RNA-Guided RNA Modifications: Biogenesis, Functions, and Applications

Targeted pseudouridylation: An approach for suppressing nonsense mutations in disease genes

(2023) Hironori Adachi et al.   MOLECULAR CELL

RIP-PEN-seq identifies a class of kink-turn RNAs as splicing regulators

(2023) Bin Li et al.   NATURE BIOTECHNOLOGY

Quantitative profiling of pseudouridylation landscape in the human transcriptome

(2023) Meiling Zhang et al.   Nature Chemical Biology

Development of a selection assay for small guide RNAs that drive efficient site-directed RNA editing

(2023) Juan Felipe Diaz Quiroz et al.   NUCLEIC ACIDS RESEARCH

Ribosomal RNA 2′-O-methylation dynamics impact cell fate decisions

(2023) Sophia J. Häfner et al.   DEVELOPMENTAL CELL

A SAM analogue-utilizing ribozyme for site-specific RNA alkylation in living cells

(2023) Takumi Okuda et al.   Nature Chemistry

Regulation and functions of non-m6A mRNA modifications

(2023) Hanxiao Sun et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

A snoRNA–tRNA modification network governs codon-biased cellular states

(2023) Minjie Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Site-Specific Synthesis of N4-Acetylcytidine in RNA Reveals Physiological Duplex Stabilization

(2022) David Bartee et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

CLUSTER guide RNAs enable precise and efficient RNA editing with endogenous ADAR enzymes in vivo

(2022) Philipp Reautschnig et al.   NATURE BIOTECHNOLOGY

Engineered circular ADAR-recruiting RNAs increase the efficiency and fidelity of RNA editing in vitro and in vivo

(2022) Zongyi Yi et al.   NATURE BIOTECHNOLOGY

Efficient in vitro and in vivo RNA editing via recruitment of endogenous ADARs using circular guide RNAs

(2022) Dhruva Katrekar et al.   NATURE BIOTECHNOLOGY

Endogenous ADAR-mediated RNA editing in non-human primates using stereopure chemically modified oligonucleotides

(2022) Prashant Monian et al.   NATURE BIOTECHNOLOGY

Structure and mechanism of the methyltransferase ribozyme MTR1

(2022) Carolin P. M. Scheitl et al.   Nature Chemical Biology

Structure and mechanism of a methyltransferase ribozyme

(2022) Jie Deng et al.   Nature Chemical Biology

Probing small ribosomal subunit RNA helix 45 acetylation across eukaryotic evolution

(2022) Marie-Line Bortolin-Cavaillé et al.   NUCLEIC ACIDS RESEARCH

A systematic dissection of determinants and consequences of snoRNA-guided pseudouridylation of human mRNA

(2022) Ronit Nir et al.   NUCLEIC ACIDS RESEARCH

Ribosomal RNA 2′- O -methylations regulate translation by impacting ribosome dynamics

(2022) Sohail Khoshnevis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ADAR1 prevents autoinflammation by suppressing spontaneous ZBP1 activation

(2022) Richard de Reuver et al.   NATURE

Box C/D snoRNA SNORD89 influences the occurrence and development of endometrial cancer through 2’-O-methylation modification of Bim

(2022) Hai-juan Bao et al.   Cell Death Discovery

Modular, programmable RNA sensing using ADAR editing in living cells

(2022) K. Eerik Kaseniit et al.   NATURE BIOTECHNOLOGY

Quantitative sequencing using BID-seq uncovers abundant pseudouridines in mammalian mRNA at base resolution

(2022) Qing Dai et al.   NATURE BIOTECHNOLOGY

Programmable eukaryotic protein synthesis with RNA sensors by harnessing ADAR

(2022) Kaiyi Jiang et al.   NATURE BIOTECHNOLOGY

snoDB 2.0: an enhanced interactive database, specializing in human snoRNAs

(2022) Danny Bergeron et al.   NUCLEIC ACIDS RESEARCH

Antisense pairing and SNORD13 structure guide RNA cytidine acetylation

(2022) Supuni Thalalla Gamage et al.   RNA

Single-base resolution mapping of 2′-O-methylation sites by an exoribonuclease-enriched chemical method

(2022) Ping Zhang et al.   Science China-Life Sciences

A dynamic rRNA ribomethylome drives stemness in acute myeloid leukemia

(2022) Fengbiao Zhou et al.   Cancer Discovery

C/D box small nucleolar RNA SNORD104 promotes endometrial cancer by regulating the 2ʹ-O-methylation of PARP1

(2022) Bingfeng Lu et al.   Journal of Translational Medicine

CRISPR-free, programmable RNA pseudouridylation to suppress premature termination codons

(2022) Jinghui Song et al.   MOLECULAR CELL

Spliceosomal snRNA Epitranscriptomics

(2021) Pedro Morais et al.   Frontiers in Genetics

Quantitative profiling of pseudouridylation dynamics in native RNAs with nanopore sequencing

(2021) Oguzhan Begik et al.   NATURE BIOTECHNOLOGY

Programmable RNA editing with compact CRISPR–Cas13 systems from uncultivated microbes

(2021) Chunlong Xu et al.   NATURE METHODS

Evolutionary driving forces of A‐to‐I editing in metazoans

(2021) Yuange Duan et al.   Wiley Interdisciplinary Reviews-RNA

Epitranscriptomic editing of the RNA N6-methyladenosine modification by dCasRx conjugated methyltransferase and demethylase

