Germinal centers(GCs)are essential for the establishment of long-lasting antibody responses.GC B cells rely on post-transcriptional RNA mechanisms to translate activation-associated transcriptional programs into funct...Germinal centers(GCs)are essential for the establishment of long-lasting antibody responses.GC B cells rely on post-transcriptional RNA mechanisms to translate activation-associated transcriptional programs into functional changes in the cell proteome.However,the critical proteins driving these key mechanisms are still unknown.Here,we show that the RNA binding proteins TIA1 and TIAL1 are required for the generation of long-lasting GC responses.TIA1-and TIAL1-deficient GC B cells fail to undergo antigen-mediated positive selection,expansion and differentiation into B-cell clones producing high-affinity antibodies.Mechanistically,TIA1 and TIAL1 control the transcriptional identity of dark-and light-zone GC B cells and enable timely expression of the prosurvival molecule MCL1.Thus,we demonstrate here that TIA1 and TIAL1 are key players in the post-transcriptional program that selects high-affinity antigen-specific GC B cells.展开更多
Targeted protein degradation(TPD)holds great promise for biological inquiry and therapeutic development.However,it still remains elusive to destruct DNA/RNA binding proteins(DBPs/RBPs)previously deemed undruggable.Her...Targeted protein degradation(TPD)holds great promise for biological inquiry and therapeutic development.However,it still remains elusive to destruct DNA/RNA binding proteins(DBPs/RBPs)previously deemed undruggable.Herein,we report ligandassisted covalent hydrophobic tagging(LACHT)as a modular strategy for TPD of these difficult-totarget proteins.Guided by a noncovalent protein ligand,LACHT leverages a reactive N-acyl-N-alkyl sulfonamide group to covalently label the protein target with a hydrophobic adamantane,which further engages the cellular quality control mechanism to induce proteolytic degradation.Using a smallmolecule ligand,we demonstrated that LACHT allowed TPD of a DBP,bromodomain-containing protein 4,in human leukemia cells with high efficiency.Mechanistic studies revealed that LACHT-mediated TPD dependent on ligand-directed irreversible tagging and the covalently labeled proteins underwent polyubiquitination before removal through both the proteasome and the lysosome.Furthermore,when an RNA ligand was employed,we showed that LACHT also enabled TPD of an RBP,Lin28a,leading to upregulation of its downstream let-7 miRNA.This study thus provides a generalizable platform to expand the TPD toolbox for biomedical applications.展开更多
BACKGROUND Colorectal cancer(CRC)causes many deaths worldwide.Synaptotagmin binding cytoplasmic RNA interacting protein(SYNCRIP)is an RNA-binding protein that plays an important role in multiple cancers by epigenetica...BACKGROUND Colorectal cancer(CRC)causes many deaths worldwide.Synaptotagmin binding cytoplasmic RNA interacting protein(SYNCRIP)is an RNA-binding protein that plays an important role in multiple cancers by epigenetically targeting some genes.Our study will examine the expression,potential effect,biological function and clinical value of SYNCRIP in CRC.AIM To examine the expression,potential effect,biological function and clinical value METHODS The expression of SYNCRIP was examined by immunohistochemistry arrays and high-throughput data.The effect of SYNCRIP gene in CRC cell growth was evaluated by CRISPR-Cas9 technology.The target genes of SYNCRIP were calculated using various algorithms,and the molecular mechanism of SYNCRIP in CRC was explored by mutation analysis and pathway analysis.The clinical value of SYNCRIP in prognosis and radiotherapy was revealed via evidence-based medicine methods.RESULTS The protein and mRNA levels of SYNCRIP were both highly expressed in CRC samples compared to nontumorous tissue based on 330 immunohistochemistry arrays and 3640 CRC samples.Cells grew more slowly in eleven CRC cell lines after knocking out the SYNCRIP gene.SYNCRIP could epigenetically target genes to promote the occurrence and development of CRC by boosting the cell cycle and affecting the tumor microenvironment.In addition,CRC patients with high SYNCRIP expression are more sensitive to radiotherapy.CONCLUSION SYNCRIP is upregulated in CRC,and highly expressed SYNCRIP can accelerate CRC cell division by exerting its epigenetic regulatory effects.In addition,SYNCRIP is expected to become a potential biomarker to predict the effect of radiotherapy.展开更多
Controlled gene regulation during gamete development is vital for maintaining reproductive potential. During the complex process of mammalian spermatogenesis, male germ cells experience extended periods of the inactiv...Controlled gene regulation during gamete development is vital for maintaining reproductive potential. During the complex process of mammalian spermatogenesis, male germ cells experience extended periods of the inactive transcription despite heavy translational requirements for continued growth and differentiation. Hence, spermatogenesis is highly reliant on mechanisms of posttranscriptional regulation of gene expression, facilitated by RNA binding proteins （RBPs）, which remain abundantly expressed throughout this process. One such group of proteins is the Musashi family, previously identified as critical regulators of testis germ cell development and meiosis in Drosophila, and also shown to be vital to sperm development and reproductive potential in the mouse. This review describes the role and function of RBPs our recent knowledge of the Musashi proteins in spermatogenesis. within the scope of male germ cell development, focusing on The functional mechanisms utilized by RBPs within the cell are outlined in depth, and the significance of sub-cellular localization and stage-specific expression in relation to the mode and impact of posttranscriptional regulation is also highlighted. We emphasize the historical role of the Musashi family of RBPs in stem cell function and cell fate determination, as originally characterized in Drosophila and Xenopus, and conclude with our current understanding of the differential roles and functions of the mammalian Musashi proteins, Musashi-1 and Musashi-2, with a primary focus on our findings in spermatogenesis. This review highlights both the essential contribution of RBPs to posttranscriptional regulation and the importance of the Musashi family as master regulators of male gamete development.展开更多
Thousands of long-distance mobile mRNAs were identified from different grafting systems,based on high-throughput sequencing technology.Moreover,the long-distance delivery of RNAs was proved to involve multiple mechani...Thousands of long-distance mobile mRNAs were identified from different grafting systems,based on high-throughput sequencing technology.Moreover,the long-distance delivery of RNAs was proved to involve multiple mechanisms.Here,we analyzed the homology,motif,and tRNA-like structure(TLS)of long-distance mobile mRNAs identified by RNA-seq as well as the RNA-binding protein(RBP)in nine grafting combinations including Arabidopsis thaliana,Vitis vinifera,Cucumis sativus,Citrullus lanatus,Nicotiana benthamiana,Malus domestica,Pyrus spp.,Glycine max and Phaseolus vulgaris.Although several mRNAs were found to be shared in herbaceous,woody,and related species,the vast majority of long-distance mobile mRNAs were species-specific.Four non-specific movement-related motifs were identified,while the TLS was not necessary for mRNA long distance mobility.In addition,we found that RBPs were conserved among herbaceous and woody plants as well as related species.This paper reports a further in-depth analysis of the endogenous mechanisms by which the species-specific transportable m RNAs were selected by bioinformatics,in order to provide insights for future research on long-distance mobile mRNAs.展开更多
