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Genetic variation of circHIBADH enhances prostate cancer risk through regulating HNRNPA1-related RNA splicing 被引量:1
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作者 Yifei Cheng Rongjie Shi +5 位作者 Shuai Ben Silu Chen Shuwei Li Junyi Xin Meilin Wang Gong Cheng 《Journal of Biomedical Research》 CAS CSCD 2024年第4期358-368,共11页
The current study aimed to investigate associations of circRNAs and related genetic variants with the risk of prostate cancer(PCa)as well as to elucidate biological mechanisms underlying the associations.We first comp... The current study aimed to investigate associations of circRNAs and related genetic variants with the risk of prostate cancer(PCa)as well as to elucidate biological mechanisms underlying the associations.We first compared expression levels of circRNAs between 25 paired PCa and adjacent normal tissues to identify riskassociated circRNAs by using the MiOncoCirc database.We then used logistic regression models to evaluate associations between genetic variants in candidate circRNAs and PCa risk among 4662 prostate cancer patients and 3114 healthy controls,and identified circHIBADH rs11973492 T>C as a significant risk-associated variant(odds ratio=1.20,95%confidence interval:1.08-1.34,P=7.06×10^(-4))in a dominant genetic model,which altered the secondary structure of the corresponding RNA chain.In the in silico analysis,we found that circHIBADH sponged and silenced 21 RNA-binding proteins(RBPs)enriched in the RNA splicing pathway,among which HNRNPA1 was identified and validated as a hub RBP using an external RNA-sequencing data as well as the in-house(four tissue samples)and publicly available single-cell transcriptomes.Additionally,we demonstrated that HNRNPA1 influenced hallmarks including MYC target,DNA repair,and E2F target signaling pathways,thereby promoting carcinogenesis.In conclusion,genetic variants in circHIBADH may act as sponges and inhibitors of RNA splicing-associated RBPs including HNRNPA1,playing an oncogenic role in PCa. 展开更多
关键词 genetic variants prostate cancer circrna rna-binding protein rna splicing sing-cell rna sequencing
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Rice FLOURY ENDOSPERM22, encoding a pentatricopeptide repeat protein, is involved in both mitochondrial RNA splicing and editing and is crucial for endosperm development 被引量:3
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作者 Hang Yang Yunlong Wang +20 位作者 Yunlu Tian Xuan Teng Zehui Lv Jie Lei Erchao Duan Hui Dong Xue Yang Yuanyan Zhang Yinglun Sun Xiaoli Chen Xiuhao Bao Rongbo Chen Chuanwei Gu Yipeng Zhang Xiaokang Jiang Wenyu Ma Pengcheng Zhang Yi Ji Yu Zhang Yihua Wang Jianmin Wan 《Journal of Integrative Plant Biology》 SCIE CAS CSCD 2023年第3期755-771,共17页
Most of the reported P-type pentatricopeptide repeat(PPR) proteins play roles in organelle RNA stabilization and splicing. However, P-type PPRs involved in both RNA splicing and editing have rarely been reported, and ... Most of the reported P-type pentatricopeptide repeat(PPR) proteins play roles in organelle RNA stabilization and splicing. However, P-type PPRs involved in both RNA splicing and editing have rarely been reported, and their underlying mechanism remains largely unknown. Here, we report a rice floury endosperm22(flo22) mutant with delayed amyloplast development in endosperm cells. Map-based cloning and complementation tests demonstrated that FLO22 encodes a mitochondrion-localized P-type PPR protein.Mutation of FLO22 resulting in defective transsplicing of mitochondrial nad1 intron 1 and perhaps causing instability of mature transcripts affected assembly and activity of complex Ⅰ, and mitochondrial morphology and function. RNA-seq analysis showed that expression levels of many genes involved in starch and sucrose metabolism were significantly down-regulated in the flo22mutant compared with the wild type, whereas genes related to oxidative phosphorylation and the tricarboxylic acid cycle were significantly upregulated. In addition to involvement in splicing as a P-type PPR protein, we found that FLO22 interacted with DYW3, a DYW-type PPR protein, and they may function synergistically in mitochondrial RNA editing. The present work indicated that FLO22 plays an important role in endosperm development and plant growth by participating in nad1 maturation and multi-site editing of mitochondrial messager RNA. 展开更多
关键词 endosperm development Oryza sativa PPR proteins rna editing rna splicing
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OsTHA8 encodes a pentatricopeptide repeat protein required for RNA editing and splicing during rice chloroplast development
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作者 Yanwei Wang Yu Duan Pengfei Ai 《The Crop Journal》 SCIE CSCD 2023年第5期1353-1367,共15页
