About

Melissa Jurica is a Professor of Molecular, Cell & Developmental Biology at UCSC. She holds a B.S. degree from Montana State University and a Ph.D. from the University of Washington/FHCRC. Her research focuses on building a mechanistic model of pre-mRNA splicing by the spliceosome, a fundamental step of human gene expression. Abnormal splicing is linked to many diseases, including cancers. Her lab aims to characterize the assembly and function of the spliceosome, which involves five small nuclear ribonucleoproteins and numerous proteins, through biochemistry and structural biology techniques. Additionally, she investigates small molecules that interfere with spliceosome activity. Her team has characterized natural products that inhibit cancer cell growth by targeting the SF3B subunit of the spliceosome and employs high-throughput chemical screening to identify new spliceosome modulators. These compounds are used as chemical probes to study spliceosome function in vitro and in cells.

Research topics

• Biology
• Cell biology
• Biochemistry
• Computational biology
• Chemistry
• Genetics

Selected publications

• The human branchpoint-interacting stem-loop sequence and structure regulates U2 snRNA expression, branchpoint recognition, and the transcriptome

  Nucleic Acids Research · 2026-03-19

  articleOpen accessSenior author

  During pre-mRNA splicing, the branch helix forms when U2 snRNP engages with introns to initiate spliceosome assembly. The branch helix is mutually exclusive with the U2 snRNA branchpoint-interacting stem loop (BSL). In yeast, BSL alteration affects branchpoint recognition, but its role in human cells, where branchpoint usage is more flexible, is unknown. To examine the impact of perturbing BSL base pairing, we used a self-contained orthogonal splicing system that pairs an engineered U2 snRNA and splicing reporter. Our results show that BSL mutations affect both U2 snRNA accumulation and splicing in human cells. We also examined the relationship between BSL stability and U2 snRNA complementarity to branchpoint sequence. The results indicate that pairing between the branchpoint sequence and BSL loop links branchpoint fidelity and intron-mediated unwinding of the BSL stem, which supports and extends a toehold-mediated strand invasion model of branch helix formation advanced by Pena and coworkers from cryo-EM structures. Finally, we investigated transcriptome-wide effects of expressing U2 snRNA with either a cancer-associated BSL mutation or with an altered branchpoint recognition sequence. Similarities in both splicing and gene expression changes between the mutants suggest a shared cellular response mechanism leading to gene upregulation linked to oncogenic pathways.

  PublisherDOI

• A Yeast-Based High-Throughput Screening Platform for the Discovery of Novel pre-mRNA Splicing Modulators

  ACS Chemical Biology · 2026-01-12

  articleOpen access

  Pre-mRNA splicing is a core process in eukaryotic gene expression, and splicing dysregulation has been linked to various diseases. However, very few small molecules have been discovered that can modulate spliced mRNA formation or inhibit the splicing machinery itself. This study presents a novel high-throughput screening (HTS) platform for identifying compounds that modulate splicing. Our platform comprises a two-tiered screening approach: A primary screen measuring growth inhibition in sensitized Saccharomyces cerevisiae (yeast) strains and a secondary screen that relies on production of a fluorescent protein as a readout for splicing inhibition. Using this approach, we identified 4 small molecules that cause accumulation of unspliced pre-mRNA in vivo in yeast. In addition, cancer cells expressing a myelodysplastic syndrome-associated splicing factor mutation (SRSF2P95H) are more sensitive to one of these compounds than those expressing the wild-type version of the protein. Transcriptome analyses showed that this compound causes widespread changes in gene expression in sensitive SRSF2P95H-expressing cells. Our results demonstrate the utility of using a yeast-based HTS to identify compounds capable of changing pre-mRNA splicing outcomes.

  PublisherDOI

• A Yeast-Based High-Throughput Screening Platform for the Discovery of Novel pre-mRNA Splicing Modulators

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-10-20

  preprintOpen access

  ABSTRACT Pre-mRNA splicing is a crucial process in eukaryotic gene expression, and splicing dysregulation has been linked to various diseases. However, very few small molecules have been discovered that can modulate spliced mRNA formation or inhibit the splicing machinery itself. This study presents a novel high-throughput screening (HTS) platform for identifying compounds that modulate splicing. Our platform comprises a two-tiered screening approach: a primary screen measuring growth inhibition in sensitized in S. cerevisiae (yeast) strains and a secondary screen that relies on production of a fluorescent protein as a readout for splicing inhibition. Using this approach, we identified 4 small molecules that cause accumulation of unspliced pre-mRNA in vivo in yeast. In addition, cancer cells expressing a myelodysplastic syndrome-associated splicing factor mutation (SRSF2 P95H ) are more sensitive to one of these compounds than those expressing the wild-type version of the protein. Transcriptome analyses showed that this compound causes widespread changes in gene expression in sensitive SRSF2 P95H -expressing cells. Our results demonstrate the utility of using a yeast-based HTS to identify compounds capable of changing pre-mRNA splicing outcomes.