Background:RNA binding proteins(RBPs)play essential roles in the regulation of RNA metabolism.Recent studies have disclosed that RBPs achieve their functions via binding to their targets in a position-dependent patter...Background:RNA binding proteins(RBPs)play essential roles in the regulation of RNA metabolism.Recent studies have disclosed that RBPs achieve their functions via binding to their targets in a position-dependent pattern on RNAs.However,few studies have systematially addressed the associations between the RBP's functions and their positional binding preferences.Methods:Here,we present large-scale analyses on the functional targets of human RBPs by integrating the enhanced cross-linking and immunoprecipitation followed by sequencing(eCLIP-seq)datasets and the shRNA knockdown followed by RNA-seq datasets that are deposited in the integrated ENCyclopedia of DNA Elements in the human genome(ENCODE)data portal.Results:We found that(1)binding to the translation termination site and the 3'untranslated region is important to most human RBP's in the RNA decay regulation;(2)RBPs’binding and regulation follow a cell-ty pe specific pattern.Conclusions:These analysis results show the strong relationship between the binding position and the functions of RBPs,which provides novel insights into the RBPs'regulation mechanisms.展开更多
Despite the conventional definition of RNA binding proteins(RBPs)as controlling the metabolism of their bound RNAs,more and more RBPs are found to function via distinct ways in complex biological processes.With the re...Despite the conventional definition of RNA binding proteins(RBPs)as controlling the metabolism of their bound RNAs,more and more RBPs are found to function via distinct ways in complex biological processes.With the recent discovery of transcriptional regulation activity of some RBPs,a hypothesis that RBPs could be multilayered regulators orchestrating gene expression has emerged.Hematopoiesis is a stepwise process that needs to be fine-tuned to keep the subtle balance between hematopoietic stem cell(HSC)stemness maintenance and downstream lineage commitment.Although the classic RBPs account for the posttranscriptional regulation in hematopoiesis,the importance and multiple regulatory capacities of RBPs have not been wellcharacterized.In this review,we summarize the recent findings of large-scale screening of novel RBPs and their novel transcriptional regulation potentials.In hematopoietic system,this kind of multifaced regulators account for nearly a half of functional RBPs.Therefore,further studies on identifying this new kind of multifaced RBPs and clarifying their regulatory mechanisms would help us better understand the precise and complex regulatory networks of gene expression in hematopoiesis.展开更多
Late-stage ovarian cancer(OC)has a poor prognosis and a high metastasis rate,but the underlying molecular mechanism is unclear.RNA binding proteins(RBPs)play important roles in posttranscriptional regulation in the co...Late-stage ovarian cancer(OC)has a poor prognosis and a high metastasis rate,but the underlying molecular mechanism is unclear.RNA binding proteins(RBPs)play important roles in posttranscriptional regulation in the contexts of neoplasia and tumor metastasis.In this study,we explored the molecular functions of a canonical RBP,Transformer 2βhomolog(TRA2B),in cancer cells.TRA2B knockdown in HeLa cells and subsequent wholetranscriptome RNA sequencing(RNA-seq)analysis revealed the TRA2B-regulated alternative splicing(AS)profile.We disrupted TRA2B expression in epithelial OC cells and performed a series of experiments to confirm the resulting effects on OC cell proliferation,apoptosis and invasion.TRA2B-regulated AS was tightly associated with the mitotic cell cycle,apoptosis and several cancer pathways.Moreover,the expression of hundreds of genes was regulated by TRA2B,and these genes were enriched in the functions of cell proliferation,cell adhesion and angiogenesis,which are related to the malignant phenotype of OC.By integrating the alternatively spliced and differentially expressed genes,we found that AS events and gene expression were regulated independently.We then explored and validated the oncogenic functions of TRA2B by knocking down its expression in OC cells.The high TRA2B expression was associated with poor prognosis in patients with OC.In ovarian tissue,TRA2B expression showed a gradual increasing trend with increasing malignancy.We demonstrated the important roles of TRA2B in ovarian neoplasia and aggressive OC behaviors and identified the underlying molecular mechanisms,facilitating the targeted treatment of OC.展开更多
BACKGROUND： High incidence of stroke at interchange period of autumn and winter was demonstrated by epidemiological survey, and the specific causes should be further investigated. OBJECTIVE： To investigate the influ...BACKGROUND： High incidence of stroke at interchange period of autumn and winter was demonstrated by epidemiological survey, and the specific causes should be further investigated. OBJECTIVE： To investigate the influence of artificial cold exposure on the incidence of stroke in renovascular hypertensive rats （RHR）, and analyze the association with blood pressure and cold-inducible RNA binding protein （CIRP） mRNA expression in brain tissue. DESIGN： A completely randomized grouping design, a randomized control animal trial. SETTINGS： Lab of Neurology, the First Affiliated Hospital of Sun Yat-sen University; Department of Chemistry, Open laboratory of Chemical Biology, Institute of Molecular Technology for Drug Discovery and Synthesis, University of Hong Kong. MATERIALS： Male SD rats （n=460）, weighing 80 - 100 g were obtained from Guangdong Province Health Animal Unit. A modified RXZ-300A intelligent artificial climate cabinet （Ningbo Jiangnan Instrument Co. ,Ltd., China）. METHODS： The experiment were processed in the Lab of Neurology, the First Affiliated Hospital of Sun Yat-sen University and the Open Laboratory of Chemical Biology, Institute of Molecular Technology for Drug Discovery and Synthesis, University of Hong Kong from October 2004 to November 2005. Rats （n = 400） were operated to establish 2-kidney 2-clip RHR model as described previously. The sham-operated rats （n =60） served as normotensive controls. Eight weeks later, 300 of RHR were randomly selected according to their systolic blood pressure （SBP） and divided into 3 sub-groups （n =100 per group）： mild hypertensive group （SBP of 160 - 200 mm Hg）, moderate hypertensive group （SBP of 200 - 220 mm Hg） and severe hypertensive group （SBP 〉 220 mm Hg）. Each group was further divided into two groups （n =50） under ACE and non-ACE. Normal sham-operated SD rats （n =60）, SBP 〈 140 mm Hg, were randomly divided into two groups： Sham-operated control group （n =30） under ACE and non-ACE. To establish the ACE and non-ACE treatment, rats were housed individually in artificial climate cabinet, and ACE was designed as three cycles of 12-hour light of 22℃ （7 ： 00 - 19 ： 00） and 12-hour dark of 4℃（19 ： 00 - 7 ： 00）. The non-ACE group was kept at 22℃ throughout the experiment. MAIN OUTCOME MEASURES： Blood Pressure changes were measured and stroke symptom were observed; Expression of the CIRP were examined by reverse transcription-polymerase chain reaction. RESULTS： Finally 360 rats were involved in the analysis of results. ①Incidence of stroke： The incidence of stroke in 2k2c RHR was significantly higher after a three-day intermittent （12-hour） ACE （29.3%） as compared with that in non-ACE （17.3%） （P 〈 0.05）. Furthermore, the severe hypertensive 2k2c RHR （BP 〉 220 mm Hg） was found to have much higher incidence of stroke （66%, 33/50） than the mild （8%, 4/50） and moderate （18%） hypertensive 2k2c RHR. ②CIRP mRNA in brain tissue： ACE treatment stimulated the mRNA expression of CIRP in non-stroke 2k2c RHR but not in stroke 2k2c RHR （P 〈 0.05）. CONCLUSION： High blood pressure and low expression of CIRP are associated with ACE induced stroke.展开更多
