Featured
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| Open AccessRNA targeting and cleavage by the type III-Dv CRISPR effector complex
Here, Schwartz, Bravo, and Ahsan et al. show how multi-subunit fusion proteins are arranged around a crRNA in a type III CRISPR-Cas effector to cleave target RNA. Structures and molecular dynamics of this complex show three distinct active sites that can be used for programmable RNA cleavage.
- Evan A. Schwartz
- , Jack P. K. Bravo
- & David W. Taylor
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Article
| Open AccessRegulation by the RNA-binding protein Unkempt at its effector interface
How RNA-binding proteins (RBPs) regulate gene expression via effectors of RNA processing is unclear. Here, the authors dissect the effector interface of an essential RBP, Unkempt, and investigate its contribution to translational control in cells.
- Kriti Shah
- , Shiyang He
- & Jernej Murn
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| Open AccessExpedient production of site specifically nucleobase-labelled or hypermodified RNA with engineered thermophilic DNA polymerases
A general method for enzymatic synthesis of base-modified RNA was developed using engineered thermostable DNA polymerases enabling introduction of site-specific modifications or synthesis of hypermodified RNA not accessible by in vitro transcription.
- Mária Brunderová
- , Vojtěch Havlíček
- & Michal Hocek
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| Open AccessPredicting nuclear G-quadruplex RNA-binding proteins with roles in transcription and phase separation
RNA G-quadruplexes are important regulatory elements, yet our knowledge of their structure-based interactions is at present limited. Here the authors combine experimental and computational methods to develop a predictive tool, G4-FUNNIES, to estimate proteins’ RNA G4-binding propensities.
- Johanna Luige
- , Alexandros Armaos
- & Ulf Andersson Vang Ørom
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| Open AccessNAP-seq reveals multiple classes of structured noncoding RNAs with regulatory functions
The genome-wide prevalence, mechanism and function of noncapped RNAs (napRNAs) are currently poorly understood. Here, the authors develop a method called NAP-seq, to globally profile the full-length sequences of napRNAs, revealing several classes of structured noncoding RNAs.
- Shurong Liu
- , Junhong Huang
- & Jianhua Yang
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Article
| Open AccessStructural and mechanistic insights into activation of the human RNA ligase RTCB by Archease
RTCB-type RNA ligases play important roles in tRNA splicing, the unfolded protein response and RNA repair. Here, Gerber et al. present structural snapshots of RTCB’s reaction cycle, and show how an activation complex with Archease primes RTCB for ligation.
- Janina Lara Gerber
- , Suria Itzel Morales Guzmán
- & Jirka Peschek
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Article
| Open AccessToll/interleukin-1 receptor (TIR) domain-containing proteins have NAD-RNA decapping activity
Toll/interleukin-1 receptor domain-containing proteins can catabolize NAD+. Here, Wang et al show that these proteins can also function as NAD-RNA decapping enzymes by releasing the NAM moiety from the NAD-RNA, resulting in the regulation of gene expression.
- Xufeng Wang
- , Dongli Yu
- & Xuemei Chen
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| Open AccessStructure-based prediction and characterization of photo-crosslinking in native protein–RNA complexes
Feng et al. developed a computational method PxR3D-map to jointly analyze crosslinked nucleotides and amino acids in protein-RNA complexes, which revealed key structural features underlying photocrosslinking of protein and RNA in cells.
- Huijuan Feng
- , Xiang-Jun Lu
- & Chaolin Zhang
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Article
| Open AccessRNA compaction and iterative scanning for small RNA targets by the Hfq chaperone
Small RNAs (sRNAs) turn bacterial genes on or off by base pairing with mRNAs. Here the authors employ single molecule fluorescence to show how sRNAs and their chaperone Hfq quickly locate the proper target by repeatedly scanning an mRNA until a stable match is found.
- Ewelina M. Małecka
- & Sarah A. Woodson
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Article
| Open AccessSpecificity, synergy, and mechanisms of splice-modifying drugs
Two small-molecule drugs, risdiplam and branaplam, have been developed for treating spinal muscular atrophy. Here the authors develop quantitative modeling methods for the sequence-specific and concentration-dependent effects of these and other splice-modifying drugs.
