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Small-molecule-catalysed deamination enables transcriptome-wide profiling of N⁶-methyladenosine in RNA

Nucleobase deamination can be used to map N⁶-methyladenosine in RNA, but existing deamination methods are harsh, limiting applications. Now a method for the N-nitrosation of RNA based on organocatalyst and Lewis acid co-catalysis has been shown to enable sensitive N⁶-methyladenosine mapping with minimal background noise and high detection efficiency.

Pingluan Wang
Chang Ye
Chuan He
Research17 Apr 2025
Nature Chemistry

Volume: 17, P: 1042-1052
Author Correction: m⁶A-SAC-seq for quantitative whole transcriptome m⁶A profiling

Ruiqi Ge
Chang Ye
Chuan He
Amendments and Corrections22 Jun 2023
Nature Protocols

Volume: 18, P: 3652
Quantitative analysis of cis-regulatory elements in transcription with KAS-ATAC-seq

Cis-regulatory elements (CREs) are crucial for gene expression. Here, authors develop a method for CRE activity quantification, which allows the identification of transcriptional regulatory sequences including Single-Stranded Transcribing Enhancers (SSTEs), and apply it to gain insights into gene regulation during neural differentiation.

Ruitu Lyu
Yun Gao
Chuan He
ResearchOpen Access10 Aug 2024
Nature Communications

Volume: 15, P: 1-17
PTPN2 copper-sensing relays copper level fluctuations into EGFR/CREB activation and associated CTR1 transcriptional repression

Copper level fluctuations are shown to modulate EGFR signal transduction via inhibition of the phosphatase PTPN2, culminating in CREB transcription factor activity, which is associated with transcriptional repression of the copper importer CTR1.

Matthew O. Ross
Yuan Xie
Chuan He
ResearchOpen Access13 Aug 2024
Nature Communications

Volume: 15, P: 1-15
Profiling of RNA-binding protein binding sites by in situ reverse transcription-based sequencing

This work introduces ARTR-seq for in situ measurement of RNA-binding protein (RBP) binding sites, which has been demonstrated in a small number of cells and for capturing dynamic RBP binding within short timeframes.

Yu Xiao
Yan-Ming Chen
Chuan He
ResearchOpen Access10 Jan 2024
Nature Methods

Volume: 21, P: 247-258
KARR-seq reveals cellular higher-order RNA structures and RNA–RNA interactions

RNA interactions and structures are determined with a chemical labeling and crosslinking method.

Tong Wu
Anthony Youzhi Cheng
Chuan He
ResearchOpen Access18 Jan 2024
Nature Biotechnology

Volume: 42, P: 1909-1920
Keth-seq for transcriptome-wide RNA structure mapping

The authors designed a chemical probe, azido-kethoxal, to specifically label guanosine in single-strand RNAs in live cells that could be used to determine transcriptome-wide RNA secondary structures.

Xiaocheng Weng
Jing Gong
Chuan He
Research03 Feb 2020
Nature Chemical Biology

Volume: 16, P: 489-492
m⁶A-SAC-seq for quantitative whole transcriptome m⁶A profiling

This protocol describes N⁶-methyladenosine (m⁶A)-SAC-seq, site-specific base-resolution m⁶A sequencing in the whole transcriptome, including preparing the enzyme and synthesizing the allyl-SAM cofactor required for library preparation, and data analysis for m⁶A sites.

Ruiqi Ge
Chang Ye
Chuan He
Protocols25 Nov 2022
Nature Protocols

Volume: 18, P: 626-657

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Small-molecule-catalysed deamination enables transcriptome-wide profiling of N⁶-methyladenosine in RNA

Author Correction: m⁶A-SAC-seq for quantitative whole transcriptome m⁶A profiling

Quantitative analysis of cis-regulatory elements in transcription with KAS-ATAC-seq

PTPN2 copper-sensing relays copper level fluctuations into EGFR/CREB activation and associated CTR1 transcriptional repression

Profiling of RNA-binding protein binding sites by in situ reverse transcription-based sequencing

KARR-seq reveals cellular higher-order RNA structures and RNA–RNA interactions

Keth-seq for transcriptome-wide RNA structure mapping

m⁶A-SAC-seq for quantitative whole transcriptome m⁶A profiling

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