Nature Search

A cohort of mRNAs undergo high-stoichiometry NSUN6-mediated site-specific m⁵C modification

mRNA modifications like m⁵C are typically introduced by tRNA-modifying enzymes, while the catalytic mechanism and function remain debated. Here, the authors show that NSUN6 catalyzes tRNA and mRNA substrates in different ways, and that NSUN6 promotes breast cancer cell migration through mRNA m⁵C modification.

Yuan-Yuan Zhang
Cai-Tao Li
Ru-Juan Liu
ResearchOpen Access04 Jul 2025
Nature Communications

Volume: 16, P: 1-19
RNA structure probing reveals the structural basis of Dicer binding and cleavage

Sequencing methods such as icSHAPE were developed to probe RNA structures transcriptome-wide in cells. To probe intact RNA structures, the authors develop icSHAPE-MaP and apply to Dicer-bound substrates showing that distance measuring is important for Dicer cleavage of pre-miRNAs.

Qing-Jun Luo
Jinsong Zhang
Qiangfeng Cliff Zhang
ResearchOpen Access07 Jun 2021
Nature Communications

Volume: 12, P: 1-12
Structural insights into branch site proofreading by human spliceosome

Here, the authors structurally characterize two sequential complexes leading to prespliceosome assembly, providing insights into the mechanism of branch site proofreading in the human spliceosome.

Xiaofeng Zhang
Xiechao Zhan
Yigong Shi
Research09 Jan 2024
Nature Structural & Molecular Biology

Volume: 31, P: 835-845
Genome-coverage single-cell histone modifications for embryo lineage tracing

Two new methods, target chromatin indexing and tagmentation (TACIT) and combined TACIT (CoTACIT), enabled single-cell profiling of the epigenome and lineage tracing from mouse zygotes to blastocysts.

Min Liu
Yanzhu Yue
Aibin He
ResearchOpen Access26 Feb 2025
Nature

Volume: 640, P: 828-839
Inward lithium-ion breathing of hierarchically porous silicon anodes

Porous silicon is highly promising as an anode material in lithium ion batteries, but its volume change upon lithiation has deleterious effects upon efficiency. Here, the authors demonstrate porous shell/hollow core Si nanospheres which exhibit negligible outward expansion and maintain performance.

Qiangfeng Xiao
Meng Gu
Mei Cai
ResearchOpen Access05 Nov 2015
Nature Communications

Volume: 6, P: 1-8
Erratum: Structural imprints in vivo decode RNA regulatory mechanisms

Robert C. Spitale
Ryan A. Flynn
Howard Y. Chang
Amendments and Corrections30 Sept 2015
Nature

Volume: 527, P: 264
Computational prediction and experimental validation identify functionally conserved lncRNAs from zebrafish to human

A new computational method coupled with a CRISPR–Cas12a screen identifies human long noncoding RNAs (lncRNAs) that lead to cell proliferation defects, which can be rescued by zebrafish homologs. Knockdown of four zebrafish lncRNAs that perturb embryonic development can be rescued by human homologs.

Wenze Huang
Tuanlin Xiong
Qiangfeng Cliff Zhang
ResearchOpen Access09 Jan 2024
Nature Genetics

Volume: 56, P: 124-135
SCALE method for single-cell ATAC-seq analysis via latent feature extraction

Single-cell ATAC-seq data is challenging to analyse for reasons such as high dimensionality and sparsity. Here, the authors develop SCALE, a deep learning method that leverages latent feature extraction for various tasks of scATACseq data analysis.

Lei Xiong
Kui Xu
Qiangfeng Cliff Zhang
ResearchOpen Access08 Oct 2019
Nature Communications

Volume: 10, P: 1-10
Single-cell transcriptome and translatome dual-omics reveals potential mechanisms of human oocyte maturation

Development of methods for simultaneous single cell analysis of transcription and translation is still underway. Here, Hu et al. develop single-cell transcriptome and translatome dual-omics on human oocytes, which enables them to identify OOSP2 as an induction factor during human oocyte maturation.

Wenqi Hu
Haitao Zeng
Kehkooi Kee
ResearchOpen Access30 Aug 2022
Nature Communications

Volume: 13, P: 1-17
Context-dependent tumor-suppressive BMP signaling in diffuse intrinsic pontine glioma regulates stemness through epigenetic regulation of CXXC5

Xi and colleagues show that BMP signaling has tumor-suppressive effects in ACVR1 wild-type diffuse intrinsic pontine glioma by modulating stemness via chromatin regulation of CXXC5, and demonstrate the therapeutic potential of this pathway using in vivo mouse models.

