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| 1 | Mapping the epigenetic modifications of DNA and RNA显示文摘Over 17 and 160 types of chemical modifications have been identified in DNA and RNA,respectively.The interest in understanding the various biological functions of DNA and RNA modifications has lead to the cutting-edged fields of epigenomics and epitranscriptomics.Developing chemical and biological tools to detect specific modifications in the genome or transcriptome has greatly facilitated their study.Here,we review the recent technological advances in this rapidly evolving field.We focus on high-throughput detection methods and biological findings for these modifications,and discuss questions to be addressed as well.We also summarize third-generation sequencing methods,which enable long-read and single-molecule sequencing of DNA and RNA modification. | Lin-Yong Zhao Jinghui Song Yibin Liu Chun-Xiao Song Chengqi Yi | 2020 | Protein & Cell2020，11，11： | 17 |
| 2 | Two RING-Finger Ubiquitin E3 Ligases Regulate the Degradation of SPX4, An Internal Phosphate Sensor, for Phosphate Homeostasis and Signaling in Rice显示文摘SPX-domain-containing proteins (SPXs) play an important role in inorganic phosphate (Pi) sensing,signaling,and transport in eukaryotes.In plants,SPXs are known to integrate cellular Pi status and negatively regulate the activity of Pi central regulators,the PHOSPATE STARVATION RESPONSE proteins (PHRs).The stability of SPXs,such as SPX4,is reduced under Pi-deficient conditions.However,the mechanisms by which SPXs are degraded remain unclear.In this study,using a yeast-twhybrid screen we iden.tified two RING-finger ubiquitin E3 ligases regulating SPX4 degradation,designated SDEL1 and SDEL2,which were post-transcriptionally induced by Pi starvation.We found that both SDELs were located in the nucleus and cytoplasm,had ubiquitin E3 ligase activity,and directly ubiquitinated the K^213 and K^299 lysine residues in SPX4 to regulate its stability.Furthermore,we found that PHR2,a Pi central regulator in rice,could compete with SDELs by interacting with SPX4 under Pi-sufficient conditions,which protected SPX4 from ubiquitination and degradation.Consistent with the biochemical function of SDEL1 and SDEL2,overexpression of SDEL1 or SDEL2 resulted in Pi overaccumulation and induced Pi-starvation signaling even under Pi-sufficient conditions.Conversely,their loss-of-function mutants displayed decreased Pi accumulation and reduced Pi-starvation signaling.Collectively,our study revealed that SDEL1 and SDEL2 facilitate the degradation of SPX4 to modulate PHR2 activity and regulate Pi homeostasis and Pi signaling in response to external Pi availability in rice. | Wenyuan Ruan Meina Guo Xueqing Wang Zhenhui Guo Zhuang Xu Lei Xu Hongyu Zhao Haiji Sun Chengqi Yan Keke Yi | 2019 | Molecular Plant2019，12，8： | 14 |
| 3 | Cap-specific, terminal N^6-methylation by a mammalian m6Am methyltransferase显示文摘Dear Editor,Dynamic and reversible N6-methyladenosine (m6A) RNA methylation has been found to greatly impact gene expression, leading to the field of epitranscriptomics.1 Unlike m6A that is an internal modification, a terminal modification at mRNA cap in higher eukaryotes exists, termed as N6,2′-O-dimethyladenosine (m6Am) (Fig. 1a). | Hanxiao Sun Meiling Zhang Kai Li Dongsheng Bai Chengqi Yi | 2019 | Cell Research2019，29，1： | 7 |
| 4 | The m^(6)A methylome of SARS-CoV-2 in host cells显示文摘The newly identified Severe Acute Respiratory Syndrome Coronavirus 2(SARS-CoV-2)has resulted in a global health emergency because of its rapid spread and high mortality.The molecular mechanism of interaction between host and viral genomic RNA is yet unclear.We demonstrate herein that SARS-CoV-2 genomic RNA,as well as the negative-sense RNA,is dynamically N6-methyladenosine(m^(6)A)-modified in human and monkey cells.Combined RIP-seq and miCLIP analyses identified a total of 8 m^(6)A sites at single-base resolution in the genome.Especially,epidemic strains with mutations at these identified m^(6)A sites have emerged worldwide,and formed a unique cluster in the US as indicated by phylogenetic analysis.Further functional experiments showed that m^(6)A methylation negatively regulates SARS-CoV-2 infection.SARS-CoV-2 infection also triggered a global increase in host m^(6)A methylome,exhibiting altered localization and motifs of m^(6)A methylation in mRNAs.Altogether,our results identify m^(6)A as a dynamic epitranscriptomic mark mediating the virus–host interaction. | Jun’e Liu Yan-Peng Xu Kai Li Qing Ye Hang-Yu Zhou Hanxiao Sun Xiaoyu Li Liu Yu Yong-Qiang Deng Rui-Ting Li Meng-Li Cheng Bo He Jia Zhou Xiao-Feng Li Aiping Wu Chengqi Yi Cheng-Feng Qin | 2021 | Cell Research2021，31，4： | 5 |
