Penn State study identifies new regulator of jumping genes

As much as half of the human genome is composed of so-called "jumping genes." These DNA sequences can make copies of themselves that are inserted back into the genome at another location, playing a significant functional role in creating the diversity that drives evolution and in regulating how other genes are turned on or off. However, their jumps can also make the genome less stable and create mutations that have been associated with neurodevelopmental disorders, autoimmune disease and cancer.

So, what keeps these jumping genes - also known as transposable elements - from hopping around and breaking things like too many kids on a trampoline? New research, led by Penn State scientists and published in the Journal of Biological Chemistry, has identified a new role for a complex of proteins as a suppressor of jumping gene activity.

CCR4-NOT is a complex of proteins that has been well characterized in yeast. In the past decade, its role in human cell lines has started to be explored, but those studies have focused mainly on characterizing its role in RNA processing and degradation. We wanted to learn more about its role in the nucleus of cells where it is involved in the production of RNA from a DNA template."

Shardul Kulkarni, assistant research professor of biochemistry and molecular biology, Penn State Eberly College of Science and lead author of the paper

In yeast, CCR4-NOT's role has been characterized in multiple phases of gene regulation, it helps to control how RNA - the molecule that carries information from DNA out of the nucleus to perform cellular functions, including protein production - is produced in the nucleus of a cell, how that RNA gets transported out the nucleus into the cell's cytoplasm, where it helps to translate the RNA into a protein and, eventually, degrade it, Kulkarni explained. The cytoplasm is the viscous liquid that fills cells and contains the organelles that help carry out the cell's function; the nucleus is the organelle that contains the cell's genetic material.

The team used a technique called auxin-induced degradation to individually knock down -or reduce expression of - CNOT1 and CNOT4, two components of the CCR4-NOT complex in a human cancer cell line obtained through the U.S. National Institutes of Health. The researchers genetically modified these two proteins to be versions that would be degraded within an hour when auxin was added to the cells. In previous work, they had shown that knock down of these two components had opposite effects in the cell's cytoplasm, but they were surprised to see that knock down of both proteins produced the same effect in the nucleus.

 "We were surprised that knock down of both CNOT1 and CNOT4 resulted in a rapid widespread increase of transcription across the genome," Kulkarni said, explaining that transcription is the process of producing RNA from a DNA template. "This included jumping genes, whose expression also increased. However, the expression of one set of genes was instead reduced. This family of genes - called the Kruppel-associated box-containing zinc nuclear finger (KZNF) family - are a known repressor of jumping gene activity."

The study demonstrated - for the first time - the role of the CCR4-NOT complex in suppressing jumping gene activity, likely through its regulation of the KZNF genes.

"The genome-wide increase in transcription, including jumping gene, is likely due to CCR4-NOT regulation of KZNF genes," Kulkarni said. "Our work reveals that a molecular complex best known for controlling RNA also acts as a guardian, helping prevent these genetic elements from being switched on. This newly identified role of CCR4-NOT is crucial for maintaining genome stability and preventing other potentially harmful effects of jumping genes. And there is a particularly interesting second layer: Our work suggests that CCR4-NOT doesn't just prevent these elements from being transcribed; it also helps control the stability of the RNA they produce. In other words, the complex provides multiple layers of defense against unwanted genetic activity."

In addition to Kulkarni, the research team at Penn State included postdoctoral researcher Alexis Morrissey; data scientist Aswathy Sebastian; graduate student Oluwasegun T. Akinniyi; Cheryl A. Keller, research professor of biochemistry and molecular biology; Istvan Albert, research professor of bioinformatics; Shaun Mahony, Dorothy Foehr Huck and J. Lloyd Huck Chair in Genomics and AI and professor of biochemistry and molecular biology; and Joseph C. Reese, distinguished professor of biochemistry and molecular biology.

The work was funded by the U.S. National Institutes of Health's National Institute of General Medical Sciences under grants R35GM136353 and R35GM144135.