Centromere inactivation is Y fusion chromosomes aren’t lost

Science Spotlight

Centromere inactivation is Y fusion chromosomes aren’t lost

Oct. 17, 2016

Schematic of the fusion of chromosomes 9 and Y in the Pacific Ocean stickleback that generated the "neo-Y" chromosome in the Japan Sea stickleback. Such fusion events are commonly observed in closely-related species.
Image provided by Jennifer Cech.

The fantastic variety of chromosome numbers across species attests to the prevalence of chromosome breakage and fusion events.  One example is human chromosome 2, which formed following a fusion of the chimpanzee chromosomes 2a and 2b.  When cells divide to reproduce, chromosomes are duplicated and each daughter cell inherits one set of chromosomes.  Centromeres are the locations on each chromosome where fibers must bind during cell division to pull each chromosome into one of the daughter cells.  Most animal chromosomes have a single centromere on each chromosome and so breakage or fusion events can lead to loss or gain of centromeres.  While loss of a centromere often leads to the chromosome being "cut" or left behind in the center of splitting cells, gain of a centromere can be equally as damaging, causing further breakage as cells attempt to pull the chromosome in opposing directions.  Despite these risks, "chromosome fusions are quite common during evolution," said Dr. Peichel.  The many examples of stable chromosome fusions across animal species, most often forming chromosomes with two centromeres called dicentrics, suggest that mechanisms exist to stabilize newly formed dicentric chromosomes and prevent their breakage during cell division.  There have been several chromosome fusion events in the stickleback family of fish (Gasterosteidae) in the past 35 million years.  In the Peichel Laboratory, formerly located in Fred Hutch Human Biology and Basic Sciences divisions but now located at University of Bern, Switzerland, former graduate student Jennifer Cech characterized a newly formed dicentric chromosome in the Japan Sea stickleback fish.  Her study was recently published in Chromosome Research.  Dr. Peichel said their study is "one of the first to identify the mechanisms that allow dicentric chromosomes with potentially deleterious effects to persist in natural populations." 

A shared characteristic of nearly all centromeres is the binding of a protein called CENP-A that forms the base of a large protein complex called the kinetochore that binds to fibers to segregate the chromosomes during cell division.  Thus, the presence of CENP-A protein implies that the centromere is functional to direct segregation during cell division. The "neo-Y" fusion chromosome in the Japan Sea species is a combination of chromosome 9 and the Y chromosome, which are not fused in the Pacific Ocean species. To determine whether both of the centromeres of the neo-Y were capable of binding CENP-A, the scientists used an antibody they generated in their previous study to locate CENP-A protein on isolated stickleback chromosomes. They found that CENP-A localized to the primary constriction point of all chromosomes of the Pacific Ocean species, including chromosome 9 and the Y chromosome.  The neo-Y chromosome of the Japan Sea stickleback, however, only had one region of CENP-A staining, which corresponded to the chromosome 9 centromere in the ancestral species.

Finding that this protein or epigenetic marker of the centromere had been lost in the Japan Sea fusion chromosome, the scientists wanted to determine whether the underlying DNA sequence had changed.  Their goal was to catch evolution in action and see what comes first: a change in the DNA sequence or a change in CENP-A binding? In their previous study, the Peichel Lab had identified a common sequence at each centromere of the Pacific Ocean stickleback fish.  In this study, they extended their analysis of the sequence of the Pacific Ocean Y chromosome and also studied the "neo-Y" fusion chromosome of the Japan Sea stickleback.  They found that their DNA probe, which labeled the centromere of all the autosomes and the X chromosome of the Pacific Ocean species, only weakly hybridized to the Y chromosome constriction point in that species.  Intriguingly, the DNA probe did not hybridize at all to the formerly Y chromosome constriction point in the neo-Y Japan Sea fusion chromosome.  In contrast, it efficiently labeled the centromere on the neo-Y that corresponded to the ancestral chromosome 9.  Lacking the sequence of the centromere on the Pacific Ocean Y chromosome, which is difficult to collect for centromeres even in well-studied organisms due to their repetitive nature, the scientists cannot determine whether the centromere sequence has been deleted or simply changed on the neo-Y.  However, they can conclude that there have been genetic changes that prevent recognition by a DNA probe that recognizes the ancestral Y centromere, albeit weakly. 

Currently, members in Dr. Peichel’s research group are working on studying the evolution of the Y chromosome in these and other stickleback species with Y chromosome fusions.  "As in humans and mice, sticklebacks have evolved a [slightly] different sequence on the Y chromosome, but we don’t know exactly how it differs, [or how it affects its function or segregation]."  "Because centromeres are really hard to sequence, this is a difficult question to answer, but we are making some progress. Stay tuned!"

Cech JN, Peichel CL.  2016.  "Centromere inactivation on a neo-Y fusion chromosome in threespine stickleback fish."  Chromosome Research.

This research was funded by the National Science Foundation, the National Institutes of Health, and the Fred Hutchinson Cancer Research Center.