  PublisherOA PDFDOI

• The human branchpoint-interacting stem loop sequence and structure regulates U2 snRNA expression, branchpoint recognition, and transcriptome

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-08-31 · 1 citations

  preprintOpen accessSenior authorCorresponding

  ABSTRACT During pre-mRNA splicing, the branch helix forms when U2 snRNP engages with introns to initiate spliceosome assembly. Its formation is mutually exclusive with the branchpoint-interacting stem loop (BSL) present in U2 snRNA. While BSL structure impacts splicing with the strict consensus branchpoint sequence of yeast introns, its influence in the flexible context of human branchpoints is unknown. We employed an orthogonal U2 snRNA and splicing reporter to examine the impact of perturbing BSL base-pairing and found differential effects on both orthogonal U2 snRNA expression and reporter splicing, indicating that BSL structure influences the biogenesis of U2 snRNP and its function in splicing. Furthermore, high complementarity between the branchpoint sequence and U2 snRNA increases splicing efficiency with wildtype and stabilized BSL, but not when BSL base-pairing is reduced. These data are consistent with complementarity between the intron and the loop of the BSL driving intron-mediated unwinding of the BSL stem. Finally, we investigated transcriptome-wide effects of expressing U2 snRNA with either a cancer-associated BSL mutation or with an altered branchpoint recognition sequence. Similar changes in splicing and gene expression suggests that while altered U2 snRNA is tolerated, cells respond by upregulating genes linked to oncogenic pathways. Main Conclusions U2 snRNA BSL base-pairing influences branchpoint sequence recognition and splicing of an orthogonal splicing reporter Propose a model for branchpoint sequence complementarity inducing BSL unwinding to promote splicing efficiency U2 snRNA BSL and BPRS mutations alter cellular gene expression regulation and splicing GRAPHICAL ABSTRACT

  PublisherOA PDFDOI

• SF3B1 thermostability as an assay for splicing inhibitor interactions

  Journal of Biological Chemistry · 2024-12-24 · 4 citations

  articleOpen accessSenior author

  The spliceosome protein, SF3B1, is associated with U2 snRNP during early spliceosome assembly for pre-mRNA splicing. Frequent somatic mutations in SF3B1 observed in cancer necessitates the characterization of its role in identifying the branchpoint adenosine of introns. Remarkably, SF3B1 is the target of three distinct natural product drugs, each identified by their potent anti-tumor properties. Structural studies indicate that SF3B1 conformational flexibility is functionally important, and suggest that drug binding blocks the transition to a closed state of SF3B1 required for the next stage of spliceosome assembly. This model is confounded, however, by the antagonistic property of an inactive herboxidiene analog. In this study, we established an assay for evaluating the thermostability of SF3B1 present in the nuclear extract preparations employed for in vitro splicing studies, to investigate inhibitor interactions with SF3B1 in a functional context. We show that both active and antagonistic analogs of natural product inhibitors affect SF3B1 thermostability, consistent with binding alone being insufficient to impair SF3B1 function. Surprisingly, SF3B1 thermostability differs among nuclear extract preparations, likely reflecting its conformational status. We also investigated a synthetic SF3B1 ligand, WX-02-23, and found that it increases SF3B1 thermostability and interferes with in vitro splicing by a mechanism that strongly resembles the activity of natural product inhibitors. We propose that altered SF3B1 thermostability can serve as an indicator of inhibitor binding to complement functional assays of their general effect on splicing. It may also provide a means to investigate the factors that influence SF3B1 conformation.

  PublisherOA PDFDOI

• Broad variation in response of individual introns to splicing inhibitors in a humanized yeast strain

  bioRxiv (Cold Spring Harbor Laboratory) · 2023-10-05 · 1 citations

  preprintOpen access

  ABSTRACT Intron branch point (BP) recognition by the U2 snRNP is a critical step of splicing, vulnerable to recurrent cancer mutations and bacterial natural product inhibitors. The BP binds a conserved pocket in the SF3B1 (human) or Hsh155 (yeast) U2 snRNP protein. Amino acids that line this pocket affect binding of splicing inhibitors like Pladienolide-B (Plad-B), such that organisms differ in their sensitivity. To study the mechanism of splicing inhibitor action in a simplified system, we modified the naturally Plad-B resistant yeast Saccharomyces cerevisiae by changing 14 amino acids in the Hsh155 BP pocket to those from human. This humanized yeast grows normally, and splicing is largely unaffected by the mutation. Splicing is inhibited within minutes after addition of Plad-B, and different introns appear inhibited to different extents. Intron-specific inhibition differences are also observed during co-transcriptional splicing in Plad-B using single-molecule intron tracking (SMIT) to minimize gene-specific transcription and decay rates that cloud estimates of inhibition by standard RNA-seq. Comparison of Plad-B intron sensitivities to those of the structurally distinct inhibitor Thailanstatin-A reveals intron-specific differences in sensitivity to different compounds. This work exposes a complex relationship between binding of different members of this class of inhibitors to the spliceosome and intron-specific rates of BP recognition and catalysis. Introns with variant BP sequences seem particularly sensitive, echoing observations from mammalian cells, where monitoring individual introns is complicated by multi-intron gene architecture and alternative splicing. The compact yeast system may hasten characterization of splicing inhibitors, accelerating improvements in selectivity and therapeutic efficacy.

