The nucleolus (dark blue) resides within the cell nucleus, surrounded by heterochromatin. Berkeley Lab researchers have discovered the molecular pathways that regulate its organization. Img: lbl.gov

Gary Karpen and Jamy Peng, researchers in the Life Sciences Division of the Department of Energy's Lawrence Berkeley National Laboratory, have now discovered two pathways that regulate the organization of the nucleolus and other features of nuclear architecture, maintaining genome stability in the fruit fly Drosophila melanogaster. Their results are published in Nature Cell Biology and are now available online to subscribers.

Because much of the genome of Drosophila is shared with human beings, learning how nuclear organization is controlled in the fruit fly can apply to human disorders like birth defects and cancer. The organization of structures in the cell's nucleus has profound effects on such essential functions as how and when genes are expressed. When regulation fails, genome aberrations accumulate, including repeated sequences of DNA or even entire extra chromosomes.

"Our project continues to point to an understanding of genome stability in humans," says Karpen, who heads Berkeley Lab's Department of Genome and Computational Biology. Karpen is also codirector of the Drosophila Genome Center (sponsored by the National Human Genome Research Institute, the National Cancer Institute, and the Department of Energy) and an adjunct professor of molecular and cell biology at the University of California at Berkeley.

The epigenetics of heterochromatin

Controlling functions of the cell and organism through nuclear architecture and spatial rearrangements is known as epigenetics — from the Greek for "on, over, or at" the genes, instead of by the DNA sequence. The chromosomal material known as heterochromatin mediates gene silencing, chromosome inheritance, and other processes. Karpen and Peng have identified the molecular pathways that regulate two of heterochromatin's important functions.

One of these is control of repeated DNA sequences in and outside the heterochromatin. The other is the organization and structure of the nucleolus, the ribosome factory, which is situated at the specific site in the heterochromatin where ribosomal DNA — consisting of large genes, repeated 300 to 400 times — codes for the production of the RNA from which ribosomes are built.  

"This work on pathways that control the organization of the nucleolus is the first to be published that deals with an organelle," says Karpen. "Even though the gross organization of chromosomes and other nuclear elements is well known in cell biology, learning about the regulation of nuclear architecture is in its early stages."

The most striking feature of any nucleus is its chromosomes. These are made of chromatin, which combines DNA with a set of proteins known as histones; four similar histones join together to form a cylindrical spool around which the DNA wraps. Each of these bundles is called a nucleosome, and many nucleosomes are bound together by the continuing strand of DNA, which forms a string of beads that further coils to form one of two kinds of chromatin, either euchromatin or heterochromatin.

Most genes reside in euchromatin, which is of relatively low density and where the DNA is more accessible to the machinery of gene transcription. By contrast, heterochromatin is dense and contains relatively few genes; most of the DNA in heterochromatin, including numerous short repeated sequences, does not code for proteins.

Heterochromatin is typically found at the ends of a chromosome, where it abuts the telomeres — chromatin structures best known for limiting, by their diminishing length, how many times a cell can replicate. Heterochromatin also flanks the centromere in the central region of the chromosome, the chromatin structure that plays a crucial role in chromosome segregation during cell division. What other functions abundant heterochromatin may perform are still an open question.

Even epigenetics ultimately has its roots in the genes; the researchers' first step was to identify which genes affect organization of the heterochromatin, then to identify the proteins expressed by these genes, and finally to learn how they act on the chromosomal material.