Objective: This study aimed to construct a bladder cancer prognostic model using bioinformatics to predict the survival of bladder cancer patients. Methods: RNA sequences and corresponding clinical data were downloade...Objective: This study aimed to construct a bladder cancer prognostic model using bioinformatics to predict the survival of bladder cancer patients. Methods: RNA sequences and corresponding clinical data were downloaded from The Cancer Genome Atlas (TCGA) database, and the differentially expressed RNA-binding proteins (RBPs) were screened for analysis using the limma software package. Then, GO enrichment analysis and KEGG pathway analysis were performed on these differentially expressed RNA-binding proteins, and a PPI network was constructed. Finally, a risk model was constructed based on the screened central RBP, and a Kaplan-Meier survival curve was drawn to evaluate the prognostic value of central RBP and predict the prognosis of bladder Cancer(BLCA) patients with this model. Finally, the human protein atlas (HPA) online database (http://www.proteinatlas.org/) was used to further detect the differential expression of central hub RBP at the protein level between tumor tissue and normal tissue. Results: The bladder cancer prognostic model constructed with these six central RBPs had good sensitivity and specificity in predicting the prognosis of bladder cancer patients. Conclusion: This study explored the genes and regulatory networks of bladder cancer prognosis-related RNA-binding protein and bladder cancer, and constructed a bladder cancer prognosis model, which provides a theoretical basis for the development of new bladder cancer prognosis biomarkers in the future.展开更多
Neurogenesis is a tightly regulated process in time and space both in the developing embryo and in adult neurogenic niches.A drastic change in the transcriptome and proteome of radial glial cells or neural stem cells ...Neurogenesis is a tightly regulated process in time and space both in the developing embryo and in adult neurogenic niches.A drastic change in the transcriptome and proteome of radial glial cells or neural stem cells towards the neuronal state is achieved due to sophisticated mechanisms of epigenetic,transcriptional,and post-transcriptional regulation.Understanding these neurogenic mechanisms is of major importance,not only for shedding light on very complex and crucial developmental processes,but also for the identification of putative reprogramming factors,that harbor hierarchically central regulatory roles in the course of neurogenesis and bare thus the capacity to drive direct reprogramming towards the neuronal fate.The major transcriptional programs that orchestrate the neurogenic process have been the focus of research for many years and key neurogenic transcription factors,as well as repressor complexes,have been identified and employed in direct reprogramming protocols to convert non-neuronal cells,into functional neurons.The post-transcriptional regulation of gene expression during nervous system development has emerged as another important and intricate regulatory layer,strongly contributing to the complexity of the mechanisms controlling neurogenesis and neuronal function.In particular,recent advances are highlighting the importance of specific RNA binding proteins that control major steps of mRNA life cycle during neurogenesis,such as alternative splicing,polyadenylation,stability,and translation.Apart from the RNA binding proteins,microRNAs,a class of small non-coding RNAs that block the translation of their target mRNAs,have also been shown to play crucial roles in all the stages of the neurogenic process,from neural stem/progenitor cell proliferation,neuronal differentiation and migration,to functional maturation.Here,we provide an overview of the most prominent post-transcriptional mechanisms mediated by RNA binding proteins and microRNAs during the neurogenic process,giving particular emphasis on the interplay of specific RNA binding proteins with neurogenic microRNAs.Taking under consideration that the molecular mechanisms of neurogenesis exert high similarity to the ones driving direct neuronal reprogramming,we also discuss the current advances in in vitro and in vivo direct neuronal reprogramming approaches that have employed microRNAs or RNA binding proteins as reprogramming factors,highlighting the so far known mechanisms of their reprogramming action.展开更多
The messenger RNA 3'-untranslated region(3'UTR)plays an important role in regulation of gene expres-sion on the posttranscriptional level. The 3'UTR con-trols gene expression via orchestrated interactionbe...The messenger RNA 3'-untranslated region(3'UTR)plays an important role in regulation of gene expres-sion on the posttranscriptional level. The 3'UTR con-trols gene expression via orchestrated interactionbetween the structural components of mRNAs(cis-ele-ment) and the specific trans-acting factors(RNA bind-ing proteins and non-coding RNAs). The crosstalk ofthese factors is based on the binding sequences and/or direct protein-protein interaction, or just functionalinteraction. Much new evidence that has accumulatedsupports the idea that several RNA binding factors canbind to common mRNA targets: to the non-overlappingbinding sites or to common sites in a competitive fash-ion. Various factors capable of binding to the sameRNA can cooperate or be antagonistic in their actions.The outcome of the collective function of all factorsbound to the same mRNA 3'UTR depends on manycircumstances, such as their expression levels, affinity to the binding sites, and localization in the cell, which can be controlled by various physiological conditions. Moreover, the functional and/or physical interactions of the factors binding to 3'UTR can change the character of their actions. These interactions vary during the cell cycle and in response to changing physiological condi-tions. Abnormal functioning of the factors can lead to disease. In this review we will discuss how alterations of these factors or their interaction can affect cancer development and promote or enhance the malignant phenotype of cancer cells. Understanding these altera-tions and their impact on 3'UTR-directed posttran-scriptional gene regulation will uncover promising new targets for therapeutic intervention and diagnostics. We will also discuss emerging new tools in cancer di-agnostics and therapy based on 3'UTR binding factors and approaches to improve them.展开更多
Protein binding is essential to the transport,decay and regulation of almost all RNA molecules.However,the structural preference of protein binding on RNAs and their cellular functions and dynamics upon changing envir...Protein binding is essential to the transport,decay and regulation of almost all RNA molecules.However,the structural preference of protein binding on RNAs and their cellular functions and dynamics upon changing environmental conditions are poorly understood.Here,we integrated various high-throughput data and introduced a computational framework to describe the global interactions between RNA binding proteins(RBPs)and structured RNAs in yeast at single-nucleotide resolution.We found that on average,in terms of percent total lengths,~15%of mRNA untranslated regions(UTRs),~37%of canonical non-coding RNAs(ncRNAs)and^11%of long ncRNAs(lncRNAs)are bound by proteins.The RBP binding sites,in general,tend to occur at single-stranded loops,with evolutionarily conserved signatures,and often facilitate a specific RNA structure conformation in vivo.We found that four nucleotide modifications of tRNA are significantly associated with RBP binding.We also identified various structural motifs bound by RBPs in the UTRs of mRNAs,associated with localization,degradation and stress responses.Moreover,we identified>200 novel lncRNAs bound by RBPs,and about half of them contain conserved secondary structures.We present the first ensemble pattern of RBP binding sites in the structured non-coding regions of a eukaryotic genome,emphasizing their structural context and cellular functions.展开更多
