Chromatin structure: More folding, more complexity than expected

New molecular technologies, some driven by the work of a researcher at the University of Illinois at Urbana-Champaign, are exposing unexpectedly high levels of DNA folding and complex protein-rich assemblages within the nucleus of cells that he says “seriously challenge the textbook models.”

“What we are seeing suggests that there may be machinery, not yet identified, that controls the folding and the movements of enzymes that turn genes on and off,” said Andrew Belmont, a professor of cell and structural biology, who is giving a talk on the subject today at the annual meeting of the American Association for the Advancement of Science.

Belmont, who also is a medical doctor, discussed current trends of research on chromatin structure during a session on “The ’New’ Nucleus: Mothership of the Human Genome.” Chromatin is a part of a cell’s nucleus that contains nucleic acids and proteins — the genetic material necessary for cell division. During mitosis, chromatin folds and condenses.

The level of folding, however, is much higher than previously thought, Belmont said, and a lot of the enzyme complexes that work on DNA, for instance to allow gene regulation, have turned out to be surprisingly large.

“In this era of genome sequencing and gene identification, the fundamental question of how DNA folds within the mitotic chromosome and interphase nucleus, and the impact of this folding on gene expression, remains largely unknown,” he said.

A startling discovery, unveiled by on-going research based on a technique to study the structure in living cells that Belmont announced in late 1996, is that chromosomes are constantly in motion. They gyrate constantly within their tiny confined territories.

Advances of his own technique allow him to watch as proteins move and come together as single packages as they approach their target receptors to activate a gene.

The genetic-engineering method developed by Belmont uses a specific protein-DNA interaction in which a protein binds to a specific target in DNA without altering chromosomal structure. Naturally occurring green fluorescent protein allows for viewing area in living cells by light microscopy or electron microscopes. The results include visual proof of chromosomal fibers 100 nanometers in diameter during folding and unfolding.

“For several decades, the basic paradigm for studying chromosome structure relied primarily on experimental approaches in which nuclei were exploded and chromosomes fragmented into small, soluble pieces that could be analyzed in the test tube using biochemical techniques,” Belmont said. “However, over the past several years, development of novel imaging tools have provided a new window, allowing direct visualization of chromosomes within living cells.”

As a result, scientific perspectives on chromosome structure and function have been dramatically altered, he said. “The picture emerging is of a cell nucleus, apparently tranquil, but concealing chromosomes and chromosomal proteins in constant motion and turnover. This highly dynamic behavior results in quasi-stable chromosome architecture poised for rapid response to signals from the cell environment.”

A current question is how large, bulky protein complexes that mediate gene transcription can find their targets and gain access to the DNA, he said.

In the February issue of the journal Current Biology, Belmont and Sevinci Memedula of the University of Bucharest suggest that large protein assemblies approach a gene target in a stepwise fashion. Individual sub-units act as pioneers. They open, or remodel, their target for subsequent binding of the larger intact protein complex