Scientists from Northwestern University and Weizmann Institute, Israel, uncovered a genomic code that can explain almost half of the nucleosome positions on DNA. Their results, appearing in an advance online publication and to be published in the August 17 issue of Nature, reveal that this code may facilitate specific chromosome functions including transcription factor binding, transcription initiation, and even remodeling of the nucleosomes themselves.
Jonathan Widom, Ph.D., of Northwestern University, the senior investigator of the study, notes “The question we asked was since almost all eukaryotic genomic DNA is wrapped up in nucleosomes, do the cells care about which parts of the DNA are coiled around the nucleosomes and which are not and the answer we got is that the cells do care.
“Nucleosomes in vivo are moving around the DNA, and we found that the nucleosomes are more likely to be near certain sequences in DNA and less likely around other sequences. The sequences recognized by the nucleosomes are in the parts of DNA that are more bendable than the other sequences. The loose sequence specificity of this code allows it to be layered over the genetic code,” he adds.
Dr. Widom says that this sequence specificity helps explain the observation that even though there are multiple transcription factor binding sites present in a stretch of DNA only the ones that are a specific length in front of a gene are recognized by the transcription machinery and result in correct transcription of the gene. He believes that the wrong sites are obscured by the nucleosomes and only the sites exposed between nucleosomes are being recognized.