- Yuma Ishigami
- , Mandy S. Wong
- & Justin B. Kinney
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Article
| Open AccessSingle-molecule RNA sizing enables quantitative analysis of alternative transcription termination
The development of RNA technologies demands accurate assessment of transcript size and heterogeneity. Here, authors report a nanopore-based approach to study full-length RNA transcripts at the single-molecule level, identify premature transcription termination and study rolling-circle transcription.
- Gerardo Patiño-Guillén
- , Jovan Pešović
- & Ulrich Felix Keyser
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Article
| Open AccessFluorogenic CRISPR for genomic DNA imaging
Conventional CRISPR-based approaches to monitor genomic loci can be hampered by high background and nonspecific nucleolar signal. Here, the authors propose a fluorogenic CRISPR (fCRISPR) tool that allows for high-contrast and sensitive imaging of genomic DNA.
- Zhongxuan Zhang
- , Xiaoxiao Rong
- & Xing Li
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Article
| Open AccessNuclear and cytoplasmic specific RNA binding proteome enrichment and its changes upon ferroptosis induction
The reported assay shows a subcellular-specific RNA labeling method for efficient enrichment and deep profiling of nuclear and cytoplasmic RBPs, the authors apply this to investigate changes of subcellular-specific RBP-RNA interactions in ferroptosis.
- Haofan Sun
- , Bin Fu
- & Weijie Qin
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Article
| Open Access2.7 Å cryo-EM structure of human telomerase H/ACA ribonucleoprotein
Here the authors captured the structure of human telomerase H/ACA ribonucleoprotein (RNP) by cryo-EM. The structure rationalizes telomere-disorder disease mutations and reveals insights into the mechanism of pseudouridylation by eukaryotic H/ACA RNPs.
- George E. Ghanim
- , Zala Sekne
- & Thi Hoang Duong Nguyen
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| Open AccessUpregulated hepatic lipogenesis from dietary sugars in response to low palmitate feeding supplies brain palmitate
The origin of brain palmitic acid (PAM) has been debated. Here, by using natural abundance carbon isotope ratios and RNA sequencing the authors show that the majority of brain PAM is maintained by hepatic PAM synthesis from dietary sugars during development and is upregulated in mice fed low PAM.
- Mackenzie E. Smith
- , Chuck T. Chen
- & Richard P. Bazinet
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Article
| Open AccessMassively parallel profiling of RNA-targeting CRISPR-Cas13d
Systematic understanding of CRISPR enzyme RNA binding specificity and cleavage is lacking. Here the authors report RNA chip-hybridised association-mapping platform (RNA-CHAMP), a workflow that repurposes next generation DNA sequencing chips to measure the binding affinity for RNA targets.
- Hung-Che Kuo
- , Joshua Prupes
- & Ilya J. Finkelstein
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Article
| Open AccessMonovalent metal ion binding promotes the first transesterification reaction in the spliceosome
Hybrid QM/MM molecular dynamics simulations reveal that the kinetics and thermodynamics of the first splicing step are regulated by a K+ ion that facilitates optimal positioning of reactive moieties.
- Jana Aupič
- , Jure Borišek
- & Alessandra Magistrato
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Article
| Open AccessAn RNA excited conformational state at atomic resolution
Excited conformation state of biomolecule is transient and high-energy conformation state. Here the authors use NMR spectroscopy and computational modeling to reveal the 3D structure of HIV-1 TAR RNA excited conformational state.
- Ainan Geng
- , Laura Ganser
- & Hashim M. Al-Hashimi
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| Open AccessExtending the toolbox for RNA biology with SegModTeX: a polymerase-driven method for site-specific and segmental labeling of RNA
It has been challenging to make long RNAs with site-specific modifications for NMR study. Here the authors present SegModTeX: a method for site-specific and segmental labeling of RNAs independent of their sequence or segment length, with applications for biological- and artificial NTP analogues at purity and scale sufficient for NMR.
- Raphael Haslecker
- , Vincent V. Pham
- & Victoria M. D’Souza
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| Open AccessDissecting the basis for differential substrate specificity of ADAR1 and ADAR2
Human ADAR1 and ADAR2 edit millions of adenosines transcriptome-wide, altering RNA structure. Here the authors show that variations in RNA binding domains influence site-specific editing, enhancing ADAR2-targeted therapeutics.