Ye Sun
Kun Yan
Qiaoran Xi
Research01 Aug 2022
Nature Cancer

Volume: 3, P: 1105-1122
A transfer-RNA-derived small RNA regulates ribosome biogenesis

A 22-nucleotide fragment of a transfer RNA regulates translation by binding to the mRNA of a ribosomal protein and increasing its expression, and downregulation of the fragment in patient-derived liver tumour cells reduces tumour growth in mice.

Hak Kyun Kim
Gabriele Fuchs
Mark A. Kay
Research29 Nov 2017
Nature

Volume: 552, P: 57-62
Differential analysis of RNA structure probing experiments at nucleotide resolution: uncovering regulatory functions of RNA structure

The authors present DiffScan, an advanced tool for normalization and differential analysis of RNA structure probing experiments, combining their power in deciphering the dynamic RNA structurome and facilitating the discovery of RNA regulatory functions.

Bo Yu
Pan Li
Lin Hou
ResearchOpen Access22 Jul 2022
Nature Communications

Volume: 13, P: 1-10
U1 snRNP regulates chromatin retention of noncoding RNAs

Long noncoding RNAs and certain unstable transcripts tend to localize to chromatin, in a process that is shown here to depend on an RNA motif that recognizes the small nuclear ribonuclear protein U1, and to rely on transcription.

Yafei Yin
J. Yuyang Lu
Xiaohua Shen
Research11 Mar 2020
Nature

Volume: 580, P: 147-150
RNA structure maps across mammalian cellular compartments

Structure maps of RNAs localized to chromatin, nucleoplasm and cytoplasm provide a rich resource with which to investigate the interplay of RNA structure, RNA–protein interactions and RNA modifications.

Lei Sun
Furqan M. Fazal
Qiangfeng Cliff Zhang
Research18 Mar 2019
Nature Structural & Molecular Biology

Volume: 26, P: 322-330
A deep learning method for recovering missing signals in transcriptome-wide RNA structure profiles from probing experiments

RNA structure profiling methods suffer from missing values in RNA structurome data. Inspired by a computer vision approach, Gong and colleagues develop a deep learning method that imputes missing RNA structure scores and increases the structural coverage of the transcriptome.

Jing Gong
Kui Xu
Qiangfeng Cliff Zhang
Research16 Nov 2021
Nature Machine Intelligence

Volume: 3, P: 995-1006
Structural imprints in vivo decode RNA regulatory mechanisms

The single-stranded nature of RNAs synthesized in the cell gives them great scope to form different structures, but current methods to measure RNA structure in vivo are limited; now, a new methodology allows researchers to examine all four nucleotides in mouse embryonic stem cells.

Robert C. Spitale
Ryan A. Flynn
Howard Y. Chang
Research18 Mar 2015
Nature

Volume: 519, P: 486-490
Pervasive downstream RNA hairpins dynamically dictate start-codon selection

Double-stranded RNA structures downstream of start codons play a role in translation initiation by regulating start-codon selection in plant immune responses, and also contribute to translational reprogramming in mammalian systems.

Yezi Xiang
Wenze Huang
Xinnian Dong
ResearchOpen Access06 Sept 2023
Nature

Volume: 621, P: 423-430
Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space

Integrative analyses of single-cell datasets are facing new challenges as data size and complexity grow. Here the authors present SCALEX, which projects cells from different datasets into a common latent space, allowing accurate online integration as well as cross-referencing with atlas-scale data.

Lei Xiong
Kang Tian
Qiangfeng Cliff Zhang
ResearchOpen Access17 Oct 2022
Nature Communications

Volume: 13, P: 1-17
One-Step Synthesis of Microporous Carbon Monoliths Derived from Biomass with High Nitrogen Doping Content for Highly Selective CO₂ Capture

Zhen Geng
Qiangfeng Xiao
Cunman Zhang
ResearchOpen Access04 Aug 2016
Scientific Reports

Volume: 6, P: 1-8
Structure-based prediction of protein–protein interactions on a genome-wide scale

Protein–protein interactions, essential for understanding how a cell functions, are predicted using a new method that combines protein structure with other computationally and experimentally derived clues.

Qiangfeng Cliff Zhang
Donald Petrey
Barry Honig
Research30 Sept 2012
Nature

Volume: 490, P: 556-560
Landscape and variation of RNA secondary structure across the human transcriptome

An RNA secondary structure (RSS) map of coding and noncoding RNA from a human family (two parents and their child) is produced; this reveals that approximately 15% of all transcribed single nucleotide variants (SNVs) alter local RNA structure, and these SNVs are depleted in certain locations, suggesting that particular RNA structures are important at those sites.

Yue Wan
Kun Qu
Howard Y. Chang
Research29 Jan 2014
Nature

Volume: 505, P: 706-709
External stress, formaldehyde, and schizophrenia: a new mouse model for mental illness research

Junhao Cheng
Zihui Sun
Zhiqian Tong
ResearchOpen Access26 Mar 2025
Schizophrenia

Volume: 11, P: 1-13
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
Transcriptome-wide interrogation of RNA secondary structure in living cells with icSHAPE

icSHAPE allows transcriptome-wide RNA structure profiling in living cells. It uses a clickable SHAPE reagent to enable biotin-based enrichment of SHAPE-modified RNA, reducing the necessary sequencing depth.

