Article
Biochemistry & Molecular Biology
Kevin R. Roy, Jason Gabunilas, Dean Neutel, Michelle Ai, Zoe Yeh, Joyce Samson, Guochang Lyu, Guillaume F. Chanfreau
Summary: The fidelity of 3'-splice site (3'SS) selection is crucial for proper gene expression. In the absence of the Prp18p splicing factor, alternative non-YAG sequences are activated and used as 3'SS in S. cerevisiae, facilitated by upstream poly(U) tracts and interaction with the first intronic nucleoside. Prp18p plays a unique role in maintaining 3'SS fidelity by interacting with other spliceosomal proteins.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Plant Sciences
Lei Liu, Xiaoyun Li, Li Yuan, Guofang Zhang, Hui Gao, Xiaodong Xu, Hongtao Zhao
Summary: This study identifies XCT as a key spliceosomal component associated with multiple splicing factors. Inactivation of XCT leads to defects in Alt 3'ss recognition, resulting in significant alterations in the 3' splice sites of LHY and TIC and a shortened circadian period.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2022)
Review
Oncology
Carlos A. Nino, Rossella Scotto di Perrotolo, Simona Polo
Summary: This review summarizes the cancer hotspot mutations in spliceosome components, focusing on the effects of mutations in U1 snRNA, SF3B1, and U2AF1 on splice site selection and cancer development.
Article
Biology
Sarah R. Hansen, David S. White, Mark Scalf, Ivan R. Correa, Lloyd M. Smith, Aaron A. Hoskins, Jonathan P. Staley
Summary: This study investigated the pathway of 5' SS selection by purified yeast U1 snRNP using colocalization single-molecule spectroscopy. The results revealed a sequence-dependent, two-step mechanism for U1 to reversibly select 5' SS, providing a kinetic basis for how U1 may rapidly surveil nascent transcripts for 5' SS.
Article
Multidisciplinary Sciences
Olexandr Dybkov, Marco Preussner, Leyla El Ayoubi, Vivi-Yun Feng, Caroline Harnisch, Kilian Merz, Paula Leupold, Peter Yudichev, Dmitry E. Agafonov, Cindy L. Will, Cyrille Girard, Christian Dienemann, Henning Urlaub, Berthold Kastner, Florian Heyd, Reinhard Luehrmann
Summary: Alternative precursor messenger RNA splicing expands the proteome of higher eukaryotes, and changes in 3'ss usage contribute to human disease. Through knockdowns and RNA sequencing, we found that proteins recruited to human C* spliceosomes regulate alternative splicing, including the selection of NAGNAG 3'ss. Cryo-electron microscopy and protein cross-linking provide insights into the molecular architecture of these proteins and how they influence 3'ss usage. Our studies reveal widespread regulation of alternative 3'ss usage and the mechanisms by which C* proteins influence NAGNAG 3'ss choices.
Article
Biochemistry & Molecular Biology
Kinneret Shefer, Ayub Boulos, Valer Gotea, Maram Arafat, Yair Ben Chaim, Aya Muharram, Sara Isaac, Amir Eden, Joseph Sperling, Laura Elnitski, Ruth Sperling
Summary: This study reveals that latent splice sites are highly abundant in human introns, and their activation under stress and in cancer leads to the generation of numerous nonsense mRNAs. The previously proposed mechanism to suppress latent splicing was shown to be independent of protein translation and dependent on initiator-tRNA. The nuclear protein nucleolin (NCL) was identified as directly and specifically interacting with initiator-tRNA in the nucleus, and its association with pre-mRNA was also demonstrated. It was further revealed that nucleolin is essential for the recovery of suppression of latent splicing by initiator-tRNA. Knockdown of nucleolin led to the activation of latent splicing in coding transcripts with important cellular functions. Therefore, nucleolin, as a component of the endogenous spliceosome, is proposed as the first protein of a nuclear quality control mechanism that regulates splice site selection to prevent defective mRNA generation.
Review
Oncology
Maram Arafat, Ruth Sperling
Summary: Splicing and alternative splicing are important in regulating gene expression and their misregulation can lead to diseases, including cancer. This review summarizes a quality control mechanism called Suppression of Splicing (SOS) that protects cells from splicing at unused intronic splice sites and its relevance to cancer. SOS is abrogated in stress and cancer, resulting in the expression of aberrant nonsense mRNAs that may be toxic to cells. These findings suggest the potential of aberrant isoforms as novel targets for cancer diagnosis and therapies.
