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Global Regulation of Alternative RNA Splicing by the SR-Rich Protein RBM39 CLIP-seq

ABSTRACT: RBM39 is extensively involved in alternative splicing of RNA and helps regulate transcript levels. RBM39 may modulate alternative splicing similarly to U2AF65 by either directly binding to RNA or recruiting other splicing factors, such as U2AF65.

ORGANISM(S): Homo sapiens

PROVIDER: GSE101631 | GEO | 2017/07/20

SECONDARY ACCESSION(S): PRJNA395038

REPOSITORIES: GEO

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Global Regulation of Alternative RNA Splicing by the SR-Rich Protein RBM39

Project description:RBM39 is extensively involved in alternative splicing of RNA and helps regulate transcript levels. RBM39 may modulate alternative splicing similarly to U2AF65 by either directly binding to RNA or recruiting other splicing factors, such as U2AF65.

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MORC2 regulates RBM39-mediated CDK5RAP2 alternative splicing to promote EMT and metastasis in colon cancer [shRBM39 mRNA-seq]

Project description:To investigate the role RBM39 plays in alternative splicing, we generated SW480 cell lines in which RBM39 was knocked down by shRNA.We then performed RNA-seq data for alternative splicing gene analysis.

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RNA-Seq of 293T cells depleted of U2AF-related proteins

Project description:Characterization of RNA processing events dependent on U2AF-related proteins PUF60 and RBM39. PUF60 (poly-U-binding factor 60 kDa, also known as FIR, Hfp or Ro-bp1) is a splicing factor homologous to the 65 kD subunit of the auxiliary factor of U2 small nuclear ribonucleoprotein (U2AF65). PUF60 has two central RNA recognition motifs and a C-terminal U2AF homology motif (UHM), but lacks the N terminal arginine/serine-rich (RS) and UHM ligand motif (ULM) domains present in U2AF65. PUF60 activity, in conjunction with U2AF, facilitates the association of U2 snRNP with the pre-mRNA. PUF60 and U2AF65 can bind SF3b155 ULMs simultaneously and noncompetitively. RBM39 (also known as CAPERα, HCC1, FSAP59 or RNPC2) is an RNA processing factor and a hormone-dependent transcriptional coactivator. RBM39 domain structure is similar to PUF60, except for the extra N-terminal RS domain with unknown function. To understand function of the two proteins on a genome-wide scale, each protein was individually depleted from human embryonic kidney cell line 293 using RNAi to systematically characterize the PUF60- and RBM39-dependent exon usage.

2018-05-25 | E-MTAB-6010 | biostudies-arrayexpress

Identification of RBM39-dependent alternative splicing events in HeLa cells

Project description:We report a comprehensive analysis of alterations in gene expression and alternative splicing upon RBM39 depletion and rescue in HeLa cells.

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Exceptional response of high-risk neuroblastoma to RBM39 degrader Indisulam (ATAC-Seq)

Project description:Indisulam selectively bridges splicing factor RBM39 to DCAF15 for proteasomal degradation. However, clinical trials indicate that patient stratification based upon the mechanism of action of indisulam may be required to achieve the best response. Here we show that neuroblastoma, a MYC-driven cancer characterized by splicing dysregulation, requires RBM39 for survival, expresses high levels of DCAF15 among different solid tumor lineages, and is the most sensitive cancer lineage to indisulam that achieves therapeutic effect by specifically targeting RBM39 in neuroblastoma. Genetic depletion or proteasomal degradation of RBM39 by indisulam induces drastic splicing event changes in neuroblastoma cells. Through specifically targeting RBM39, indisulam induces exceptional tumor response in multiple high-risk neuroblastoma models. Collectively we demonstrate that high RBM39 dependency and high-level expression of DCAF15 provide indisulam a more efficacious therapeutic window to treating high-risk neuroblastoma.

2021-11-24 | GSE164504 | GEO

Exceptional response of high-risk neuroblastoma to RBM39 degrader Indisulam (RNA-Seq)

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Identification of RBM39-dependent alternative splicing events in HeLa cells

Project description:Identification of RBM39-dependent alternative splicing events in HeLa cells

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MORC2 regulates RBM39-mediated CDK5RAP2 alternative splicing to promote EMT and metastasis in colon cancer [RBM39 RIP-seq]

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E7820, an Anti-Cancer Sulfonamide, Degrades RBM39 in Patients with Splicing Factor Mutant Myeloid Malignancies: A Phase II Clinical Trial

Project description:Mutations in RNA splicing factor genes (SF3B1, SRSF2, and U2AF1) are common in AML and MDS and recent studies demonstrate pharmacologic degradation of the RNA splicing factor RBM39 results in preferential killing of splicing factor mutant cells. We therefore conducted a phase II clinical trial (NCT05024994) of the oral RBM39 degrader E7820 at the recommended phase II dose in patients with R/R MDS/AML and a splicing factor mutation. No patients met the primary endpoint of overall response rate in the first 12 patients enrolled, leading to study termination. However, E7820 was well-tolerated and achieved >50% RBM39 degradation in blood and disruption of splicing. At the same time, the degree of splicing disruption was far less than seen with in vitro doses exhibiting preclinical efficacy, providing potential explanation for limited clinical efficacy. Overall, this study demonstrates on-target safety and feasibility of RBM39 degradation in patients and supports future combination therapies with E7820.

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Structural complementarity offsets low receptor affinity in E7820-mediated RBM39 degradation by CRL4DCAF15

Project description:The investigational drugs E7820, indisulam and tasisulam (aryl-sulfonamides) promote the degradation of the splicing factor RBM39 in a proteasome and CRL4DCAF15 ubiquitin ligase-dependent mechanism, however the molecular details of this activity remain elusive. Here we present the cryo-EM structure of DDB1-DCAF15-DDA1 bound to RBM39 and E7820 at 4.4 Å resolution, together with crystal structures of engineered subcomplexes. We show that DCAF15 adopts a novel fold stabilized by DDA1, and that extensive protein-protein contacts between the ligase and substrate mitigate the low affinity interaction between aryl-sulfonamides and DCAF15. Our data demonstrates how aryl-sulfonamides neo-functionalize a shallow, non-conserved pocket on DCAF15 to selectively bind and degrade RBM39 and RBM23 without the requirement for a high affinity ligand, which has broad implications for the de novo discovery of molecular glue degraders.

2019-07-10 | PXD014536 | Pride

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