In higher plants, the chloroplast is the most important organelle for photosynthesis and for numerous essential metabolic processes in the cell. Although many genes involved in chloroplast development have been identi... In higher plants, the chloroplast is the most important organelle for photosynthesis and for numerous essential metabolic processes in the cell. Although many genes involved in chloroplast development have been identified, the mechanisms underlying such development are not fully understood. In this study, a rice(Oryza sativa) mutant exhibiting pale green color and seedling lethality was isolated from a mutant library. The mutated gene was identified as an ortholog of THA8(thylakoid assembly 8) in Arabidopsis and maize. This gene is designated as OsTHA8 hereafter. OsTHA8 showed a typical pentatricopeptide repeat(PPR) characteristic of only four PPR motifs. Inactivation of OsTHA8 led to a deficiency in chloroplast development in the rice seedling stage. OsTHA8 was expressed mainly in young leaves and leaf sheaths.The OsTHA8 protein was localized to the chloroplast. Loss of function of OsTHA8 weakened the editing efficiency of ndhB-611/737 and rps8-182 transcripts under normal conditions. Y2H and BiFC indicated that OsTHA8 facilitates RNA editing by forming an editosome with multiple organellar RNA editing factor(OsMORF8) and thioredoxin z(OsTRXz), which function in RNA editing in rice chloroplasts. Defective OsTHA8 impaired chloroplast ribosome assembly and resulted in reduced expression of PEP-dependent genes and photosynthesis-related genes. Abnormal splicing of the chloroplast gene ycf3 was detected in ostha8. These findings reveal a synergistic regulatory mechanism of chloroplast biogenesis mediated by RNA, broaden the function of the PPR family, and shed light on the RNA editing complex in rice. 展开更多
关键词 Oryza sativa L. Chloroplast biogenesis Pentatricopeptide repeat protein rna editing rna splicing
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RNA splicing alterations in lung cancer pathogenesis and therapy
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作者 Yueren Yan Yunpeng Ren +1 位作者 Yufang Bao Yongbo Wang 《Cancer Pathogenesis and Therapy》 2023年第4期272-283,共12页
RNA splicing alterations are widespread and play critical roles in cancer pathogenesis and therapy.Lung cancer is highly heterogeneous and causes the most cancer-related deaths worldwide.Large-scale multi-omics studie... RNA splicing alterations are widespread and play critical roles in cancer pathogenesis and therapy.Lung cancer is highly heterogeneous and causes the most cancer-related deaths worldwide.Large-scale multi-omics studies have not only characterized the mutational landscapes but also discovered a plethora of transcriptional and post-transcriptional changes in lung cancer.Such resources have greatly facilitated the development of new diagnostic markers and therapeutic options over the past two decades.Intriguingly,altered RNA splicing has emerged as an important molecular feature and therapeutic target of lung cancer.In this review,we provide a brief overview of splicing dysregulation in lung cancer and summarize the recent progress on key splicing events and splicing factors that contribute to lung cancer pathogenesis.Moreover,we describe the general strategies targeting splicing alterations in lung cancer and highlight the potential of combining splicing modulation with currently approved therapies to combat this deadly disease.This review provides new mechanistic and therapeutic insights into splicing dysregulation in cancer. 展开更多
关键词 rna splicing splicing factors splicing alterations Lung cancer
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Nuclearly Encoded Splicing Factors Implicated in RNA Splicing in Higher Plant Organelles 被引量:11
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作者 Andeol Falcon de Longevialle lan D. Small Claire Lurin 《Molecular Plant》 SCIE CAS CSCD 2010年第4期691-705,共15页
Plant organelles arose from two independent endosymbiosis events. Throughout evolutionary history, tight control of chloroplasts and mitochondria has been gained by the nucleus, which regulates most steps of organelle... Plant organelles arose from two independent endosymbiosis events. Throughout evolutionary history, tight control of chloroplasts and mitochondria has been gained by the nucleus, which regulates most steps of organelle genome expression and metabolism. In particular, RNA maturation, including RNA splicing, is highly dependent on nuclearly encoded splicing factors. Most introns in organelles are group II introns, whose catalytic mechanism closely resembles that of the nuclear spliceosome. Plant group II introns have lost the ability to self-splice in vivo and require nuclearly encoded proteins as cofactors. Since the first splicing factor was identified in chloroplasts more than 10 years ago, many other proteins have been shown to be involved in splicing of one or more introns in chloroplasts or mitochondria. These new proteins belong to a variety of different families of RNA binding proteins and provide new insights into ribonucleoprotein complexes and RNA splicing machineries in organelles. In this review, we describe how splicing factors, encoded by the nucleus and targeted to the organelles, take part in post-transcriptional steps in higher plant organelle gene expression. We go on to discuss the potential for these factors to regulate organelle gene expression. 展开更多
关键词 rna splicing CHLOROPLAST MITOCHONDRIA splicing factors.
