Table 3.
Differentially expressed genes are nuclear scaffold associated
| Chromosomes | Gene name | Biological process/function | SAR within 10-kb upstream | SAR within gene |
|---|---|---|---|---|
| 14 | SCFD1 | Exocytosis | − | + |
| 14 | C14orf11 | Stimulates proliferation | + | + |
| 14 | KIAA0423 | Mitosis | + | + |
| 14 | MAP4K5 | Protein phosphorylation | − | + |
| 14 | PYGL | Glycogen metabolism | − | + |
| 14 | KIAA0831 | Chromosome partitioning | − | + |
| 14 | DACT1 | Regulates WNT signaling | − | + |
| 14 | FUT8 | Transferase activity | − | + |
| 14 | PCNX | Neurogenesis | + | + |
| 14 | SIPA1L1 | Cell adhesion | − | + |
| 14 | RBM25 | Pre-mRNA processing | − | − |
| 14 | JDP2 | mRNA transcription regulation/tumor suppressor | − | + |
| 14 | C14orf179 | Cytoskeleton | − | − |
| 14 | FLRT2 | Cell surface receptor mediated signal transduction | − | + |
| 14 | BTBD7 | Homo/heteromeric protein dimerization | − | + |
| 15 | AQR | Viral RNA-dependent RNA polymerase | − | + |
| 15 | EIF2AK4 | Protein phosphorylation/translational regulation | + | + |
| 15 | FLJ43339 | Unclassified | + | − |
| 15 | CCDC32 | Unclassified | − | + |
| 15 | AP4E1 | Receptor-mediated endocytosis | − | + |
| 15 | LEO1 | mRNA transcription elongation | − | − |
| 15 | TPM1 | Cell motility | − | − |
| 15 | OAZ2 | Apoptosis/oncogenesis | − | + |
| 15 | ITGA11 | Cell adhesion | + | + |
| 15 | SIN3A | mRNA transcription regulation | + | + |
| 15 | UBE2Q2 | Protein modification | − | + |
| 15 | CHSY1 | Protein glycosylation | − | + |
| 16 | CREBBP | mRNA transcription regulation | − | + |
| 16 | KIAA0350 | Autoimmunity | − | + |
| 16 | ARHGAP17 | Signal transduction/cell structure | − | + |
| 16 | NSMCE1 | Genome stability | + | + |
| 16 | XPO6 | Nuclear export to cytoplasm | − | + |
| 16 | CHD9 | mRNA transcription regulation | − | + |
| 16 | AMFR | Proteolysis | + | + |
| 16 | GTL3 | Unclassified | − | − |
| 16 | CDH11 | Cell adhesion | + | + |
| 16 | CMTM4 | Inflammatory response/migration | − | + |
| 16 | AP1G1 | Receptor-mediated endocytosis | − | + |
| 17 | C17orf25 | Carbon metabolism | + | + |
| 17 | TTC19 | Unclassified | − | − |
| 17 | ZNF207 | Nucleic acid metabolism | − | − |
| 17 | CCDC47 | Unclassified | − | − |
| 17 | ERN1 | Protein phosphorylation | − | + |
| 17 | TEX2 | Unclassified | − | − |
| 17 | PRKCA | Protein phosphorylation/cell proliferation and differentiation | − | + |
| 17 | WIPI1 | Protein complex assembly | + | − |
| 18 | EPB41L3 | Tumor progression | − | + |
| 18 | RNMT | mRNA capping | + | + |
| 18 | CABLES1 | Proliferation/differentiation | − | − |
| 18 | CDH2 | Cell adhesion | + | + |
| 18 | HDHD2 | Phosphate metabolism | − | + |
| 18 | KIAA0427 | Protein biosynthesis | − | + |
| 18 | DYM | Skeletal development/brain function | − | + |
Genes expressed in AoAF cells, but bound to the nuclear matrix and silenced in HeLa cells, were analyzed for nuclear scaffold attachment within and up to 10 kb upstream of each gene. The majority of genes (81%) were found to contain a SAR either within the gene, upstream of the gene or both suggesting a scaffold-mediated mechanism for tissue-specific expression.