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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Increased expression levels of the RNA splicing regulator Transformer2fl (abbreviated Tra2fl) have been reported in several types of cancer. Recent work has revealed an intimate cross-regulation between Tra2fl and t...Increased expression levels of the RNA splicing regulator Transformer2fl (abbreviated Tra2fl) have been reported in several types of cancer. Recent work has revealed an intimate cross-regulation between Tra2fl and the highly similar Tra2a protein in human breast cancer cells, though these two proteins are encoded by separate genes created by a gene duplication that occurred over 500 million years ago. This cross-regulation involves splicing control of a special class of exons, called poison exons. Down-regulation of Tra2fl reduces splicing inclu- sion of a poison exon in the mRNA encoding Tra2a, thereby up-regulating Tra2a protein expression. This buffers any splicing changes that might be caused by individual depletion of Tra2fl alone. Discovery of this cross-regulation pathway, and its by-pass by joint deple- tion of both human Tra2 proteins, revealed Tra2 proteins are essential for breast cancer cell viability, and led to the identification of important targets for splicing control. These exons include a critical exon within the checkpoint kinase 1 (CHK1) gene that plays a crucial function in the protection of cancer cells from replication stress. Breast cancer cells depleted for Tra2 proteins have reduced CHK1 protein levels and accumulate DNA damage. These data suggest Tra2 proteins and/or their splicing targets as possible cancer drug targets.展开更多
Recently an article published in Molecular Cell reveals the mechanism of a nuclear N6-methyladenosine(m^6A)reader,the YTH domain-containing protein 1(YTHDC1),in regulating pre-m RNA splicing[1].Meanwhile,two addit...Recently an article published in Molecular Cell reveals the mechanism of a nuclear N6-methyladenosine(m^6A)reader,the YTH domain-containing protein 1(YTHDC1),in regulating pre-m RNA splicing[1].Meanwhile,two additional articles published in Nature and Nature Chemical Biology report the展开更多
Pentatricopeptide repeat(PPR) proteins function in post-transcriptional regulation of organellar gene expression. Although several PPR proteins are known to function in chloroplast development in rice(Oryza sativa), t...Pentatricopeptide repeat(PPR) proteins function in post-transcriptional regulation of organellar gene expression. Although several PPR proteins are known to function in chloroplast development in rice(Oryza sativa), the detailed molecular functions of many PPR proteins remain unclear.Here, we characterized a rice young leaf white stripe(ylws) mutant, which has defective chloroplast development during early seedling growth.Map-based cloning revealed that YLWS encodes a novel P-type chloroplast-targeted PPR protein with 11 PPR motifs. Further expression analyses showed that many nuclear-and plastid-encoded genes in the ylws mutant were significantly changed at the RNA and protein levels. The ylws mutant was impaired in chloroplast ribosome biogenesis and chloroplast development under low-temperature conditions. The ylws mutation causes defects in the splicing of atpF, ndhA, rpl2,and rps12, and editing of ndhA, ndhB, and rps14transcripts. YLWS directly binds to specific sites in the atpF, ndhA, and rpl2 pre-mRNAs. Our results suggest that YLWS participates in chloroplast RNA group II intron splicing and plays an important role in chloroplast development during early leaf development.展开更多
基金supported by the Medical Research Project of Jiangsu Commission of Health(Grant No.M2022015).
文摘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.
基金supported by grants from the National Key R&D Program of China (2021YFF1000200)National Natural Science Foundation of China (31901513)+6 种基金the “JBGS” Project of Seed Industry Revitalization in Jiangsu Province (JBGS [2021]008)Jiangsu Province Agriculture Independent Innovation Fund Project (CX(19)1002)the Fundamental Research Funds for the Central Universities (KJQN202005)the China Postdoctoral Science Foundation (2019M661864)also supported by the Key Laboratory of Biology, Genetics, and Breeding of Japonica Rice in Mid-lower Yangtze River, Ministry of Agriculture, Chinathe Jiangsu Collaborative Innovation Center for Modern Crop ProductionNational Observation and Research Station of Rice Germplasm Resources, Nanjing, Jiangsu。
文摘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.
基金supported by the Natural Science Foundation of Hebei Province (C2021208014)the Key R&D Program of Hebei Province (22326312D, 21326332D)。
文摘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.
基金This work was supported by the National Natural Science Foundation of China(Nos.81871878,31371299)the Shanghai Municipal Natural Science Fund(No.20ZR1406500)the Innovation Research Team of High-level Local Universities in Shanghai.
文摘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.
文摘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.
基金This work was supported by the Natural Science Foundation of Zhejiang province(LR20C13002)the special support plan for high level talents in Zhejiang Province(2019R52032)Agricultural Sciences and Technologies Innovation Program of the Chinese Academy of Agricultural Sciences.
文摘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.
