Author
Jonathan P. Staley
Other affiliations: University of Illinois at Chicago, University of California, San Francisco, Massachusetts Institute of Technology
Bio: Jonathan P. Staley is an academic researcher from University of Chicago. The author has contributed to research in topics: RNA splicing & Spliceosome. The author has an hindex of 28, co-authored 42 publications receiving 4198 citations. Previous affiliations of Jonathan P. Staley include University of Illinois at Chicago & University of California, San Francisco.
Topics: RNA splicing, Spliceosome, Intron, RNA, Small nuclear RNA
Papers
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TL;DR: This work aims to provide a history of canine coronavirus infection in the context of central giant cell granuloma and aims to establish a cause-and-effect relationship between infection and disease progression.
1,163 citations
TL;DR: By lengthening the U1:5' splice site duplex, this work impeded this switch in a temperature-dependent manner and prevented formation of the spliceosome's catalytic core.
315 citations
TL;DR: It is shown that the U6 snRNA catalyses both of the two splicing reactions by positioning divalent metals that stabilize the leaving groups during each reaction, indicating that RNA mediates catalysis within the spliceosome.
Abstract: In nuclear pre-messenger RNA splicing, introns are excised by the spliceosome, a dynamic machine composed of both proteins and small nuclear RNAs (snRNAs) Over thirty years ago, after the discovery of self-splicing group II intron RNAs, the snRNAs were proposed to catalyse splicing However, no definitive evidence for a role of either RNA or protein in catalysis by the spliceosome has been reported so far By using metal rescue strategies in spliceosomes from budding yeast, here we show that the U6 snRNA catalyses both of the two splicing reactions by positioning divalent metals that stabilize the leaving groups during each reaction Notably, all of the U6 catalytic metal ligands we identified correspond to the ligands observed to position catalytic, divalent metals in crystal structures of a group II intron RNA These findings indicate that group II introns and the spliceosome share common catalytic mechanisms and probably common evolutionary origins Our results demonstrate that RNA mediates catalysis within the spliceosome
285 citations
TL;DR: In addition to unwinding RNA, the DExD/H box proteins may affect RNA-RNA rearrangements by antagonizing specific RNA-stabilizing proteins.
209 citations
TL;DR: The findings indicate that Snu114p functions as a classic regulatory G protein that serves as a signal-dependent switch that transduces signals to Brr2p to control spliceosome dynamics.
187 citations
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TL;DR: The structure, assembly, and function of the posttranslational modification with ubiquitin, a process referred to as ubiquitylation, controls almost every process in cells.
Abstract: The posttranslational modification with ubiquitin, a process referred to as ubiquitylation, controls almost every process in cells. Ubiquitin can be attached to substrate proteins as a single moiety or in the form of polymeric chains in which successive ubiquitin molecules are connected through specific isopeptide bonds. Reminiscent of a code, the various ubiquitin modifications adopt distinct conformations and lead to different outcomes in cells. Here, we discuss the structure, assembly, and function of this ubiquitin code.
2,762 citations
TL;DR: This review describes what is currently known of the molecular mechanisms that control changes in splice site choice and starts with the best-characterized systems from the Drosophila sex determination pathway, and then describes the regulators of other systems about whose mechanisms there is some data.
Abstract: Alternative pre-mRNA splicing is a central mode of genetic regulation in higher eukaryotes. Variability in splicing patterns is a major source of protein diversity from the genome. In this review, I describe what is currently known of the molecular mechanisms that control changes in splice site choice. I start with the best-characterized systems from the Drosophila sex determination pathway, and then describe the regulators of other systems about whose mechanisms there is some data. How these regulators are combined into complex systems of tissue-specific splicing is discussed. In conclusion, very recent studies are presented that point to new directions for understanding alternative splicing and its mechanisms.
2,590 citations
TL;DR: The spliceosome exhibits exceptional compositional and structural dynamics that are exploited during substrate-dependent complex assembly, catalytic activation, and active site remodeling in the pre-mRNAs.
2,316 citations
TL;DR: The pathway of ncRNA research is described, where every established "rule" seems destined to be overturned.
1,875 citations
TL;DR: This work presents a census of 1,542 manually curated RBPs that are analysed for their interactions with different classes of RNA, their evolutionary conservation, their abundance and their tissue-specific expression, a critical step towards the comprehensive characterization of proteins involved in human RNA metabolism.
Abstract: Post-transcriptional gene regulation (PTGR) concerns processes involved in the maturation, transport, stability and translation of coding and non-coding RNAs. RNA-binding proteins (RBPs) and ribonucleoproteins coordinate RNA processing and PTGR. The introduction of large-scale quantitative methods, such as next-generation sequencing and modern protein mass spectrometry, has renewed interest in the investigation of PTGR and the protein factors involved at a systems-biology level. Here, we present a census of 1,542 manually curated RBPs that we have analysed for their interactions with different classes of RNA, their evolutionary conservation, their abundance and their tissue-specific expression. Our analysis is a critical step towards the comprehensive characterization of proteins involved in human RNA metabolism.
1,479 citations