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Journal articles on the topic 'Nucleotide modification'

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Published: 4 June 2021

Last updated: 1 February 2022

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Ding, Hongxu, Andrew D. Bailey, Miten Jain, Hugh Olsen, and Benedict Paten. "Gaussian mixture model-based unsupervised nucleotide modification number detection using nanopore-sequencing readouts." Bioinformatics 36, no. 19 (2020): 4928–34. http://dx.doi.org/10.1093/bioinformatics/btaa601.

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Abstract Motivation Nucleotide modification status can be decoded from the Oxford Nanopore Technologies nanopore-sequencing ionic current signals. Although various algorithms have been developed for nanopore-sequencing-based modification analysis, more detailed characterizations, such as modification numbers, corresponding signal levels and proportions are still lacking. Results We present a framework for the unsupervised determination of the number of nucleotide modifications from nanopore-sequencing readouts. We demonstrate the approach can effectively recapitulate the number of modifications, the corresponding ionic current signal levels, as well as mixing proportions under both DNA and RNA contexts. We further show, by integrating information from multiple detected modification regions, that the modification status of DNA and RNA molecules can be inferred. This method forms a key step of de novo characterization of nucleotide modifications, shedding light on the interpretation of various biological questions. Availability and implementation Modified nanopolish: https://github.com/adbailey4/nanopolish/tree/cigar_output. All other codes used to reproduce the results: https://github.com/hd2326/ModificationNumber. Supplementary information Supplementary data are available at Bioinformatics online.

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Hoffmann, Anne, Lieselotte Erber, Heike Betat, Peter F. Stadler, Mario Mörl, and Jörg Fallmann. "Changes of the tRNA Modification Pattern during the Development of Dictyostelium discoideum." Non-Coding RNA 7, no. 2 (2021): 32. http://dx.doi.org/10.3390/ncrna7020032.

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Dictyostelium discoideum is a social amoeba, which on starvation develops from a single-cell state to a multicellular fruiting body. This developmental process is accompanied by massive changes in gene expression, which also affect non-coding RNAs. Here, we investigate how tRNAs as key regulators of the translation process are affected by this transition. To this end, we used LOTTE-seq to sequence the tRNA pool of D. discoideum at different developmental time points and analyzed both tRNA composition and tRNA modification patterns. We developed a workflow for the specific detection of modifications from reverse transcriptase signatures in chemically untreated RNA-seq data at single-nucleotide resolution. It avoids the comparison of treated and untreated RNA-seq data using reverse transcription arrest patterns at nucleotides in the neighborhood of a putative modification site as internal control. We find that nucleotide modification sites in D. discoideum tRNAs largely conform to the modification patterns observed throughout the eukaroytes. However, there are also previously undescribed modification sites. We observe substantial dynamic changes of both expression levels and modification patterns of certain tRNA types during fruiting body development. Beyond the specific application to D. discoideum our results demonstrate that the developmental variability of tRNA expression and modification can be traced efficiently with LOTTE-seq.

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Jang, Eui Kyoung, Ryeo Gang Son, and Seung Pil Pack. "Novel enzymatic single-nucleotide modification of DNA oligomer: prevention of incessant incorporation of nucleotidyl transferase by ribonucleotide-borate complex." Nucleic Acids Research 47, no. 17 (2019): e102-e102. http://dx.doi.org/10.1093/nar/gkz612.

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Abstract Terminal deoxynucleotidyl transferase (TdT), which mediates template-independent polymerization with low specificity for nucleotides, has been used for nucleotide extension of DNA oligomers. One concern is that it is difficult to control the number of incorporated nucleotides, which is a limitation on the use of TdT for single-nucleotide incorporation of DNA oligomers. Herein, we uncovered an interesting inhibitory effect on TdT when ribonucleotide substrates (rNTPs) were employed in a borate buffer. On the basis of unique inhibitory effects of the ribonucleotide–borate complex, we developed a novel enzymatic method for single-nucleotide incorporation of a DNA oligomer with a modified rNTP by TdT. Single-nucleotide incorporation of a DNA oligomer with various modified rNTPs containing an oxanine, biotin, aminoallyl or N6-propargyl group was achieved with a high yield. The ‘TdT in rNTP-borate’ method is quite simple and efficient for preparing a single-nucleotide modified DNA oligomer, which is useful for the design of functional DNA-based systems.

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Price, Neil P. J., Michael A. Jackson, Karl E. Vermillion, Judith A. Blackburn, and Trina M. Hartman. "Rhodium-catalyzed reductive modification of pyrimidine nucleosides, nucleotide phosphates, and sugar nucleotides." Carbohydrate Research 488 (February 2020): 107893. http://dx.doi.org/10.1016/j.carres.2019.107893.

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Behm-Ansmant, Isabelle, Mark Helm, and Yuri Motorin. "Use of Specific Chemical Reagents for Detection of Modified Nucleotides in RNA." Journal of Nucleic Acids 2011 (2011): 1–17. http://dx.doi.org/10.4061/2011/408053.

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Naturally occurring cellular RNAs contain an impressive number of chemically distinct modified residues which appear posttranscriptionally, as a result of specific action of the corresponding RNA modification enzymes. Over 100 different chemical modifications have been identified and characterized up to now. Identification of the chemical nature and exact position of these modifications is typically based on 2D-TLC analysis of nucleotide digests, on HPLC coupled with mass spectrometry, or on the use of primer extension by reverse transcriptase. However, many modified nucleotides are silent in reverse transcription, since the presence of additional chemical groups frequently does not change base-pairing properties. In this paper, we give a summary of various chemical approaches exploiting the specific reactivity of modified nucleotides in RNA for their detection.

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Mullally, Grace, Kara van Aelst, Mohsin M. Naqvi, et al. "5′ modifications to CRISPR–Cas9 gRNA can change the dynamics and size of R-loops and inhibit DNA cleavage." Nucleic Acids Research 48, no. 12 (2020): 6811–23. http://dx.doi.org/10.1093/nar/gkaa477.