基金This work was supported by the National Natural Science Foundation of China(grants 31991190,31730052,31525015,31861143042,31561130153,31671444,31871352)the National Key R&D Program of China(2017YFA0503501,2019YFA0508401,and 2017YFA0102900)。
文摘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.
基金This work was supported by grants from the National Natural Science Foundation of China(31901427)the National Transgenic Science and Technology Program(2019ZX08010-003)+1 种基金the Agricultural Science and Technology Innovation Program of CAAS(CAAS-ZDXT2018001)the Young Talent of CAAS to Yulong Ren.
文摘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.
文摘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.
基金This work was supported by a research grant from Prostate Cancer Canada#673 to MP.
文摘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.
基金supported by the National Natural Science Foundation of China(31830045,32025005,32100429)。
文摘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.
文摘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.
基金Chongqing Science Fund for Distinguished Young Scholars(No.CSTB2022NSCQJQX0032)Chongqing University Innovation Research Group Project(No.CXQT21011)+2 种基金Chongqing Medical University Youth Innovation in Future Medicine(No.W0156)the National Natural Science Foundation of China(No.82200123)Natural Science Foundation of Chongqing,China,(No.CSTB2023NSCQ-MSX0280).
文摘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.
基金supported by the National Natural Science Foundation of China(Nos.31620103903 and 31621001)partially by the 111 projectsupported by the Peking-Tsinghua Joint Center for Life Sciences
文摘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.
基金supported by the grants from the National Natural Science Foundation of China(31600117)the Natural Science Basic Research Program of Shaanxi,China(2020JM-165)。
文摘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.
文摘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.
文摘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.
文摘Increased expression levels of the RNA splicing regulator Transformer2fl (abbreviated Tra2fl) have been reported in several types of cancer. Recent work has revealed an intimate cross-regulation between Tra2fl and the highly similar Tra2a protein in human breast cancer cells, though these two proteins are encoded by separate genes created by a gene duplication that occurred over 500 million years ago. This cross-regulation involves splicing control of a special class of exons, called poison exons. Down-regulation of Tra2fl reduces splicing inclu- sion of a poison exon in the mRNA encoding Tra2a, thereby up-regulating Tra2a protein expression. This buffers any splicing changes that might be caused by individual depletion of Tra2fl alone. Discovery of this cross-regulation pathway, and its by-pass by joint deple- tion of both human Tra2 proteins, revealed Tra2 proteins are essential for breast cancer cell viability, and led to the identification of important targets for splicing control. These exons include a critical exon within the checkpoint kinase 1 (CHK1) gene that plays a crucial function in the protection of cancer cells from replication stress. Breast cancer cells depleted for Tra2 proteins have reduced CHK1 protein levels and accumulate DNA damage. These data suggest Tra2 proteins and/or their splicing targets as possible cancer drug targets.
基金supported by the National Basic Research Program of China (973 ProgramGrant No.2014CB964900)the National Natural Science Foundation of China (Grant Nos.21432002,21372022,and 21210003)
文摘Recently an article published in Molecular Cell reveals the mechanism of a nuclear N6-methyladenosine(m^6A)reader,the YTH domain-containing protein 1(YTHDC1),in regulating pre-m RNA splicing[1].Meanwhile,two additional articles published in Nature and Nature Chemical Biology report the
基金supported by the Key Laboratory of Biology, GeneticsBreeding of Japonica Rice in the Mid-lower Yangtze River, Ministry of Agriculture, China+5 种基金Jiangsu Plant Gene Engineering Research CenterJiangsu Collaborative Innovation Center for Modern Crop ProductionThis research was also supported by grants from the National Natural Science Foundation (92035301)Jiangsu Science and Technology Development Program (BE2021360)Jiangsu Agricultural Science and Technology Innovation Fund Project (SCX (19)1079)the Fundamental Research Funds for the Central Universities (JCQY201902)。
文摘Pentatricopeptide repeat(PPR) proteins function in post-transcriptional regulation of organellar gene expression. Although several PPR proteins are known to function in chloroplast development in rice(Oryza sativa), the detailed molecular functions of many PPR proteins remain unclear.Here, we characterized a rice young leaf white stripe(ylws) mutant, which has defective chloroplast development during early seedling growth.Map-based cloning revealed that YLWS encodes a novel P-type chloroplast-targeted PPR protein with 11 PPR motifs. Further expression analyses showed that many nuclear-and plastid-encoded genes in the ylws mutant were significantly changed at the RNA and protein levels. The ylws mutant was impaired in chloroplast ribosome biogenesis and chloroplast development under low-temperature conditions. The ylws mutation causes defects in the splicing of atpF, ndhA, rpl2,and rps12, and editing of ndhA, ndhB, and rps14transcripts. YLWS directly binds to specific sites in the atpF, ndhA, and rpl2 pre-mRNAs. Our results suggest that YLWS participates in chloroplast RNA group II intron splicing and plays an important role in chloroplast development during early leaf development.