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Molecular Plant 2024年第4期17卷 531-551页

作者： Sheng Fan Yu Zhang Shaobo Zhu Lisha Shen Temasek Life Sciences Laboratory 1 Research LinkNational University of Singapore1 Research LinkSingapore 117604Singapore Department of Biological Sciences National University of Singapore14 Science Drive 4Singapore 117543Singapore

rna-binding proteins(RBPs)accompany rna from synthesis to decay,mediating every aspect of rna metabolism and impacting diverse cellular and developmental processes in eukaryotes.Many RBPs undergo phase separation along with their bound rna to form and function in dynamic membraneless biomolecular condensates for spatiotemporal coordination or regulation of rna metabolism.Increasing evidence suggests that phase-separating RBPs with rna-binding domains and intrinsically disordered regions play important roles in plant development and stress adaptation.Here,we summarize the current knowledge about how dynamic partitioning of RBPs into condensates controls plant development and enables sensing of experimental changes to confer growth plasticity under stress conditions,with a focus on the dynamics and functional mechanisms of RBP-rich nuclear condensates and cytoplasmic granules in mediating rna metabolism.We also discuss roles of multiple factors,such as environmental signals,protein modifications,and N6-methyladenosine rna methylation,in modulating the phase separation behaviors of RBPs,and highlight the prospects and challenges for future research on phase-separating RBPs in crops.

关键词： rna-binding proteins phase separation biomolecular condensates rna metabolism development stress resilience

Genes for rna-binding proteins involved in neuralspecific functions and diseases are downregulated in Rubinstein-Taybi iNeurons

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Neural Regeneration Research 2022年第1期17卷 5-14页

作者： Lidia Larizza Luciano Calzari Valentina Alari Silvia Russo Cytogenetics and Molecular Genetics Laboratory IRCCS Istituto Auxologico ItalianoMilanoItaly

Taking advantage of the fast-growing knowledge of rna-binding proteins(RBPs)we review the signature of downregulated genes for RBPs in the transcriptome of induced pluripotent stem cell neurons(iNeurons)modelling the neurodevelopmental Rubinstein Taybi Syndrome(RSTS)caused by mutations in the genes encoding CBP/p300 acetyltransferases.We discuss top and functionally connected downregulated genes sorted to“rna processing”and“Ribonucleoprotein complex biogenesis”Gene Ontology clusters.The first set of downregulated RBPs includes members of hnRNHP(A1,A2B1,D,G,H2-H1,MAGOHB,PAPBC),core subunits of U small nuclear ribonucleoproteins and Serine-Arginine splicing regulators families,acting in precursor messenger rna alternative splicing and processing.Consistent with literature findings on reduced transcript levels of serine/arginine repetitive matrix 4(SRRM4)protein,the main regulator of the neural-specific microexons splicing program upon depletion of Ep300 and Crebbp in mouse neurons,RSTS iNeurons show downregulated genes for proteins impacting this network.We link downregulated genes to neurological disorders including the new HNRNPH1-related intellectual disability syndrome with clinical overlap to RSTS.The set of downregulated genes for Ribosome biogenesis includes several components of ribosomal subunits and nucleolar proteins,such NOP58 and fibrillarin that form complexes with snornas with a central role in guiding post-transcriptional modifications needed for rrna maturation.These nucleolar proteins are“dual”players as fibrillarin is also required for epigenetic regulation of ribosomal genes and conversely NOP58-associated snorna levels are under the control of NOP58 interactor BMAL1,a transcriptional regulator of the circadian rhythm.Additional downregulated genes for“dual specificity”RBPs such as RUVBL1 and METTL1 highlight the links between chromatin and the RBP-ome and the contribution of perturbations in their cross-talk to RSTS.We underline the hub position of CBP/p300 in chromatin regulation,the impact of

关键词： alternative splicing CBP/p300 chromatin regulators downregulated genes induced pluripotent stem cell-neurons neurodevelopmental disorders ribosome biogenesis rna-binding proteins rnaSeq Rubinstein-Taybi

Post-transcriptional regulation of grain weight and shape by the RBP-A-J-K complex in rice

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Journal of Integrative Plant Biology 2024年第1期66卷 66-85页

