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Thesis
Integrative proteomic and genomic approaches reveal nuclear role of SMN in chromatin and RNA regulation
Master of Science (M.S.), Drexel University
Jun 2025
DOI:
https://doi.org/10.17918/00011111
Abstract
Survival Motor Neuron (SMN) protein is essential for RNA metabolism, but its broader role in nuclear organization and gene regulation remains incompletely understood. Here, we show that SMN is critical for maintaining the structural and functional integrity of Cajal bodies (CBs) in HeLa cells. Using inducible SMN knockdown, we demonstrate that SMN loss disrupts CB composition and localization, alters chromatin-associated proteomes, and impairs histone gene expression. Proteomic analyses revealed widespread solubility shifts, including the depletion of replication-dependent histones and U7 snRNP components from the chromatin-bound fraction. These changes were accompanied by defective histone pre-mRNA processing, marked by the accumulation of aberrant polyadenylated transcripts. Chromatin profiling by CUT&RUN further revealed that SMN is required for CB-chromatin interactions, notably coilin occupancy at snRNA and snoRNA genes. Additional analysis of cell-cycle specific phases revealed similar enrichment patterns of coilin and the histone locus body (HLB) marker NPAT. Coilin was enriched at snRNA/snoRNA genomic loci and NPAT at histone gene clusters during S phase, which is not observed in the G1 phase. In addition to the reported proximity between the two bodies, the similar, cell cycle-specific association of these structures at their distinct genomic targets hints at an existing functional relationship. Finally, nascent RNA labeling uncovered a global attenuation of transcription and northern blot analysis revealed a connection between CB integrity and the buildup of smaller, truncated RNA species, suggesting a breakdown of co-transcriptional processing and RNA quality control as a result of disrupted SMN and CB function. Collectively, our findings establish SMN as a central regulator of nuclear architecture, chromatin interaction, and gene expression. These insights not only shed light on the molecular pathology of spinal muscular atrophy but also suggest broader implications for diseases such as cancer, where nuclear organization, epigenetic changes and efficient gene expression programs are critical for proliferation.
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Details
- Title
- Integrative proteomic and genomic approaches reveal nuclear role of SMN in chromatin and RNA regulation
- Creators
- Emily Nicole Pochet
- Contributors
- Lu Chen (Advisor)
- Awarding Institution
- Drexel University
- Degree Awarded
- Master of Science (M.S.)
- Publisher
- Drexel University; Philadelphia, Pennsylvania
- Number of pages
- 74 pages
- Resource Type
- Thesis
- Language
- English
- Academic Unit
- Biochemistry and Molecular Biology; College of Medicine; Drexel University
- Other Identifier
- 991022064041904721