- Periodicals (Báo – Tạp chí)
Authors : Rosenblum, Sydney L; Lorenz, Daniel A; Garner, Amanda L (2020) - Recent efforts in genome-wide sequencing and proteomics have revealed the fundamental roles that RNA-binding proteins (RBPs) play in the life cycle and function of both coding and non-coding RNAs. While these methodologies provide a systems-level view of the networking of RNA and proteins, approaches to enable the cellular validation of discovered interactions are lacking. Leveraging the power of bioorthogonal chemistry- and split-luciferase-based assay technologies, w...
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- Journal article
Authors : Sawant, Anupam A. (2023) - RNA-based genetic code is thought to be central to life’s emergence due to its dual ability for information transfer and catalysis. Nonetheless, the genetic code of early life was potentially not restricted to canonical genetic alphabets alone. The presence of an extensive repertoire of modified nucleobases in extant biology as ‘signatures of the past’, highlights the relevance of non-canonical alphabets, ably strengthened by experiments demonstrating their r...
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- Journal article
Authors : Doval, Carmela Garcia; Schwede, Frank; Berk, Christian (2020) - Upon target RNA recognition, type III CRISPR-Cas systems produce cyclic oligoadenylate second messengers to activate downstream effectors including Csm6-family ribonucleases via their CARF domains. Here we show that Enteroccocus italicus Csm6 (EiCsm6) degrades its cognate cyclic hexa-AMP (cA6) activator and report the crystal structure of EiCsm6 bound to a cA6 mimic. The structure, combined with biochemical and in vivo functional assays, reveal how cA6 recognition ...
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- Journal article
Authors : Wielenberg, Kevin; Wang, Miao; Yang, Min (2020) - Nucleic acid crosslinkers that covalently join commentary strands have applications as both pharmaceuticals and biochemical probes. Psoralen is a popular crosslinker moiety that reacts with double stranded DNA and RNA upon irradiation with long wave UV light. A commercially available compound EZ-Link Psoralen-PEG3-Biotin has been used in many studies to crosslink DNA and double strand RNA for genome-wide investigations. Here we present a novel probe, AP3B, wh...
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- Journal article
Authors : Johanna, Hörberg (2023) - Transcription factors (TFs) regulate eukaryotic transcription through selecting DNA-binding,
can also specifically interact with RNA, which may present another layer of transcriptional
control. The mechanisms of the TFs-DNA recognition are often well-characterised, while the
details of TFs-RNA complexation are less understood. Here we investigate the dual
recognition mechanism of the glucocorticoid receptor (GR), which interacts with similar
affinities with consen...
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- Journal Article
Authors : Thompson, Valery F. (2023) - The protein FUS (FUSed in sarcoma) is a metazoan RNA-binding protein that influences RNA production by all three nuclear polymerases. FUS also binds nascent transcripts, RNA processing factors, RNA polymerases, and transcription machinery. We explored the role of FUS binding interactions for activity during transcription. In vitro run-off transcription assays revealed FUS enhanced RNA produced by a non-eukaryote polymerase. Activity also reduced the formation of R...
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- Journal article
Authors : Murugan, Karthik; Seetharam, Arun S; Severin, Andrew J (2020) - Cas9 is an RNA-guided endonuclease in the bacterial CRISPR-Cas immune system and a popular tool for genome editing. The most commonly used Cas9 variant, Streptococcus pyogenes Cas9 (SpCas9), is relatively non-specific and prone to off-target genome editing. Other Cas9 orthologs and engineered variants of SpCas9 have been reported to be more specific than wild-type (WT) SpCas9. However, systematic comparisons of the cleavage activities of these Cas9 variants&#...
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- Journal article
Authors : Fos, Santi Mestre; Ito, Chieri; Moore, Courtney M (2020) - The in vitro formation of stable G-quadruplexes (G4s) in human ribosomal RNA (rRNA) was recently reported. However, their formation in cells and their cellular roles have not been resolved. Here, by taking a chemical biology approach that integrates results from immunofluorescence, G4 ligands, heme affinity reagents, and a genetically encoded fluorescent heme sensor, we report that human ribosomes can form G4s in vivo that regulate heme bioavailability. ...
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- Periodicals (Báo – Tạp chí)
Authors : Halder, Antarip; Kumar, Sunil; Valsson, Omar (2020) - RNA molecules selectively bind to specific metal ions to populate their functional active states making it important to understand their source of ion selectivity. In large RNA systems, metal ions interact with the RNA at multiple locations making it difficult to decipher the precise role of ions in folding. To overcome this complexity, we studied the role of different metal ions (Mg2+, Ca2+ and K+) in the folding of a small RNA ...
