ArticleNucleic acids research2021
Nucleotide resolution profiling of m3C RNA modification by HAC-seq.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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Who cites it
51 citing papers in PubMed, 91 citations in OpenAlex.
- tRNA methylation: functional insights and epitranscriptomic regulation.Cell communication and signaling : CCS · 2026Review
- RNA modification-mediated multidimensional crosstalk: a novel perspective on gene expression regulation.Genome biology · 2026Review
- Enzyme-mediated alkynylation enables transcriptome-wide identification of pseudouridine modifications.Nature communications · 2026Article
- Hidden in plain sight: illuminating the tRNA landscape by sequencing.Genome biology · 2026Review
- Article
- Mapping the RNA methylome under drought: techniques, mechanisms, and agricultural implications.Frontiers in plant science · 2026Review
- tRNA modifications: greasing the wheels of translation and beyond.RNA biology · 2025Review
- Nanopore direct RNA sequencing reveals METTL2A-mediated mGenome research · 2025Article
- Targeting tRNA methyltransferases: from molecular mechanisms to drug discovery.Science China. Life sciences · 2025Review
- MapID-based quantitative mapping of chemical modifications and expression of human transfer RNA.Cell chemical biology · 2025Article
- Transcriptome-wide mapping of N3-methylcytidine modification at single-base resolution.Nucleic acids research · 2025Article
- Chemical reactivity of RNA and its modifications with hydrazine.Communications chemistry · 2025Article
- Human TRMT1 and TRMT1L paralogs ensure the proper modification state, stability, and function of tRNAs.Cell reports · 2025Article
- Genome-wide profiling of tRNA modifications by Induro-tRNAseq reveals coordinated changes.Nature communications · 2025Article
- Mapping epigenetic modifications by sequencing technologies.Cell death and differentiation · 2025Review
- RNA modifications and their role in gene expression.Frontiers in molecular biosciences · 2025Review
- High-throughput detection of RNA modifications at single base resolution.FEBS letters · 2025Review
- Structural basis of tRNA recognition by the mNature structural & molecular biology · 2024Article
- RluA is the major mRNA pseudouridine synthase in Escherichia coli.PLoS genetics · 2024Article
- Dysregulation of tRNA methylation in cancer: Mechanisms and targeting therapeutic strategies.Cell death discovery · 2024Review
Corrections and comments
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Authors and funding
5 authors at 1 institution in 2 countries.
Funding
Abstract
Cellular RNAs are subject to a myriad of different chemical modifications that play important roles in controlling RNA expression and function. Dysregulation of certain RNA modifications, the so-called 'epitranscriptome', contributes to human disease. One limitation in studying the functional, physiological, and pathological roles of the epitranscriptome is the availability of methods for the precise mapping of individual RNA modifications throughout the transcriptome. 3-Methylcytidine (m3C) modification of certain tRNAs is well established and was also recently detected in mRNA. However, methods for the specific mapping of m3C throughout the transcriptome are lacking. Here, we developed a m3C-specific technique, Hydrazine-Aniline Cleavage sequencing (HAC-seq), to profile the m3C methylome at single-nucleotide resolution. We applied HAC-seq to analyze ribosomal RNA (rRNA)-depleted total RNAs in human cells. We found that tRNAs are the predominant m3C-modified RNA species, with 17 m3C modification sites on 11 cytoplasmic and 2 mitochondrial tRNA isoacceptors in MCF7 cells. We found no evidence for m3C-modification of mRNA or other non-coding RNAs at comparable levels to tRNAs in these cells. HAC-seq provides a novel method for the unbiased, transcriptome-wide identification of m3C RNA modification at single-nucleotide resolution, and could be widely applied to reveal the m3C methylome in different cells and tissues.
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