作者： Ding Ren Hui Liu Xuejun Sun Fan Zhang Ling Jiang Ying Wang Ning Jiang Peiwen Yan Jinhao Cui Jinshui Yang Zhikang Li Pingli Lu Xiaojin Luo State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology School of Life SciencesFudan UniversityShanghai 200438China State Key Laboratory of Crop Stress Adaptation and Improvement School of Life SciencesHenan UniversityKaifeng 475004China MOE Key Laboratory of Crop Physiology Ecology and Genetic Breeding College of AgronomyJiangxi Agricultural UniversityNanchang 330045China State Key Laboratory of Crop Gene Resources and Breeding Institute of Crop SciencesChinese Academy of Agricultural Sciences(CAAS)Beijing 100081China College of Agronomy Anhui Agricultural UniversityHefei 230036China

rna-binding proteins(RBPs)are components of the post-transcriptional regulatory system,but their regulatory effects on complex traits remain unknown.Using an integrated strategy involving map-based cloning,functional characterizations,and transcriptomic and population genomic analyses,we revealed that RBP-K(LOC_Os08g23120),RBP-A(LOC_Os11g41890),and RBP-J(LOC_Os10g33230)encode proteins that form an RBP-A-J-K complex that negatively regulates rice yield-related traits.Examinations of the RBP-A-J-K complex indicated RBP-K functions as a relatively non-specific RBP chaperone that enables RBP-A and RBP-J to function normally.Additionally,RBP-J most likely affects GA pathways,resulting in considerable increases in grain and panicle lengths,but decreases in grain width and thickness.In contrast,RBP-A negatively regulates the expression of genes most likely involved in auxin-regulated pathways controlling cell wall elongation and carbohydrate transport,with substantial effects on the rice grain filling process as well as grain length and weight.Evolutionarily,RBP-K is relatively ancient and highly conserved,whereas RBP-J and RBP-A are more diverse.Thus,the RBP-A-J-K complex may represent a typical functional model for many RBPs and protein complexes that function at transcriptional and post-transcriptional levels in plants and animals for increased functional consistency,efficiency,and versatility,as well as increased evolutionary potential.Our results clearly demonstrate the importance of RBP-mediated post-transcriptional regulation for the diversity of complex traits.Furthermore,rice grain yield and quality may be enhanced by introducing various complete or partial loss-of-function mutations to specific RBP genes using clustered regularly interspaced palindromic repeats(CRISPR)/CRISPR-associated protein 9 technology and by exploiting desirable natural tri-genic allelic combinations at the loci encoding the components of the RBP-A-J-K complex through marker-assisted selection.

关键词： GL11 grain weight and shape post-transcriptional regulation rna-binding proteins

Non-Protein-Coding rnas and their Interacting rna-binding proteins in the Plant Cell Nucleus

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Molecular Plant 2010年第4期3卷 729-739页

作者： Celine Charon Ana Beatriz Moreno Florian Bardou Martin Crespi University Paris-Sud Institut de Biologie des Plantes UMR8618 Orsay Cedex F-91405 France CNRS Orsay Cedex F-91405 France Institut des Sciences du Vegetal CNRS F-91198 Gif-sur-Yvette Cedex France

The complex responses of eukaryotic cells to external factors are governed by several transcriptional and post-transcriptional processes. Several of them occur in the nucleus and have been linked to the action of non-proteincoding rnas （or npcrnas）, both long and small npcrnas, that recently emerged as major regulators of gene expression. Regulatory npcrnas acting in the nucleus include silencing-related rnas, intergenic npcrnas, natural antisense rnas, and other aberrant rnas resulting from the interplay between global transcription and rna processing activities （such as Dicers and rna-dependent polymerases）. Generally, the resulting npcrnas exert their regulatory effects through interactions with rna-binding proteins （or RBPs） within ribonucleoprotein particles （or RNPs）. A large group of RBPs are implicated in the silencing machinery through small interfering rnas （sirnas） and their localization suggests that several act in the nucleus to trigger epigenetic and chromatin changes at a whole-genome scale. Other nuclear RBPs interact with npcrnas and change their localization. In the fission yeast, the rna-binding Mei2p protein, playing pivotal roles in meiosis, interact with a meiotic npcrna involved in its nuclear re-localization. Related processes have been identified in plants and the ENOD40 npcrna was shown to re-localize a nuclear-speckle RBP from the nucleus to the cytoplasm in Medicago truncatula. Plant RBPs have been also implicated in rna-mediated chromatin silencing in the FLC locus through interaction with specific antisense transcripts. In this review, we discuss the interactions between RBPs and npcrnas in the context of nuclear-related processes and their implication in plant development and stress responses. We propose that these interactions may add a regulatory layer that modulates the interactions between the nuclear genome and the environment and, consequently, control plant developmental plasticity.