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CDE4 encodes a pentatricopeptide repeat protein involved in chloroplast RNA splicing and affects chloroplast development under low-temperature conditions in rice 被引量:3
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作者 Xinyong Liu Xichun Zhang +8 位作者 Ruijie Cao Guiai Jiao Shikai Hu Gaoneng Shao Zhonghua Sheng Lihong Xie Shaoqing Tang Xiangjin Wei Peisong Hu 《Journal of Integrative Plant Biology》 SCIE CAS CSCD 2021年第10期1724-1739,共16页
Pentatricopeptide repeat(PPR)proteins play important roles in the post-transcriptional modification of organellar RNAs in plants.However,the function of most PPR proteins remains unknown.Here,we characterized the rice... Pentatricopeptide repeat(PPR)proteins play important roles in the post-transcriptional modification of organellar RNAs in plants.However,the function of most PPR proteins remains unknown.Here,we characterized the rice(Oryza sativa L.)chlorophyll deficient 4(cde4)mutant which exhibits an albino phenotype during early leaf development,with decreased chlorophyll contents and abnormal chloroplasts at low-temperature(20℃).Positional cloning revealed that CDE4 encodes a P-type PPR protein localized in chloroplasts.In the cde4 mutant,plastid-encoded polymerase(PEP)-dependent transcript levels were significantly reduced,but transcript levels of nuclear-encoded genes were increased compared to wild-type plants at 20℃.CDE4 directly binds to the transcripts of the chloroplast genes rpl2,ndhA,and ndhB.Intron splicing of these transcripts was defective in the cde4 mutant at 20℃,but was normal at 32℃.Moreover,CDE4 interacts with the guanylate kinase VIRESCENT 2(V2);overexpression of V2 enhanced CDE4 protein stability,thereby rescuing the cde4 phenotype at 20℃.Our results suggest that CDE4 participates in plastid RNA splicing and plays an important role in rice chloroplast development under lowtemperature conditions. 展开更多
关键词 CDE4 chloroplast development pentatricopeptide repeat(PPR)protein rna splicing LOW-TEMPERATURE Oryza sativa L.
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Global impact of RNA splicing on transcriptome remodeling in the heart 被引量:2
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作者 Chen GAO Yibin WANG 《Journal of Zhejiang University-Science B(Biomedicine & Biotechnology)》 SCIE CAS CSCD 2012年第8期603-608,共6页
In the eukaryotic transcriptome, both the numbers of genes and different RNA species produced by each gene contribute to the overall complexity. These RNA species are generated by the utilization of different transcri... In the eukaryotic transcriptome, both the numbers of genes and different RNA species produced by each gene contribute to the overall complexity. These RNA species are generated by the utilization of different transcriptional initiation or termination sites, or more commonly, from different messenger RNA (mRNA) splicing events. Among the 30 000+ genes in human genome, it is estimated that more than 95% of them can generate more than one gene product via alternative RNA splicing. The protein products generated from different RNA splicing variants can have different intracellular localization, activity, or tissue-distribution. Therefore, alternative RNA splicing is an important molecular process that contributes to the overall complexity of the genome and the functional specificity and diversity among different cell types. In this review, we will discuss current efforts to unravel the full complexity of the cardiac transcriptome using a deep-sequencing approach, and highlight the potential of this technology to uncover the global impact of RNA splicing on the transcriptome during development and diseases of the heart. 展开更多
关键词 Alternative rna splicing Transcriptome Gene regulation HEART rna-SEQ
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Cilia regeneration requires an RNA splicing factor from the ciliary base 被引量:1
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作者 Kaiming Xu Guangshuo Ou 《Cell Regeneration》 2022年第1期303-314,共12页
Cilia are microtubule-based organelles projected from most eukaryotic cell surfaces performing cell motility and signaling.Several previously recognized non-ciliary proteins play crucial roles in cilium formation and ... Cilia are microtubule-based organelles projected from most eukaryotic cell surfaces performing cell motility and signaling.Several previously recognized non-ciliary proteins play crucial roles in cilium formation and function.Here,we provide additional evidence that the Caenorhabditis elegans RNA splicing factor PRP-8/PRPF8 regulates ciliogen-esis and regeneration from the ciliary base.Live imaging of GFP knock-in animals reveals that the endogenous PRP-8 localizes in the nuclei and the ciliary base.A weak loss-of-function allele of prp-8 affects ciliary structure but with little impact on RNA splicing.Conditional degradation of PRP-8 within ciliated sensory neurons showed its direct and spe-cific roles in cilium formation.Notably,the penetrance of ciliary defects correlates with the reduction of PRP-8 at the ciliary base but not nuclei,and sensory neurons regenerated cilia accompanying PRP-8 recovery from the ciliary base rather than the nuclei.We suggest that PRP-8 at the ciliary base contributes to cilium formation and regeneration. 展开更多
