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Science China(Life Sciences) 2022年第7期65卷 1285-1324页

作者： Bingbing Xu Yanda Zhu Changchang Cao Hao Chen Qiongli Jin Guangnan Li Junfeng Ma Siwy Ling Yang Jieyu Zhao Jianghui Zhu Yiliang Ding Xianyang Fang Yongfeng Jin Chun Kit Kwok Aiming Ren Yue Wan Zhiye Wang Yuanchao Xue Huakun Zhang Qiangfeng Cliff Zhang Yu Zhou MOE Laboratory of Biosystems Homeostasis&Protection Innovation Center for Cell Signaling NetworkCollege of Life SciencesZhejiang UniversityHangzhou 310058China Key Laboratory of rna Biology Institute of BiophysicsChinese Academy of SciencesBeijing 100101China Life Sciences Institute Zhejiang UniversityHangzhou 310058China State Key Laboratory of Plant Physiology and Biochemistry College of Life SciencesZhejiang UniversityHangzhou 310058China State Key Laboratory of Virology College of Life SciencesWuhan UniversityWuhan 430072China Beijing Advanced Innovation Center for Structural Biology School of Life SciencesTsinghua UniversityBeijing 100084China Stem Cell and Regenerative Biology Genome Institute of SingaporeA*STARSingaporeSingapore Department of Chemistry and State Key Laboratory of Marine PollutionCity University of Hong KongHong KongChina MOE Key Laboratory of Bioinformatics Beijing Advanced Innovation Center for Structural Biology and Frontier Research Center for Biological StructureCenter for Synthetic and Systems BiologySchool of Life SciencesTsinghua UniversityBeijing 100084China Tsinghua-Peking Center for Life Sciences Beijing 100084China Department of Cell and Developmental Biology John Innes CentreNorwich Research ParkNorwich NR47UHUnited Kingdom Shenzhen Research Institute of City University of Hong Kong Shenzhen 518057China University of Chinese Academy of Sciences Beijing 100101China Key Laboratory of Molecular Epigenetics of the Ministry of Education Northeast Normal UniversityChangchun 130024China

rna structures are essential to support rna functions and regulation in various biological processes. Recently, a range of novel technologies have been developed to decode genome-wide rna structures and novel modes of functionality across a wide range of species. In this review, we summarize key strategies for probing the rna structurome and discuss the pros and cons of representative technologies. In particular, these new technologies have been applied to dissect the structural landscape of the SARS-CoV-2 rna genome. We also summarize the functionalities of rna structures discovered in different regulatory layers-including rna processing, transport, localization, and mrna translation-across viruses, bacteria, animals, and plants. We review many versatile rna structural elements in the context of different physiological and pathological processes(e.g., cell differentiation, stress response, and viral replication). Finally, we discuss future prospects for rna structural studies to map the rna structurome at higher resolution and at the single-molecule and single-cell level, and to decipher novel modes of rna structures and functions for innovative applications.

关键词： rna structurome high-throughput techniques genome-wide 3D structure rna secondary structure SARS-CoV-2 decoding function

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rna Regulations and Functions Decoded by Transcriptome-wide rna Structure Probing

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Genomics, Proteomics & Bioinformatics 2017年第5期15卷 267-278页

作者： meiling piao lei sun qiangfeng cliff zhang moe key laboratory of bioinformatics beijing advanced innovation center for structural biologycenter for synthetic and systems biologytsinghua-peking joint center for life sciencesschool of life sciencestsinghua universityBeijing 100084China

rna folds into intricate structures that are crucial for its functions and regulations. To date, a multitude of approaches for probing structures of the whole transcriptome, i.e., rna struc- turomes, have been developed. Applications of these approaches to different cell lines and tissues have generated a rich resource for the study of rna structure-function relationships at a systems biology level. In this review, we first introduce the designs of these methods and their applications to study different rna structuromes. We emphasize their technological differences especially their unique advantages and caveats. We then summarize the structural insights in rna functions and regulations obtained from the studies of rna structuromes. And finally, we propose potential directions for future improvements and studies.

关键词： rna structure probing rna structurome rna secondary structure Structure-function relation-ship rna regulation

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An ultra low-input method for global rna structure probing uncovers Regnase-1-mediated regulation in macrophages

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Fundamental Research 2022年第1期2卷 2-13页

作者： Meiling Piao Pan Li Xiaomin Zeng Xi-Wen Wang Lan Kang Jinsong Zhang Yifan Wei Shaojun Zhangas Lei Tang Jianghui Zhu Chun Kit Kwok Xiaoyu Hu Qiangfeng Cliff Zhang MOE Key Laboratory of Bioinformatics Center for Synthetic and Systems BiologySchool of Life SciencesTsinghua UniversityBeijing 100084China Beijing Advanced Innovation Center for Structural Biology&Frontier Research Center for Biological Structure School of Life SciencesTsinghua UniversityBeijing 100084China Tsinghua-Peking Center for Life Sciences Beijing 100084China Institute for Immunology and School of Medicine Tsinghua UniversityBeijingChina Beijing Key Laboratory for Immunological Research on Chronic Diseases Tsinghua-Peking Center for Life SciencesTsinghua UniversityBeijingChina department of Chemistry City University of Hong KongTat Chee AvenueKowloon TongHong KongChina Shenzhen Research Institute of City University of Hong Kong ShenzhenChina

To enable diverse functions and precise regulation,an rna sequence often folds into complex yet distinct structures in different cellular *** rna in its native environment is essential to uncovering rna structures of biological ***,current methods generally require large amounts of input rna and are challenging for physiologically relevant ***,we report smartSHAPE,a new rna structure probing method that requires very low amounts of rna input due to the largely reduced artefact of probing signals and increased efficiency of library *** smartSHAPE,we showcased the profiling of the rna structure landscape of mouse intestinal macrophages upon inflammation,and provided evidence that rna conformational changes regulate immune *** results demonstrate that smartSHAPE can greatly expand the scope of rna structure-based investigations in practical biological systems,and also provide a research paradigm for the study of post-transcriptional regulation.

关键词： rna structure probing method Low-input rna structure element Macrophage rna structure rna structurome

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