| 5 | Liquid biopsies:DNA methylation analyses in circulating cell-free DNA显示文摘Analysis of patient's materials like cells or nucleic acids obtained in a minimally invasive or noninvasive manner through the sampling of blood or other body fluids serves as liquid biopsies, which has huge potential for numerous diagnostic applications. Circulating cell-free DNA(cfDNA) is explored as a prognostic or predictive marker of liquid biopsies with the improvements in genomic and molecular methods. DNA methylation is an important epigenetic marker known to affect gene expression. cfDNA methylation detection is a very promising approach as abnormal distribution of DNA methylation is one of the hallmarks of many cancers and methylation changes occur early during carcinogenesis. This re?view summarizes the various investigational applications of cfDNA methylation and its oxidized de?rivatives as biomarkers for cancer diagnosis, prenatal diagnosis and organ transplantation monitoring.The review also provides a brief overview of the technologies for cfDNA methylation analysis based on next generation sequencing. | Hu Zeng Bo He Chengqi Yi Jinying Peng | 2018 | Journal of Genetics and Genomics2018，45，4： | 4 |
| 6 | Epitranscriptomics:Toward A Better Understanding of RNA Modifications显示文摘Ever since the first RNA nucleoside modification was characterized in 1957~[1],over 100 distinct chemical modifications have been identified in RNA to date~[2].Most of these modifications were characterized in non-coding RNAs(nc RNAs),including t RNA,r RNA,and small nuclear RNA(sn RNA)~[3].Studies in the past few decades have located various modifications in these nc RNAs and revealed their functional roles~[3].For instance,N1-methyladenosine(m^1A),which is | Xushen Xiong Chengqi Yi Jinying Peng | 2017 | Genomics, Proteomics & Bioinformatics2017，15，3： | 3 |
| 7 | Mitigation Strategy against Cascading Failures on Social Networks显示文摘Cascading failures are common phenomena in many of real-world networks,such as power grids,Internet,transportation networks and social networks.It's worth noting that once one or a few users on a social network are unavailable for some reasons,they are more likely to influence a large portion of social network.Therefore,an effective mitigation strategy is very critical for avoiding or reducing the impact of cascading failures.In this paper,we firstly quantify the user loads and construct the processes of cascading dynamics,then elaborate the more reasonable mechanism of sharing the extra user loads with considering the features of social networks,and further propose a novel mitigation strategy on social networks against cascading failures.Based on the realworld social network datasets,we evaluate the effectiveness and efficiency of the novel mitigation strategy.The experimental results show that this mitigation strategy can reduce the impact of cascading failures effectively and maintain the network connectivity better with lower cost.These findings are very useful for rationally advertising and may be helpful for avoiding various disasters of cascading failures on many real-world networks. | YI Chengqi BAO Yuanyuan JIANG Jingchi XUE Yibo | 2014 | China Communications2014，11，8： | 3 |
| 8 | Single-base resolution analysis of DNA epigenome via high-throughput sequencing显示文摘Epigenetic changes caused by DNA methylation and histone modifications play important roles in the regulation of various cellular processes and development. Recent discoveries of 5-methylcytosine(5m C) oxidation derivatives including 5-hydroxymethylcytosine(5hm C), 5-formylcytsine(5f C) and 5-carboxycytosine(5ca C) in mammalian genome further expand our understanding of the epigenetic regulation. Analysis of DNA modification patterns relies increasingly on sequencing-based profiling methods. A number of different approaches have been established to map the DNA epigenomes with single-base resolution, as represented by the bisulfite-based methods, such as classical bisulfite sequencing(BS-seq), TAB-seq(TET-assisted bisulfite sequencing), ox BS-seq(oxidative bisulfite sequencing) and etc. These methods have been used to generate base-resolution maps of 5m C and its oxidation derivatives in genomic samples. The focus of this review will be to discuss the chemical methodologies that have been developed to detect the cytosine derivatives in the genomic DNA. | Jinying Peng Bo Xia Chengqi Yi | 2016 | Science China(Life Sciences)2016，59，3： | 2 |
