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HGNC Approved Gene Symbol: RBM39
Cytogenetic location: 20q11.22 Genomic coordinates (GRCh38): 20:35,701,347-35,742,260 (from NCBI)
RBM39 is a nuclear protein involved in precursor mRNA (pre-mRNA) splicing (Han et al., 2017).
Autoantibodies to intracellular components can occur in patients with autoimmune disease and occasionally in patients with other diseases. The antibodies often recognize determinants corresponding to functional sites. Using serum from a patient who progressed from liver cirrhosis to hepatocellular carcinoma (HCC) to screen a liver cell cDNA library, Imai et al. (1993) isolated full-length cDNA clones encoding a nuclear protein that they called HCC1. The HCC1 clones encode deduced proteins of 530 amino acids (clone HCC1.4) and 524 amino acids (clone HCC1.3), and the authors suggested that these represent splice variants. Sequence analysis of HCC1 revealed the presence of 15 arginine-serine (RS) motifs, characteristic of mRNA splicing factors (e.g., SFRS1; 600812). Imai et al. (1993) also noted the presence of ribonucleoprotein consensus sequences (see SNRPA; 182285) and a structural resemblance to U2AF65 (191318). Western blot analysis showed expression of a 64-kD cellular protein. Immunofluorescence microscopy demonstrated the presence of nuclear speckles that colocalized with SFRS2 (600813) and a 5-prime cap structure of U-snRNAs (e.g., RNU2; 180690). Northern blot analysis detected 2 major HCC1 transcripts of 2.3 and 3.2 kb, as well as 2 minor transcripts of 4.3 and 5.0 kb, in human cancer cell lines and in all normal tissues tested, with higher expression in pancreas, skeletal muscle, lung, and brain, and lower expression in kidney, liver, and heart.
Using ASC2 (NCOA6; 605299) as bait to screen a mouse liver cDNA library, Jung et al. (2002) cloned Rnpc2, which they called Caper. The deduced protein contains an N-terminal RS-rich domain, followed by 3 RNA recognition motifs (RRMs). An autonomous transactivation domain partly overlaps RNA recognition motifs 2 and 3.
Han et al. (2017) stated that human RBM39 contains an N-terminal RS domain followed by 3 predicted RRMs.
Stumpf (2020) mapped the RBM39 gene to chromosome 20q11.22 based on an alignment of the RBM39 sequence (GenBank AK299678) with the genomic sequence (GRCh38).
By yeast 2-hybrid analysis, Jung et al. (2002) found that mouse Caper specifically interacted with the AP1 component Jun (165160) and estradiol-bound ligand-binding domains of estrogen receptor (ER)-alpha (ESR1; 133430) and ER-beta (ESR2; 601663), but not with any other transcription factor tested. Binding to estradiol-bound ER activated the cryptic autonomous transactivation function of Caper.
Indisulam is an aryl sulfonamide with selective anticancer activity. Using a forward genetic strategy, Han et al. (2017) identified mutations in RBM39 that caused resistance to indisulam in cancer cells in vitro and in mice with tumor xenografts in vivo. The mutations were clustered in the second RRM of RBM39 and were sufficient to confer indisulam resistance in cancer cells. Indisulam promoted interaction of RBM39 with DCAF15 (620109), followed by DCAF15-mediated recruitment of the CUL4 (see 603137)-DCAF15 E3 ubiquitin ligase complex, which triggered ubiquitination and proteolytic degradation of RBM39. Degradation of RBM39 caused pre-mRNA splicing defects, resulting in cytotoxicity and death of the cancer cells. Cancer cells containing mutations in RBM39 that blocked its recruitment to the CUL4-DCAF15 complex were resistant to indisulam. In support of these results, DCAF15 levels correlated with indisulam sensitivity, as cancer cells expressing high levels of DCAF15 exhibited hypersensitivity to indisulam. Other aryl sulfonamides with anticancer activity shared a similar mechanism of action with indisulam.
