The precise location of the nucleosomes along the DNA is known to play an important role in the cell's day to day function, since access to DNA wrapped in a nucleosome is blocked for many proteins, including those responsible for some of life's most basic processes. Among these barred proteins are factors that initiate DNA replication, transcription (the transfer of genetic information from DNA to RNA) and DNA repair. Thus, the positioning of nucleosomes defines the segments in which these processes can and can't take place. These limitations are considerable: Most of the DNA is packaged into nucleosomes. A single nucleosome contains about 150 genetic bases (the "letters" that make up a genetic sequence), while the free area between neighboring nucleosomes is only about 20 bases long. It is in these nucleosome-free regions that processes such as transcription can be initiated.
For many years, scientists have been unable to agree whether the placement of nucleosomes in live cells is controlled by the genetic sequence itself. Segal and his colleagues managed to prove that the DNA sequence indeed encodes "zoning" information on where to place nucleosomes. They also characterized this code and then, using the DNA sequence alone, were able to accurately predict a large number of nucleosome positions in yeast cells.
Segal and his colleagues accomplished this by examining around 200 different nucleosome sites on the DNA and asking whether their sequences have something in common. Mathematical analysis revealed similarities between the nucleosome-bound sequences and eventually uncovered a specific "code word." This "code word" consists of a periodic signal that appears every 10 bases on the sequence. The regular repetition of this signal helps the DNA segment to bend sharply into the spherical shape required to form a nucleosome. To identify this nucleosome positioning code, the research team used probabilistic models to characterize the sequences bound by nucleosomes, and they then developed a computer algorithm to predict the encoded organization of nucleosomes along an entire chromosome.
The team's findings provided insight into another mystery that has long been puzzling molecular biologists: How do cells direct transcription factors to their intended sites on the DNA, as opposed to the many similar but functionally irrelevant sites along the genomic sequence? The short binding sites themselves do not contain enough information for the transcription factors to discern between them. The scientists showed that basic information on the functional relevance of a binding site is at least partially encoded in the nucleosome positioning code: The intended sites are found in nucleosome-free segments, thereby allowing them to be accessed by the various transcription factors. In contrast, spurious binding sites with identical structures that could potentially sidetrack transcription factors are conveniently situated in segments that form nucleosomes, and are thus mostly inaccessible.
Since the proteins that form the core of the nucleosome are among the most evolutionarily conserved in nature, the scientists believe the genetic code they identified should also be conserved in many organisms, including humans. Several diseases, such as cancer, are typically accompanied or caused by mutations in the DNA and the way it organizes into chromosomes. Such mutational processes may be influenced by the relative accessibility of the DNA to various proteins and by the organization of the DNA in the cell nucleus. Therefore, the scientists believe that the nucleosome positioning code they discovered may aid scientists in the future in understanding the mechanisms underlying many diseases.
Jennifer Manning | EurekAlert!
First time-lapse footage of cell activity during limb regeneration
25.10.2016 | eLife
Phenotype at the push of a button
25.10.2016 | Institut für Pflanzenbiochemie
Ultrafast lasers have introduced new possibilities in engraving ultrafine structures, and scientists are now also investigating how to use them to etch microstructures into thin glass. There are possible applications in analytics (lab on a chip) and especially in electronics and the consumer sector, where great interest has been shown.
This new method was born of a surprising phenomenon: irradiating glass in a particular way with an ultrafast laser has the effect of making the glass up to a...
Terahertz excitation of selected crystal vibrations leads to an effective magnetic field that drives coherent spin motion
Controlling functional properties by light is one of the grand goals in modern condensed matter physics and materials science. A new study now demonstrates how...
Researchers from the Institute for Quantum Computing (IQC) at the University of Waterloo led the development of a new extensible wiring technique capable of controlling superconducting quantum bits, representing a significant step towards to the realization of a scalable quantum computer.
"The quantum socket is a wiring method that uses three-dimensional wires based on spring-loaded pins to address individual qubits," said Jeremy Béjanin, a PhD...
In a paper in Scientific Reports, a research team at Worcester Polytechnic Institute describes a novel light-activated phenomenon that could become the basis for applications as diverse as microscopic robotic grippers and more efficient solar cells.
A research team at Worcester Polytechnic Institute (WPI) has developed a revolutionary, light-activated semiconductor nanocomposite material that can be used...
By forcefully embedding two silicon atoms in a diamond matrix, Sandia researchers have demonstrated for the first time on a single chip all the components needed to create a quantum bridge to link quantum computers together.
"People have already built small quantum computers," says Sandia researcher Ryan Camacho. "Maybe the first useful one won't be a single giant quantum computer...
14.10.2016 | Event News
14.10.2016 | Event News
12.10.2016 | Event News
26.10.2016 | Awards Funding
26.10.2016 | Power and Electrical Engineering
26.10.2016 | Health and Medicine