  PublisherOA PDFDOI

• Broad variation in response of individual introns to splicing inhibitors in a humanized yeast strain

  RNA · 2023-11-28 · 12 citations

  articleOpen access

  Intron branchpoint (BP) recognition by the U2 snRNP is a critical step of splicing, vulnerable to recurrent cancer mutations and bacterial natural product inhibitors. The BP binds a conserved pocket in the SF3B1 (human) or Hsh155 (yeast) U2 snRNP protein. Amino acids that line this pocket affect the binding of splicing inhibitors like Pladienolide-B (Plad-B), such that organisms differ in their sensitivity. To study the mechanism of splicing inhibitor action in a simplified system, we modified the naturally Plad-B resistant yeast Saccharomyces cerevisiae by changing 14 amino acids in the Hsh155 BP pocket to those from human. This humanized yeast grows normally, and splicing is largely unaffected by the mutation. Splicing is inhibited within minutes after the addition of Plad-B, and different introns appear inhibited to different extents. Intron-specific inhibition differences are also observed during cotranscriptional splicing in Plad-B using single-molecule intron tracking to minimize gene-specific transcription and decay rates that cloud estimates of inhibition by standard RNA-seq. Comparison of Plad-B intron sensitivities to those of the structurally distinct inhibitor Thailanstatin-A reveals intron-specific differences in sensitivity to different compounds. This work exposes a complex relationship between the binding of different members of this class of inhibitors to the spliceosome and intron-specific rates of BP recognition and catalysis. Introns with variant BP sequences seem particularly sensitive, echoing observations from mammalian cells, where monitoring individual introns is complicated by multi-intron gene architecture and alternative splicing. The compact yeast system may hasten the characterization of splicing inhibitors, accelerating improvements in selectivity and therapeutic efficacy.

  PublisherOA PDFDOI

• A model for DHX15 mediated disassembly of A-complex spliceosomes

  RNA · 2022 · 34 citations

  Senior authorCorresponding
  • Biology
  • Biochemistry
  • Cell biology

  A critical step of pre-mRNA splicing is the recruitment of U2 snRNP to the branch point sequence of an intron. U2 snRNP conformation changes extensively during branch helix formation, and several RNA-dependent ATPases are implicated in the process. However, the molecular mechanisms involved remain to be fully dissected. We took advantage of the differential nucleotide triphosphates requirements for DExD/H-box enzymes to probe their contributions to in vitro spliceosome assembly. Both ATP and GTP hydrolysis support the formation of A-complex, indicating the activity of a DEAH-enzyme because DEAD-enzymes are selective for ATP. We immunodepleted DHX15 to assess its involvement, and although splicing efficiency decreases with reduced DHX15, A-complex accumulation incongruently increases. DHX15 depletion also results in the persistence of the atypical ATP-independent interaction between U2 snRNP and a minimal substrate that is otherwise destabilized in the presence of either ATP or GTP. These results lead us to hypothesize that DHX15 plays a quality control function in U2 snRNP's engagement with an intron. In efforts to identify the RNA target of DHX15, we determined that an extended polypyrimidine tract is not necessary for disruption of the atypical interaction between U2 snRNP and the minimal substrate. We also examined U2 snRNA by RNase H digestion and identified nucleotides in the branch binding region that become accessible with both ATP and GTP hydrolysis, again implicating a DEAH-enzyme. Together, our results demonstrate that multiple ATP-dependent rearrangements are likely involved in U2 snRNP addition to the spliceosome and that DHX15 may have an expanded role in maintaining splicing fidelity.

