Protein duo thwarts chromosomal scrambling and DNA breakage

Over the past few decades it has become increasingly clear that epigenetic changes - heritable changes in the cell that do not result from DNA sequence alteration - may be just as important as gene mutations in cancer development. Researchers have identified a host of factors involved in epigenetic control of gene expression and development, but many of the precise mechanisms underlying this type of regulation remain unclear.

A new study by Mark Bedford, Ph.D., professor of Molecular Carcinogenesis, and colleagues published in Molecular Cell sheds light on the mechanism by which TDRD3 — a protein that "reads" epigenetic marks on chromosomal proteins — turns on certain genes.

The study establishes a link between TDRD3 and an enzyme that unwinds DNA at regions of active gene expression, and provides evidence that this partnership can prevent DNA breakage and chromosomal translocations - two of the hallmarks of cancer.

Decoding epigenetic marks

DNA is tightly packaged into chromosomes along with histone proteins. Chemical modification of these histones is one way that the cell regulates the packing and unpacking of the DNA and its associated proteins (collectively called chromatin), which in turn helps to determine whether a given gene is activated or repressed.

Several types of chemical modifications of the five major histone protein families give rise to a complex "histone code" that signals the transcriptional machinery to turn genes on or off.

The Bedford lab studies one such modification, the methylation of arginine amino acids in histones and other chromatin-associated proteins. This is accomplished by a class of enzymes called protein arginine methyltransferases (PRMTs). A few years ago the lab identified TDRD3, a protein that "reads" methyl-arginine marks on histone tails.

Until now, the function of TDR3 had been unclear. "Over 10 years ago, arginine methylation of histone tails was identified as an epigenetic mark that was linked to gene activation. But the mechanism behind this link was unknown," says Bedford.

Proteins team up at sites of gene expression

The authors set out to find clues to TDRD3's function by looking for physical interactions between TDRD3 and other proteins in the cell. They found that TDRD3 forms a complex with a protein called topoisomerase 3B (TOP3B), an enzyme that unwinds DNA and, in so doing, prevents DNA structures from forming that impede gene transcription.

The researchers studied the two proteins in breast cancer cell lines, where they discovered that TDRD3 recruits TOP3B to active chromatin (where genes are turned on) that is marked by arginine methylation.

Avoiding potentially detrimental R-loops in DNA

When genes are heavily transcribed, they have a tendency to form single-stranded DNA loops, called R-loops, near their promoter. R-loop accumulation at a gene can prevent transcription, and these loops are also often sites of DNA breaks.

It is these R-loop structures that are targeted by TOP3B. The research team observed that in mice lacking the TDRD3 gene there was an increase in both R-loop formation and chromosomal translocations.

"These paired proteins (TDRD3 and TOP3B) thus work together to make sure that transcription is not interrupted, and they also reduce the frequency of DNA breaks and translocations, which are often the driving force behind may cancers," says Bedford.

The lead author of the study is Yanzhong Yang, Ph.D., an instructor in Bedford's lab. The study benefitted from strong collaborations with Kevin McBride, Ph.D., assistant professor of Molecular Carcinogenesis, and Frederic Chedin, Ph.D., associate professor in Molecular & Cellular Biology at the University of California, Davis. Yue Lu, Ph.D., assistant professor of Molecular Carcinogenesis, performed the bioinformatics analysis.

Bedford is the senior author, and is a member of the Center for Cancer Epigenetics at MD Anderson. The research was funded by grants from the National Institutes of Health (DK062248 and GM094299).