Ryan A Flynn
Qiangfeng Cliff Zhang
Howard Y Chang
Protocols14 Jan 2016
Nature Protocols

Volume: 11, P: 273-290
Advances and opportunities in RNA structure experimental determination and computational modeling

This Review summarizes recent methodological advances in experimental and computational tools developed in studying RNA structures, which provides a bridge for communication between both experimentalists and computational experts.

Jinsong Zhang
Yuhan Fei
Qiangfeng Cliff Zhang
Reviews06 Oct 2022
Nature Methods

Volume: 19, P: 1193-1207
Comparison of viral RNA–host protein interactomes across pathogenic RNA viruses informs rapid antiviral drug discovery for SARS-CoV-2

Shaojun Zhang
Wenze Huang
Qiangfeng Cliff Zhang
ResearchOpen Access04 Nov 2021
Cell Research

Volume: 32, P: 9-23
Transcriptional profiling provides new insights into the role of nitric oxide in enhancing Ganoderma oregonense resistance to heat stress

Cheng Chen
Qiang Li
Rongtao Fu
ResearchOpen Access16 Nov 2017
Scientific Reports

Volume: 7, P: 1-14
RNA structure probing uncovers RNA structure-dependent biological functions

This Review summarizes the recent technical advances in probing RNA secondary structures and discusses their connection with RNA regulatory functions in various biological processes and future directions in RNA structure-probing methods.

Xi-Wen Wang
Chu-Xiao Liu
Qiangfeng Cliff Zhang
Reviews25 Jun 2021
Nature Chemical Biology

Volume: 17, P: 755-766
Predicting dynamic cellular protein–RNA interactions by deep learning using in vivo RNA structures

Lei Sun
Kui Xu
Qiangfeng Cliff Zhang
ResearchOpen Access23 Feb 2021
Cell Research

Volume: 31, P: 495-516
Multivalent m⁶A motifs promote phase separation of YTHDF proteins

Yifei Gao
Gaofeng Pei
Pilong Li
Correspondence06 Aug 2019
Cell Research

Volume: 29, P: 767-769

Search

A cohort of mRNAs undergo high-stoichiometry NSUN6-mediated site-specific m⁵C modification

RNA structure probing reveals the structural basis of Dicer binding and cleavage

Structural insights into branch site proofreading by human spliceosome

Genome-coverage single-cell histone modifications for embryo lineage tracing

Inward lithium-ion breathing of hierarchically porous silicon anodes

Erratum: Structural imprints in vivo decode RNA regulatory mechanisms

Computational prediction and experimental validation identify functionally conserved lncRNAs from zebrafish to human

SCALE method for single-cell ATAC-seq analysis via latent feature extraction

Single-cell transcriptome and translatome dual-omics reveals potential mechanisms of human oocyte maturation

Context-dependent tumor-suppressive BMP signaling in diffuse intrinsic pontine glioma regulates stemness through epigenetic regulation of CXXC5

A transfer-RNA-derived small RNA regulates ribosome biogenesis

Differential analysis of RNA structure probing experiments at nucleotide resolution: uncovering regulatory functions of RNA structure

U1 snRNP regulates chromatin retention of noncoding RNAs

RNA structure maps across mammalian cellular compartments

A deep learning method for recovering missing signals in transcriptome-wide RNA structure profiles from probing experiments

Structural imprints in vivo decode RNA regulatory mechanisms

Pervasive downstream RNA hairpins dynamically dictate start-codon selection

Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space

One-Step Synthesis of Microporous Carbon Monoliths Derived from Biomass with High Nitrogen Doping Content for Highly Selective CO₂ Capture

Structure-based prediction of protein–protein interactions on a genome-wide scale

Landscape and variation of RNA secondary structure across the human transcriptome

External stress, formaldehyde, and schizophrenia: a new mouse model for mental illness research

Keth-seq for transcriptome-wide RNA structure mapping

Transcriptome-wide interrogation of RNA secondary structure in living cells with icSHAPE

Advances and opportunities in RNA structure experimental determination and computational modeling

Comparison of viral RNA–host protein interactomes across pathogenic RNA viruses informs rapid antiviral drug discovery for SARS-CoV-2

Transcriptional profiling provides new insights into the role of nitric oxide in enhancing Ganoderma oregonense resistance to heat stress

RNA structure probing uncovers RNA structure-dependent biological functions

Predicting dynamic cellular protein–RNA interactions by deep learning using in vivo RNA structures

Multivalent m⁶A motifs promote phase separation of YTHDF proteins

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