关键词： Abiotic/environmental stress gene silencing Arabidopsis rna-binding proteins non-protein-coding rnas nucleus.

rna-binding proteins in mouse male germline stem cells:a mammalian perspective

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Cell Regeneration 2016年第1期5卷 1-11页

作者： Huayu Qi Key Laboratory of Regenerative Biology Guangdong Provincial Key Laboratory of Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhou 510530China

Adult stem cells that reside in particular types of tissues are responsible for tissue homeostasis and regeneration.Cellular functions of adult stem cells are intricately related to the gene expression programs in those cells.Past research has demonstrated that regulation of gene expression at the transcriptional level can decisively alter cell fate of stem cells.However,cellular contents of mrnas are sometimes not equivalent to proteins,the functional units of cells.It is increasingly realized that post-transcriptional and translational regulation of gene expression are also fundamental for stem cell functions.Compared to differentiated somatic cells,effects on cellular status manifested by varied expression of rna-binding proteins and global protein synthesis have been demonstrated in several stem cell systems.Through the cooperation of both cis-elements of mrnas and trans-acting rna-binding proteins that are intimately associated with them,regulation of localization,stability,and translational status of mrnas directly influences the self-renewal and differentiation of stem cells.Previous studies have uncovered some of the molecular mechanisms that underlie the functions of rna-binding proteins in stem cells in invertebrate species.However,their roles in adult stem cells in mammals are just beginning to be unveiled.This review highlights some of the rna-binding proteins that play important functions during the maintenance and differentiation of mouse male germline stem cells,the adult stem cells in the male reproductive organ.

关键词： Adult stem cells rna-binding proteins Post-transcriptional regulation Translational regulation Protein synthesis

Transcriptome-wide discovery of coding and noncoding rna-binding proteins by click chemistry-assisted rna interactome capture（CARIC）

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Transcriptome-wide discovery of coding and noncoding RNA-bin...

KHSRP combines transcriptional and posttranscriptional mechanisms to regulate monocytic differentiation

第十届全国化学生物学学术会议

作者： Rongbing Huang Mengting Han Liying Meng Xing Chen College of Chemistry and Molecular Engineering Peking University Peking-Tsinghua Center for Life Sciences Peking University Synthetic and Functional Biomolecules Center Peking University Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University

Identification of rna-binding proteins（RBPs） is a prerequisite for understanding the posttranscriptional gene regulation networks. However, current large-scale RBP identification strategies are mostly based on the capture of polyadenylated rnas along with their binding proteins, leaving RBPs on non-poly（A） rnas, including most noncoding rnas（ncrnas） and pre-mrnas, largely undiscovered. Here we present a click chemistry-assisted rna interactome capture（CARIC） strategy, which enables transcriptome-wide identification of RBPs, independent of the polyadenylation state of rnas. CARIC combines metabolic labeling of rnas with an alkynyl uridine analog and in vivo rna-protein photocrosslinking, followed by click reaction with azide-biotin, affinity enrichment, and proteomic analysis. Applying CARIC, we identified 783 RBPs in HeLa cells, including 219 previously unknown RBPs. The CARIC strategy can be broadly applied to various organisms including bacterium whose rnas are mostly non-polyadenylated.

