Eukaryotic gene expression is regulated at multiple levels in the cell nucleus, from histone modification and chromatin compaction to the synthesis, processing and export of mRNA. The precise execution of transcriptional programs during cell differentiation and development relies on faithful reproduction of a specific chromatin state through mitosis. Failure to maintain these epigenetic programs through multiple cell divisions commonly leads to pathological conditions such as cancer. Thus, understanding how chromatin organization is established and propagated will enhance the understanding of how disease-causing errors in gene expression can occur and be prevented. The central hypothesis guiding this proposal is that the nuclear pore component Nup98 plays an essential role in transcriptional activation of developmentally regulated genes. Biochemical, genetic, genomic and cell biological methods will be used to investigate the potential interaction between Nup98 and the members of the trithorax protein complex, a well-known chromatin regulator and mediator of developmental active gene memory. First, the molecular composition of the intranuclear Nup98 complex will be established, its recruitment mechanism to chromatin identified and thus provide key functional insights into the link between Nup98 and epigenetic memory. Second, the molecular function of Nup98 at genomic target sites will be investigated. For instance, the consequences of Nup98 knockdown and over-expression will be analyzed by chromatin immune- precipitation to investigate which binding partners, histone modifications and RNA polymerase II phosphorylation events depend on Nup98. In addition, a potential effect of Nup98 on mRNA processing and export will be determined by RNA fluorescence in situ hybridization and analysis of recruitment of mRNA processing and nuclear export factors. Furthermore, Nup98 recruitment in developing tissues that activate targets genes as well as genetic effects of Nup98 on established Trx mutant phenotypes will be analyzed. Finally, a potential role of Nup98 in long-range gene interactions and organization of active chromatin domains will be investigated with genome-wide techniques. These studies will provide important information about the role of Nup98 in transcriptional initiation and establishment of active chromatin. Third, the interaction between Nup98 and mammalian MLL and Wdr5 may prove to be important in understanding Acute Myelogenous Leukemia (AML) and development-associated roles of these proteins. Proposed is a comprehensive genome-wide analysis of Nup98 binding in human cell lines and in mouse hematopoietic cell lines. The latter have been transformed by a known leukemia-inducing gene fusion Nup98- NSD1 and will be compared relative to normal hematopoietic cells. These approaches have the potential to reveal the gene regulatory role of mammalian Nup98 and provide insight into its leukemia-causing potential.

Public Health Relevance

Aberrant nuclear organization is a key pathological feature of cancer cells and has been linked to various human diseases such as muscular dystrophies, neurodegenerative disorders and the premature aging disease progeria. Studying the molecular communication between chromatin and the nuclear pore complex has the potential to uncover novel levels of gene regulation and to improve our understanding of nuclear organization in normal and pathological cells. Ultimately, our studies might provide new insights into the onset of Acute Myelogenous Leukemia (AML) and lead to the generation of new tools to interfere with malignant cell proliferation and repair dysfunctional genetic programs in aberrant cells.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Nuclear and Cytoplasmic Structure/Function and Dynamics Study Section (NCSD)
Program Officer
Carter, Anthony D
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Salk Institute for Biological Studies
La Jolla
United States
Zip Code
Franks, Tobias M; McCloskey, Asako; Shokirev, Maxim Nikolaievich et al. (2017) Nup98 recruits the Wdr82-Set1A/COMPASS complex to promoters to regulate H3K4 trimethylation in hematopoietic progenitor cells. Genes Dev 31:2222-2234
Hatch, Emily M; Hetzer, Martin W (2016) Nuclear envelope rupture is induced by actin-based nucleus confinement. J Cell Biol 215:27-36
Franks, Tobias M; Benner, Chris; Narvaiza, IƱigo et al. (2016) Evolution of a transcriptional regulator from a transmembrane nucleoporin. Genes Dev 30:1155-71
Ibarra, Arkaitz; Benner, Chris; Tyagi, Swati et al. (2016) Nucleoporin-mediated regulation of cell identity genes. Genes Dev 30:2253-2258
Ibarra, Arkaitz; Hetzer, Martin W (2015) Nuclear pore proteins and the control of genome functions. Genes Dev 29:337-49
Gomez-Cavazos, J Sebastian; Hetzer, Martin W (2015) The nucleoporin gp210/Nup210 controls muscle differentiation by regulating nuclear envelope/ER homeostasis. J Cell Biol 208:671-81
Jacinto, Filipe V; Benner, Chris; Hetzer, Martin W (2015) The nucleoporin Nup153 regulates embryonic stem cell pluripotency through gene silencing. Genes Dev 29:1224-38
Buchwalter, Abigail L; Liang, Yun; Hetzer, Martin W (2014) Nup50 is required for cell differentiation and exhibits transcription-dependent dynamics. Mol Biol Cell 25:2472-84
Hatch, Emily; Hetzer, Martin (2014) Breaching the nuclear envelope in development and disease. J Cell Biol 205:133-41
Toyama, Brandon H; Hetzer, Martin W (2013) Protein homeostasis: live long, won't prosper. Nat Rev Mol Cell Biol 14:55-61

Showing the most recent 10 out of 16 publications