关键词 PRP-8/PRPF8 rna splicing factor CILIOGENESIS Cilium regeneration
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Mitochondrion-targeted PENTATRICOPEPTIDE REPEAT5 is required for cis-splicing of nad4 intron 3 and endosperm development in rice 被引量:4
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作者 Long Zhang Yanzhou Qi +10 位作者 Mingming Wu Lei Zhao Zhichao Zhao Cailin Lei Yuanyuan Hao Xiaowen Yu Yinglun Sun Xin Zhang Xiuping Guo Yulong Ren Jianmin Wan 《The Crop Journal》 SCIE CSCD 2021年第2期282-296,共15页
Endosperm as the storage organ of starch and protein in cereal crops largely determines grain yield and quality.Despite the fact that several pentatricopeptide repeat(PPR)proteins required for endosperm development ha... Endosperm as the storage organ of starch and protein in cereal crops largely determines grain yield and quality.Despite the fact that several pentatricopeptide repeat(PPR)proteins required for endosperm development have been identified in rice,the molecular mechanisms of many P-type PPR proteins in endosperm development remains unclear.Here,we isolated a rice floury endosperm mutant ppr5 that developed small starch grains and an abnormal aleurone layer,accompanied by decreased starch,protein,and amylose contents.Map-based cloning combined with a complementation test demonstrated that PPR5 encodes a P-type PPR protein that is localized to the mitochondria.The mutation in PPR5 caused reduced splicing efficiency of mitochondrial NADH dehydrogenase 4(nad4)gene intron 3 and reduced complex I assembly and activity.Loss of PPR5 function greatly upregulated expression of alternative oxidases(AOXs),reduced ATP production,and affected mitochondrial morphology.We demonstrate that PPR5,as a P-type PPR protein,is required for mitochondrial function and endosperm development by controlling the cis-splicing of mitochondrial nad4 intron 3. 展开更多
关键词 Floury endosperm PPR MITOCHONDRIA rna splicing Oryza sativa
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Circular RNA and its potential as prostate cancer biomarkers 被引量:1
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作者 Dwayne Tucker Wei Zheng +1 位作者 Da-Hong Zhang Xuesen Dong 《World Journal of Clinical Oncology》 CAS 2020年第8期563-572,共10页
Advancing knowledge of the transcriptome has revealed that circular RNAs(circRNAs)are widely expressed and evolutionarily conserved molecules that may serve relevant biological roles.More interesting is the accumulati... Advancing knowledge of the transcriptome has revealed that circular RNAs(circRNAs)are widely expressed and evolutionarily conserved molecules that may serve relevant biological roles.More interesting is the accumulating evidence which demonstrates the implication of circRNAs in diseases,especially cancers.This revelation has helped to form the rationale for many studies exploring their utility as clinical biomarkers.CircRNAs are highly stable due to their unique structures,exhibit some tissue specificity,and are enriched in exosomes,which facilitate their detection in a range of body fluids.These properties make circRNAs ideal candidates for biomarker development in many diseases.This review will outline the discovery,biogenesis,and proposed functions of circRNAs. 展开更多
关键词 Circular rna rna splicing Prostate cancer BIOMARKER Cell-free rna
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Investigation of androgen receptor-dependent alternative splicing has identified a unique subtype of lethal prostate cancer
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作者 Sean Seltzer Paresa N Giannopoulos +2 位作者 Tarek A Bismar Mark Trifiro Miltiadis Paliouras 《Asian Journal of Andrology》 SCIE CAS CSCD 2023年第3期296-308,共13页
A complete proteomics study characterizing active androgen receptor(AR)complexes in prostate cancer(PCa)cells identified a diversity of protein interactors with tumorigenic annotations,including known RNA splicing fac... A complete proteomics study characterizing active androgen receptor(AR)complexes in prostate cancer(PCa)cells identified a diversity of protein interactors with tumorigenic annotations,including known RNA splicing factors.Thus,we chose to further investigate the functional role of AR-mediated alternative RNA splicing in PCa disease progression.We selected two AR-interacting RNA splicing factors,Src associated in mitosis of 68 kDa(SAM68)and DEAD(Asp-Glu-Ala-Asp)box helicase 5(DDX5)to examine their associative roles in AR-dependent alternative RNA splicing.To assess the true physiological role of AR in alternative RNA splicing,we assessed splicing profiles of LNCaP PCa cells using exon microarrays and correlated the results