- Marlon S. Zambrano-Mila
- , Monika Witzenberger
- & Schraga Schwartz
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| Open AccessIn vivo RNA interactome profiling reveals 3’UTR-processed small RNA targeting a central regulatory hub
Here the authors report a new approach to profile RNA-RNA interactions in live bacterial cells. The charted RNA interaction networks unveil a key mRNA regulatory hub targeted by twelve small RNAs, including a novel RNA involved in fatty acid metabolism.
- Fang Liu
- , Ziying Chen
- & Yanjie Chao
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Article
| Open AccessStructural insights into the role of GTPBP10 in the RNA maturation of the mitoribosome
The biogenesis of ribosomes is a highly coordinated process. Here, Nguyen et al. uncover how the mitochondria-specific interplay of the GTPases GTPBP10 and GTPBP7 ensures proper maturation of the catalytic RNA center of the human mitoribosome.
- Thu Giang Nguyen
- , Christina Ritter
- & Eva Kummer
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| Open AccessObservation of coordinated RNA folding events by systematic cotranscriptional RNA structure probing
RNA begins to fold as the nascent transcript emerges from a transcribing RNA polymerase. Here, the authors develop a concise method for mapping RNA folding pathways that couples in vitro transcription with high-throughput RNA chemical probing.
- Courtney E. Szyjka
- & Eric J. Strobel
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Article
| Open AccessA single pseudouridine on rRNA regulates ribosome structure and function in the mammalian parasite Trypanosoma brucei
Trypanosomes are the causative agent of sleeping sickness. Here the authors demonstrate that the loss of single pseudouridine in ribosomal RNA affects the stoichiometry of ribosomal proteins and translation of a subset of proteins.
- K. Shanmugha Rajan
- , Hava Madmoni
- & Shulamit Michaeli
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| Open AccessStructural and dynamic mechanisms for coupled folding and tRNA recognition of a translational T-box riboswitch
T-box riboswitches are RNA-based gene regulators, composed of highly structured noncoding RNAs: the T-box and a tRNA ligand. Here, the authors assess the folding of a translational T-box aptamer and dissect the role of Mg2+, intra- and intermolecular RNA-RNA interactions in modulating its folding and function.
- Xiaolin Niu
- , Zhonghe Xu
- & Xianyang Fang
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Article
| Open AccessProfiling stress-triggered RNA condensation with photocatalytic proximity labeling
Stress granules (SGs) are highly dynamic cytoplasmic membraneless organelles that assemble when cells are challenged by stress. Herein, the authors apply a proximity-dependent RNA labeling method, CAP-seq, to comprehensively investigate the content of SG-proximal transcriptome and the dynamic change in SG-proximal transcriptome along the time course of granule assembly and disassembly processes in live mammalian cells.
- Ziqi Ren
- , Wei Tang
- & Peng Zou
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Article
| Open AccessIntra- and inter-molecular regulation by intrinsically-disordered regions governs PUF protein RNA binding
FBF-2 and LST-1 repress gld-1 mRNA expression to maintain C. elegans germline stem cells. The authors show that an intrinsically-disordered region of FBF-2 autoinhibits its RNA binding. LST-1 antagonizes this interaction to promote RNA binding.
- Chen Qiu
- , Zihan Zhang
- & Traci M. Tanaka Hall
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Article
| Open AccessThe E3 ligase Riplet promotes RIG-I signaling independent of RIG-I oligomerization
Riplet conjugates K63-Ub chain to RIG-I in order to induce a robust antiviral response, but the mechanism of action remains unclear. Here, the authors show that Riplet recognizes RIG-I regardless of its RNA-bound status and promotes RIG-I signaling independent of RIG-I oligomerization.
- Wenshuai Wang
- , Benjamin Götte
- & Anna Marie Pyle
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Article
| Open AccessRational design of microRNA-responsive switch for programmable translational control in mammalian cells
Artificial regulation of translation by intracellular RNAs has many potential applications. Here, authors design a platform capable of miRNA-triggered upregulation or downregulation using a single RNA construct, and demonstrate its use in constructing logic gates and cell-type classifiers.
- Hui Ning
- , Gan Liu
- & Zhen Xie
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| Open AccessMePMe-seq: antibody-free simultaneous m6A and m5C mapping in mRNA by metabolic propargyl labeling and sequencing
Methylation is the dominant modification in mRNA and occurs at a variety of sites. Here, Hartstock et al. show that a clickable analogue of the key cosubstrate S-adenosyl-L-methionine (SAM) can be produced in cells, allowing for identification and mapping of different methylated nucleosides in mRNA.