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Abstract A key aim in exploiting CRISPR–Cas is gRNA engineering to introduce additional functionalities, ranging from individual nucleotide changes that increase efficiency of on-target binding to the inclusion of larger functional RNA aptamers or ribonucleoproteins (RNPs). Cas9–gRNA interactions are crucial for complex assembly, but several distinct regions of the gRNA are amenable to modification. We used in vitro ensemble and single-molecule assays to assess the impact of gRNA structural alterations on RNP complex formation, R-loop dynamics, and endonuclease activity. Our results indicate that RNP formation was unaffected by any of our modifications. R-loop formation and DNA cleavage activity were also essentially unaffected by modification of the Upper Stem, first Hairpin and 3′ end. In contrast, we found that 5′ additions of only two or three nucleotides could reduce R-loop formation and cleavage activity of the RuvC domain relative to a single nucleotide addition. Such modifications are a common by-product of in vitro transcribed gRNA. We also observed that addition of a 20 nt RNA hairpin to the 5′ end of a gRNA still supported RNP formation but produced a stable ∼9 bp R-loop that could not activate DNA cleavage. Consideration of these observations will assist in successful gRNA design.

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Munoz-Tello, Paola, Lional Rajappa, Sandrine Coquille, and Stéphane Thore. "Polyuridylation in Eukaryotes: A 3′-End Modification Regulating RNA Life." BioMed Research International 2015 (2015): 1–12. http://dx.doi.org/10.1155/2015/968127.

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In eukaryotes, mRNA polyadenylation is a well-known modification that is essential for many aspects of the protein-coding RNAs life cycle. However, modification of the 3′ terminal nucleotide within various RNA molecules is a general and conserved process that broadly modulates RNA function in all kingdoms of life. Numerous types of modifications have been characterized, which are generally specific for a given type of RNA such as the CCA addition found in tRNAs. In recent years, the addition of nontemplated uridine nucleotides or uridylation has been shown to occur in various types of RNA molecules and in various cellular compartments with significantly different outcomes. Indeed, uridylation is able to alter RNA half-life both in positive and in negative ways, highlighting the importance of the enzymes in charge of performing this modification. The present review aims at summarizing the current knowledge on the various processes leading to RNA 3′-end uridylation and on their potential impacts in various diseases.

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Stepanov, Grigory, Evgenii Zhuravlev, Victoria Shender, et al. "Nucleotide Modifications Decrease Innate Immune Response Induced by Synthetic Analogs of snRNAs and snoRNAs." Genes 9, no. 11 (2018): 531. http://dx.doi.org/10.3390/genes9110531.

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Short nuclear regulatory RNAs play a key role in the main stages of maturation of the precursors of the major RNA species. Small nuclear RNAs (snRNAs) form the core of the spliceosome and are responsible for the splicing of pre-mRNA molecules. Small nucleolar RNAs (snoRNAs) direct post-transcriptional modification of pre-rRNAs. A promising strategy for the development of non-coding RNA (ncRNAs) mimicking molecules is the introduction of modified nucleotides, which are normally present in natural ncRNAs, into the structure of synthetic RNAs. We have created a set of snoRNAs and snRNA analogs and studied the effect of base modifications, specifically, pseudouridine (Ψ) and 5-methylcytidine (m5C), on the immune-stimulating and cytotoxic properties of these RNAs. Here, we performed a whole-transcriptome study of the influence of synthetic snoRNA analogs with various modifications on gene expression in human cells. Moreover, we confirmed the role of PKR in the recognition of snoRNA and snRNA analogs using the short hairpin RNA (shRNA) technique. We believe that the data obtained will contribute to the understanding of the role of nucleotide modification in ncRNA functions, and can be useful for creating the agents for gene regulation based on the structure of natural snoRNAs and snRNAs.

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Yip, W. S. Vincent, Nicholas G. Vincent, and Susan J. Baserga. "Ribonucleoproteins in Archaeal Pre-rRNA Processing and Modification." Archaea 2013 (2013): 1–14. http://dx.doi.org/10.1155/2013/614735.

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Given that ribosomes are one of the most important cellular macromolecular machines, it is not surprising that there is intensive research in ribosome biogenesis. Ribosome biogenesis is a complex process. The maturation of ribosomal RNAs (rRNAs) requires not only the precise cleaving and folding of the pre-rRNA but also extensive nucleotide modifications. At the heart of the processing and modifications of pre-rRNAs in Archaea and Eukarya are ribonucleoprotein (RNP) machines. They are called small RNPs (sRNPs), in Archaea, and small nucleolar RNPs (snoRNPs), in Eukarya. Studies on ribosome biogenesis originally focused on eukaryotic systems. However, recent studies on archaeal sRNPs have provided important insights into the functions of these RNPs. This paper will introduce archaeal rRNA gene organization and pre-rRNA processing, with a particular focus on the discovery of the archaeal sRNP components, their functions in nucleotide modification, and their structures.

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MILLER, Richard W., Robert R. EADY, Carol GORMAL, Shirley A. FAIRHURST, and Barry E. SMITH. "Covalent modification of nitrogenase MoFe protein by ADP." Biochemical Journal 322, no. 3 (1997): 737–44. http://dx.doi.org/10.1042/bj3220737.

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MgADP- reacted with the nitrogenase molybdenum–iron (MoFe) protein of Klebsiella pneumoniae (Kp1) over a period of 2 h to yield a stable, catalytically active conjugate. The isolated protein exhibited a new, broad 31P NMR resonance at -1 p.p.m. lacking phosphorus J coupling. The adenine ring of [8-14C]ADP remained associated with the conjugate. A covalently bound nucleotide was identified as AMP by NMR and TLC. Extended dialysis of Kp1 against MgADP- resulted in further AMP binding at the protein surface. ADP was initially bound tightly to Kp1 at a site distinct from the AMP sites. ATP did not replace ADP. The time course of the formation of the Kp1-AMP was altered by the nitrogenase iron protein (Kp2) and was dependent on redox potential. Kp1-AMP was stable to concentration and oxidation with ferricyanide ion at -350 mV. Slow hydrolysis of Kp1-AMP over a period of 6 h yielded AMP and unaltered Kp1. The adenine ring of ADP exchanged with adenine of MgATP2- during reductant-limited turnover of nitrogenase under N2, indicating reversibility of ATP hydrolysis at 15 °C. [32P]Pi exchanged with the terminal phosphate group of both ADP and ATP on incubation with Kp1. 32P exchange and the catalytic activity of Kp1 were inhibited by a 20-fold molar excess of the lysine-modifying reagent, o-phthalaldehyde (OPT). Preincubation with MgADP- protected against OPT inactivation. Two potentially reactive lysine residues on the α chain of the MoFe protein near a putative hydrophobic docking site for the nitrogenase Fe protein are proposed as sites of OPT and nucleotide binding. Azotobacter vinelandiiMoFe protein (Av1) also formed an AMP adduct but Kp2 did not. Catalase did not interact with ADP. The reactions of the nitrogenase MoFe protein with adenine nucleotides have no counterpart in known protein–nucleotide interactions.

