Brian Strahl and colleagues identify another piece of the āhistone codeā puzzle
UNC-CHAPEL HILL ā DNA is often called the blueprint of life, but the four letter combinations that make up the genetic code are just part of the story. Ā Built upon the DNA lies additional āepigeneticā information in the form of a complex ensemble of chemical tags attached to the DNA itself and on proteins that package our DNA ā called histones ā which ultimately control how our genetic code is accessed and used.Ā Interestingly, histones are decorated with many types of chemical tags, and their particular combinations have been referred to as the āhistone codeā.Ā But understanding how this ācodeā is interpreted by the cell has proven challenging due its sheer complexity and a lack of tools to study the ācodeā inside the cell.
Now research from the University of North Carolina at Chapel Hill School of Medicine has shown how a protein called UHRF1 āreadsā the āhistone codeā in a specific way to perform an important cellular function. āBecause the protein has been found to be defective in cancer, the finding not only lends new insight into functions downstream of the āhistone codeā but could also point the way toward novel strategies for cancer treatment and prevention,ā said senior study author Brian Strahl, PhD, associate professor of biochemistry and biophysics and member of the UNC Lineberger Comprehensive Cancer Center.
The research, which appears June 1st, 2013, in the journal Genes and Development, is the latest of many studies to investigate the āhistone codeā hypothesized more than ten years ago by Strahl and his former postdoctoral advisor C. David Allis. The hypothesis suggests that distinct combinations of histone modifications work together to form a ācode,ā akin to the classic genetic code, in which three-letter combinations of nucleotides make an amino acid. These histone modifications ā chemical changes like phosphorylation, acetylation and methylation -- generate an epigenetic language that is interpreted through the ability to recruit proteins to DNA and histones that in turn modulate cellular functions.
āThis study provides important support for the āhistone codeā hypothesis, and also reiterates how difficult it will be to crack this ācode.ā It is not enough to understand how one tag works in isolation, we now have to look at all different combinations of tags on both histones and DNA to piece together the puzzle encrypting this second layer of information,ā said Strahl.
Over the last decade, researchers have pinpointed a number of different ādomainsā that proteins use to interact with, or read, the āhistone codeā. Scott Rothbart, PhD, a postdoctoral research fellow in Strahlās laboratory, previously showed that one such domain on the protein UHFR1 ā called the tandem Tudor -- helps it bind to a histone in the cell that is methylated at a specific place. Adjacent to the Tudor was another domain called a PHD finger that helped the protein also bind the unmodified end of a histone. Rothbart and Strahl wondered if these neighboring domains might function together to help UHRF1 to read the āhistone codeā and, subsequently, influence its ability to function in the cell.Ā
To investigate this question, the researchers used a highly sophisticated peptide microarray technology developed in the Strahl lab. Just as DNA microarrays contain sections of DNA sequence spotted on glass slides, these peptide arrays contained sections of modified histone proteins. When the researchers applied the UHRF1 protein to the array, they found it bound the histone differently when it contained the linked Tudor and PHD domains than when it contained the domains in isolation. They then used biochemical techniques to show that the two domains of UHRF1 functioned together in cells ā whereby each domain is making a key contribution to promote binding to the histone protein in a specific way.
One of the main functions of UHRF1 is the maintenance of a critical modification known as DNA methylation. The researchers showed that when these domains of UHRF1 were not functioning together to read the āhistone codeā, DNA methylation patterns in the cell were eventually lost.
āAbnormalities in the patterning of DNA methylation are a hallmark of many cancers. In addition, UHRF1 has been found to be defective in a number of cancers including prostate, breast, kidney, and lung cancer,ā said Scott Rothbart, PhD, who is lead author of the study.
āUHRF1ās function in maintaining DNA methylation seems to be reversible ā if you take it out of the cell you lose DNA methylation, but if you add it back you restore DNA methylation. We therefore think that by using small molecules to disrupt the recognition of the āhistone codeā by UHRF1, we may be able to reprogram DNA methylation patterns in cancer cells.ā
The research was supported in part by the National Institutes of Health, the Carolina Partnership and the University Cancer Research Fund, the Natural Sciences and Engineering Research Council of Canada, and the American Cancer Society.
Study co-authors from UNC were Bradley M. Dickson, PhD, postdoctoral research associate; Krzysztof Krajewski, PhD, research assistant professor; and Dmitri B. Kireev, PhD, research professor. Ā Other collaborators on the story were Cheryl Arrowsmith, PhD, professor; Michelle Ong, postdoctoral research associate; and Scott Houliston from the University of Toronto.