August 31, 2012

The role of H3K9 in bringing order to the nucleus

Scientists from the Friedrich Miescher Institute for Biomedical Research have elucidated the histone modifications that lead to the sequestration of silent genes at the nuclear periphery. In a study published in the latest issue of Cell they show that at least two levels of histone H3 lysine 9 methylation trigger the anchoring of heterochromatin to the nuclear envelope.

The cell nucleus is a hotbed of activity, in which DNA and numerous species of RNA are implicated in gene expression, genome duplication and repair, as well as the regulation of these essential processes. The organization of DNA into chromatin, which entails the folding of long DNA fibers around bead-like units containing 8 histone proteins, is the defining feature of the eukaryotic genome. Once organized into these nucleosomes, chromatin can be compacted into condensed chromosomal structures, or unfolded to allow enzymes to act on their DNA substrate. Chromatin-controlled access to the DNA fiber regulates essentially all functions of the genome in a eukaryotic cell.

Intriguingly, as embryonic cells differentiate to form a multicellular organism, regions of the genome become packaged into compact silent domains, called heterochromatin. The total amount of heterochromatin in the cell increases as pluripotent precursor cells differentiate into restricted cell types. Different genes are repressed in different tissues. The silent domains also become spatially segregated from the transcriptionally active ones, being shifted to the periphery of the nucleus. This spatial segregation of active and inactive domains of the genome is conserved in all eukaryotic cells. The Gasser laboratory at the Friedrich Miescher Institute for Biomedical Research studies the physiological implications of this spatial organization. They have now elucidated in the worm C. elegans how the sequestration of genes at the nuclear periphery is achieved.

Benjamin Towbin, during the course of his PhD studies in Susan Gasser's laboratory, found that an enzyme called SAM synthetase, which generates the universal donor for lysine methylation, S-adenosylmethionine (SAM), is critical for the proper spatial segregation of chromatin in the nucleus. When he interfered with SAM synthesis he observed a strong drop in histone methylation, activation of what should have been silent genes in a heterochromatic context, and loss of their sequestration at the nuclear edge.

Assuming that the methylation of specific lysines within histones might be the signal for heterochromatin sequestration, Towbin then went on to determine which of the many enzymes that transfer a methyl group from SAM to a histone substrate, were necessary for heterochromatin anchoring. He identified two histone methyltransferases (HMTs), which act sequentially to generate a trimethylated lysine 9 in histone H3: MET-2 is a homologue of the mammalian SET DB1 enzyme, and deposits the first and second methyl group on this specific residue, while a new HMT, SET-25, was able to deposit the third methyl group, generating H3K9me3. Each progressive stage of modification, the mono-, di- and tri-methylated forms of H3K9, provided a signal that triggered the transfer of the modified nucleosomes to the nuclear envelope. Intriguingly, mono- and di-methylated nucleosomes were not transcriptionally silent, but were necessary for the tri-methylation mark, which then closed down expression and sealed the bond to the periphery.

Towbin and colleagues could further show that SET-25 co-localizes with peripheral heterochromatin bearing tri-methylated H3K9. SET-25 is thus sequestered at the nuclear periphery by the product of its own methylation reaction. "We believe that SET-25 accumulates at the nuclear periphery to promote heterochromatic repression of the genes that are brought there due to deposition of the mono- and di-methyl marks. This also ensures that heterochromatin is targeted by the SET-25 enzyme as the chromatin replicates, an event that would favor the propagation of both a repressed state and its spatial positioning," says Towbin.

Although the results were gained in the model organism C. elegans, mammalian homologues exist for the identified proteins and similar processes have been described in mammalian cells, albeit in less detail. "The analogies to mammalian silencing suggest that the principles identified here are relevant from worms to man," said Gasser.

On Benjamin Towbin and Susan M. Gasser
Benjamin Towbin just finished his PhD thesis in the research group of Susan Gasser. Susan Gasser's research interests focus on how nuclear organization impinges on mechanisms of repair and replication fork stability and on epigenetic inheritance of cell fate decisions. Her laboratory combines genome-wide mapping, synthetic lethal screens, quantitative live fluorescence imaging, C elegans genetics, siRNA screens and standard yeast molecular genetics to address these questions at the molecular and cellular levels.
» More about Susan Gasser

Original publication
Towbin BD, González-Aguilera C, Sack R, Gaidatzis D, Kalck V, Meister P, Askjaer P, Gasser SM (2012) Step-wise methylation of histone H3K9 positions chromosome arms at the nuclear periphery in C. elegans embryos. Cell 150:934-947

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