to PCa clinical datasets.As a result,we were able to highlight alternative splicing events of clinical significance.Initial use of exon-mini gene cassettes illustrated hormone-dependent AR-mediated exon-inclusion splicing events with SAM68 or exon-exclusion splicing events with DDX5 overexpression.The physiological significance in PCa was investigated through the application of clinical exon array analysis,where we identified exon-gene sets that were able to delineate aggressive disease progression profiles and predict patient disease-free outcomes independently of pathological clinical criteria.Using a clinical dataset with patients categorized as prostate cancer-specific death(PCSD),these exon gene sets further identified a select group of patients with extremely poor disease-free outcomes.Overall,these results strongly suggest a nonclassical role of AR in mediating robust alternative RNA splicing in PCa.Moreover,AR-mediated alternative spicing contributes to aggressive PCa progression,where we identified a new subtype of lethal PCa defined by AR-dependent alternative splicing. 展开更多
关键词 alternative rna splicing androgen receptor exon-gene sets lethal prostate cancer subtype prostate cancer
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A repertoire of intronic lariat RNAs reveals tissue-specific regulation and target mimicry potential in plants
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作者 Yong Zhang Xiaotuo Zhang +7 位作者 Qi Tang Lei Li Ting Jiang Yixiao Fang Hong Zhang Jixian Zhai Guodong Ren Binglian Zheng 《Science China(Life Sciences)》 SCIE CAS CSCD 2024年第6期1280-1291,共12页
Lariat RNA is concomitantly produced by excised intron during RNA splicing,which is usually debranched by DBR1,an RNA debranching enzyme.However,increasing evidence showed that some lariat RNA could escape debranching... Lariat RNA is concomitantly produced by excised intron during RNA splicing,which is usually debranched by DBR1,an RNA debranching enzyme.However,increasing evidence showed that some lariat RNA could escape debranching.Little is known about how and why these lariat RNAs could be retained.By comparing the atlas of lariat RNAs between the non-dividing cell(mature pollen)and three actively dividing tissues(young shoot apex,young seeds,and young roots),we identified hundreds to thousands of lariat RNA naturally retained in each tissue,and the incidence of lariat RNA retention is much less in shoot apex while much more in pollen.Many lariat RNAs derived from the same intron or different lariat RNAs from the same pre-m RNA could be retained in one tissue while degraded in the other tissues.By deciphering lariat RNA sequences,we identified an AG-rich(RAAAAVAAAR)motif and a UC-rich(UCUCUYUCUC)motif for pollen-specific and the other three tissues-retained lariat RNAs,respectively.Reconstitution of the pollen-specific AG-rich motif indeed enhanced lariat RNA retention in plants.Biologically,hundreds of lariat RNAs harbored mi RNA binding sites,and dual-luciferase reporter assay showed that these natural lariat RNAs had the potential to protect expression of mi RNA target genes.Collectively,our results uncover that selective retention of lariat RNA is an actively regulatory process,and provide new insights into understanding how lariat RNA metabolism may impact mi RNA activity. 展开更多
关键词 intron turnover lariat rna mirna rna splicing DBR1
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GhCTSF1,a short PPR protein with a conserved role in chloroplast development and photosynthesis,participates in intron splicing of rpoC1 and ycf3-2 transcripts in cotton
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作者 Yuzhu Huo Mengxue Cheng +6 位作者 Meiju Tang Meng Zhang Xiaofan Yang Yating Zheng Tong Zhao Peng He Jianing Yu 《Plant Communications》 SCIE CSCD 2024年第6期213-229,共17页
Cotton is one of the most important textile fibers worldwide.As crucial agronomic traits,leaves play an essential role in the growth,disease resistance,fiber quality,and yield of cotton plants.Pentatricopeptide repeat... Cotton is one of the most important textile fibers worldwide.As crucial agronomic traits,leaves play an essential role in the growth,disease resistance,fiber quality,and yield of cotton plants.Pentatricopeptide repeat(PPR)proteins are a large family of nuclear-encoded proteins involved in organellar or nuclear RNA metabolism.Using a virus-induced gene silencing assay,we found that cotton plants displayed variegated yellow leaf phenotypes with decreased chlorophyll content when expression of the PPR gene GhCTSF1 was silenced.GhCTSF1 encodes a chloroplast-localized protein that contains only two PPR motifs.Disruption of GhCTSF1 substantially reduces the splicing efficiency of rpoC1 intron 1 and ycf3 intron 2.Loss of function of the GhCTSF1 ortholog EMB1417 causes splicing defects in rpoC1 and ycf3-2,leading to impaired chloroplast structure and decreased photosynthetic rates in Arabidopsis.We also found that GhCTSF1 interacts with two splicing factors,GhCRS2 and GhWTF1.Defects in GhCRS2 and GhWTF1 severely affect intron splicing of rpoC1 and ycf3-2 in cotton,leading to defects in chloroplast development and a reduction in photosynthesis.Our results suggest that GhCTSF1 is specifically required for splicing rpoC1 and ycf3-2 in cooperation with GhCRS2 and GhWTF1. 展开更多
