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Peri-centrosomal localization of small interfering rnas in C. elegans

Science China Life Sciences 2025年

作者： Qile Jin Xuezhu Feng Minjie Hong Ke Wang Xiangyang Chen Jiewei Cheng Yan Kuang Xiaoyue Si Mingjing Xu Xinya Huang Shouhong Guang Chengming Zhu Department of Obstetrics and Gynecology The First Affiliated Hospital of USTC The USTC RNA Institute Hefei National Research Center for Physical Sciences at the Microscale School of Life Sciences Division of Life Sciences and Medicine Biomedical Sciences and Health Laboratory of Anhui Province University of Science and Technology of China School of Basic Medicine Anhui Medical University

The centrosome is the microtubule-organizing center and a crucial part of cell division. Centrosomal rnas(cnrnas) have been reported to enable precise spatiotemporal control of gene expression during cell division in many species. Whether and how cnrnas exist in C. elegans are unclear. Here, using the nuclear rnai Argonaute protein NRDE-3 as a reporter, we observed potential peri-centrosome localized small interfering(si)rnas in C. elegans. NRDE-3 was previously shown to associate with pre-mrnas and pre-rrnas via a process involving the presence of complementary sirnas. We generated a GFP-NRDE-3 knock-in transgene through CRISPR/Cas9 technology and observed that NRDE-3 formed peri-centrosomal foci neighboring the tubulin protein TBB-2, other centriole proteins and pericentriolar material(PCM)components in C. elegans embryos. The peri-centrosomal accumulation of NRDE-3 depends on rna-dependent rna polymerase(RdRP)-synthesized 22G sirnas and the PAZ domain of NRDE-3, which is essential for sirna binding. Mutation of eri-1, ergo-1, or drh-3 significantly increased the percentage of pericentrosome-enriched NRDE-3. At the metaphase of the cell cycle, NRDE-3 was enriched in both the peri-centrosomal region and the spindle. Moreover, the integrity of centriole proteins and pericentriolar material(PCM) components is also required for the peri-centrosomal accumulation of NRDE-3. Therefore, we concluded that sirnas could accumulate in the pericentrosomal region in C. elegans and suggested that the peri-centrosomal region may also be a platform for rnai-mediated gene regulation.

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Marking rna:m^6A writers,readers,and functions in Arabidopsis

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Journal of Molecular Cell Biology 2019年第10期11卷 899-910页

作者： Marlene Reichel Tino Koster Dorothee Staiger rna Biology and Molecular Physiology Faculty of BiologyBielefeld University33615 BielefeldGermany

N^6-methyladenosine(m^6A)emerges as an important modification in eukaryotic mrnas.m^6A has first been reported in 1974,and its functional significance in mammalian gene regulation and importance for proper development have been well *** arsenal of writer,eraser,and reader proteins accomplish deposition,removal,and interpretation of the m^6A mark,resulting in dynamic *** led to the concept of an epitranscriptome,the compendium of rna species with chemical modification ofthe nucleobases in the cell,in analogy to the *** m^6A has long been known to also exist in plant mrnas,proteins involved in m^6A metabolism have only recently been detected by mutant analysis,homology search,and mrna interactome capture in the reference plant Arabidopsis *** ofthe m^6A modification causes severe developmental abnormalities of leaves and roots and altered timing of reproductive ***,m^6A modification affects viral ***,we discuss recent progress in identifying m^6A sites transcriptome-wide,in identifying the molecular players involved in writing,removing,and reading the mark,and in assigning functions to this rna modification in *** highlight similarities and differences to m^6A modification in mammals and provide an outlook on important questions that remain to be addressed.

关键词： Arabidopsis m^6A mrna interactome posttranscriptional rna-binding protein

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Tangled but ordered human mitochondrial trna maturation

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Science China Life Sciences 2025年

作者： Shi-Ying Yao Xiao-Long Zhou Key Laboratory of rna Innovation Science and Engineering CAS Center for Excellence in Molecular Cell Science Shanghai Institute of Biochemistry and Cell Biology Chinese Academy of Sciences University of Chinese Academy of Sciences Key Laboratory of Systems Health Science of Zhejiang Province School of Life Science Hangzhou Institute for Advanced Study University of Chinese Academy of Sciences

Mitochondria are cellular organelles that originate from an endosymbiotic bacterial ancestor and are primarily responsible for ATP generation via oxidative phosphorylation (OXPHOS). OXPHOS is conducted by five mitochondrial respiratory complexes in the inner mitochondrial membrane. Human mitochondria possess a distinct genome, a small, circular, doublestranded DNA (mtDNA) of 16,569 base pairs.