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Yang, Jie, Hong Zhang, Weibin Gong та ін. "S-Glutathionylation of human inducible Hsp70 reveals a regulatory mechanism involving the C-terminal α-helical lid". Journal of Biological Chemistry 295, № 24 (2020): 8302–24. http://dx.doi.org/10.1074/jbc.ra119.012372.

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Heat shock protein 70 (Hsp70) proteins are a family of ancient and conserved chaperones. Cysteine modifications have been widely detected among different Hsp70 family members in vivo, but their effects on Hsp70 structure and function are unclear. Here, we treated HeLa cells with diamide, which typically induces disulfide bond formation except in the presence of excess GSH, when glutathionylated cysteines predominate. We show that in these cells, HspA1A (hHsp70) undergoes reversible cysteine modifications, including glutathionylation, potentially at all five cysteine residues. In vitro experiments revealed that modification of cysteines in the nucleotide-binding domain of hHsp70 is prevented by nucleotide binding but that Cys-574 and Cys-603, located in the C-terminal α-helical lid of the substrate-binding domain, can undergo glutathionylation in both the presence and absence of nucleotide. We found that glutathionylation of these cysteine residues results in unfolding of the α-helical lid structure. The unfolded region mimics substrate by binding to and blocking the substrate-binding site, thereby promoting intrinsic ATPase activity and competing with binding of external substrates, including heat shock transcription factor 1 (Hsf1). Thus, post-translational modification can alter the structure and regulate the function of hHsp70.

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Bernofsky, Carl, and Sean W. O'dea. "Nucleotide Modification, A Radical Mechanism of Oxidative Toxicity." Free Radical Research Communications 2, no. 3 (1986): 129–36. http://dx.doi.org/10.3109/10715768609088064.

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Flierl, Ulrike, Tracy L. Nero, Bock Lim, et al. "Phosphorothioate backbone modifications of nucleotide-based drugs are potent platelet activators." Journal of Experimental Medicine 212, no. 2 (2015): 129–37. http://dx.doi.org/10.1084/jem.20140391.

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Nucleotide-based drug candidates such as antisense oligonucleotides, aptamers, immunoreceptor-activating nucleotides, or (anti)microRNAs hold great therapeutic promise for many human diseases. Phosphorothioate (PS) backbone modification of nucleotide-based drugs is common practice to protect these promising drug candidates from rapid degradation by plasma and intracellular nucleases. Effects of the changes in physicochemical properties associated with PS modification on platelets have not been elucidated so far. Here we report the unexpected binding of PS-modified oligonucleotides to platelets eliciting strong platelet activation, signaling, reactive oxygen species generation, adhesion, spreading, aggregation, and thrombus formation in vitro and in vivo. Mechanistically, the platelet-specific receptor glycoprotein VI (GPVI) mediates these platelet-activating effects. Notably, platelets from GPVI function–deficient patients do not exhibit binding of PS-modified oligonucleotides, and platelet activation is fully abolished. Our data demonstrate a novel, unexpected, PS backbone–dependent, platelet-activating effect of nucleotide-based drug candidates mediated by GPVI. This unforeseen effect should be considered in the ongoing development programs for the broad range of upcoming and promising DNA/RNA therapeutics.

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Schuster, W., R. Hiesel, B. Wissinger, and A. Brennicke. "RNA editing in the cytochrome b locus of the higher plant Oenothera berteriana includes a U-to-C transition." Molecular and Cellular Biology 10, no. 5 (1990): 2428–31. http://dx.doi.org/10.1128/mcb.10.5.2428.

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RNA editing in the cytochrome b locus of Oenothera berteriana mitochondria modified a number of cytidine nucleotides to uridines, mostly altering codon identities. One nucleotide alteration involved a reverse modification changing a genomic thymidine to a cytidine in the cDNA sequence. The enzymatic editing activity in higher-plant mitochondria thus appears to be able to catalyze the interconversion of pyrimidines in both directions at specific nucleotides in the mRNA template.

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Greig, Kylie T., Jennifer Antonchuk, Donald Metcalf, et al. "Agm1/Pgm3-Mediated Sugar Nucleotide Synthesis Is Essential for Hematopoiesis and Development." Molecular and Cellular Biology 27, no. 16 (2007): 5849–59. http://dx.doi.org/10.1128/mcb.00802-07.

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ABSTRACT Carbohydrate modification of proteins includes N-linked and O-linked glycosylation, proteoglycan formation, glycosylphosphatidylinositol anchor synthesis, and O-GlcNAc modification. Each of these modifications requires the sugar nucleotide UDP-GlcNAc, which is produced via the hexosamine biosynthesis pathway. A key step in this pathway is the interconversion of GlcNAc-6-phosphate (GlcNAc-6-P) and GlcNAc-1-P, catalyzed by phosphoglucomutase 3 (Pgm3). In this paper, we describe two hypomorphic alleles of mouse Pgm3 and show there are specific physiological consequences of a graded reduction in Pgm3 activity and global UDP-GlcNAc levels. Whereas mice lacking Pgm3 die prior to implantation, animals with less severe reductions in enzyme activity are sterile, exhibit changes in pancreatic architecture, and are anemic, leukopenic, and thrombocytopenic. These phenotypes are accompanied by specific rather than wholesale changes in protein glycosylation, suggesting that while universally required, the functions of certain proteins and, as a consequence, certain cell types are especially sensitive to reductions in Pgm3 activity.

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Kropp, Heike Maria, Simon Leonard Dürr, Christine Peter, Kay Diederichs, and Andreas Marx. "Snapshots of a modified nucleotide moving through the confines of a DNA polymerase." Proceedings of the National Academy of Sciences 115, no. 40 (2018): 9992–97. http://dx.doi.org/10.1073/pnas.1811518115.

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DNA polymerases have evolved to process the four canonical nucleotides accurately. Nevertheless, these enzymes are also known to process modified nucleotides, which is the key to numerous core biotechnology applications. Processing of modified nucleotides includes incorporation of the modified nucleotide and postincorporation elongation to proceed with the synthesis of the nascent DNA strand. The structural basis for postincorporation elongation is currently unknown. We addressed this issue and successfully crystallized KlenTaq DNA polymerase in six closed ternary complexes containing the enzyme, the modified DNA substrate, and the incoming nucleotide. Each structure shows a high-resolution snapshot of the elongation of a modified primer, where the modification “moves” from the 3′-primer terminus upstream to the sixth nucleotide in the primer strand. Combining these data with quantum mechanics/molecular mechanics calculations and biochemical studies elucidates how the enzyme and the modified substrate mutually modulate their conformations without compromising the enzyme’s activity significantly. The study highlights the plasticity of the system as origin of the broad substrate properties of DNA polymerases and facilitates the design of improved systems.