关键词 CHLOROPLAST rna splicing PPR protein COTTON photosynthesis
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Post-transcriptional regulation of DEAD-box RNA helicases in hematopoietic malignancies
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作者 Jiankun Fan Zhigang Li +1 位作者 Li Pei Yu Hou 《Genes & Diseases》 SCIE CSCD 2024年第5期315-323,共9页
Hematopoiesis represents a meticulously regulated and dynamic biological process.Genetic aberrations affecting blood cells,induced by various factors,frequently give rise to hematological tumors.These instances are of... Hematopoiesis represents a meticulously regulated and dynamic biological process.Genetic aberrations affecting blood cells,induced by various factors,frequently give rise to hematological tumors.These instances are often accompanied by a multitude of abnormal post-transcriptional regulatory events,including RNA alternative splicing,RNA localization,RNA degradation,and storage.Notably,post-transcriptional regulation plays a pivotal role in preserving hematopoietic homeostasis.The DEAD-Box RNA helicase genes emerge as crucial post-transcriptional regulatory factors,intricately involved in sustaining normal hematopoiesis through diverse mechanisms such as RNA alternative splicing,RNA modification,and ribosome assembly.This review consolidates the existing knowledge on the role of DEAD-box RNA helicases in regulating normal hematopoiesis and underscores the pathogenicity of mutant DEADBox RNA helicases in malignant hematopoiesis.Emphasis is placed on elucidating both the positive and negative contributions of DEAD-box RNA helicases within the hematopoietic system. 展开更多
关键词 DEAD-box rna helicase Hemopoietic system Post-transcriptional regulation Ribosomes assembly rna alternative splicing
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Extending the functions of the homeotic transcription factor Cdx2 in the digestive system through nontranscriptional activities 被引量:5
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作者 Jean-Noel Freund Isabelle Duluc +2 位作者 Jean-Marie Reimund Isabelle Gross Claire Domon-Dell 《World Journal of Gastroenterology》 SCIE CAS 2015年第5期1436-1443,共8页
The homeoprotein encoded by the intestinal-specific Cdx2 gene is a major regulator of gut development and homeostasis,also involved in colon cancer as well as in intestinal-type metaplasias when it is abnormally expre... The homeoprotein encoded by the intestinal-specific Cdx2 gene is a major regulator of gut development and homeostasis,also involved in colon cancer as well as in intestinal-type metaplasias when it is abnormally expressed outside the gut.At the molecular level,structure/function studies have demonstrated that the Cdx2 protein is a transcription factor containing a conserved homeotic DNA-binding domain made ofthree alpha helixes arranged in a helix-turn-helix motif,preceded by a transcriptional domain and followed by a regulatory domain.The protein interacts with several thousand sites on the chromatin and widely regulates intestinal functions in stem/progenitor cells as well as in mature differentiated cells.Yet,this transcription factor also acts trough original nontranscriptional mechanisms.Indeed,the identification of novel protein partners of Cdx2 and also of a splicing variant revealed unexpected functions in the control of signaling pathways like the Wnt and NF-k B pathways,in double-strand break DNA repair and in premessenger RNA splicing.These novel functions of Cdx2 must be considered to fully understand the complexity of the role of Cdx2 in the healthy intestine and in diseases. 展开更多
关键词 HOMEOBOX Transcription Signaling DNA repair rna splicing INTESTINE Development Cancer HOMEOSTASIS
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Novel DYW-type pentatricopeptide repeat(PPR) protein BLX controls mitochondrial RNA editing and splicing essential for early seed development of Arabidopsis 被引量:2
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作者 Yan Sun Jiaying Huang +3 位作者 Sheng Zhong Hongya Gu Shan He Li-Jia Qu 《Journal of Genetics and Genomics》 SCIE CAS CSCD 2018年第3期155-168,共14页