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Viral Regulation of rna Granules in Infected Cells

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Virologica Sinica 2019年第2期34卷 175-191页

作者： Qiang Zhang Nishi R. Sharma Zhi-Ming Zheng Mingzhou Chen State Key Laboratory of Virology and Modern Virology Research Center College of Life Sciences Wuhan UniversityWuhan 430072 China Tumor Virus rna Biology Section RNA Biology Laboratory National Cancer Institute National Institutes of Health Frederick MD 21702 USA

rna granules are cytoplasmic, microscopically visible, non-membrane ribo-nucleoprotein structures and are important posttranscriptional regulators in gene expression by controlling rna translation and stability. TIA/G3BP/PABP-specific stress granules(SG) and GW182/DCP-specific rna processing bodies(PB) are two major distinguishable rna granules in somatic cells and contain various ribosomal subunits, translation factors, scaffold proteins, rna-binding proteins, rna decay enzymes and helicases to exclude m rnas from the cellular active translational pool. Although SG formation is inducible due to cellular stress, PB exist physiologically in every cell. Both rna granules are important components of the host antiviral defense. Virus infection imposes stress on host cells and thus induces SG formation. However, both rna and DNA viruses must confront the hostile environment of host innate immunity and apply various strategies to block the formation of SG and PB for their effective infection and multiplication. This review summarizes the current research development in the field and the mechanisms of how individual viruses suppress the formation of host SG and PB for virus production.

关键词： Stress granules (SG) P-bodies (PB) rna virus - DNA virus

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Mapping transcriptome-wide protein-rna interactions to elucidate rna regulatory programs

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Frontiers of Electrical and Electronic Engineering in China 2018年第3期6卷 228-238页

作者： Molly M.Hannigan Leah L.Zagore Donny D.Licatalosi Center for rna Science and Therapeutics Case Western Reserve UniversityClevelandOH 44106USA

Background： Our understanding of post-transcriptional gene regulation has increased exponentially with the development of robust methods to define protein-rna interactions across the transcriptome. In this review, we highlight the evolution and successful applications of crosslinking and immunoprecipitation （CLIP） methods to interrogate protein-rna interactions in a transcriptome-wide manner. Results： Here, we survey the vast array of in vitro and in vivo approaches used to identify protein-rna interactions, including but not limited to electrophoretic mobility shift assays, systematic evolution of ligands by exponential enrichment （SELEX）, and RIP-seq. We particularly emphasize the advancement of CLIP technologies, and detail protocol improvements and computational tools used to analyze the output data. Importantly, we discuss how profiling protein-rna interactions can delineate biological functions including splicing regulation, alternative polyadenylation, cytoplasmic decay substrates, and mirna targets. Conclusions： In summary, this review summarizes the benefits of characterizing rna-protcin networks to further understand the regulation of gene expression and disease pathogenesis. Our review comments on how future CLIP technologies can be adapted to address outstanding questions related to many aspects of rna metabolism and further advance our understanding of rna biology.

关键词： rna binding proteins CLIP post-transcriptional regulation rna networks

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Sequence-and structure-selective m rna m5C methylation by NSUN6 in animals

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National Science Review 2021年第6期8卷 136-147页

作者： Jianheng Liu Tao Huang Yusen Zhang Tianxuan Zhao Xueni Zhao Wanying Chen Rui Zhang MOE Key Laboratory of Gene Function and Regulation State Key Laboratory of BiocontrolSchool of Life SciencesRNA Biomedical InstituteSun Yat-Sen Memorial HospitalSun Yat-Sen University

mrna m5C,which has recently been implicated in the regulation of mrna mobility,metabolism and translation,plays important regulatory roles in various biological *** types of m5C sites are found in *** Ⅰ m5C sites,which contain a downstream G-rich triplet motif and are computationally predicted to be located at the 5' end of putative hairpin structures,are methylated by *** Ⅱ m5C sites contain a downstream UCCA motif and are computationally predicted to be located in the loops of putative hairpin ***,their biogenesis remains *** we identified NSUN6,a methyltransferase that is known to methylate C72 of trnaThrand trnaCys,as an mrna methyltransferase that targets Type Ⅱ m5C *** the rna secondary structure prediction,miCLIP,and results from a high-throughput mutagenesis analysis,we determined the rna sequence and structural features governing the specificity of NSUN6-mediated mrna *** these features into an NSUN6-rna structural model,we identified an NSUN6 variant that largely loses trna methylation but retains mrna methylation ***,we revealed a weak negative correlation between m5C methylation and translation *** findings uncover that mrna m5C is tightly controlled by an elaborate two-enzyme system,and the protein-rna structure analysis strategy established maybe applied to other rna modification writers to distinguish the functions of different rna substrates of a writer protein.

关键词： mrnam5C NSUN6 rna modification protein-rna complex structure

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Emerging roles of non-coding rnas in epigenetic regulation

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Science China(Life Sciences) 2016年第3期59卷 227-235页

作者： Juan Chen Yuanchao Xue Key Lab of rna biology Institute of Biophysics Chinese academy of Sciences

Recent deep sequencing surveys of mammalian genomes have unexpectedly revealed pervasive and complex transcription and identified tens of thousands of rna transcripts that do not code for proteins. These non-coding rnas(nc rnas) highlight the central role of rna in gene regulation. nc rnas are arbitrarily divided into two main groups: The first includes small rnas, such as mi rnas, pi rnas, and endogenous si rnas, that usually range from 20 to 30 nt, while the second group includes long non-coding rnas(lnc rnas), which are typically more than 200 nt in length. These nc rnas were initially thought to merely regulate gene expression at the post-transcriptional level, but recent studies have indicated that nc rnas, especially lnc rnas, are extensively associated with diverse chromatin remodeling complexes and target them to specific genomic loci to alter DNA methylation or histone status. These findings suggest an emerging theme of nc rnas in epigenetic regulation. In this review, we discuss the wide spectrum of nc rnas in the regulation of DNA methylation and chromatin state, as well as the key questions that needs to be investigated and acknowledging the elegant design of these intriguing macromolecules.