Article
Biology
Lauren A. Levesque, Scott Roy, Nicole Salazar
Summary: Through investigating the expression and splicing events of CXCR3 in breast cancer, its association with breast cancer progression and immune infiltration was revealed. The importance of A3SS in regulating CXCR3 was validated, while the splicing events in breast cancer indicated the role of A3SS in the integrated splicing network.
Article
Multidisciplinary Sciences
Yuma Ishigami, Takayuki Ohira, Yui Isokawa, Yutaka Suzuki, Tsutomu Suzuki
Summary: The modification of N-6-methyladenosine on spliceosomal U6 snRNA facilitates efficient recognition of the splice sites through cooperation with U5 snRNA, allowing for variation in the 5' exon sequence and contributing to protein sequence diversity.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Karli A. Lipinski, Katherine A. Senn, Natalie J. Zeps, Aaron A. Hoskins
Summary: Splicing is a crucial step in gene expression in eukaryotes, and FAM192A is an important splicing factor. By studying the potential homolog of FAM192A in yeast, FYv6, it was found that FYv6 is also a splicing factor involved in exon ligation and regulates splicing by influencing 3' splice site usage.
Article
Biochemistry & Molecular Biology
Francisco Carranza, Hossein Shenasa, Klemens J. Hertel
Summary: Alternative splicing is a highly combinatorial mechanism that allows higher eukaryotes to increase mRNA diversity. The selection of alternative splice sites is influenced by sequence, cis-regulatory elements, exon and intron length, and RNA secondary structures. The study showed that the mode of splice site recognition, either intron or exon definition, plays a role in alternative splicing decisions.
Article
Biology
Matthew T. Parker, Beth K. Soanes, Jelena Kusakina, Antoine Larrieu, Katarzyna Knop, Nisha Joy, Friedrich Breidenbach, Anna Sherwood, Geoffrey J. Barton, Sebastian M. Fica, Brendan H. Davies, Gordon G. Simpson, Jonathan P. Staley
Summary: Alternative splicing is associated with the evolution of complex eukaryotes. The m(6)A modification of U6 snRNA plays a crucial role in splicing accuracy and efficiency. The sequence composition of splice sites and the cooperative roles of U5 and U6 snRNA are important in splice site selection. U6 snRNA m(6)A modification influences the usage of 3' splice sites. Two major classes of 5' splice site were identified in diverse eukaryotes.
Article
Biochemistry & Molecular Biology
John G. Conboy
Summary: A translationally silent single nucleotide mutation in exon 44 of the von Willebrand factor gene is associated with inefficient splicing in a von Willebrand disease patient. The mutation introduces a cryptic splice donor site that interferes with the function of the annotated site to favor intron retention. Competition between the cryptic site and annotated site may affect splicing efficiency.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Stefanie Ebersberger, Clara Hipp, Miriam M. Mulorz, Andreas Buchbender, Dalmira Hubrich, Hyun-Seo Kang, Santiago Martinez-Lumbreras, Panajot Kristofori, F. X. Reymond Sutandy, Lidia Llacsahuanga Allcca, Jonas Schoenfeld, Cem Bakisoglu, Anke Busch, Heike Haenel, Kerstin Tretow, Mareen Welzel, Antonella Di Liddo, Martin M. Moeckel, Kathi Zarnack, Ingo Ebersberger, Stefan Legewie, Katja Luck, Michael Sattler, Julian Koenig
Summary: In this study, the RNA-binding protein FUBP1 was identified as a key splicing factor that stabilizes key components at the 3' splice site, U2AF2 and SF1. FUBP1 plays an important role in efficient splicing of long introns, which is impaired in cancer patients with FUBP1 mutations. It was found that FUBP1 interacts with multiple U1 snRNP-associated proteins, suggesting a unique role in splice site bridging for long introns. A compelling model for 3' splice site recognition of long introns is proposed.
Article
Biochemistry & Molecular Biology
Adam A. Mol, Marc Vogel, Beatrix Suess
Summary: A synthetic genetic device was developed to control nuclear and cytosolic localization in human cells through controlled alternative splicing. By manipulating a TetR aptamer and adding doxycycline, specific splice sites can be selected to produce two isoforms. This technology allows integration of different target sequences for research on protein localization and alternative splicing mechanisms in human cells.