- Katja Hartstock
- , Nadine A. Kueck
- & Andrea Rentmeister
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| Open AccessRNA-based translation activators for targeted gene upregulation
Many diseases are driven by the insufficient expression of critical genes, but few technologies are capable of rescuing these endogenous protein levels. Here, Cao et al. present an RNA-based technology that boosts protein production from endogenous mRNAs by upregulating their translation.
- Yang Cao
- , Huachun Liu
- & Bryan C. Dickinson
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Article
| Open AccessPAPγ associates with PAXT nuclear exosome to control the abundance of PROMPT ncRNAs
Pervasive transcription of the human genome generates an abundance of RNAs that must be processed and degraded by the nuclear RNA exosome. Here the authors show that polyA polymerase gamma (PAPγ) associates with PAXT providing key insights into the direct targeting of PROMPT ncRNAs by PAXT at their genomic sites.
- Xavier Contreras
- , David Depierre
- & Rosemary Kiernan
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Article
| Open AccessThe SMN complex drives structural changes in human snRNAs to enable snRNP assembly
Sm protein binding to pre-snRNA is a key step in snRNP biogenesis catalyzed by the SMN complex. Here, the authors show that pre-snRNAs adopt compact structures incompatible with Sm protein binding and that Gemin3 and 4 are required for pre-snRNA rearrangement to allow Sm protein interaction.
- Josef Pánek
- , Adriana Roithová
- & David Staněk
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| Open AccessChemoproteomic capture of RNA binding activity in living cells
Here the authors introduce a photo-activatable-competition and chemoproteomic enrichment (PACCE) method to localize protein-RNA interfaces using photoactivatable cellular RNA to protect RNA binding regions on proteins from electrophilic purine probe labeling.
- Andrew J. Heindel
- , Jeffrey W. Brulet
- & Ku-Lung Hsu
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Article
| Open AccessSecondary structures that regulate mRNA translation provide insights for ASO-mediated modulation of cardiac hypertrophy
The GAT4A transcription factor mediates cardiac development. Here the authors identify that the 5′ UTR of GATA4 mRNA contains a double stranded structure downstream of an upstream open reading frame (uORF) that promotes uORF-mediated suppression of the main ORF.
- Omar M. Hedaya
- , Kadiam C. Venkata Subbaiah
- & Peng Yao
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| Open AccessEpitranscriptomic subtyping, visualization, and denoising by global motif visualization
The current available tools lack the ability to accurately classify and visually represent epitranscriptomic profiling data. Here, the authors provide a framework that offers a general solution for the visualization and interpretation of such data.
- Jianheng Liu
- , Tao Huang
- & Rui Zhang
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| Open AccessSignal-noise metrics for RNA binding protein identification reveal broad spectrum protein-RNA interaction frequencies and dynamics
The identification of RNA-bound proteomes is hampered by a lack of quantitative metrics for evaluating RNA binding function. Here, the authors report LEAP-RBP as a method for purification of RNA-bound proteins and introduce signal-based metrics for robust profiling of RNA-bound proteomes.
- JohnCarlo Kristofich
- & Christopher V. Nicchitta
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Article
| Open AccessDiscovery of the major 15–30 nt mammalian small RNAs, their biogenesis and function
The authors uncover the major 15-30 nt mouse and human small RNAs (sRNAs), which mainly end with 2’,3’-cyclic phosphate, and show that many of these sRNAs can be generated by Angiogenin or RNase 4 and function in Ago2 complex as miRNAs.
- Hejin Lai
- , Ning Feng
- & Qiwei Zhai
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Article
| Open AccessThe master energy homeostasis regulator PGC-1α exhibits an mRNA nuclear export function
PGC-1α is a master regulator activating the transcription of key genes controlling the cell’s energy production. Here the authors show that PGC-1α has a function in the NXF1-dependent nuclear export of mRNAs.
- Simeon R. Mihaylov
- , Lydia M. Castelli
- & Guillaume M. Hautbergue
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Article
| Open AccessDynamically regulated two-site interaction of viral RNA to capture host translation initiation factor
RNA viruses use elements of their genomic RNA to commandeer the host translational machinery. Here, the authors use NMR and cryo-EM to reveal the sophisticated strategy by which a viral RNA engages host translational factors in a dynamically regulated two-site interaction.