关键词： rna-binding proteins metabolic labeling click chemistry proteomics

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Blood Science 2022年第3期4卷 103-115页

作者： Jiayue Xu Dongsheng Wang Hongliu Ma Xueying Zhai Yue Huo Yue Ren Weiqian Li Le Chang Dongxu Lu Yuehong Guo Yanmin Si Yufeng Gao Xiaoshuang Wang Yanni Ma Fang Wang Jia Yu State Key Laboratory of Medical Molecular Biology Haihe Laboratory of Cell EcosystemInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijing 100005China Key Laboratory of rna and Hematopoietic Regulation Chinese Academy of Medical SciencesBeijing 100005China Department of Clinical Laboratory Sichuan Cancer Hospital and InstituteSichuan Cancer CenterSchool of MedicineUniversity of Electronic Science and Technology of ChinaChengdu 610041China Department of Gynecology Dian Jiang People’s Hospital of Chong QingChongqing 408300China Medical Epigenetic Research Center Chinese Academy of Medical SciencesBeijing 100005China

rna-binding proteins(RBPs)are widely involved in the transcriptional and posttranscriptional regulation of multiple biological processes.The transcriptional regulatory ability of RBPs was indicated by the identification of chromatin-enriched RBPs(Che-RBPs).One of these proteins,KH-type splicing regulatory protein(KHSRP),is a multifunctional RBP that has been implicated in mrna decay,alternative splicing,and mirna biogenesis and plays an essential role in myeloid differentiation by facilitating the maturation of miR-129.In this study,we revealed that KHSRP regulates monocytic differentiation by regulating gene transcription and rna splicing.KHSRP-occupied specific genomic sites in promoter and enhancer regions to regulate the expression of several hematopoietic genes through transcriptional activation and bound to pre-mrna intronic regions to modulate alternative splicing during monocytic differentiation.Of note,KHSRP had co-regulatory effects at both the transcriptional and posttranscriptional levels on MOGOH and ADARB1.Taken together,our analyses revealed the dual DNA-and rna-binding activities of KHSRP and have provided a paradigm to guide the analysis of other functional Che-RBPs in different biological systems.

关键词： KHSRP Monocytic differentiation rna-binding proteins Transcriptional regulation

Regnase-1, a rapid response ribonuclease regulating nflammation and stress responses

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Cellular & Molecular Immunology 2017年第5期14卷 412-422页

作者： Renfang Mao Riyun Yang Xia Chen Edward W Harhaj Xiaoying Wang Yihui Fan Basic Medical Research Center School of Medicine Nantong University Nantong Jiangsu 226001 People's Republic of China Department of Oncology Sidney Kimmel Comprehensive Cancer Center Johns Hopkins School of Medicine Baltimore MD 21287 USA Department of Immunology School of Medicine Nantong University Nantong Jiangsu 226001 People's Republic of China

rna-binding proteins （RBPs） are central players in post-transcriptional regulation and immune homeostasis. The ribonuclease and RBP Regnase-1 exerts critical roles in both immune cells and non-immune cells. Its expression is rapidly induced under diverse conditions including microbial infections, treatment with inflammatory cytokines and chemical or mechanical stimulation. Regnase-1 activation is transient and is subject to negative feedback mechanisms including proteasome-mediated degradation or mucosa-associated lymphoid tissue 1 （MALT1） mediated cleavage. The major function of Regnase-1 is promoting mrna decay via its ribonuclease activity by specifically targeting a subset of genes in different cell types. In monocytes, Regnase-1 downregulates IL-6 and IL-12B mrnas, thus mitigating inflammation, whereas in T cells, it restricts T-cell activation by targeting c-Rel, Ox40 and 11-2 transcripts. In cancer cells, Regnase-1 promotes apoptosis by inhibiting anti-apoptotic genes including Bcl2L1, Bcl2A1, RelB and Bcl3. Together with up-frameshift protein-1 （UPF1）, Regnase-1 specifically cleaves mrnas that are active during translation by recognizing a stem-loop （SL） structure within the 3＇UTRs of these genes in endoplasmic reticulum-bound ribosomes. Through this mechanism, Regnase-1 rapidly shapes mrna profiles and associated protein expression, restricts inflammation and maintains immune homeostasis. Dysregulation of Regnase-1 has been described in a multitude of pathological states including autoimmune diseases, cancer and cardiovascular diseases. Here, we provide a comprehensive update on the function, regulation and molecular mechanisms of Regnase-1, and we propose that Regnase-1 may function as a master rapid response gene for cellular adaption triggered by microenvironmental changes.