In plants, RNA editing is a post-transcriptional process that changes specific cytidine to uridine in both mitochondria and plastids. Most pentatricopeptide repeat(PPR) proteins are involved in organelle RNA editing... In plants, RNA editing is a post-transcriptional process that changes specific cytidine to uridine in both mitochondria and plastids. Most pentatricopeptide repeat(PPR) proteins are involved in organelle RNA editing by recognizing specific RNA sequences. We here report the functional characterization of a PPR protein from the DYW subclass, Baili Xi(BLX), which contains five PPR motifs and a DYW domain. BLX is essential for early seed development, as plants lacking the BLX gene was embryo lethal and the endosperm failed to initiate cellularization. BLX was highly expressed in the embryo and endosperm, and the BLX protein was specifically localized in mitochondria, which is essential for BLX function. We found that BLX was required for the efficient editing of 36 editing sites in mitochondria. Moreover, BLX was involved in the splicing regulation of the fourth intron of nad1 and the first intron of nad2. The loss of BLX function impaired the mitochondrial function and increased the reactive oxygen species(ROS) level. Genetic complementation with truncated variants of BLX revealed that, in addition to the DYW domain, only the fifth PPR motif was essential for BLX function. The upstream sequences of the BLX-targeted editing sites are not conserved, suggesting that BLX serves as a novel and major mitochondrial editing factor(MEF) via a new non-RNA-interacting manner. This finding provides new insights into how a DYW-type PPR protein with fewer PPR motifs regulates RNA editing in plants. 展开更多
关键词 ARABIDOPSIS PPR rna editing rna splicing Embryo and endosperm development
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Mutations in FgPrp6 suppressive to the Fgprp4 mutant in Fusarium graminearum
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作者 LI Chao-hui FAN Zhi-li +4 位作者 HUANG Xin-yi WANG Qin-hu JIANG Cong XU Jin-rong JIN Qiao-jun 《Journal of Integrative Agriculture》 SCIE CAS CSCD 2022年第5期1375-1388,共14页
The pre-mRNA processing factor Prp6 is an essential component of the U4/U6.U5 tri-small nuclear ribonucleoprotein(snRNP).In a previous study,mutations were identified in the PRP6 ortholog in four suppressors of Fgprp4... The pre-mRNA processing factor Prp6 is an essential component of the U4/U6.U5 tri-small nuclear ribonucleoprotein(snRNP).In a previous study,mutations were identified in the PRP6 ortholog in four suppressors of Fgprp4 that was deleted of the only kinase FgPrp4 among the spliceosome components in the plant pathogenic fungus Fusarium graminearum.In this study,we identified additional suppressor mutations in FgPrp6 and determined the suppressive effects of selected mutations.In total,12 mutations of FgPRP6 were identified in 20 suppressors of Fgprp4 by sequencing analysis.Whereas three mutation sites are in the linker region of FgPrp6,seven are in the first two HAT repeats.RNA-seq analysis showed that suppressor mutations on different sites caused different splicing efficiency recovery.The suppressive effects of E308K and R230H were verified.Similar to human and fission yeast,the FgPrp6 was phosphorylated by the FgPrp4 kinase.Interestingly,the conserved Prp4-phosphorylation sites T261,T219&T221,and predicted phosphorylation sites T199&T200 on FgPrp6 were dispensable for the function of FgPrp6 in hyphal growth and sexual reproduction but important in plant infection.They are required for the infectious growth of F.graminearum in wheat lemma.RNA-seq analysis of the wheat lemma infected with Fgprp6/FgPRP6^(Δ199-221)-GFP or Fgprp6/FgPRP6^(Δ250-262)-GFP showed that 28 and 35% introns had splicing defects,respectively,which may be responsible for their defects in plant infection. 展开更多
关键词 rna splicing FgPrp6 SUPPRESSOR plant infection PHOSPHORYLATION
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Human hematopoietic cells express two forms of thecytokine receptor common γ-chain (γc)
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作者 SHI YU FANG MARY HILL +4 位作者 ANTON NOVAK ZHIQING CHEN RUO XIANG WANG CHOONGCHIN LIEW GORDON B. MILLS (Oncology Research, The Toronto Hospital, 200 ElizabcthSt., Toronto, Ontario, Canada MSG 2C4Department of Immunology, Holland Laboratoryof American Red Cr 《Cell Research》 SCIE CAS CSCD 1997年第2期195-205,共11页
Recent studies have revealed that the γ-chain of theIL-2 receptor is shared by the receptors for IL-4, IL7, IL-9, IL-13, and IL-15, and it is therefore also referred toas the common γ-chain (γc). Mutations of γc r... Recent studies have revealed that the γ-chain of theIL-2 receptor is shared by the receptors for IL-4, IL7, IL-9, IL-13, and IL-15, and it is therefore also referred toas the common γ-chain (γc). Mutations of γc result inX-linked severe combined immunodeficiency syndrome inhumans, indicating that rye is essential for normal development and function of the immune system. We demonstratethat human hematopoietic cells express two γc transcriptsdiffering in their carboxyl terminal coding region. Onetranscript is the previously reported sequence (γc-long),whereas the newly identified sequence exhibits a deletion of72 nucleotides close to the 3’-end of the open reading frame(γc-short). This alteration predicts a loss of 24 amino acidsincluding a conserved tyrosine residue which is shared byseveral members of the cytokine receptor family. Thepresence