07/22/2026
Out today in Nature: Neurosurgeon-scientist Daniel Lim, MD, PhD, and colleagues UCSF have discovered that genes are controlled not only by DNA sequence and chemical epigenetic marks, but also by where they are located inside the nucleus.
During human brain development, hundreds of genes physically move from the quiet outer edge of the nucleus (the lamina) to active interior hubs (the speckles), where their activity can increase by as much as eightfold. Remarkably, genes forced to remain at the nuclear edge stayed silent even after a major repressive epigenetic mark was removed.
These findings establish a new paradigm: a gene's spatial location is fundamental to understanding its regulation and function. Because this principle likely applies across many cell types, it has broad implications for human biology and for diseases linked to altered gene regulation—including brain tumors, neurodegeneration, and age-related decline.
Citation: Sajad Hamid Ahanger, Evan R. Semenza, Chujing Zhang, Eugene Gil, Mitchel A. Cole, Serena Huei-An Lu, Li Wang, Arnold R. Kriegstein, Daniel A. Lim. Subnuclear genome compartmentalization controls bivalent chromatin activity. Nature. 2026 July 22. doi: 10.1038/s41586-026-10832-w
This publication is Open Access! Read it here:https://www.nature.com/articles/s41586-026-10832-w.pdf
Learn more about the Lim lab's research at: https://danlimlab.ucsf.edu/
——————————
Images:
Slide 1: Text laid over micrograph reads: “A New Dimension of Gene Expression. Just published in Nature, UCSF scientists show that where a gene sits inside the nucleus is fundamental to how it is regulated.”
Slide 2: Drawing of switch from lamina-associated domains (LAD) to speckles-associated domains (SPAD) during differentiation from radial glia (RG) to excitatory neurons (EN). Created by the Lim lab with BioRender.
Slide 3: Representative DNA-FISH micrographs of the STY1 gene loci (red) relocating LAD to SPAD, with lamin B1 and SON immunostaining (green) in cells of the germinal zone (left) and cortical plate (right).
Slide 4: The fold change in expression of bivalent genes that resolve to the H3K4me3-monovalent state during RG-to-EN differentiation stratified by LAD to SPAD dynamics. (WG = whole genome).
Slide 5: Text reads “These findings have major implications for our understanding of brain development, neurodegenerative disease, cancer and aging” with icons representing each of these words.