关键词： Autoimmune diseases Regnase-1 ribonuclease rna-binding proteins microenvironment

Deregulation of splicing factors and breast cancer development

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分子细胞生物学报:英文版 2015年第5期7卷 388-401页

作者： Marco Silipo Hannah Gautrey Alison Tyson-Capper Institute of Cellular Medicine Faculty of Medical SciencesNewcastle UniversityNewcastle upon Tyne NE24HHUK

It is well known that many genes implicated in the development and progression of breast cancer undergo aberrant alternative splicing events to produce proteinswithpro-cancerproperties.These changes in alternative splicingcan arise frommutations or single-nucleotide polymorphisms(SNPs)within the DNA sequences of cancer-related genes,which can strongly affect the activity of splicing factors and influence the splice site choice.However,it is important to note that absence of mutations is not sufficient to prevent misleading choices in splice site selection.There is nowincreasing evidence to demonstrate that the expression profile of ten splicing factors(including SRs and hnRNPs)and eight rna-binding proteins changes in breast cancer cells compared with normal cells.These modifications strongly influence the alternative splicing pattern of many cancer-related genes despite the absence of any detrimental mutations within their DNA sequences.Thus,a comprehensive assessment of the splicing factor status in breast cancer is important to provide insights into the mechanisms that lead to breast cancer development and metastasis.Whilst most studies focus on mutations that affect alternative splicing in cancer-related genes,this review focuses on splicing factors and rna-binding proteins that are themselves deregulated in breast cancer and implicated in cancer-related alternative splicing events.

关键词： alternative splicing splicing factors rna-binding proteins breast cancer

Global Profiling of the Lysine Crotonylome in Different Pluripotent States

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Genomics, Proteomics & Bioinformatics 2021年第1期19卷 80-93页

作者： Yuan Lv Chen Bu Jin Meng Carl Ward Giacomo Volpe Jieyi Hu Mengling Jiang Lin Guo Jiekai Chen Miguel A.Esteban Xichen Bao Zhongyi Cheng Laboratory of Integrative Biology Guangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhou 510530China CAS Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine Guangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhou 510530China University of Chinese Academy of Sciences Beijing 100049China Jingjie PTM BioLab(Hangzhou)Co.Ltd Hangzhou 310018China Joint School of Life Sciences Guangzhou Institutes of Biomedicine and Health and Guangzhou Medical UniversityGuangzhou 511436China Bioland Laboratory(Guangzhou Regenerative Medicine and Health Guangdong Laboratory) Guangzhou 510005China Institute of Stem Cells and Regeneration Chinese Academy of SciencesBeijing 100101China Laboratory of rna Molecular Biology Guangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhou 510530China

Pluripotent stem cells(PSCs)can be expanded in vitro in different culture conditions,resulting in a spectrum of cell states with distinct properties.Understanding how PSCs transition from one state to another,ultimately leading to lineage-specific differentiation,is important for developmental biology and regenerative medicine.Although there is significant information regarding gene expression changes controlling these transitions,less is known about post-translational modifications of proteins.Protein crotonylation is a newly discovered post-translational modification where lysine residues are modified with a crotonyl group.Here,we employed affinity purification of crotonylated(LC–MS/MS)to systematically profile protein crotonylation in mouse PSCs in different states including ground,metastable,and primed states,as well as metastable PSCs undergoing early pluripotency exit.We successfully identified 3628 high-confidence crotonylated sites in 1426 proteins.These crotonylated proteins are enriched for factors involved in functions/processes related to pluripotency such as rna biogenesis,central carbon metabolism,and proteasome function.Moreover,we found that increasing the cellular levels of crotonyl-coenzyme A(crotonyl-CoA)through crotonic acid treatment promotes proteasome activity in metastable PSCs and delays their differentiation,consistent with previous observations showing that enhanced proteasome activity helps to sustain pluripotency.Our atlas of protein crotonylation will be valuable for further studies of pluripotency regulation and may also provide insights into the role of metabolism in other cell fate transitions.

关键词： Metabolism Crotonylation Pluripotency rna-binding proteins Proteasome