| 9 | Genome-wide Mapping of Cellular Protein–RNA Interactions Enabled by Chemical Crosslinking显示文摘RNA–protein interactions influence many biological processes. Identifying the binding sites of RNA-binding proteins(RBPs) remains one of the most fundamental and important challenges to the studies of such interactions. Capturing RNA and RBPs via chemical crosslinking allows stringent purification procedures that significantly remove the non-specific RNA and protein interactions. Two major types of chemical crosslinking strategies have been developed to date, i.e., UV-enabled crosslinking and enzymatic mechanism-based covalent capture. In this review, we compare such strategies and their current applications, with an emphasis on the technologies themselves rather than the biology that has been revealed. We hope such methods could benefit broader audience and also urge for the development of new methods to study RNA RBP interactions. | Xiaoyu Li Jinghui Song Chengqi Yi | 2014 | Genomics, Proteomics & Bioinformatics2014，12，2： | 1 |
| 10 | Epitranscriptomic technologies and analyses显示文摘RNA can interact with RNA-binding proteins(RBPs),mRNA,or other non-coding RNAs(ncRNAs)to form complex regulatory networks.High-throughput CLIP-seq,degradome-seq,and RNA-RNA interactome sequencing methods represent powerful approaches to identify biologically relevant ncRNA-target and protein-ncRNA interactions.However,assigning ncRNAs to their regulatory target genes or interacting RNA-binding proteins(RBPs)remains technically challenging.Chemical modifications to mRNA also play important roles in regulating gene expression.Investigation of the functional roles of these modifications relies highly on the detection methods used.RNA structure is also critical at nearly every step of the RNA life cycle.In this review,we summarize recent advances and limitations in CLIP technologies and discuss the computational challenges of and bioinformatics tools used for decoding the functions and regulatory networks of ncRNAs.We also summarize methods used to detect RNA modifications and to probe RNA structure. | Xiaoyu Li Qiao-Xia Liang Jin-Ran Lin Jinying Peng Jian-Hua Yang Chengqi Yi Yang Yu Qiangfeng Cliff Zhang Ke-Ren Zhou | 2020 | Science China(Life Sciences)2020，63，4： | 1 |
| 11 | SnoRNP is essential for thermospermine-mediated development in Arabidopsis thaliana显示文摘Polyamines have been discovered for hundreds of years and once considered as a class of phytohormones.Polyamines play critical roles in a range of developmental processes.However,the molecular mechanisms of polyamine signaling pathways remain poorly understood.Here,we measured the contents of main types of polyamines,and found that endogenous level of thermospermine(T-Spm)in Arabidopsis thaliana is comparable to those of classic phytohormones and is significantly lower than those of putrescine(Put),spermidine(Spd),and spermine(Spm).We further found a nodule-like structure around the junction area connecting the shoot and root of the T-Spm biosynthetic mutant acl5 and obtained more than 50 suppressors of acl5 nodule structure(san)through suppressor screening.An in-depth study of two san suppressors revealed that NAP57 and NOP56,core components of box H/ACA and C/D snoRNPs,were essential for T-Spm-mediated nodule-like structure formation and plant height.Furthermore,analyses of rRNA modifications showed that the overall levels of pseudouridylation and 2′-O-methylation were compromised in san1 and san2 respectively.Taken together,these results establish a strong genetic relationship between rRNA modification and T-Spm-mediated growth and development,which was previously undiscovered in all organisms. | Xilong Li Zongyun Yan Meiling Zhang Jiayin Wang Peiyong Xin Shujing Cheng Liquan Kou Xiaoting Zhang Songlin Wu Jinfang Chu Chengqi Yi Keqiong Ye Bing Wang Jiayang Li | 2023 | Science China(Life Sciences)2023，66，1： | 0 |
| 12 | RNA Modifications and Epitranscriptomics显示文摘More than 170 distinct chemical modifications have been identified in non-coding and coding RNAs.Accumulating evidence suggests that RNA modifications play pivotal roles at both the molecular and physiological levels.Dysregulation of RNAmodifying enzymes has been linked to various human cancers and developmental diseases.The expanding understanding of RNA modifications in molecular and cellular functions further suggests promising prospects for therapeutic applications.Recently,the creation of effective mRNA vaccines against coronavirus disease 2019(COVID-19),based on RNA base modification,was honored with the Nobel Prize in Physiology or Medicine 2023(http://gffzzd4f86938af8b41c7sp0qopkou59pf6cxb.ffgz.tsg.suse.edu.cn/prizes/medicine/2023/press-release/).Aiming to provide a forum for emerging advances in detection and functional studies of epitranscriptomic modifications,we have organized a special issue'RNA Modifications and Epitranscriptomics'for the journal Genomics,Proteomics&Bioinformatics(GPB).This special issue encompasses a wide range of topics,including:(1)dynamic landscapes of RNA modifications in various organisms,including animals,plants,and viruses;(2)mechanistic regulation of m^(6)A and m5 C modifications in human diseases and plant responses to stresses;(3)an online platform for unveiling the context-specific m^(6)A methylation and m^(6)Aaffecting mutation;and(4)the regulatory role of non-coding RNAs(ncRNAs),including tRNAs and circular RNAs(circRNAs),in gene expression regulation. | Chengqi Yi Jianhua Yang | 2023 | Genomics, Proteomics & Bioinformatics2023，21，4： | 0 |