(2021) Zhen Xia et al.   NUCLEIC ACIDS RESEARCH

A natural riboswitch scaffold with self-methylation activity

(2021) Laurin Flemmich et al.   Nature Communications

Guide RNA acrobatics: positioning consecutive uridines for pseudouridylation by H/ACA pseudouridylation loops with dual guide capacity

(2021) Beáta E. Jády et al.   GENES & DEVELOPMENT

The identification and characterization of a selected SAM-dependent methyltransferase ribozyme that is present in natural sequences

(2021) Hengyi Jiang et al.   Nature Catalysis

Sense–antisense miRNA pairs constitute an elaborate reciprocal regulatory circuit

(2020) Yulong Song et al.   GENOME RESEARCH

Dynamic RNA acetylation revealed by quantitative cross-evolutionary mapping

(2020) Aldema Sas-Chen et al.   NATURE

Programmable m6A modification of cellular RNAs with a Cas13-directed methyltransferase

(2020) Christopher Wilson et al.   NATURE BIOTECHNOLOGY

Re-assessment of the involvement of Snord115 in the serotonin 2C receptor pathway in a genetically relevant mouse model

(2020) Jade Hebras et al.   eLife

In vivo RNA editing of point mutations via RNA-guided adenosine deaminases

(2019) Dhruva Katrekar et al.   NATURE METHODS

Precise RNA editing by recruiting endogenous ADARs with antisense oligonucleotides

(2019) Tobias Merkle et al.   NATURE BIOTECHNOLOGY

Programmable RNA-Guided RNA Effector Proteins Built from Human Parts

(2019) Simone Rauch et al.   CELL

Cooperative 2′-O-methylation of the wobble cytidine of human elongator tRNAMet(CAT) by a nucleolar and a Cajal body-specific box C/D RNP

(2019) Patrice Vitali et al.   GENES & DEVELOPMENT

Programmable RNA editing by recruiting endogenous ADAR using engineered RNAs

(2019) Liang Qu et al.   NATURE BIOTECHNOLOGY

Pseudouridines on Trypanosoma brucei spliceosomal small nuclear RNAs and their implication for RNA and protein interactions

(2019) K Shanmugha Rajan et al.   NUCLEIC ACIDS RESEARCH

A cytosine deaminase for programmable single-base RNA editing

(2019) Omar O. Abudayyeh et al.   SCIENCE

Modification of messenger RNA by 2′-O-methylation regulates gene expression in vivo

(2019) Brittany A. Elliott et al.   Nature Communications

Programmable RNA N6-methyladenosine editing by CRISPR-Cas9 conjugates

(2019) Xiao-Min Liu et al.   Nature Chemical Biology

Direct in Vitro Selection of Trans-Acting Ribozymes for Posttranscriptional, Site-Specific, and Covalent Fluorescent Labeling of RNA

(2019) Mohammad Ghaem Maghami et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

2′-O-methylation in mRNA disrupts tRNA decoding during translation elongation

(2018) Junhong Choi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

2′-O-methylation in mRNA disrupts tRNA decoding during translation elongation

(2018) Junhong Choi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Acetylation of Cytidine in mRNA Promotes Translation Efficiency

(2018) Daniel Arango et al.   CELL

Epitranscriptome sequencing technologies: decoding RNA modifications

(2017) Xiaoyu Li et al.   NATURE METHODS

Detecting RNA modifications in the epitranscriptome: predict and validate

(2017) Mark Helm et al.   NATURE REVIEWS GENETICS

RMBase v2.0: deciphering the map of RNA modifications from epitranscriptome sequencing data

(2017) Jia-Jia Xuan et al.   NUCLEIC ACIDS RESEARCH

RNA editing with CRISPR-Cas13

(2017) David B. T. Cox et al.   SCIENCE

Specialized box C/D snoRNPs act as antisense guides to target RNA base acetylation

(2017) Sunny Sharma et al.   PLoS Genetics

Pseudouridylation of 7SK snRNA promotes 7SK snRNP formation to suppress HIV‐1 transcription and escape from latency

(2016) Yang Zhao et al.   EMBO REPORTS

High-throughput determination of RNA structure by proximity ligation

(2015) Vijay Ramani et al.   NATURE BIOTECHNOLOGY

Transcriptome-wide dynamics of RNA pseudouridylation

(2015) John Karijolich et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Human NAT10 Is an ATP-dependent RNA Acetyltransferase Responsible forN4-Acetylcytidine Formation in 18 S Ribosomal RNA (rRNA)

(2014) Satoshi Ito et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Insights into snoRNA biogenesis and processing from PAR-CLIP of snoRNA core proteins and small RNA sequencing

(2013) Shivendra Kishore et al.   GENOME BIOLOGY

Transcriptome-wide identification of A > I RNA editing sites by inosine specific cleavage

(2012) P. B. Cattenoz et al.   RNA

Cross-linking, ligation, and sequencing of hybrids reveals RNA-RNA interactions in yeast

(2011) G. Kudla et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The box C/D and H/ACA snoRNPs: key players in the modification, processing and the dynamic folding of ribosomal RNA

(2011) Nicholas J. Watkins et al.   Wiley Interdisciplinary Reviews-RNA

Targeted 2'-O Methylation at a Nucleotide within the Pseudoknot of Telomerase RNA Reduces Telomerase Activity In Vivo

(2010) C. Huang et al.   MOLECULAR AND CELLULAR BIOLOGY

Inosine cyanoethylation identifies A-to-I RNA editing sites in the human transcriptome

(2010) Masayuki Sakurai et al.   Nature Chemical Biology

Regulation of pre-mRNA splicing in Xenopus oocytes by targeted 2'-O-methylation

(2010) J. Ge et al.   RNA