Article
Biochemistry & Molecular Biology
Arka Chakraborty, Sebastien Lyonnais, Federica Battistini, Adam Hospital, Giorgio Medici, Rafel Prohens, Modesto Orozco, Josep Vilardell, Maria Sola
NUCLEIC ACIDS RESEARCH
(2017)
Article
Cell Biology
Agnieszka Tudek, Manfred Schmid, Marius Makaras, J. David Barrass, Jean D. Beggs, Torben Heick Jensen
Article
Biochemistry & Molecular Biology
Gonzalo I. Mendoza-Ochoa, J. David Barrass, Barbara R. Terlouw, Isabella E. Maudlin, Susana de Lucas, Emanuela Sani, Vahid Aslanzadeh, Jane A. E. Reid, Jean D. Beggs
Article
Biochemistry & Molecular Biology
Amit Gautam, Jean D. Beggs
Article
Multidisciplinary Sciences
J. David Barrass, Gonzalo Mendoza-Ochoa, Isabella E. Maudlin, Emanuela Sani, Jean D. Beggs
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2019)
Article
Biochemistry & Molecular Biology
Gonzalo I. Mendoza-Ochoa, J. David Barrass, Isabella E. Maudlin, Jean D. Beggs
Article
Multidisciplinary Sciences
J. David Barrass, Jean D. Beggs
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2019)
Article
Cell Biology
Marek Adamowicz, Richard Hailstone, Annie A. Demin, Emilia Komulainen, Hana Hanzlikova, Jan Brazina, Amit Gautam, Sophie E. Wells, Keith W. Caldecott
Summary: Toxic PARP1 activity induced by mutations in XRCC1 impairs global transcription recovery during DNA base excision repair by promoting aberrant recruitment and activity of the ubiquitin protease USP3. Inhibition or deletion of PARP1 or USP3 restores transcriptional recovery in XRCC1-deficient cells, suggesting them as potential therapeutic targets in neurological disease.
NATURE CELL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Alina Vaitsiankova, Kamila Burdova, Margarita Sobol, Amit Gautam, Oldrich Benada, Hana Hanzlikova, Keith W. Caldecott
Summary: PARP inhibitors hinder the maturation of nascent DNA strands during DNA replication, particularly unligated Okazaki fragments and other discontinuities, resulting in cytotoxic effects. The activation of PARP1 is elevated in cells lacking the FEN1 nuclease, suggesting its involvement in the detection and processing of these DNA replication intermediates. PARP inhibitors disrupt the integrity of nascent DNA strands in both normal and FEN1(-/-) cells, leading to the formation of single-strand nicks or gaps. These findings highlight the importance of unligated Okazaki fragments and other discontinuities in the cytotoxicity of PARP inhibitors.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Almudena Serrano-Benitez, Sophie E. Wells, Lylah Drummond-Clarke, Lilian C. Russo, John Christopher Thomas, Giovanna A. Leal, Mark Farrow, James Michael Edgerton, Shankar Balasubramanian, Ming Yang, Christian Frezza, Amit Gautam, Jan Brazina, Kamila Burdova, Nicolas C. Hoch, Stephen P. Jackson, Keith W. Caldecott
Summary: DNA single-strand breaks (SSBs) play a role in disrupting DNA replication and causing chromosome breakage. This study investigates whether SSBs induce chromosome breakage when located behind or ahead of replication forks, and finds that only SSBs ahead of replication forks trigger fork collapse and chromosome breakage. Furthermore, the study shows that CldU, a thymidine analogue, is cytotoxic to cells lacking SSB repair mechanisms and its incorporation in template DNA is particularly harmful during the following cell cycle. Additionally, BRCA-defective cells are highly sensitive to CldU, suggesting its potential clinical utility.
Article
Biochemistry & Molecular Biology
Amit Gautam, Heather Fawcett, Kamila Burdova, Jan Brazina, Keith W. Caldecott
Summary: This study identified a DNA base excision repair process in normal human cells that can rapidly remove a subset of photodimers induced by UV irradiation. This repair process functions independently of nucleotide excision repair.
Article
Biotechnology & Applied Microbiology
J. David Barrass, Jane E. A. Reid, Yuanhua Huang, Ralph D. Hector, Guido Sanguinetti, Jean D. Beggs, Sander Granneman