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Abdrabou, Abdalla, and Zhixiang Wang. "Post-Translational Modification and Subcellular Distribution of Rac1: An Update." Cells 7, no. 12 (2018): 263. http://dx.doi.org/10.3390/cells7120263.

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Rac1 is a small GTPase that belongs to the Rho family. The Rho family of small GTPases is a subfamily of the Ras superfamily. The Rho family of GTPases mediate a plethora of cellular effects, including regulation of cytoarchitecture, cell size, cell adhesion, cell polarity, cell motility, proliferation, apoptosis/survival, and membrane trafficking. The cycling of Rac1 between the GTP (guanosine triphosphate)- and GDP (guanosine diphosphate)-bound states is essential for effective signal flow to elicit downstream biological functions. The cycle between inactive and active forms is controlled by three classes of regulatory proteins: Guanine nucleotide exchange factors (GEFs), GTPase-activating proteins (GAPs), and guanine-nucleotide-dissociation inhibitors (GDIs). Other modifications include RNA splicing and microRNAs; various post-translational modifications have also been shown to regulate the activity and function of Rac1. The reported post-translational modifications include lipidation, ubiquitination, phosphorylation, and adenylylation, which have all been shown to play important roles in the regulation of Rac1 and other Rho GTPases. Moreover, the Rac1 activity and function are regulated by its subcellular distribution and translocation. This review focused on the most recent progress in Rac1 research, especially in the area of post-translational modification and subcellular distribution and translocation.

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Lockhart, John, John Canfield, Ezinne Francess Mong, Jeffrey VanWye, and Hana Totary-Jain. "Nucleotide Modification Alters MicroRNA-Dependent Silencing of MicroRNA Switches." Molecular Therapy - Nucleic Acids 14 (March 2019): 339–50. http://dx.doi.org/10.1016/j.omtn.2018.12.007.

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Helm, M. "Post-transcriptional nucleotide modification and alternative folding of RNA." Nucleic Acids Research 34, no. 2 (2006): 721–33. http://dx.doi.org/10.1093/nar/gkj471.

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Helm, M. "Post-transcriptional nucleotide modification and alternative folding of RNA." Nucleic Acids Research 35, no. 20 (2007): 7041. http://dx.doi.org/10.1093/nar/gkm819.

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Decatur, Wayne A., and Maurille J. Fournier. "RNA-guided Nucleotide Modification of Ribosomal and Other RNAs." Journal of Biological Chemistry 278, no. 2 (2002): 695–98. http://dx.doi.org/10.1074/jbc.r200023200.

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Stephan, Niklas C., Anne B. Ries, Daniel Boehringer, and Nenad Ban. "Structural basis of successive adenosine modifications by the conserved ribosomal methyltransferase KsgA." Nucleic Acids Research 49, no. 11 (2021): 6389–98. http://dx.doi.org/10.1093/nar/gkab430.

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Abstract Biogenesis of ribosomal subunits involves enzymatic modifications of rRNA that fine-tune functionally important regions. The universally conserved prokaryotic dimethyltransferase KsgA sequentially modifies two universally conserved adenosine residues in helix 45 of the small ribosomal subunit rRNA, which is in proximity of the decoding site. Here we present the cryo-EM structure of Escherichia coli KsgA bound to an E. coli 30S at a resolution of 3.1 Å. The high-resolution structure reveals how KsgA recognizes immature rRNA and binds helix 45 in a conformation where one of the substrate nucleotides is flipped-out into the active site. We suggest that successive processing of two adjacent nucleotides involves base-flipping of the rRNA, which allows modification of the second substrate nucleotide without dissociation of the enzyme. Since KsgA is homologous to the essential eukaryotic methyltransferase Dim1 involved in 40S maturation, these results have also implications for understanding eukaryotic ribosome maturation.

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Kumar, Pawan, Rohan Degaonkar, Dale C. Guenther, et al. "Chimeric siRNAs with chemically modified pentofuranose and hexopyranose nucleotides: altritol-nucleotide (ANA) containing GalNAc–siRNA conjugates: in vitro and in vivo RNAi activity and resistance to 5′-exonuclease." Nucleic Acids Research 48, no. 8 (2020): 4028–40. http://dx.doi.org/10.1093/nar/gkaa125.

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Abstract In this report, we investigated the hexopyranose chemical modification Altriol Nucleic Acid (ANA) within small interfering RNA (siRNA) duplexes that were otherwise fully modified with the 2′-deoxy-2′-fluoro and 2′-O-methyl pentofuranose chemical modifications. The siRNAs were designed to silence the transthyretin (Ttr) gene and were conjugated to a trivalent N-acetylgalactosamine (GalNAc) ligand for targeted delivery to hepatocytes. Sense and antisense strands of the parent duplex were synthesized with single ANA residues at each position on the strand, and the resulting siRNAs were evaluated for their ability to inhibit Ttr mRNA expression in vitro. Although ANA residues were detrimental at the 5′ end of the antisense strand, the siRNAs with ANA at position 6 or 7 in the seed region had activity comparable to the parent. The siRNA with ANA at position 7 in the seed region was active in a mouse model. An Oligonucleotide with ANA at the 5′ end was more stable in the presence of 5′-exonuclease than an oligonucleotide of the same sequence and chemical composition without the ANA modification. Modeling studies provide insight into the origins of regiospecific changes in potency of siRNAs and the increased protection against 5′-exonuclease degradation afforded by the ANA modification.

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Kane, S. E., and K. Beemon. "Precise localization of m6A in Rous sarcoma virus RNA reveals clustering of methylation sites: implications for RNA processing." Molecular and Cellular Biology 5, no. 9 (1985): 2298–306. http://dx.doi.org/10.1128/mcb.5.9.2298.