- Shunsuke Imai
- , Hiroshi Suzuki
- & Ichio Shimada
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Article
| Open AccessStructural mechanism of R2D2 and Loqs-PD synergistic modulation on DmDcr-2 oligomers
R2D2 and Loqs-PD are cofactors of Drosophila Dicer-2 (DmDcr-2), which generates siRNAs. Here the authors report the cryo-EM structures of DmDcr-2/R2D2/Loqs-PD with dsRNAs showing that these complexes can form oligomers and assemble into fibers.
- Ting Deng
- , Shichen Su
- & Jia Wang
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Article
| Open AccessStructural basis for a degenerate tRNA identity code and the evolution of bimodal specificity in human mitochondrial tRNA recognition
Aminoacyl-tRNA synthetases catalyze the ligation of amino acids to their cognate tRNAs. Here the authors report the cryo-EM structure of a human mitochondrial seryl-tRNA synthetase•mtRNASer complex showing how strong mutation pressure on mtRNA genes drove a rewiring of intermolecular recognition rules.
- Bernhard Kuhle
- , Marscha Hirschi
- & Paul Schimmel
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Article
| Open AccessModulation of translational decoding by m6A modification of mRNA
m6A is an mRNA modification that slows down translation elongation. Here, Jain et al. show that m6A delays decoding and increases tRNA drop-off from the ribosome by favoring alternative codon conformations that are rejected by the ribosome.
- Sakshi Jain
- , Lukasz Koziej
- & Marina V. Rodnina
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Article
| Open AccessMolecular basis of the pleiotropic effects by the antibiotic amikacin on the ribosome
Here the authors use fast kinetics, X-ray crystallography, and cryo-EM to uncover the mechanism of ribosome inhibition by amikacin and kanamycin. They find that amikacin binds near the P-site tRNA, offering new strategies to fight antibiotic resistance.
- Savannah M. Seely
- , Narayan P. Parajuli
- & Matthieu G. Gagnon
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Article
| Open AccessStructural basis for specific RNA recognition by the alternative splicing factor RBM5
The RNA binding protein RBM5 regulates alternative splicing of genes implicated in cancer. Here the authors show structural mechanisms how multiple RNA binding domains of RBM5 cooperate to recognize specific target RNA sequences.
- Komal Soni
- , Pravin Kumar Ankush Jagtap
- & Michael Sattler
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Article
| Open AccessExon-intron boundary inhibits m6A deposition, enabling m6A distribution hallmark, longer mRNA half-life and flexible protein coding
m6A mRNA modification is not typically found near splice junctions in mRNAs. Here the authors show exon-intron boundary inhibits m6A deposition at ~100 nt region nearby splice site, enabling m6A distribution hallmark, more stable mRNA and flexible protein coding.
- Zhiyuan Luo
- , Qilian Ma
- & Shengdong Ke
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Article
| Open AccessFast-exchanging spirocyclic rhodamine probes for aptamer-based super-resolution RNA imaging
Live-cell RNA imaging with high spatial and temporal resolution remains a major challenge. Here the authors design spirocyclic rhodamine probes that enable a fluorescent light-up aptamer system suitable for visualizing RNAs in live or fixed cells with two different super-resolution microscopy modalities SMLM and STED.
- Daniel Englert
- , Eva-Maria Burger
- & Murat Sunbul
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Article
| Open AccessThe mRNA methyltransferase Mettl3 modulates cytokine mRNA stability and limits functional responses in mast cells
The m6A mRNA modification is essential for immune cell function. Here, the Monticelli lab optimized methods of gene editing by CRISPR-Cas9 in mast cells and revealed how the m6A machinery is required to sustain proliferation and to limit the production of inflammatory cytokines by these cells.
- Cristina Leoni
- , Marian Bataclan
- & Silvia Monticelli
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Article
| Open AccessAn unnatural enzyme with endonuclease activity towards small non-coding RNAs
Endonucleases play crucial roles in various biological processes but endonucleases that target small non-coding RNAs have not been reported. Here, the authors combined the metal binding non-canonical amino acid BpyAla and a high affinity binder to engineer a catalyst that degrades small non-coding RNAs.
- Noreen Ahmed
- , Nadine Ahmed
- & John Paul Pezacki