Using a FRET assay with purified recombinant proteins, Faust et al. (2020) showed that DCAF15 bound aryl sulfonamides with low affinity. Recruitment of RBM39 to CRL4-DCAF15 was mediated by the RRM2 domain of RBM39 and depended on aryl sulfonamides. The authors determined the 3-dimensional structure of the DDB1 (600045)-DCAF15-DDA1 core complex bound to RRM2 of RBM39 and the sulfonamide E7820 at 4.4-angstrom resolution by cryoelectron microscopy. They also determined the crystal structures of engineered subcomplexes. The structures showed that DCAF15 adopted a novel fold stabilized by DDA1, and that extensive protein-protein contacts between the ligase and substrate mitigated the low-affinity interactions between aryl sulfonamides and DCAF15. The data revealed how aryl sulfonamides used a shallow, nonconserved pocket on DCAF15 to selectively bind and degrade RBM39, as well as the closely related splicing factor RBM23, without the requirement for a high-affinity ligand.
Using an in vitro reconstitution assay, Bussiere et al. (2020) showed that a purified recombinant DCAF15-DDB1-DDA1 complex bound to the purified recombinant RRM2 domain of RBM39 and formed a functional quaternary complex only in the presence of indisulam. Indisulam bound to the DCAF15-DDB1-DDA1 complex with weak affinity and did not bind RBM39, but it bound potently to the quaternary complex. Using X-ray crystallography and cryoelectron microscopy, the authors determined the structures of DCAF15-DDB1-DDA1-RBM39(RRM2) complexes with indisulam to 2.3- and 3.5-angstrom resolution, respectively. DCAF15 had a distinct topology that embraced the RRM2 domain of RBM39 largely via nonpolar interactions, and indisulam bound between DCAF15 and RMB39(RRM2), coordinating additional interactions between the proteins. DDA1 stabilized the DCAF15-DDB1 complex. Further analysis validated the structural model and defined the alpha-helical degron motif, which is present only in RBM39 and RBM23. Consequently, only RBM39 and RBM23 were downregulated in indisulam-treated HCT116 cells.
Bussiere, D. E., Xie, L., Srinivas, H., Shu, W., Burke, A., Be, C., Zhao, J., Godbole, A., King, D., Karki, R. G., Hornak, V., Xu, F., and 15 others. Structural basis of indisulam-mediated RBM39 recruitment to DCAF15 E3 ligase complex. Nature Chem. Biol. 16: 15-23, 2020. Note: Erratum: Nature Chem. Biol. 16: 361 only, 2020. [PubMed: 31819272] [Full Text: https://doi.org/10.1038/s41589-019-0411-6]
Faust, T. B., Yoon, H., Nowak, R. P., Donovan, K. A., Li, Z., Cai, Q., Eleuteri, N. A., Zhang, T., Gray, N. S., Fischer, E. S. Structural complementarity facilitates E7820-mediated degradation of RBM39 by DCAF15. Nature Chem. Biol. 16: 7-14, 2020. [PubMed: 31686031] [Full Text: https://doi.org/10.1038/s41589-019-0378-3]
Han, T., Goralski, M., Gaskill, N., Capota, E., Kim, J., Ting, T. C., Xie, Y., Williams, N. S., Nijhawan, D. Anticancer sulfonamides target splicing by inducing RBM39 degradation via recruitment to DCAF15. Science 356: eaal3755, 2017. Note: Erratum: Science 356: eaan7977, 2017. [PubMed: 28302793] [Full Text: https://doi.org/10.1126/science.aal3755]
Imai, H., Chan, E. K. L., Kiyosawa, K., Fu, X.-D., Tan, E. M. Novel nuclear autoantigen with splicing factor motifs identified with antibody from hepatocellular carcinoma. J. Clin. Invest. 92: 2419-2426, 1993. [PubMed: 8227358] [Full Text: https://doi.org/10.1172/JCI116848]
Jung, D.-J., Na, S.-Y., Na, D. S., Lee, J. W. Molecular cloning and characterization of CAPER, a novel coactivator of activating protein-1 and estrogen receptors. J. Biol. Chem. 277: 1229-1234, 2002. [PubMed: 11704680] [Full Text: https://doi.org/10.1074/jbc.M110417200]
Stumpf, A. M. Personal Communication. Baltimore, Md. 03/04/2020.