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N6-methyladenosine (m6A) residues are present as internal base modifications in most higher eucaryotic mRNAs; however, the biological function of this modification is not known. We describe a method for localizing and quantitating m6A within a large RNA molecule, the genomic RNA of Rous sarcoma virus. Specific fragments of 32P-labeled Rous sarcoma virus RNA were isolated by hybridization with complementary DNA restriction fragments spanning nucleotides 6185 to 8050. RNA was digested with RNase and finger-printed, and individual oligonucleotides were analyzed for the presence of m6A by paper electrophoresis and thin-layer chromatography. With this technique, seven sites of methylation in this region of the Rous sarcoma virus genome were localized at nucleotides 6394, 6447, 6507, 6718, 7414, 7424, and 8014. Further, m6A was observed at two additional sites whose nucleotide assignments remain ambiguous. A clustering of two or more m6A residues was seen at three positions within the RNA analyzed. Modification at certain sites was found to be heterogeneous, in that different molecules of RNA appeared to be methylated differently. Previous studies have determined that methylation occurs only in the sequences Gm6AC and Am6AC. We observed a high frequency of methylation at PuGm6ACU sequences. The possible involvement of m6A in RNA splicing events is discussed.

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Kristen, Marco, Johanna Plehn, Virginie Marchand, et al. "Manganese Ions Individually Alter the Reverse Transcription Signature of Modified Ribonucleosides." Genes 11, no. 8 (2020): 950. http://dx.doi.org/10.3390/genes11080950.

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Reverse transcription of RNA templates containing modified ribonucleosides transfers modification-related information as misincorporations, arrest or nucleotide skipping events to the newly synthesized cDNA strand. The frequency and proportion of these events, merged from all sequenced cDNAs, yield a so-called RT signature, characteristic for the respective RNA modification and reverse transcriptase (RT). While known for DNA polymerases in so-called error-prone PCR, testing of four different RTs by replacing Mg2+ with Mn2+ in reaction buffer revealed the immense influence of manganese chloride on derived RT signatures, with arrest rates on m1A positions dropping from 82% down to 24%. Additionally, we observed a vast increase in nucleotide skipping events, with single positions rising from 4% to 49%, thus implying an enhanced read-through capability as an effect of Mn2+ on the reverse transcriptase, by promoting nucleotide skipping over synthesis abortion. While modifications such as m1A, m22G, m1G and m3C showed a clear influence of manganese ions on their RT signature, this effect was individual to the polymerase used. In summary, the results imply a supporting effect of Mn2+ on reverse transcription, thus overcoming blockades in the Watson-Crick face of modified ribonucleosides and improving both read-through rate and signal intensity in RT signature analysis.

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Heaton, Steven M., Natalie A. Borg, and Vishva M. Dixit. "Ubiquitin in the activation and attenuation of innate antiviral immunity." Journal of Experimental Medicine 213, no. 1 (2015): 1–13. http://dx.doi.org/10.1084/jem.20151531.

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Viral infection activates danger signals that are transmitted via the retinoic acid–inducible gene 1–like receptor (RLR), nucleotide-binding oligomerization domain-like receptor (NLR), and Toll-like receptor (TLR) protein signaling cascades. This places host cells in an antiviral posture by up-regulating antiviral cytokines including type-I interferon (IFN-I). Ubiquitin modifications and cross-talk between proteins within these signaling cascades potentiate IFN-I expression, and inversely, a growing number of viruses are found to weaponize the ubiquitin modification system to suppress IFN-I. Here we review how host- and virus-directed ubiquitin modification of proteins in the RLR, NLR, and TLR antiviral signaling cascades modulate IFN-I expression.

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Middendorf, Thomas R., Richard W. Aldrich, and Denis A. Baylor. "Modification of Cyclic Nucleotide–Gated Ion Channels by Ultraviolet Light." Journal of General Physiology 116, no. 2 (2000): 227–52. http://dx.doi.org/10.1085/jgp.116.2.227.

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We irradiated cyclic nucleotide–gated ion channels in situ with ultraviolet light to probe the role of aromatic residues in ion channel function. UV light reduced the current through excised membrane patches from Xenopus oocytes expressing the α subunit of bovine retinal cyclic nucleotide–gated channels irreversibly, a result consistent with permanent covalent modification of channel amino acids by UV light. The magnitude of the current reduction depended only on the total photon dose delivered to the patches, and not on the intensity of the exciting light, indicating that the functionally important photochemical modification(s) occurred from an excited state reached by a one-photon absorption process. The wavelength dependence of the channels' UV light sensitivity (the action spectrum) was quantitatively consistent with the absorption spectrum of tryptophan, with a small component at long wavelengths, possibly due to cystine absorption. This spectral analysis suggests that UV light reduced the currents at most wavelengths studied by modifying one or more “target” tryptophans in the channels. Comparison of the channels' action spectrum to the absorption spectrum of tryptophan in various solvents suggests that the UV light targets are in a water-like chemical environment. Experiments on mutant channels indicated that the UV light sensitivity of wild-type channels was not conferred exclusively by any one of the 10 tryptophan residues in a subunit. The similarity in the dose dependences of channel current reduction and tryptophan photolysis in solution suggests that photochemical modification of a small number of tryptophan targets in the channels is sufficient to decrease the currents.

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Johansson, Tommy, Annika Kers, and Jacek Stawinski. "2-Pyridylphosphonates: a new type of modification for nucleotide analogues." Tetrahedron Letters 42, no. 11 (2001): 2217–20. http://dx.doi.org/10.1016/s0040-4039(01)00115-0.

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Ito, Hiroyuki, Atsuko Sadaoka, Hirokazu Kotani, Nobutsugu Hiraoka, and Teruya Nakamura. "Cloning, nucleotide sequence, and expression of theHincll restriction-modification system." Nucleic Acids Research 18, no. 13 (1990): 3903–11. http://dx.doi.org/10.1093/nar/18.13.3903.

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Ivanovskaya, M. G., M. B. Gottikh, and Z. A. Shabarova. "Modification of Oligo (Poly) Nucleotide Phosphomonoester Groups in Aqueous Solutions." Nucleosides and Nucleotides 6, no. 5 (1987): 913–34. http://dx.doi.org/10.1080/15257778708073437.

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Grosjean, H., G. Björk, and B. E. H. Maden. "Nucleotide modification and base conversion of RNA: Summary and outlook." Biochimie 77, no. 1-2 (1995): 3–6. http://dx.doi.org/10.1016/0300-9084(96)88097-7.

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Lin, Shuibin, Qi Liu, Yi-Zhou Jiang, and Richard I. Gregory. "Nucleotide resolution profiling of m7G tRNA modification by TRAC-Seq." Nature Protocols 14, no. 11 (2019): 3220–42. http://dx.doi.org/10.1038/s41596-019-0226-7.