of these two distinct forms of rye transcripts wasdemonstrated by sequencing of reversely transcribed andpolymerase chain reaction (RT-PCR) amplified mRNA, restriction digestion of the RT-PCR products, RNAse protection, and Northern blotting from human cell lines andhuman peripheral blood lymphocytes. Furthermore, thetwo variants were present in peripheral blood lymphocytesfrom both female and male donors, which rules out allelicvariants since rye is a single copy gene located on the Xchromosome. A truncation mutant at a site near the observed changes in γc-short has been reported by othersto alter biochemical events activated by cytokines. Thiscombined with the loss of a potential SH2 "docking" sitein γc-short suggests that γc-long and γc-short may link todifferent signaling pathways and may play an importantrole in determining the cellular response to IL-2, IL-4, IL-7, IL-9, IL-13, IL-15. 展开更多
关键词 IL-2 receptor γ-chain cytokine receptor common γ-chain IL-2 receptor cytokine receptors rna splicing
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A Novel Chloroplast-Localized Pentatricopeptide Repeat Protein Involved in Splicing Affects Chloroplast Development and Abiotic Stress Response in Rice 被引量:21
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作者 Junjie Tan Zhenhua Tan +12 位作者 Fuqing Wu Peike Sheng Yueqin Heng Xinhua Wang Yulong Ren Jiulin Wang Xiuping Guo Xin Zhang Zhijun Cheng Ling Jiang Xuanming Liu Haiyang Wang Jianmin Wan 《Molecular Plant》 SCIE CAS CSCD 2014年第8期1329-1349,共21页
Pentatricopeptide repeat (PPR) proteins comprise a large family in higher plants and modulate organellar gene expression by participating in various aspects of organellar RNA metabolism. In rice, the family contains... Pentatricopeptide repeat (PPR) proteins comprise a large family in higher plants and modulate organellar gene expression by participating in various aspects of organellar RNA metabolism. In rice, the family contains 477 members, and the majority of their functions remain unclear. In this study, we isolated and characterized a rice mutant, white stripe leaf (wsl), which displays chlorotic striations early in development. Map-based cloning revealed that WSL encodes a newly identified rice PPR protein which targets the chloroplasts. In wsl mutants, PEP-dependent plastid gene expression was significantly down-regulated, and plastid rRNAs and translation products accumulate to very low levels. Consistently with the observations, wsl shows a strong defect in the splicing of chloroplast transcript rpl2, resulting in aberrant transcript accumulation and its product reduction in the mutant. The wsl shows enhanced sensitivity to ABA, salinity, and sugar, and it accumulates more H2O2 than wild-type. These results suggest the reduced translation efficiency may affect the response of the mutant to abiotic stress. 展开更多
关键词 PPR protein WSL ABA CHLOROPLAST rna splicing rpl2 abiotic stress responses.
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The U6 Biogenesis-Like I Plays an Important Role in Maize Kernel and Seedling Development by Affecting the 3' End Processing of U6 snRNA 被引量:8
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作者 Jiankun Li Junjie Fu +8 位作者 Yan Chen Kaijian Fan Cheng He Zhiqiang Zhang Li Li Yunjun Liu Jun Zheng Dongtao Ren Guoying Wang 《Molecular Plant》 SCIE CAS CSCD 2017年第3期470-482,共13页
Regulation of gene expression at the post-transcriptional level is of crucial importance in the development of an organism. Here we present the characterization of a maize gene, U6 biogenesis-like 1 (UBL1), which pl... Regulation of gene expression at the post-transcriptional level is of crucial importance in the development of an organism. Here we present the characterization of a maize gene, U6 biogenesis-like 1 (UBL1), which plays an important role in kernel and seedling development by influencing pre-mRNA splicing. The ubll mutant, exhibiting small kernel and weak seedling, was isolated from a Mutator-tagged population. Trans- genic complementation and three independent mutant alleles confirmed that UBL1, which encodes a putative RNA exonuclease belonging to the 2H phosphodiesterase superfamily, is responsible for the phenotype of ubll. We demonstrated that UBL1 possess the RNA exonuclease activity in vitro and found that loss of UBL1 function in ubll causes decreased level and abnormal 3' end constitution of snRNA U6, resulting in splicing defect of mRNAs. Through the in vitro and in vivo studies replacing two histidines with alanines in the H-X-T/S-X (X is a hydrophobic residue) motifs we demonstrated that these two motifs are essential for the normal function of UBL1. We further showed that the function of UBL1 may be conserved across a wide phylogenetic distance as the heterologous expression of maize UBL1 could complement the Arabidopsis ubll mutant. 展开更多
关键词 UBL1 U6 snrna rna splicing intron retention kernel development MAIZE
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