The secondary structures of hepatitis C virus （HCV） RNA and the cellular proteins that bind to them are important for modulating both translation and RNA replication. However, the sets of RNA-binding proteins involv...The secondary structures of hepatitis C virus （HCV） RNA and the cellular proteins that bind to them are important for modulating both translation and RNA replication. However, the sets of RNA-binding proteins involved in the regulation of HCV translation, replication and encapsidation remain unknown. Here, we identified RNA binding motif protein 24 （RBM24） as a host factor par- ticipated in HCV translation and replication. Knockdown of RBM24 reduced HCV propagation in Huh7.5.1 cells. An enhanced translation and delayed RNA synthesis during the early phase of infection was observed in RBM24 silencing cells. However, both overexpression of RBM24 and recombinant human RBM24 protein sup- pressed HCV IRES-mediated translation. Further analy- sis revealed that the assembly of the 80S ribosome on the HCV IRES was interrupted by RBM24 protein through binding to the 5＇-UTR. RBM24 could also inter- act with HCV Core and enhance the interaction of Core and 5＇-UTR, which suppresses the expression of HCV. Moreover, RBM24 enhanced the interaction between the 5＇- and 3＇-UTRs in the HCV genome, which probably explained its requirement in HCV genome replication. Therefore, RBM24 is a novel host factor involved in HCV replication and may function at the switch from trans- lation to replication.展开更多
Background and Aims:The survival rate of patients with hepatocellular carcinoma is variable.The abnormal expression of RNA-binding proteins(RBPs)is closely related to the occurrence and development of malignant tumors...Background and Aims:The survival rate of patients with hepatocellular carcinoma is variable.The abnormal expression of RNA-binding proteins(RBPs)is closely related to the occurrence and development of malignant tumors.The primary aim of this study was to identify RBPs related to the prognosis of liver cancer and to construct a prognostic model of liver cancer.Methods:We downloaded the hepatocellular carcinoma gene sequencing data from The Cancer Genome Atlas(cancergenome.nih.gov/)database,constructed a protein-protein interaction network,and used Cytoscape to realize the visualization.From among 325 abnormally expressed genes for RBPs,9(XPO5,enhancer of zeste 2 polycomb repressive complex 2 subunit[EZH2],CSTF2,BRCA1,RRP12,MRPL54,EIF2AK4,PPARGC1A,and SEPSECS)were selected for construction of the prognostic model.Then,we further verified the results through the Gene Expression Omnibus(www.ncbi.nlm.nih.gov/geo/)database and in vitro experiments.Results:A prognostic model was constructed,which determined that the survival time of patients in the high-risk group was significantly shorter than that of the low-risk group(p<0.01).Univariate and multivariate Cox regression analysis suggested that the risk score was an independent prognostic factor(p<0.01).We also constructed a nomogram based on the risk score,survival time,and survival status.At the same time,we verified the high expression and cancer-promoting effects of EZH2 in tumors.Conclusions:Survival,receiver operating characteristic curve and independent prognostic analyses demonstrated that we constructed a good prognostic model,which might be useful for estimating the survival of patients with hepatocellular carcinoma.展开更多
Although initially argued to be a feature of immature neurons with incomplete polarization, there is clear evidence that neurons in the peripheral nervous system retain the capacity for intra-axonal protein synthe- si...Although initially argued to be a feature of immature neurons with incomplete polarization, there is clear evidence that neurons in the peripheral nervous system retain the capacity for intra-axonal protein synthe- sis well into adulthood. This localized protein synthesis has been shown to contribute to injury signaling and axon regeneration in peripheral nerves. Recent works point to potential for protein synthesis in axons of the vertebrate central nervous system, mRNAs and protein synthesis machinery have now been docu- mented in lamprey, mouse, and rat spinal cord axons. Intra-axonal protein synthesis appears to be activated in adult vertebrate spinal cord axons when they are regeneration-competent. Rat spinal cord axons regen- erating into a peripheral nerve graft contain mRNAs and markers of activated translational machinery. Indeed, levels of some growth-associated mRNAs in these spinal cord axons are comparable to the regen- erating sciatic nerve. Markers of active translation tend to decrease when these axons stop growing, but can be reactivated by a second axotomy. These emerging observations raise the possibility that mRNA transport into and translation within axons could be targeted to facilitate regeneration in both the peripheral and central nervous systems.展开更多
Background Sam68 plays an important role as a multiple functional RNA binding nuclear protein in cell cycle progress, RNA usage, signal transduction, and tyrosine phosphorylation by Src during mitosis. However, its pr...Background Sam68 plays an important role as a multiple functional RNA binding nuclear protein in cell cycle progress, RNA usage, signal transduction, and tyrosine phosphorylation by Src during mitosis. However, its precise impact on these essential cellular functions remains unclear. The purpose of this study is to further elucidate Sam68 functions in RNA metabolism, signal transduction regulation of cell growth and cell proliferation in DT40 cell line. Methods By using gene targeting method, we isolated a mutation form of Sam68 in DT40 cells and described its effect on cell growth process and signal transduction. Southern, Northern, and Western blot, phosphorylation and flow-cytometric analyses were performed to investigate the Sam68 functions. Results A slower growth rate （2.1 hours growth elongation） and longer S phase （1.7 hours elongation） was observed in the Sam68 mutant cells. Serum depletion resulted in increased amounts of dead cells, and expansion of S phase in mutant cells. Upon B cell cross-linking, the maximal level of tyrosine phosphorylation on BLNK was observed to be significantly lower in mutant cells.Conclusions The proline rich domain of Sam68 is involved in cell growth control by modulating the function of mRNAs in S phase or earlier and the functions as an adaptor molecule in B cell signal transduction pathways.展开更多
