Epitranscriptomic mapping of RNA modifications at single-nucleotide resolution using rhodamine sequencing (Rho-seq)
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Summary
The protocol for Rho-Seq is described, which enables the mapping of dihydrouridine RNA modification at single-nucleotide resolution, and is applicable to other modifications including 7-methylguanosine or 4-thiouridine.
- Type
- article
- Published
- 2022-05-05
- Cited by
- 7
- References
- 37
- Access
- Open access
- OpenAlex
- https://openalex.org/W4229028821
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:248644931
Keywords
Nucleotide, RNA-Seq, Computational biology, RNA, Biology
References
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- Transcriptome-wide identification of adenosine-to-inosine editing using the ICE-seq method
- Preparation of a pG‐fragment from tRNAPhe yeast by chemical scission at the dihydrouracil, and inhibition of tRNAPhe yeast charging by this fragment when combined with the ‐CCA half of this tRNA
- 1-Methyladenosine. Dimroth rearrangement and reversible reduction.
- Independent filtering increases detection power for high-throughput experiments
- Photoreduction of uridine and reduction of dihydrouridine with sodium borohydride.
- Selective reduction of yeast transfer ribonucleic acid with sodium borohydride.
- Replacement of wybutine by hydrazines and its effect on the active conformation of yeast tRNAPhe.
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- A simple strand-specific RNA-Seq library preparation protocol combining the Illumina TruSeq RNA and the dUTP methods.
- The Sequence Alignment/Map format and SAMtools
- Controlling the false discovery rate: a practical and powerful approach to multiple testing
- Trimmomatic: a flexible trimmer for Illumina sequence data
- Fluorescent labeling of tRNAs for dynamics experiments.
Cited by
- The Dihydrouridine landscape from tRNA to mRNA: a perspective on synthesis, structural impact and function
- Self-attention enabled deep learning of dihydrouridine (D) modification on mRNAs unveiled a distinct sequence signature from tRNAs
- A novel cell biological tool to explain mechanics and dynamics in fission yeast
- The molecular basis of tRNA selectivity by human pseudouridine synthase 3
- Advancements in chemically inducible modified tRNA sequencing techniques: Elucidating novel insights into tRNA epitranscriptomics.
- Quantitative CRACI reveals transcriptome-wide distribution of RNA dihydrouridine at base resolution
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