关键词： non-coding rnas lncrnas DNA methylation chromatin remodeling

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Transfer rna:A dancer between charging and mis-charging for protein biosynthesis

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Science China(Life Sciences) 2013年第10期56卷 921-932页

作者： ZHOU XiaoLong WANG EnDuo Center for rna Research State Key Laboratory of Molecular BiologyInstitute of Biochemistry and Cell BiologyShanghai Institutes for Biological SciencesChinese Academy of Sciences

Transfer rna plays a fundamental role in the protein biosynthesis as an adaptor molecule by functioning as a biological link between the genetic nucleotide sequence in the mrna and the amino acid sequence in the *** perform its role in protein biosynthesis,it has to be accurately recognized by aminoacyl-trna synthetases(aaRSs)to generate aminoacyl-trnas(aa-trnas).The correct pairing between an amino acid with its cognate trna is crucial for translational quality *** and utilization of mis-charged trnas are usually detrimental for all the species,resulting in cellular *** aa-trnas formation is collectively controlled by aaRSs with distinct mechanisms and/or other ***,in very limited instances,mis-charged trnas are intermediate for specific pathways or essential components for the translational ***,from the point of accuracy in trna charging,we review our understanding about the mechanism ensuring correct aa-trna *** addition,some unique mis-charged trna species necessary for the organism are also briefly described.

关键词： trna aminoacyl-trna synthetase aminoacylation editing

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Crystal structure of E. coli arginyl-trna synthetase and ligand binding studies revealed key residues in arginine recognition

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Protein & Cell 2014年第2期5卷 151-159页

作者： Kelei Bi Yueting Zheng Feng G"ao Jianshu Dong Jiangyun Wang Yi Wang Weimin Gong Laboratory of Non-coding rna Institute of Biophysics Chinese Academy of Sciences

The arginyl-trna synthetase(ArgRS) catalyzes the esterification reaction between L-arginine and its cognate trnaArg. Previously reported structures of ArgRS shed considerable light on the trna recognition mechanism, while the aspect of amino acid binding in ArgRS remains largely unexplored. Here we report the first crystal structure of E. coli ArgRS(eArgRS) complexed with L-arginine, and a series of mutational studies using isothermal titration calorimetry(ITC). Combined with previously reported work on ArgRS, our results elucidated the structural and functional roles of a series of important residues in the active site, which furthered our understanding of this unique enzyme.

关键词： arginyl-trna synthetase amino acyl-trna synthetase isothermal titration calorimetry site-directed mutation X-ray crystal structure E. coli

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rna-dependent pseudouridylation catalyzed by box H/ACA RNPs

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Frontiers in Biology 2018年第1期13卷 1-10页

作者： Meemanage D. De Zoysa Yi-Tao Yu University of Rochester Medical Center Department of Biochemistry and Biophysics Center for RNA Biology 601 Elmwood AvenueRochester NY14642 USA

BACKGROUND： Pseudouridine （Ψ） is the most abundant post-transcriptionally modified nucleotide found in rna. ~ is clustered in functionally important and evolutionary conserved regions of rnas in all three domains of life. Pseudouridylation is catalyzed by two distinct mechanisms： an rna-independent and an rna-dependent mechanism. The former involves a group of stand-alone protein enzymes, and the latter involves a family of complex enzymes called box H/ACA RNPs, each of which consists of one rna （box H/ACA rna） and a set of four core proteins. Over the years, the mechanism of rna- dependent pseudouridylation has been extensively studied. The crystal structures of partial and complete box H/ACA RNP have been solved. However, the detailed picture of rna-dependent pseudouridylation is still not entirely clear. OBJECTIVE： In this work, we review what is known about box H/ACA RNP and the mechanism by which box H/ACA RNP catalyzes rna-dependent pseudouridylation. We also discuss some examples of the dual nature and redundancy of box H/ ACA RNPs that deviate from the usual mechanism. METHODS： A methodical literature search was performed using the Pubmed central search engine and International Digital Publishing Forum （EPUB） using the following keywords：＂pseudouridylation,＂＂pseudouridine,＂ and ＂box H/ACA RNP.＂ The necessary information was extracted and cited. RESULTS： A detailed introduction is made including the discovery, mechanism and crystal structure of box H/ACA RNP. Three sequence/structural requirements for box H/ACA rna-guided pseudouridylation are discussed and the exceptions to those rules are explored. CONCLUSION： Over the years, box H/ACA RNP-catalyzed pseudouridylation has been extensively studied, generating fruitful results. However, a detailed picture regarding the mechanism of this reaction is still to be deciphered. More work is needed to fully understand box H/ACA RNP-catalyzed pseudouridylation.

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