The RNA‐binding glycine‐rich protein（RB‐GRP）family is characterized by the presence of a glycine‐rich domain arranged in（Gly）n‐X repeats and an RNA‐recognition motif（RRM）. RB‐GRPs participate in varied ph...The RNA‐binding glycine‐rich protein（RB‐GRP）family is characterized by the presence of a glycine‐rich domain arranged in（Gly）n‐X repeats and an RNA‐recognition motif（RRM）. RB‐GRPs participate in varied physiological and biochemical processes especially in the stress response of plants. In this study, a total of 23 RB‐GRPs distributed on 10 chromosomes were identified in maize（Zea mays L.）, and they were divided into four subgroups according to their conserved domain architecture. Five pairs of paralogs were identified,while none of them was located on the same chromosomal region, suggesting that segmental duplication is predominant in the duplication events of the RB‐GRPs in maize. Comparative analysis of RB‐GRPs in maize, Arabidopsis（Arabidopsis thaliana L.）, rice（Oryza sativa L.）, and wheat（Triticum aestivum）revealed that two exclusive subgroups were only identified in maize. Expression of eight ZmRB‐GRPs was significantly regulated by at least two kinds of stresses. In addition, cis‐elements predicted in the promoter regions of the ZmRB‐GRPs also indicated that these ZmRB‐GRPs would be involved in stress response of maize. The preliminary genome‐wide analysis of the RB‐GRPs in maize would provide useful information for further study on the function of the ZmRB‐GRPs.展开更多
Background:Long non-coding RNA colon cancer-associated transcript 1(CCAT1)is involved in transforming multiple cancers into malignant cancer types.Previous studies underlining the mechanisms of the functions of CCAT1 ...Background:Long non-coding RNA colon cancer-associated transcript 1(CCAT1)is involved in transforming multiple cancers into malignant cancer types.Previous studies underlining the mechanisms of the functions of CCAT1 primarily focused on its decoy for miRNAs(micro RNAs).However,the regulatory mechanism of CCAT1-protein interaction associated with tumor metastasis is still largely unknown.The present study aimed to identify proteome-wide CCAT1 partners and explored the CCAT1-protein interaction mediated tumor metastasis.Methods:CCAT1-proteins complexes were purified and identified using RNA antisense purification coupled with the mass spectrometry(RAP-MS)method.The database for annotation,visualization,and integrated discovery and database for eukaryotic RNA binding proteins(EuRBPDB)websites were used to bioinformatic analyzing CCAT1 binding proteins.RNA pull-down and RNA immunoprecipitation were used to validate CCAT1-Vimentin interaction.Transwell assay was used to evaluate the migration and invasion abilities of HeLa cells.Results:RAP-MS method worked well by culturing cells with nucleoside analog 4-thiouridine,and cross-linking was performed using 365 nm wavelength ultraviolet.There were 631 proteins identified,out of which about 60%were RNA binding proteins recorded by the EuRBPDB database.Vimentin was one of the CCAT1 binding proteins and participated in the tumor metastasis pathway.Knocked down vimetin(VIM)and rescued the downregulation by overexpressing CCAT1 demonstrated that CCAT1 could enhance tumor migration and invasion abilities by stabilizing Vimentin protein.Conclusion:CCAT1 may bind with and stabilize Vimentin protein,thus enhancing cancer cell migration and invasion abilities.展开更多
Muscle formation is a coordinated process driven by extensive gene expression changes where single cells fuse together to form multinucleated muscle fibers. Newly synthesized m RNAs are then regulated by RNA binding p...Muscle formation is a coordinated process driven by extensive gene expression changes where single cells fuse together to form multinucleated muscle fibers. Newly synthesized m RNAs are then regulated by RNA binding proteins(RBPs), affecting post-transcriptional transcript metabolism. Here, we determined how large-scale gene expression changes affect the catalog of RBPs by studying proliferating and differentiated muscle cells in healthy and dystrophic conditions. Transcriptomic analysis showed that the expression of more than 7000 genes was affected during myogenesis. We identified 769 RBPs, of which 294 were muscle-specific and 49 were uniquely shared with cardiomyocytes. A subset of 32 RBPs(half of which were muscle-specific) was found to be preferentially associated with target mRNAs in either myoblasts(MBs) or myotubes(MTs). A large proportion of catalytic proteins were bound to mRNAs even though they lack classical RNA binding domains. Finally, we showed how the identification of cell-specific RBPs enabled the identification of biomarkers that can separate healthy individuals from dystrophic patients. Our data show how interactome data can shed light on new basic RNA biology as well as provide cell-specific data that can be used for diagnostic purposes.展开更多
基金We thank all personnel from the Toulouse animal facility CREFRE and from the flow cytometry,imaging,transcriptomics and bioinformatics technical platforms of INFINITy.M.D.D-M.is supported by ATIP-Avenir-Plan Cancer(C18003BS),ANR(ANR-20-CE15-0007)foundation ARSEP R19201BB,foundation ARC,La Ligue Contre Le Cancer and INSPIRE(Region Occitanie,Inserm and CHU Toulouse)M.T.is supported with a BBSRC core funding grant and a Wellcome Investigator award(200823/Z/16/Z).D.C.-S.is supported by Boehringer Ingelheim Fonds.
文摘Germinal centers(GCs)are essential for the establishment of long-lasting antibody responses.GC B cells rely on post-transcriptional RNA mechanisms to translate activation-associated transcriptional programs into functional changes in the cell proteome.However,the critical proteins driving these key mechanisms are still unknown.Here,we show that the RNA binding proteins TIA1 and TIAL1 are required for the generation of long-lasting GC responses.TIA1-and TIAL1-deficient GC B cells fail to undergo antigen-mediated positive selection,expansion and differentiation into B-cell clones producing high-affinity antibodies.Mechanistically,TIA1 and TIAL1 control the transcriptional identity of dark-and light-zone GC B cells and enable timely expression of the prosurvival molecule MCL1.Thus,we demonstrate here that TIA1 and TIAL1 are key players in the post-transcriptional program that selects high-affinity antigen-specific GC B cells.
基金supported by the Natural Science Foundation of Jiangsu Province(grant nos.BK20202004 and BE2022835)the National Natural Science Foundation of China(grant nos.22077063,22225703,22137003,21877058,and 21977043).
文摘Targeted protein degradation(TPD)holds great promise for biological inquiry and therapeutic development.However,it still remains elusive to destruct DNA/RNA binding proteins(DBPs/RBPs)previously deemed undruggable.Herein,we report ligandassisted covalent hydrophobic tagging(LACHT)as a modular strategy for TPD of these difficult-totarget proteins.Guided by a noncovalent protein ligand,LACHT leverages a reactive N-acyl-N-alkyl sulfonamide group to covalently label the protein target with a hydrophobic adamantane,which further engages the cellular quality control mechanism to induce proteolytic degradation.Using a smallmolecule ligand,we demonstrated that LACHT allowed TPD of a DBP,bromodomain-containing protein 4,in human leukemia cells with high efficiency.Mechanistic studies revealed that LACHT-mediated TPD dependent on ligand-directed irreversible tagging and the covalently labeled proteins underwent polyubiquitination before removal through both the proteasome and the lysosome.Furthermore,when an RNA ligand was employed,we showed that LACHT also enabled TPD of an RBP,Lin28a,leading to upregulation of its downstream let-7 miRNA.This study thus provides a generalizable platform to expand the TPD toolbox for biomedical applications.
基金Supported by Guangxi Zhuang Autonomous Region Health Commission Scientific Research Project,No.Z-A20220415 and No.Z20210442The First Affiliated Hospital of Guangxi Medical University Provincial and Ministerial Key Laboratory Cultivation Project:Guangxi Laboratory of Enhanced Recovery after Surgery for Gastrointestinal Cancer,No.21-220-18.
