High-throughput and site-specific identification of 2′-<i>O</i>-methylation sites using ribose oxidation sequencing (RibOxi-seq)

Zhu, Yinzhou; Pirnie, Stephan P.; Carmichael, Gordon G.

doi:10.1261/rna.061549.117

Cited by 76 publications

(74 citation statements)

References 34 publications

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“…Nm-seq uncovered over 7,000 potential methylation sites in human mRNA revealing a consensus sequence and enrichment within three amino acid codons and extensive ribose methylation in all four bases. The same approach has been used to map these sites in rRNA (Dai et al, 2017; Zhu et al, 2017). …”

Section: Ribose Modificationmentioning

confidence: 99%

Dynamic RNA Modifications in Gene Expression Regulation

Roundtree

Evans

Pan

et al. 2017

Cell

2,464

2,401

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Over one hundred types of chemical modifications have been identified in cellular RNAs. While the 5’ cap modification and the poly(A) tail of eukaryotic messenger RNA play key roles in regulation, internal modifications are gaining attention for their roles in mRNA metabolism. The most abundant internal modification is N6-methyladenosine (m6A), and identification of proteins that install, recognize, and remove this and other marks have revealed roles for mRNA modification in nearly every aspect of the mRNA lifecycle, as well as in various cellular, developmental, and disease processes. Abundant noncoding RNAs such as transfer RNAs, ribosomal RNAs and spliceosomal RNAs are also heavily modified and depend on the modifications for their biogenesis and function. Our understanding of the biological contributions of these different chemical modifications is beginning to take shape, but it’s clear that in both coding and noncoding RNA, dynamic modifications represent a new layer of control of genetic information.

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Section: Ribose Modificationmentioning

confidence: 99%

Dynamic RNA Modifications in Gene Expression Regulation

Roundtree

Evans

Pan

et al. 2017

Cell

2,464

2,401

View full text Add to dashboard Cite

show abstract

“…In 2′ome-Seq, reverse transcription stops at an Nm site under low-dNtP conditions 140 . Nm-seq and ribooxiSeq utilize the resistance of 3′-end Nm to periodate cleavage (Io 4 -) 141,142 . All three of these chemical Nm-mapping methods provide single-nucleotide resolution.…”

Section: Box 2 | Techniques Used To Map Epitranscriptomic Modificationsmentioning

confidence: 99%

Epigenetic and epitranscriptomic regulation of viral replication

2020

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Eukaryotic gene expression is regulated not only by genomic enhancers and promoters, but also by covalent modifications added to both chromatin and RNAs. Whereas cellular gene expression may be either enhanced or inhibited by specific epigenetic modifications deposited on histones (in particular, histone H3), these epigenetic modifications can also repress viral gene expression, potentially functioning as a potent antiviral innate immune response in DNA virus-infected cells. However, viruses have evolved countermeasures that prevent the epigenetic silencing of their genes during lytic replication, and they can also take advantage of epigenetic silencing to establish latent infections. By contrast, the various covalent modifications added to RNAs, termed epitranscriptomic modifications, can positively regulate mRNA translation and/or stability, and both DNA and RNA viruses have evolved to utilize epitranscriptomic modifications as a means to maximize viral gene expression. As a consequence, both chromatin and RNA modifications could serve as novel targets for the development of antivirals. In this Review, we discuss how host epigenetic and epitranscriptomic processes regulate viral gene expression at the levels of chromatin and RNA function, respectively, and explore how viruses modify, avoid or utilize these processes in order to regulate viral gene expression.

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“…Assorted archaeal and eukaryotic snoRNAs, many of which are Box C/D snoRNAs, aid in assembling the snoRNPs NOP56, NOP58, fibrillarin, and 15.5K/Snu13/L7Ae. This protein complex then coordinates 2 0 -Omethylation events on pre-rRNA transcripts and other RNAs (reviewed in Sloan et al, 2017;Yip, Shigematsu, Taylor, & Baserga, 2016;Zhu, Pirnie, & Carmichael, 2017). Moreover, snoRNAs are also used by archaeal species to conduct 2 0 -Omethylation events on tRNA.…”

Section: 0 -O-methyl Rna Modifications Exist In Otherwise Unmodifmentioning

confidence: 99%

Naturally occurring modified ribonucleosides

et al. 2020

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The chemical identity of RNA molecules beyond the four standard ribonucleosides has fascinated scientists since pseudouridine was characterized as the "fifth" ribonucleotide in 1951. Since then, the ever-increasing number and complexity of modified ribonucleosides have been found in viruses and throughout all three domains of life. Such modifications can be as simple as methylations, hydroxylations, or thiolations, complex as ring closures, glycosylations, acylations, or aminoacylations, or unusual as the incorporation of selenium. While initially found in transfer and ribosomal RNAs, modifications also exist in messenger RNAs and noncoding RNAs. Modifications have profound cellular outcomes at various levels, such as altering RNA structure or being essential for cell survival or organism viability. The aberrant presence or absence of RNA modifications can lead to human disease, ranging from cancer to various metabolic and developmental illnesses such as Hoyeraal-Hreidarsson syndrome, Bowen-Conradi syndrome, or Williams-Beuren syndrome. In this review article, we summarize the characterization of all 143 currently known modified ribonucleosides by describing their taxonomic distributions, the enzymes that generate the modifications, and any implications in cellular processes, RNA structure, and disease. We also highlight areas of active research, such as specific RNAs that contain a particular type of modification as well as methodologies used to identify novel RNA modifications.

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High-throughput and site-specific identification of 2′-O-methylation sites using ribose oxidation sequencing (RibOxi-seq)

Cited by 76 publications

References 34 publications

Dynamic RNA Modifications in Gene Expression Regulation

Dynamic RNA Modifications in Gene Expression Regulation

Epigenetic and epitranscriptomic regulation of viral replication

Naturally occurring modified ribonucleosides

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