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Han, Chunhua, Ran Zhao, John Kroger, et al. "UV radiation-induced SUMOylation of DDB2 regulates nucleotide excision repair." Carcinogenesis 38, no. 10 (2017): 976–85. http://dx.doi.org/10.1093/carcin/bgx076.

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Abstract Subunit 2 of DNA damage-binding protein complex (DDB2) is an early sensor of nucleotide excision repair (NER) pathway for eliminating DNA damage induced by UV radiation (UVR) and cisplatin treatments of mammalian cells. DDB2 is modified by ubiquitin and poly(ADP-ribose) (PAR) in response to UVR, and these modifications play a crucial role in regulating NER. Here, using immuno-analysis of irradiated cell extracts, we have identified multiple post-irradiation modifications of DDB2 protein. Interestingly, although the DNA lesions induced by both UVR and cisplatin are corrected by NER, only the UV irradiation, but not the cisplatin treatment, induces any discernable DDB2 modifications. We, for the first time, show that the appearance of UVR-induced DDB2 modifications depend on the binding of DDB2 to the damaged chromatin and the participation of functionally active 26S proteasome. The in vitro and in vivo analysis revealed that SUMO-1 conjugations comprise a significant portion of these UVR-induced DDB2 modifications. Mapping of SUMO-modified sites demonstrated that UVR-induced SUMOylation occurs on Lys-309 residue of DDB2 protein. Mutation of Lys-309 to Arg-309 diminished the DDB2 SUMOylation observable both in vitro and in vivo. Moreover, K309R mutated DDB2 lost its function of recruiting XPC to the DNA damage sites, as well as the ability to repair cyclobutane pyrimidine dimers following cellular UV irradiation. Taken together, our results indicate that DDB2 is modified by SUMOylation upon UV irradiation, and this post-translational modification plays an important role in the initial recognition and processing of UVR-induced DNA damage occurring within the context of chromatin.

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Xu, Zhao-Chun, Peng-Mian Feng, Hui Yang, Wang-Ren Qiu, Wei Chen, and Hao Lin. "iRNAD: a computational tool for identifying D modification sites in RNA sequence." Bioinformatics 35, no. 23 (2019): 4922–29. http://dx.doi.org/10.1093/bioinformatics/btz358.

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Abstract Motivation Dihydrouridine (D) is a common RNA post-transcriptional modification found in eukaryotes, bacteria and a few archaea. The modification can promote the conformational flexibility of individual nucleotide bases. And its levels are increased in cancerous tissues. Therefore, it is necessary to detect D in RNA for further understanding its functional roles. Since wet-experimental techniques for the aim are time-consuming and laborious, it is urgent to develop computational models to identify D modification sites in RNA. Results We constructed a predictor, called iRNAD, for identifying D modification sites in RNA sequence. In this predictor, the RNA samples derived from five species were encoded by nucleotide chemical property and nucleotide density. Support vector machine was utilized to perform the classification. The final model could produce the overall accuracy of 96.18% with the area under the receiver operating characteristic curve of 0.9839 in jackknife cross-validation test. Furthermore, we performed a series of validations from several aspects and demonstrated the robustness and reliability of the proposed model. Availability and implementation A user-friendly web-server called iRNAD can be freely accessible at http://lin-group.cn/server/iRNAD, which will provide convenience and guide to users for further studying D modification.

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Cao, Bo, Xiaolin Wu, Jieliang Zhou, et al. "Nick-seq for single-nucleotide resolution genomic maps of DNA modifications and damage." Nucleic Acids Research 48, no. 12 (2020): 6715–25. http://dx.doi.org/10.1093/nar/gkaa473.

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Abstract DNA damage and epigenetic marks are well established to have profound influences on genome stability and cell phenotype, yet there are few technologies to obtain high-resolution genomic maps of the many types of chemical modifications of DNA. Here we present Nick-seq for quantitative, sensitive, and accurate mapping of DNA modifications at single-nucleotide resolution across genomes. Pre-existing breaks are first blocked and DNA modifications are then converted enzymatically or chemically to strand-breaks for both 3′-extension by nick-translation to produce nuclease-resistant oligonucleotides and 3′-terminal transferase tailing. Following library preparation and next generation sequencing, the complementary datasets are mined with a custom workflow to increase sensitivity, specificity and accuracy of the map. The utility of Nick-seq is demonstrated with genomic maps of site-specific endonuclease strand-breaks in purified DNA from Eschericia coli, phosphorothioate epigenetics in Salmonella enterica Cerro 87, and oxidation-induced abasic sites in DNA from E. coli treated with a sublethal dose of hydrogen peroxide. Nick-seq applicability is demonstrated with strategies for &gt;25 types of DNA modification and damage.

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Ayllón, María A., Siddarame Gowda, Tatineni Satyanarayana, et al. "Effects of Modification of the Transcription Initiation Site Context on Citrus Tristeza Virus Subgenomic RNA Synthesis." Journal of Virology 77, no. 17 (2003): 9232–43. http://dx.doi.org/10.1128/jvi.77.17.9232-9243.2003.

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ABSTRACT Citrus tristeza virus (CTV), a member of the Closteroviridae, has a positive-sense RNA genome of about 20 kb organized into 12 open reading frames (ORFs). The last 10 ORFs are expressed through 3′-coterminal subgenomic RNAs (sgRNAs) regulated in both amounts and timing. Additionally, relatively large amounts of complementary sgRNAs are produced. We have been unable to determine whether these sgRNAs are produced by internal promotion from the full-length template minus strand or by transcription from the minus-stranded sgRNAs. Understanding the regulation of 10 sgRNAs is a conceptual challenge. In analyzing commonalities of a replicase complex in producing so many sgRNAs, we examined initiating nucleotides of the sgRNAs. We mapped the 5′ termini of intermediate- (CP and p13) and low- (p18) produced sgRNAs that, like the two highly abundant sgRNAs (p20 and p23) previously mapped, all initiate with an adenylate. We then examined modifications of the initiation site, which has been shown to be useful in defining mechanisms of sgRNA synthesis. Surprisingly, mutation of the initiating nucleotide of the CTV sgRNAs did not prevent sgRNA accumulation. Based on our results, the CTV replication complex appears to initiate sgRNA synthesis with purines, preferably with adenylates, and is able to initiate synthesis using a nucleotide a few positions 5′ or 3′ of the native initiation nucleotide. Furthermore, the context of the initiation site appears to be a regulatory mechanism for levels of sgRNA production. These data do not support either of the established mechanisms for synthesis of sgRNAs, suggesting that CTV sgRNA production utilizes a different mechanism.