文摘BACKGROUND Colorectal cancer(CRC)causes many deaths worldwide.Synaptotagmin binding cytoplasmic RNA interacting protein(SYNCRIP)is an RNA-binding protein that plays an important role in multiple cancers by epigenetically targeting some genes.Our study will examine the expression,potential effect,biological function and clinical value of SYNCRIP in CRC.AIM To examine the expression,potential effect,biological function and clinical value METHODS The expression of SYNCRIP was examined by immunohistochemistry arrays and high-throughput data.The effect of SYNCRIP gene in CRC cell growth was evaluated by CRISPR-Cas9 technology.The target genes of SYNCRIP were calculated using various algorithms,and the molecular mechanism of SYNCRIP in CRC was explored by mutation analysis and pathway analysis.The clinical value of SYNCRIP in prognosis and radiotherapy was revealed via evidence-based medicine methods.RESULTS The protein and mRNA levels of SYNCRIP were both highly expressed in CRC samples compared to nontumorous tissue based on 330 immunohistochemistry arrays and 3640 CRC samples.Cells grew more slowly in eleven CRC cell lines after knocking out the SYNCRIP gene.SYNCRIP could epigenetically target genes to promote the occurrence and development of CRC by boosting the cell cycle and affecting the tumor microenvironment.In addition,CRC patients with high SYNCRIP expression are more sensitive to radiotherapy.CONCLUSION SYNCRIP is upregulated in CRC,and highly expressed SYNCRIP can accelerate CRC cell division by exerting its epigenetic regulatory effects.In addition,SYNCRIP is expected to become a potential biomarker to predict the effect of radiotherapy.
文摘Controlled gene regulation during gamete development is vital for maintaining reproductive potential. During the complex process of mammalian spermatogenesis, male germ cells experience extended periods of the inactive transcription despite heavy translational requirements for continued growth and differentiation. Hence, spermatogenesis is highly reliant on mechanisms of posttranscriptional regulation of gene expression, facilitated by RNA binding proteins （RBPs）, which remain abundantly expressed throughout this process. One such group of proteins is the Musashi family, previously identified as critical regulators of testis germ cell development and meiosis in Drosophila, and also shown to be vital to sperm development and reproductive potential in the mouse. This review describes the role and function of RBPs our recent knowledge of the Musashi proteins in spermatogenesis. within the scope of male germ cell development, focusing on The functional mechanisms utilized by RBPs within the cell are outlined in depth, and the significance of sub-cellular localization and stage-specific expression in relation to the mode and impact of posttranscriptional regulation is also highlighted. We emphasize the historical role of the Musashi family of RBPs in stem cell function and cell fate determination, as originally characterized in Drosophila and Xenopus, and conclude with our current understanding of the differential roles and functions of the mammalian Musashi proteins, Musashi-1 and Musashi-2, with a primary focus on our findings in spermatogenesis. This review highlights both the essential contribution of RBPs to posttranscriptional regulation and the importance of the Musashi family as master regulators of male gamete development.
基金supported by the 111 Project(Grant No.B17043)the 2115 Talent Development Program of China Agricultural University。
文摘Thousands of long-distance mobile mRNAs were identified from different grafting systems,based on high-throughput sequencing technology.Moreover,the long-distance delivery of RNAs was proved to involve multiple mechanisms.Here,we analyzed the homology,motif,and tRNA-like structure(TLS)of long-distance mobile mRNAs identified by RNA-seq as well as the RNA-binding protein(RBP)in nine grafting combinations including Arabidopsis thaliana,Vitis vinifera,Cucumis sativus,Citrullus lanatus,Nicotiana benthamiana,Malus domestica,Pyrus spp.,Glycine max and Phaseolus vulgaris.Although several mRNAs were found to be shared in herbaceous,woody,and related species,the vast majority of long-distance mobile mRNAs were species-specific.Four non-specific movement-related motifs were identified,while the TLS was not necessary for mRNA long distance mobility.In addition,we found that RBPs were conserved among herbaceous and woody plants as well as related species.This paper reports a further in-depth analysis of the endogenous mechanisms by which the species-specific transportable m RNAs were selected by bioinformatics,in order to provide insights for future research on long-distance mobile mRNAs.
基金Z.O.acknowledges the National Institute of General Medical Sciences(https://www.nigms.nih.gov/)grant R35GM124998.
文摘Background:RNA binding proteins(RBPs)play essential roles in the regulation of RNA metabolism.Recent studies have disclosed that RBPs achieve their functions via binding to their targets in a position-dependent pattern on RNAs.However,few studies have systematially addressed the associations between the RBP's functions and their positional binding preferences.Methods:Here,we present large-scale analyses on the functional targets of human RBPs by integrating the enhanced cross-linking and immunoprecipitation followed by sequencing(eCLIP-seq)datasets and the shRNA knockdown followed by RNA-seq datasets that are deposited in the integrated ENCyclopedia of DNA Elements in the human genome(ENCODE)data portal.Results:We found that(1)binding to the translation termination site and the 3'untranslated region is important to most human RBP's in the RNA decay regulation;(2)RBPs’binding and regulation follow a cell-ty pe specific pattern.Conclusions:These analysis results show the strong relationship between the binding position and the functions of RBPs,which provides novel insights into the RBPs'regulation mechanisms.
基金supported by the National Natural Science Foundation of China(81530007 and 31725013)CAMS Innovation Fund for Medical Sciences(2017-I2M-3-009 and 2017-I2M-1-015)+4 种基金CAMS Young Talents Award Program(2018RC310013)the National Key Research and Development Program of China(2016YFA0100601)the National Key Basic Research Program of China(2015CB943001)the CAMS(2017-I2M-B&R-04)Grant from Medical Epigenetics Research Center,CAMS(2017PT31035).
文摘Despite the conventional definition of RNA binding proteins(RBPs)as controlling the metabolism of their bound RNAs,more and more RBPs are found to function via distinct ways in complex biological processes.With the recent discovery of transcriptional regulation activity of some RBPs,a hypothesis that RBPs could be multilayered regulators orchestrating gene expression has emerged.Hematopoiesis is a stepwise process that needs to be fine-tuned to keep the subtle balance between hematopoietic stem cell(HSC)stemness maintenance and downstream lineage commitment.Although the classic RBPs account for the posttranscriptional regulation in hematopoiesis,the importance and multiple regulatory capacities of RBPs have not been wellcharacterized.In this review,we summarize the recent findings of large-scale screening of novel RBPs and their novel transcriptional regulation potentials.In hematopoietic system,this kind of multifaced regulators account for nearly a half of functional RBPs.Therefore,further studies on identifying this new kind of multifaced RBPs and clarifying their regulatory mechanisms would help us better understand the precise and complex regulatory networks of gene expression in hematopoiesis.
基金supported by the National Natural Science Foundation of China(81572563)the National Science Foundations of HUBEI(2018CFB235).
文摘Late-stage ovarian cancer(OC)has a poor prognosis and a high metastasis rate,but the underlying molecular mechanism is unclear.RNA binding proteins(RBPs)play important roles in posttranscriptional regulation in the contexts of neoplasia and tumor metastasis.In this study,we explored the molecular functions of a canonical RBP,Transformer 2βhomolog(TRA2B),in cancer cells.TRA2B knockdown in HeLa cells and subsequent wholetranscriptome RNA sequencing(RNA-seq)analysis revealed the TRA2B-regulated alternative splicing(AS)profile.We disrupted TRA2B expression in epithelial OC cells and performed a series of experiments to confirm the resulting effects on OC cell proliferation,apoptosis and invasion.TRA2B-regulated AS was tightly associated with the mitotic cell cycle,apoptosis and several cancer pathways.Moreover,the expression of hundreds of genes was regulated by TRA2B,and these genes were enriched in the functions of cell proliferation,cell adhesion and angiogenesis,which are related to the malignant phenotype of OC.By integrating the alternatively spliced and differentially expressed genes,we found that AS events and gene expression were regulated independently.We then explored and validated the oncogenic functions of TRA2B by knocking down its expression in OC cells.The high TRA2B expression was associated with poor prognosis in patients with OC.In ovarian tissue,TRA2B expression showed a gradual increasing trend with increasing malignancy.We demonstrated the important roles of TRA2B in ovarian neoplasia and aggressive OC behaviors and identified the underlying molecular mechanisms,facilitating the targeted treatment of OC.