| 13 | Multi-omics for COVID-19:driving development of therapeutics and vaccines显示文摘The ongoing COVID-19 pandemic caused by SARS-CoV-2 has raised global concern for public health and economy.The development of therapeutics and vaccines to combat this virus is continuously progressing.Multi-omics approaches,including genomics,transcriptomics,proteomics,metabolomics,epigenomics and metallomics,have helped understand the structural and molecular features of the virus,thereby assisting in the design of potential therapeutics and accelerating vaccine development for COVID-19.Here,we provide an up-to-date overview of the latest applications of multi-omics technologies in strategies addressing COVID-19,in order to provide suggestions towards the development of highly effective knowledge-based therapeutics and vaccines. | Mengyu Guo Muya Xiong Jinying Peng Tong Guan Haixia Su Yanyi Huang Cai-Guang Yang Yang Li Diana Boraschi Thanigaimalai Pillaiyar Guanbo Wang Chengqi Yi Yechun Xu Chunying Chen | 2023 | National Science Review2023，10，9： | 0 |
| 14 | Metatranscriptomic analysis of host response and vaginal microbiome of patients with severe COVID-19显示文摘Dear Editor,The pandemic of coronavirus disease 2019(COVID-19)caused by severe acute respiratory syndrome coronavirus 2(SARS-Co V-2)has become a global public health threat.Here we use a TRACE-seq-based metatranscriptomic analysis to compare host responses and vaginal microbiome of postmenopausal female patients with underlying severe COVID-19 disease with those of healthy females,thereby providing insights into the changes in the microenvironment of women's reproductive system. | Meng Xiao Bo Lu Rui Ding Xia Liu Xian Wu Yaqian Li Xudong Liu Lin Qiu Zhibo Zhang Jing Xie Yu Chen Dong Zhang Liting Dong Meiling Zhang Jinying Peng Hua Yang Timothy Kudihna Yingchun Xu Taisheng Li Chengqi Yi Lan Zhu | 2022 | Science China(Life Sciences)2022，65，7： | 0 |
| 15 | Sequencing methods and functional decoding of mRNA modifications显示文摘More than 160 types of post-transcriptional RNA modifications have been reported;there is substantial variation in modification type,abundance,site,and function across species,tissues,and RNA type.The recent development of high-throughput detection technology has enabled identification of diverse dynamic and reversible RNA modifications,including N6,2′-O-dimethyladenosine(m6Am),N1-methyladenosine(m1A),5-methylcytosine(m5C),N6-methyladenosine(m6A),pseudouridine(Ψ),and inosine(I).In this review,we focus on eukaryotic mRNA modifications.We summarize their biogenesis,regulatory mechanisms,and biological functions,as well as highthroughput methods for detection of mRNA modifications.We also discuss challenges that must be addressed in mRNA modification research. | Kai Li Jinying Peng Chengqi Yi | 2023 | Fundamental Research2023，3，5： | 0 |
| 16 | Transformation of 5-Carboxylcytosine to Cytosine Through C-C Bond Cleavage in Human Cells Constitutes a Novel Pathway for DNA Demethylation显示文摘Active demethylation of 5-methylcytosine(5mC)can be realized through ten-eleven translocation(TET)dioxygenase-mediated oxidation of 5mC to 5-hydroxymethylcytosine(5hmC),5-formylcytosine(5fC),and 5-carboxylcytosine(5caC),followed by thymine DNA glycosylase(TDG)-initiated base excision repair(BER).The TDG-BER pathwaymay lead to the generation of DNA strand breaks,potentially compromising genome integrity.Alternatively,direct decarboxylation of TET-produced 5caC is highly attractive because this mechanism allows for conversion of 5mC to cytosine without the formation of DNA strand breaks.However,cleavage of the C–C bond in 5caC in human cells remains an open question.We examined this reaction in cell extract and live cells using 5caC-carrying hairpin DNA substrate.After incubation with whole-cell protein extract or transfection into human cells,we monitored the transformation of 5caC to cytosine through direct decarboxylation or BER using liquid chromatography–tandem mass spectrometry(LCMS/MS)analyses at both the mononucleotide and oligodeoxynucleotide levels.Our results clearly showed the direct conversion of 5caC to cytosine in human cells,providing evidence to support a novel pathway for active DNA demethylation. | Yang Feng Neng-Bin Xie Wan-Bing Tao Jiang-Hui Ding Xue-Jiao You Cheng-Jie Ma Xiaoxue Zhang Chengqi Yi Xiang Zhou Bi-Feng Yuan Yu-Qi Feng | 2021 | CCS Chemistry2021，3，4： | 0 |
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