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Ganot, Philippe, Beáta E. Jády, Marie-Line Bortolin, Xavier Darzacq, and Tamás Kiss. "Nucleolar Factors Direct the 2′-O-Ribose Methylation and Pseudouridylation of U6 Spliceosomal RNA." Molecular and Cellular Biology 19, no. 10 (1999): 6906–17. http://dx.doi.org/10.1128/mcb.19.10.6906.

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ABSTRACT The nucleolus has long been known as a functionally highly specialized subnuclear compartment where synthesis, posttranscriptional modification, and processing of cytoplasmic rRNAs take place. In this study, we demonstrate that the nucleolus contains all thetrans-acting factors that are responsible for the accurate and efficient synthesis of the eight 2′-O-methylated nucleotides and three pseudouridine residues carried by the mammalian U6 spliceosomal small nuclear RNA. Factors mediating the formation of pseudouridine residues in the U3 small nucleolar RNA are also present and functionally active in the nucleolus. For selection of the correct target nucleotides in the U6 and U3 RNAs, the nucleolar 2′-O-methylation and pseudouridylation factors rely on short sequences located around the target nucleotide to be modified. This observation further underscores a recently proposed role for small nucleolar guide RNAs in the 2′-O-methylation of the U6 spliceosomal RNA (K. T. Tycowski, Z.-H. You, P. J. Graham, and J. A. Steitz, Mol. Cell 2:629–638, 1998). We demonstrate that a novel 2′-O-methylated nucleotide can be generated in the yeast U6 RNA by use of an artificial 2′-O-methylation small nucleolar guide RNA. We also show that a short fragment of the 5.8S rRNA, when expressed as part of the human U6 RNA, is faithfully 2′-O-methylated and pseudouridylated. These results are most consistent with a trafficking pathway in which the U6 spliceosomal RNA cycles through the nucleolus to undergo nucleolar RNA-directed modifications.

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MEULLER, Johan, Junwei ZHANG, Cynthia HOU, Philip D. BRAGG, and Jan RYDSTRÖM. "Properties of a cysteine-free proton-pumping nicotinamide nucleotide transhydrogenase." Biochemical Journal 324, no. 2 (1997): 681–87. http://dx.doi.org/10.1042/bj3240681.

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Nicotinamide nucleotide transhydrogenase from Escherichia coli was investigated with respect to the roles of its cysteine residues. This enzyme contains seven cysteines, of which five are located in the α subunit and two are in the β subunit. All cysteines were replaced by site-directed mutagenesis. The final construct (αC292T, αC339T, αC395S, αC397T, αC435S, βC147S, βC260S) was inserted normally in the membrane and underwent the normal NADPH-dependent conformational change of the β subunit to a trypsin-sensitive state. Reduction of NADP+ by NADH driven by ATP hydrolysis or respiration was between 32% and 65% of the corresponding wild-type activities. Likewise, the catalytic and proton pumping activities of the purified cysteine-free enzyme were at least 30% of the purified wild-type enzyme activities. The H+/H- ratio for both enzymes was 0.5, although the cysteine-free enzyme appeared to be more stable than the wild-type enzyme in proteoliposomes. No bound NADP(H) was detected in the enzymes. Modification of transhydrogenase by diethyl pyrocarbonate and the subsequent inhibition of the enzyme were unaffected by removal of the cysteines, indicating a lack of involvement of cysteines in this process. Replacement of cysteine residues in the α subunit resulted in no or little change in activity, suggesting that the basis for the decreased activity was probably the modification of the conserved β-subunit residue Cys-260 or (less likely) the non-conserved β-subunit residue Cys-147. It is concluded that the cysteine-free transhydrogenase is structurally and mechanistically very similar to the wild-type enzyme, with minor modifications of the properties of the NADP(H) site, possibly mediated by the βC260S mutation. The cysteine-free construct will be a valuable tool for studying structure–function relationships of transhydrogenases.

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Di Serio, Francesco, Enza Maria Torchetti, José-Antonio Daròs, and Beatriz Navarro. "Reassessment of Viroid RNA Cytosine Methylation Status at the Single Nucleotide Level." Viruses 11, no. 4 (2019): 357. http://dx.doi.org/10.3390/v11040357.

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Composed of a few hundreds of nucleotides, viroids are infectious, circular, non-protein coding RNAs able to usurp plant cellular enzymes and molecular machineries to replicate and move in their hosts. Several secondary and tertiary RNA structural motifs have been implicated in the viroid infectious cycle, but whether modified nucleotides, such as 5C-methylcytosine (m5C), also play a role has not been deeply investigated so far. Here, the possible existence of m5C in both RNA polarity strands of potato spindle tuber viroid and avocado sunblotch viroid -which are representative members of the nucleus- and chloroplast-replicating viroids, respectively- has been assessed at single nucleotide level. We show that a standard bisulfite protocol efficiently used for identifying m5C in cellular RNAs may generate false positive results in the case of the highly structured viroid RNAs. Applying a bisulfite conversion protocol specifically adapted to RNAs with high secondary structure, no m5C was identified in both polarity strands of both viroids, indicating that this specific nucleotide modification does not likely play a role in viroid biology.

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Limanskaya, O. Yu, T. N. Fesenko, V. A. Pokrovskiy, et al. "Characterization of oligonucleotides with LNA-monomers for PCR detection of point mutations in mycobacteria tuberculosis genome." Biomeditsinskaya Khimiya 58, no. 2 (2012): 199–210. http://dx.doi.org/10.18097/pbmc20125802199.

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Point mutations associated with isoniazid resistance in Mycobacterium tuberculosis (MTB) have been analyzed in codon 315 of the katG gene by conventional polymerase chain reaction (PCR) using primers containing locked nucleic acid (LNA) modified nucleotides. Purity and structure of primers containing 5 LNA monomers of 17 nucleotides in length were characterized by matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) and a 17-mer duplex formed by two complementary oligonucleotides was characterized by the method of thermal denaturation. The duplex containing five LNA monomers per each strand was characterized by a higher melting temperature than it was expected using extrapolation of theoretical calculation for nucleotide modification of one strand of the duplex. Detection of any of six possible mutations in katG codon 315 (i.e. discrimination between sensitive and resistant MTB) requires just one PCR employing a set of two primers with one LNA-modified primer; this is an important advantage of oligonucleotides containing LNA over unmodified nucleotides: employment of multiplex PCR would require up to 12 primers. Problems of control of oligonucleotide modification by LNA monomers are discussed.