基金the National Natural Science Foundation of China, No. 30471917the Hong Kong Research Grant Council,No. HKU 7198/01
文摘BACKGROUND： High incidence of stroke at interchange period of autumn and winter was demonstrated by epidemiological survey, and the specific causes should be further investigated. OBJECTIVE： To investigate the influence of artificial cold exposure on the incidence of stroke in renovascular hypertensive rats （RHR）, and analyze the association with blood pressure and cold-inducible RNA binding protein （CIRP） mRNA expression in brain tissue. DESIGN： A completely randomized grouping design, a randomized control animal trial. SETTINGS： Lab of Neurology, the First Affiliated Hospital of Sun Yat-sen University; Department of Chemistry, Open laboratory of Chemical Biology, Institute of Molecular Technology for Drug Discovery and Synthesis, University of Hong Kong. MATERIALS： Male SD rats （n=460）, weighing 80 - 100 g were obtained from Guangdong Province Health Animal Unit. A modified RXZ-300A intelligent artificial climate cabinet （Ningbo Jiangnan Instrument Co. ,Ltd., China）. METHODS： The experiment were processed in the Lab of Neurology, the First Affiliated Hospital of Sun Yat-sen University and the Open Laboratory of Chemical Biology, Institute of Molecular Technology for Drug Discovery and Synthesis, University of Hong Kong from October 2004 to November 2005. Rats （n = 400） were operated to establish 2-kidney 2-clip RHR model as described previously. The sham-operated rats （n =60） served as normotensive controls. Eight weeks later, 300 of RHR were randomly selected according to their systolic blood pressure （SBP） and divided into 3 sub-groups （n =100 per group）： mild hypertensive group （SBP of 160 - 200 mm Hg）, moderate hypertensive group （SBP of 200 - 220 mm Hg） and severe hypertensive group （SBP 〉 220 mm Hg）. Each group was further divided into two groups （n =50） under ACE and non-ACE. Normal sham-operated SD rats （n =60）, SBP 〈 140 mm Hg, were randomly divided into two groups： Sham-operated control group （n =30） under ACE and non-ACE. To establish the ACE and non-ACE treatment, rats were housed individually in artificial climate cabinet, and ACE was designed as three cycles of 12-hour light of 22℃ （7 ： 00 - 19 ： 00） and 12-hour dark of 4℃（19 ： 00 - 7 ： 00）. The non-ACE group was kept at 22℃ throughout the experiment. MAIN OUTCOME MEASURES： Blood Pressure changes were measured and stroke symptom were observed; Expression of the CIRP were examined by reverse transcription-polymerase chain reaction. RESULTS： Finally 360 rats were involved in the analysis of results. ①Incidence of stroke： The incidence of stroke in 2k2c RHR was significantly higher after a three-day intermittent （12-hour） ACE （29.3%） as compared with that in non-ACE （17.3%） （P 〈 0.05）. Furthermore, the severe hypertensive 2k2c RHR （BP 〉 220 mm Hg） was found to have much higher incidence of stroke （66%, 33/50） than the mild （8%, 4/50） and moderate （18%） hypertensive 2k2c RHR. ②CIRP mRNA in brain tissue： ACE treatment stimulated the mRNA expression of CIRP in non-stroke 2k2c RHR but not in stroke 2k2c RHR （P 〈 0.05）. CONCLUSION： High blood pressure and low expression of CIRP are associated with ACE induced stroke.
文摘Objective: This study aimed to construct a bladder cancer prognostic model using bioinformatics to predict the survival of bladder cancer patients. Methods: RNA sequences and corresponding clinical data were downloaded from The Cancer Genome Atlas (TCGA) database, and the differentially expressed RNA-binding proteins (RBPs) were screened for analysis using the limma software package. Then, GO enrichment analysis and KEGG pathway analysis were performed on these differentially expressed RNA-binding proteins, and a PPI network was constructed. Finally, a risk model was constructed based on the screened central RBP, and a Kaplan-Meier survival curve was drawn to evaluate the prognostic value of central RBP and predict the prognosis of bladder Cancer(BLCA) patients with this model. Finally, the human protein atlas (HPA) online database (http://www.proteinatlas.org/) was used to further detect the differential expression of central hub RBP at the protein level between tumor tissue and normal tissue. Results: The bladder cancer prognostic model constructed with these six central RBPs had good sensitivity and specificity in predicting the prognosis of bladder cancer patients. Conclusion: This study explored the genes and regulatory networks of bladder cancer prognosis-related RNA-binding protein and bladder cancer, and constructed a bladder cancer prognosis model, which provides a theoretical basis for the development of new bladder cancer prognosis biomarkers in the future.
基金supported by Stavros Niarhos FoundationGreek‘Flagship Action for the Study of Neurodegenerative Diseases on the Basis of Precision Medicine’(to DT).
文摘Neurogenesis is a tightly regulated process in time and space both in the developing embryo and in adult neurogenic niches.A drastic change in the transcriptome and proteome of radial glial cells or neural stem cells towards the neuronal state is achieved due to sophisticated mechanisms of epigenetic,transcriptional,and post-transcriptional regulation.Understanding these neurogenic mechanisms is of major importance,not only for shedding light on very complex and crucial developmental processes,but also for the identification of putative reprogramming factors,that harbor hierarchically central regulatory roles in the course of neurogenesis and bare thus the capacity to drive direct reprogramming towards the neuronal fate.The major transcriptional programs that orchestrate the neurogenic process have been the focus of research for many years and key neurogenic transcription factors,as well as repressor complexes,have been identified and employed in direct reprogramming protocols to convert non-neuronal cells,into functional neurons.The post-transcriptional regulation of gene expression during nervous system development has emerged as another important and intricate regulatory layer,strongly contributing to the complexity of the mechanisms controlling neurogenesis and neuronal function.In particular,recent advances are highlighting the importance of specific RNA binding proteins that control major steps of mRNA life cycle during neurogenesis,such as alternative splicing,polyadenylation,stability,and translation.Apart from the RNA binding proteins,microRNAs,a class of small non-coding RNAs that block the translation of their target mRNAs,have also been shown to play crucial roles in all the stages of the neurogenic process,from neural stem/progenitor cell proliferation,neuronal differentiation and migration,to functional maturation.Here,we provide an overview of the most prominent post-transcriptional mechanisms mediated by RNA binding proteins and microRNAs during the neurogenic process,giving particular emphasis on the interplay of specific RNA binding proteins with neurogenic microRNAs.Taking under consideration that the molecular mechanisms of neurogenesis exert high similarity to the ones driving direct neuronal reprogramming,we also discuss the current advances in in vitro and in vivo direct neuronal reprogramming approaches that have employed microRNAs or RNA binding proteins as reprogramming factors,highlighting the so far known mechanisms of their reprogramming action.
