleagues used a technique called chromosome conformation capture (3C), which allows isolation and analysis of physically touching DNA-bound proteins. The authors consistently detected physical contact between Xic loci, with the strongest interaction on day four of differentiation.
The researchers next conducted genetic deletion studies to determine the genes responsible for these interactions. Studies in mice have shown that counting and/or choice can be disrupted if Tsix or Xite is deleted-- cells often end up with two active or two inactive X chromosomes, which suggests that these deletions lead to loss of trans communication, Lee said. She and her colleagues found that deleting Tsix and Xite impairs X pairing, which they say signifies a tight link between chromosomal cross-talk and counting/choice.
The authors also introduced Tsix or Xite fragments into embryonic stem cells to observe their effects on autosomes. They found that both fragments induced ectopic pairing between X chromosomes and autosomes, further solidifying the two genes' involvement in chromosomal pairing.
Edith Heard of the Curie Institute in Paris is publishing a study extremely similar to Lee's, which will appear online in Nature Cell Biology sometime next week, Heard told The Scientist. Heard and her colleagues also found transient X pairing just prior to X inactivation, but she said that neither paper shows absolute proof that pairing cross-talk is necessary to trigger counting and choice.
"It's clear that mutants that affect those processes also affect cross-talk," she said, "so it's clear that they're linked, but the actual causality I think is not necessarily totally clear."
It also remains possible that interactions between the two X chromosomes are not direct, Heard said. Even with the 3C technique, it's impossible to tell if DNA is directly interacting, she said. "It could be that the X-inactivation centers have to be in the same nuclear compartment?in order for some kind of a process to count them."
Lee's and Heard's studies may have implications outside of X inactivation, according to York Marahrens of the University of California, Los Angeles, who did not participate in either study. For instance, trans interactions at imprinted loci and at autosomal loci that express only one allele may rely on homologous pairing, Marahrens told The Scientist.
"This is going to happen at many epigenetically regulated loci," Lee agreed. "It's going to be a general mechanism of gene regulation."
Melissa Lee Phillips
Links within this article
N. Xu et al., "Transient homologous chromosome pairing marks the onset of X inactivation," Science, January 19, 2006
C. Choi, "XX mouse cell instability explained," The Scientist, October 24, 2005.
S. Pincock, "X sequence published," The Scientist, March 16, 2005.
Y. Marahrens, "X-inactivation by chromosomal pairing events," Genes & Development, October 15, 1999.
J. Dekker et al., "Capturing chromosome conformation," Science, February 15, 2002.
J.T. Lee, "Homozygous Tsix mutant mice reveal a sex-ratio distortion and revert to random X-inactivation," Nature Genetics, September 2002.
Y. Ogawa, J.T. Lee, "Xite, X-inactivation intergenic transcription elements that regulate the probability of choice," Molecular Cell, March 2003.
http://www.curie.fr/recherche/themes/equipe_histoire.cfm/id_equipe/63/lang/_gb.htmNature Cell Biologyhttp://www.nature.com/ncb/
J.M. LaSalle, M. Lalande, "Homologous association of oppositely imprinted chromosomal domains," Science, May 3, 1996.
N. Singh et al., "Coordination of the random asynchronous replication of autosomal loci," Nature Genetics, March 2003.