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- Journal article
Authors : Montemayor, Eric J; Virta, Johanna M; Hayes, Samuel M (2020) - Eukaryotes possess eight highly conserved Lsm (like Sm) proteins that assemble into circular, heteroheptameric complexes, bind RNA, and direct a diverse range of biological processes. Among the many essential functions of Lsm proteins, the cytoplasmic Lsm1-7 complex initiates mRNA decay, while the nuclear Lsm2-8 complex acts as a chaperone for U6 spliceosomal RNA. It has been unclear how these complexes perform their distinct functions while differing by ...
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- Journal article
Authors : Fleming, Aaron M. (2023) - Direct RNA sequencing with a commercial nanopore platform was used to sequence RNA containing uridine (U), pseudouridine (Ψ), or N1-methylpseudouridine (m1Ψ) generated by in vitro transcription (IVT). The base calling data as well as the ionic currents and dwell times for U, Ψ, or m1Ψ as they translocated through the helicase and nanopore proteins identified diagnostic signatures for Ψ and m1Ψ; however, the two modifications yielded similar patterns ...
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- Periodicals (Báo – Tạp chí)
Authors : Carlson, Christopher R; Asfaha, Jonathan B; Ghent, Chloe M (2020) - The nucleocapsid (N) protein of coronaviruses serves two major functions: compaction of the RNA genome in the virion and regulation of viral gene transcription in the infected cell1–3. The N protein contains two globular RNA-binding domains surrounded by regions of intrinsic disorder4. Phosphorylation of the central disordered region is required for normal viral genome transcription5,6, which occurs in a cytoplasmic structure called the replication transcription c...
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- Journal article
Authors : Costanzo, Giovanna; Cirigliano, Angela; Pino, Samanta (2020) - A cornerstone of molecular evolution leading to the emergence of life on our planet is associated with appearance of the first catalytic RNA molecules. A question remains regarding the nature of the simplest catalytic centers that could mediate the chemistry needed for RNA-catalysis. In the current paper we provide a new example supporting our previously suggested model proposing that transiently formed open loop geometries could serve as temporary ...
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- Journal Article
Authors : wicks, sarah L. (2023) - The use of small molecules to modulate RNA structure and function has become invaluable for
studying the many roles of RNA in biological processes1 as well as discovering effective
therapeutic treatments.2-5 Early on, the promise of RNA as a ‘druggable’ target was demonstrated
by the identification of several RNA-targeting small molecule classes such as aminoglycosides.6,
7 These ligands bound highly abundant and structured ribosomal RNA (r...
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- Journal article
Authors : DasGupta, Saurja (2023) - Demonstrating RNA catalysis within prebiotically relevant models of primordial cells (protocells)
remains a challenge in Origins of life research. Fatty acid vesicles encapsulating genomic and
catalytic RNAs (ribozymes) are attractive models for protocells; however, RNA catalysis has
largely been incompatible with fatty acid vesicles due to their instability in the presence of Mg2+ at
concentrations required for ribozyme function. Here, we report a r...
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- Journal article
Authors : Neugroschl, Atara (2023) - Nucleic acid probes are valuable tools in biology and chemistry and are indispensable for PCR amplification of DNA, RNA quantification and visualization, and downregulation of gene expression. Recently, triplex forming oligonucleotides (TFO) have received increased attention due to their improved selectivity and sensitivity in recognizing purine-rich double-stranded RNA regions at physiological pH by incorporating backbone and base modifications. For example, triplex forming pep...
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- Journal article
Authors : Malinen, Anssi M. (2021) - The expression of most bacterial genes commences with the binding of RNA polymerase (RNAP)–s70
holoenzyme to the promoter DNA. This initial RNAP–promoter closed complex undergoes a series of
conformational changes, including the formation of a transcription bubble on the promoter and the
loading of template DNA strand into the RNAP active site; these changes lead to the catalytically active
open complex (RPO) state. Recent cryo-electron mic...
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- Periodicals (Báo – Tạp chí)
Authors : Mäkinen, Janne J; Shin, Yeonoh (2020) - RNA polymerases (RNAPs) synthesize RNA from NTPs, whereas DNA polymerases synthesize DNA from 2’dNTPs. DNA polymerases select against NTPs by using steric gates to exclude the 2’ OH, but RNAPs have to employ alternative selection strategies. In single-subunit RNAPs, a conserved Tyr residue discriminates against 2’dNTPs, whereas selectivity mechanisms of multi-subunit RNAPs remain hitherto unknown. Here we show that a conserved Arg residue uses a two-pronged s...
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- Journal article
Authors : Rasmussen, Rebecca A. (2023) - Bacteria can adapt in response to numerous stress conditions. One such stress condition is zinc depletion. The zinc-sensing transcription factor Zur regulates the way enteric bacteria respond to severe changes in zinc availability. Under zinc sufficient conditions, Zn-loaded Zur (Zn2-Zur) is well-known to repress transcription of genes encoding zinc uptake transporters and paralogues of a few ribosomal subunits. Here, we report the discovery and mechanistic basis&...
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