  PublisherOA PDFDOI

• A Model for DHX15 Mediated Disassembly of A-Complex Spliceosomes

  bioRxiv (Cold Spring Harbor Laboratory) · 2021-09-12 · 2 citations

  preprintOpen accessSenior authorCorresponding

  Abstract A critical step of pre-mRNA splicing is the recruitment of U2 snRNP to the branch point sequence of an intron. U2 snRNP conformation changes extensively during branch helix formation and several RNA-dependent-ATPases are implicated in the process. However, the molecular mechanisms involved remain to be fully dissected. We took advantage of the differential nucleotide triphosphates requirements for DExD/H-box enzymes to probe their contributions to in vitro spliceosome assembly. Both ATP and GTP hydrolysis support the formation of A-complex, indicating the activity of a DEAH-enzyme because DEAD-enzymes are selective for ATP. We immunodepleted DHX15 to assess its involvement and although splicing efficiency decreases with reduced DHX15, A-complex accumulation incongruently increases. DHX15 depletion also results in the persistence of the atypical ATP-independent interaction between U2 snRNP and a minimal substrate that is otherwise destabilized in the presence of either ATP or GTP. These results lead us to hypothesize that DHX15 plays a quality control function in U2 snRNP’s engagement with an intron. In efforts to identify the RNA target of DHX15, we determined that an extended polypyrimidine tract is not necessary for disruption of the atypical interaction between U2 snRNP and the minimal substrate. We also examined U2 snRNA by RNase H digestion and identified nucleotides in the branch binding region that become accessible with both ATP and GTP hydrolysis, again implicating a DEAH-enzyme. Together, our results demonstrate that multiple ATP-dependent rearrangements are likely involved in U2 snRNP addition to the spliceosome and that DHX15 can have an expanded role in splicing.

  PublisherOA PDFDOI

• Abstract 1832: Development of a splicing modulator-based ADC payload class with immune stimulatory properties for cancer therapy

  Cancer Research · 2021-07-01

  article

  Abstract Background: Thailanstatins are naturally occurring anti-proliferative compounds that target spliceosomes and modulate pre-mRNA splicing. Alterations in splicing machinery and mRNA splicing is common in cancer and represents a potential susceptibility that can be exploited by targeted delivery of a splicing modulator to tumors with antibody drug conjugates (ADCs). Results: PH1 payload is a novel derivative of Thailanstatin optimized for metabolic stability and anti-tumor activity. PH1 is an efficient modulator of splicing in vitro and in vivo and a poor substrate for the MDR1 transporter. Transcriptome analysis of PH1- treated NCI-N87 cells revealed multiple classes of mis-splicing events including elevated expression of transcripts with skipped exons (3364 genes/4x change) and retained introns (332 genes/2.5x change). Translation of transcripts with retained introns and novel exon-exon junctions results in generation of neoepitopes. Upon conjugation to Trastuzumab, Tras PH1 ADC exhibited nanomolar potency specific to HER2-expressing cancer cells, with durable anti-tumor response in vivo and favorable pharmacokinetic exposure in mice. Due to the potential for generation of neoepitopes, combination studies of Tras PH1 with a checkpoint inhibitor antibody was performed in a syngeneic MC38-HuHer2 model. Single agent and combination treatments induced tumor recruitment of CD11b+ positive myeloid cell subsets. While the combination treatment eradicated tumors, the treated animals also developed tumor-specific immunity. A toxicology study performed in cynomolgus monkeys confirmed favorable PK profile and a wide safety margin for Tras PH1 ADC. Conclusions: We present the development of a splicing modulator-based payload class with the ability to target tumor mRNA splicing, induce tumor neoepitopes, recruit myeloid cells and generate anti-tumor immunity. These findings support the development of ADCs using this novel class of immunostimulatory payload. Citation Format: Satyajit K. Mitra, Vasu Jammalamadaka, Jeffrey Kang, Teodora Losic, Greg Tuffy, Tony W. Liang, Kim Tipton, Adriana Lopez, Scott Savage, William Monteith, William E. Haskins, Melissa S. Jurica, Sanjeev Satyal, Mary Do. Development of a splicing modulator-based ADC payload class with immune stimulatory properties for cancer therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1832.

  PublisherDOI

Recent grants

• University of California, Santa Cruz IMSD Program

  NIH · $20.2M · 1999–2021

• Mechanisms of the spliceosome protein SF3B1 and inhibitors

  NIH · $1.8M · 2017–2022

• NIH Grant R01CA136762

  NIH · $908k · 2014

• Interpreting the Structure of the Spliceosome

  NIH · $2.7M · 2006–2018

• NIH Grant P41RR001614

  NIH · $8.0M · 2015

Frequent coauthors

• Melissa J. Moore

  University of Massachusetts Chan Medical School

  26 shared

• Arun K. Ghosh

  Purdue University West Lafayette

  24 shared

• Barry Stoddard

  Seattle University

  14 shared

• Kerstin A. Effenberger

  PTC Therapeutics (United States)

  13 shared

• Barry Stoddard

  Fred Hutch Cancer Center

  12 shared

• Andrew D. Mesecar

  Purdue University West Lafayette

  12 shared

• Nikolaus Grigorieff

  Howard Hughes Medical Institute

  10 shared

• Andrew J. MacRae

  10 shared