Genome organization and function in fungi

The National Institute of General Medical Sciences, part of the Department of Health and Human Services National Institutes of Health, awarded The Regents of the University of Colorado, University of Colorado Colorado Springs $325,938 on June 1, 2026, under the Biomedical Research and Research Training program (CFDA 93.859).

The Klocko Laboratory will conduct fundamental research on genome organization and function in fungi, specifically examining how eukaryotic genomes are precisely organized within the nucleus to support proper gene expression and chromatin formation. The research uses Neurospora crassa as a model organism to understand epigenetic regulation and chromatin properties, with findings applicable to understanding genome organization in fungal pathogens and informing human disease mechanisms such as oncogenic tumor formation in neuroblastoma and pancreatic cancers. The laboratory will assess high-resolution genome organization in wild-type fungal species and characterize the mechanisms underlying heterochromatin and euchromatin formation and gene expression regulation across several fungal species.

Work is performed in Colorado Springs, Colorado. The award period runs from June 1, 2026, through May 31, 2031. This is a Project Grant, the standard assistance type for NIGMS investigator-initiated research supporting basic research that advances understanding of biological processes and disease diagnosis, treatment, and prevention.

Abstract

Klocko laboratory research overview: eukaryotic genomes are precisely and non-stochastically organized in the nucleus for proper function, including gene expression and chromatin formation. In humans, genome disorder can cause to aberrant gene expression and uncontrolled cellular growth, leading to oncogenic tumor formation, as observed in neuroblastoma and pancreatic cancers. However, a complete understanding of the mechanisms necessary to organize eukaryotic genomes is not known in any species, which is a critical GAP in our collective knowledge. Specifically, many (EPI)genetic factors have not been examined for roles in organizing genomic DNA, including for how silent heterochromatin is segregated at the nuclear periphery from active euchromatin. We use the innovative fungal organism neurospora crassa as a model for humans, given the similarities of its epigenetic regulation and extent of DNA compaction with humans. The neurospora genome contains active euchromatin and silent heterochromatin, marked by identical histone post-translational modifications that are catalyzed by homologous proteins as humans. However, the small, genetically tractable, haploid neurospora genome allows cost-efficient genomic studies, and its chromatin machinery is not essential, as strains harboring single deletions of chromatin modifying proteins are viable. By using neurospora crassa as a model fungus, we can also directly understand how chromatin properties affect the genome organization of fungal pathogens of humans. My lab assesses the high-resolution genome organization of wild type fungal species, including neurospora crassa, and studies how chromatin composition or the genome synteny changes impact genome organization and function. We are also characterizing the fundamental mechanisms underlying hetero- or euchromatin formation and the regulation of gene expression in several fungal species, focusing on neurospora and ogataea clade yeasts. Five-year goals: I want to complete several manuscripts for which we already have significant data collected, including the impact of translocations on neurospora genome organization and the characterization of chromatin and genome organization in ogataea species. I will continue to guide/mentor uccs (UNDER)graduate students on new experiments, and their subsequent data analysis, that assess the contribution of DNA binding proteins, telomeres, and histone deacetylases/acetyltransferases on chromatin composition and genome organization. I will have uccs students present their research at international conferences to enhance their research training. Klocko research program vision: my long-term goal is to substantially contribute to our collective knowledge for how fungal genomes are organized, including the underlying mechanisms required for genome organization, and how changes to organization alter genome function. Specifically, I want to explore the inherent principles of chromatin formation and how they contribute to gene regulation in heterochromatic and euchromatic genome regions using novel experimental directions on which I guide uccs (UNDER)graduate students. I strive to mentor the next generation of research scientists in preparation for biomedical research careers.