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Suzuki, Toshihiko, Emi Sugimoto, Yasutaka Tahara, and Yuzo Yamada. "Cloning and Nucleotide Sequence ofApaLI Restriction-modification System fromAcetobacter pasteurianusIFO 13753†." Bioscience, Biotechnology, and Biochemistry 60, no. 9 (1996): 1401–5. http://dx.doi.org/10.1271/bbb.60.1401.

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Som, Subhendu, Ashok S. Bhagwat, and Stanley Friedman. "Nucleotide sequence and expression of the gene encoding theEcoRII modification enzyme." Nucleic Acids Research 15, no. 1 (1987): 313–32. http://dx.doi.org/10.1093/nar/15.1.313.

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Maden, B. Edward H., and John M. X. Hughes. "Eukaryotic ribosomal RNA: the recent excitement in the nucleotide modification problem." Chromosoma 105, no. 7-8 (1997): 391–400. http://dx.doi.org/10.1007/s004120050200.

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Gehrig, Stefanie, Mariel-Esther Eberle, Flavia Botschen, et al. "Identification of modifications in microbial, native tRNA that suppress immunostimulatory activity." Journal of Experimental Medicine 209, no. 2 (2012): 225–33. http://dx.doi.org/10.1084/jem.20111044.

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Naturally occurring nucleotide modifications within RNA have been proposed to be structural determinants for innate immune recognition. We tested this hypothesis in the context of native nonself-RNAs. Isolated, fully modified native bacterial transfer RNAs (tRNAs) induced significant secretion of IFN-α from human peripheral blood mononuclear cells in a manner dependent on TLR7 and plasmacytoid dendritic cells. As a notable exception, tRNATyr from Escherichia coli was not immunostimulatory, as were all tested eukaryotic tRNAs. However, the unmodified, 5′-unphosphorylated in vitro transcript of tRNATyr induced IFN-α, thus revealing posttranscriptional modifications as a factor suppressing immunostimulation. Using a molecular surgery approach based on catalytic DNA, a panel of tRNATyr variants featuring differential modification patterns was examined. Out of seven modifications present in this tRNA, 2′-O-methylated Gm18 was identified as necessary and sufficient to suppress immunostimulation. Transplantation of this modification into the scaffold of yeast tRNAPhe also resulted in blocked immunostimulation. Moreover, an RNA preparation of an E. coli trmH mutant that lacks Gm18 2′-O-methyltransferase activity was significantly more stimulatory than the wild-type sample. The experiments identify the single methyl group on the 2′-oxygen of Gm18 as a natural modification in native tRNA that, beyond its primary structural role, has acquired a secondary function as an antagonist of TLR7.

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Lu, Xuefeng, and Tae Hyun. "The role of epigenetic modifications in plant responses to stress." Botanica Serbica 45, no. 1 (2021): 3–12. http://dx.doi.org/10.2298/botserb2101003l.

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Epigenetics is the study of hereditary changes in gene expression under the premise that the nucleotide sequence is not changed. Such hereditary changes mainly involve DNA methylation, histone modification, and chromatin remodeling. These covalent modifications play indispensable roles in regulating gene expression; DNA replication, recombination, and repair; and cell differentiation. Epigenetic modifications can be partially inherited by daughter cells during mitosis and meiosis and influenced by external factors, such as environmental stresses and supply deficits. In this review, we summarize the current knowledge regarding epigenetic factors, such as DNA methylation, histone acetylation, and regulation by non-coding RNAs, in the development and stress response of plants.

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Hardy, Alexis, Mélody Matelot, Amandine Touzeau, et al. "DNAModAnnot: a R toolbox for DNA modification filtering and annotation." Bioinformatics 37, no. 17 (2021): 2738–40. http://dx.doi.org/10.1093/bioinformatics/btab032.

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Abstract Motivation Long-read sequencing technologies can be employed to detect and map DNA modifications at the nucleotide resolution on a genome-wide scale. However, published software packages neglect the integration of genomic annotation and comprehensive filtering when analyzing patterns of modified bases detected using Pacific Biosciences (PacBio) or Oxford Nanopore Technologies (ONT) data. Here, we present DNA Modification Annotation (DNAModAnnot), a R package designed for the global analysis of DNA modification patterns using adapted filtering and visualization tools. Results We tested our package using PacBio sequencing data to analyze patterns of the 6-methyladenine (6mA) in the ciliate Paramecium tetraurelia, in which high 6mA amounts were previously reported. We found P. tetraurelia 6mA genome-wide distribution to be similar to other ciliates. We also performed 5-methylcytosine (5mC) analysis in human lymphoblastoid cells using ONT data and confirmed previously known patterns of 5mC. DNAModAnnot provides a toolbox for the genome-wide analysis of different DNA modifications using PacBio and ONT long-read sequencing data. Availability and implementation DNAModAnnot is distributed as a R package available via GitHub (https://github.com/AlexisHardy/DNAModAnnot). Supplementary information Supplementary data are available at Bioinformatics online.

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Stojković, Vanja, Alexander G. Myasnikov, Iris D. Young, Adam Frost, James S. Fraser, and Danica Galonić Fujimori. "Assessment of the nucleotide modifications in the high-resolution cryo-electron microscopy structure of the Escherichia coli 50S subunit." Nucleic Acids Research 48, no. 5 (2020): 2723–32. http://dx.doi.org/10.1093/nar/gkaa037.

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Abstract Post-transcriptional ribosomal RNA (rRNA) modifications are present in all organisms, but their exact functional roles and positions are yet to be fully characterized. Modified nucleotides have been implicated in the stabilization of RNA structure and regulation of ribosome biogenesis and protein synthesis. In some instances, rRNA modifications can confer antibiotic resistance. High-resolution ribosome structures are thus necessary for precise determination of modified nucleotides’ positions, a task that has previously been accomplished by X-ray crystallography. Here, we present a cryo-electron microscopy (cryo-EM) structure of the Escherichia coli 50S subunit at an average resolution of 2.2 Å as an additional approach for mapping modification sites. Our structure confirms known modifications present in 23S rRNA and additionally allows for localization of Mg2+ ions and their coordinated water molecules. Using our cryo-EM structure as a testbed, we developed a program for assessment of cryo-EM map quality. This program can be easily used on any RNA-containing cryo-EM structure, and an associated Coot plugin allows for visualization of validated modifications, making it highly accessible.

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