The human genome contains an estimated 30,000 genes encoded in approximately 3 billion base pairs. This vast amount of genetic information resides within a cell’s nucleus, an area with an average diameter of around 6 micrometers. A new study led by Ecology and Evolutionary Biology Assistant Professor Grace Yuh Chwen Lee and UC Berkeley Professor Gary Karpen discovered that a genome’s 3D shape in the cell nucleus could influence how it functions. The study has been published in the journal PLOS Genetics.

The genomes of multi-cellular organisms like humans are complex collections of DNA and associated proteins bound together in a small area of the cell known as the nucleus. Over the years, scientists have learned that the 3D orientation of DNA within the nucleus can impact genome processing. Professor Lee has recently published a paper investigating the impact of “the dark matter” of the genome on its role in genome organization.  Known as pericentromeric heterochromatin (PCH), these regions have been poorly studied in the past because they are highly repetitive and lack coding genes, despite encompass more than 20% of human genomes. Working with the fruit fly genetics model, Professor Lee and her colleagues developed a new method that overcame some of the technical challenges of analyzing PCH DNA and generated a comprehensive picture of its 3D organization. The team found that the PCH domains were organized into distinct regions within the genome and that they interacted with euchromatic or coding rich regions of the genome with specific properties. Their results have implications for how seemingly “junk” DNA could impact the functions of our genes.