文摘The messenger RNA 3'-untranslated region(3'UTR)plays an important role in regulation of gene expres-sion on the posttranscriptional level. The 3'UTR con-trols gene expression via orchestrated interactionbetween the structural components of mRNAs(cis-ele-ment) and the specific trans-acting factors(RNA bind-ing proteins and non-coding RNAs). The crosstalk ofthese factors is based on the binding sequences and/or direct protein-protein interaction, or just functionalinteraction. Much new evidence that has accumulatedsupports the idea that several RNA binding factors canbind to common mRNA targets: to the non-overlappingbinding sites or to common sites in a competitive fash-ion. Various factors capable of binding to the sameRNA can cooperate or be antagonistic in their actions.The outcome of the collective function of all factorsbound to the same mRNA 3'UTR depends on manycircumstances, such as their expression levels, affinity to the binding sites, and localization in the cell, which can be controlled by various physiological conditions. Moreover, the functional and/or physical interactions of the factors binding to 3'UTR can change the character of their actions. These interactions vary during the cell cycle and in response to changing physiological condi-tions. Abnormal functioning of the factors can lead to disease. In this review we will discuss how alterations of these factors or their interaction can affect cancer development and promote or enhance the malignant phenotype of cancer cells. Understanding these altera-tions and their impact on 3'UTR-directed posttran-scriptional gene regulation will uncover promising new targets for therapeutic intervention and diagnostics. We will also discuss emerging new tools in cancer di-agnostics and therapy based on 3'UTR binding factors and approaches to improve them.
基金supported by the National Natural Science Foundation of China(31271402 and 31100601)the National Key Basic Research Program(2012CB316503)
文摘Protein binding is essential to the transport,decay and regulation of almost all RNA molecules.However,the structural preference of protein binding on RNAs and their cellular functions and dynamics upon changing environmental conditions are poorly understood.Here,we integrated various high-throughput data and introduced a computational framework to describe the global interactions between RNA binding proteins(RBPs)and structured RNAs in yeast at single-nucleotide resolution.We found that on average,in terms of percent total lengths,~15%of mRNA untranslated regions(UTRs),~37%of canonical non-coding RNAs(ncRNAs)and^11%of long ncRNAs(lncRNAs)are bound by proteins.The RBP binding sites,in general,tend to occur at single-stranded loops,with evolutionarily conserved signatures,and often facilitate a specific RNA structure conformation in vivo.We found that four nucleotide modifications of tRNA are significantly associated with RBP binding.We also identified various structural motifs bound by RBPs in the UTRs of mRNAs,associated with localization,degradation and stress responses.Moreover,we identified>200 novel lncRNAs bound by RBPs,and about half of them contain conserved secondary structures.We present the first ensemble pattern of RBP binding sites in the structured non-coding regions of a eukaryotic genome,emphasizing their structural context and cellular functions.
文摘The secondary structures of hepatitis C virus （HCV） RNA and the cellular proteins that bind to them are important for modulating both translation and RNA replication. However, the sets of RNA-binding proteins involved in the regulation of HCV translation, replication and encapsidation remain unknown. Here, we identified RNA binding motif protein 24 （RBM24） as a host factor par- ticipated in HCV translation and replication. Knockdown of RBM24 reduced HCV propagation in Huh7.5.1 cells. An enhanced translation and delayed RNA synthesis during the early phase of infection was observed in RBM24 silencing cells. However, both overexpression of RBM24 and recombinant human RBM24 protein sup- pressed HCV IRES-mediated translation. Further analy- sis revealed that the assembly of the 80S ribosome on the HCV IRES was interrupted by RBM24 protein through binding to the 5＇-UTR. RBM24 could also inter- act with HCV Core and enhance the interaction of Core and 5＇-UTR, which suppresses the expression of HCV. Moreover, RBM24 enhanced the interaction between the 5＇- and 3＇-UTRs in the HCV genome, which probably explained its requirement in HCV genome replication. Therefore, RBM24 is a novel host factor involved in HCV replication and may function at the switch from trans- lation to replication.
基金Our work was supported by the Research Fund of the Health Commission of Hubei Province(WJ2021M255)the Cancer Research and Translational Platform Project of Zhongnan Hospital of Wuhan University(ZLYNXM202004)+1 种基金the Translational Medicine and Interdisciplinary Research Joint Fund Project of Zhongnan Hospital of Wuhan University(ZNJC201918)and a grant from the National Key Research and Development Program of China(SQ2019YFC200078/02).
文摘Background and Aims:The survival rate of patients with hepatocellular carcinoma is variable.The abnormal expression of RNA-binding proteins(RBPs)is closely related to the occurrence and development of malignant tumors.The primary aim of this study was to identify RBPs related to the prognosis of liver cancer and to construct a prognostic model of liver cancer.Methods:We downloaded the hepatocellular carcinoma gene sequencing data from The Cancer Genome Atlas(cancergenome.nih.gov/)database,constructed a protein-protein interaction network,and used Cytoscape to realize the visualization.From among 325 abnormally expressed genes for RBPs,9(XPO5,enhancer of zeste 2 polycomb repressive complex 2 subunit[EZH2],CSTF2,BRCA1,RRP12,MRPL54,EIF2AK4,PPARGC1A,and SEPSECS)were selected for construction of the prognostic model.Then,we further verified the results through the Gene Expression Omnibus(www.ncbi.nlm.nih.gov/geo/)database and in vitro experiments.Results:A prognostic model was constructed,which determined that the survival time of patients in the high-risk group was significantly shorter than that of the low-risk group(p<0.01).Univariate and multivariate Cox regression analysis suggested that the risk score was an independent prognostic factor(p<0.01).We also constructed a nomogram based on the risk score,survival time,and survival status.At the same time,we verified the high expression and cancer-promoting effects of EZH2 in tumors.Conclusions:Survival,receiver operating characteristic curve and independent prognostic analyses demonstrated that we constructed a good prognostic model,which might be useful for estimating the survival of patients with hepatocellular carcinoma.
基金Research in the authors’laboratories that is related to the topic of this review has been supported by grants from the National Institutes of Health(R01-NS041596 and R01-NS089663 to JLTP01-NS055976 to JDH)+3 种基金National Science Foundation(MCB-1020970 to JLT)Department of Defense/Congressionally Mandated Research Program(W81XWH-13-1-0308 to JLT)US-Israel Binational Science Foundation(2011329 to JLT)Dr.Miriam and Sheldon G.Adelson Medical Research Foundation(to JLT)
文摘Although initially argued to be a feature of immature neurons with incomplete polarization, there is clear evidence that neurons in the peripheral nervous system retain the capacity for intra-axonal protein synthe- sis well into adulthood. This localized protein synthesis has been shown to contribute to injury signaling and axon regeneration in peripheral nerves. Recent works point to potential for protein synthesis in axons of the vertebrate central nervous system, mRNAs and protein synthesis machinery have now been docu- mented in lamprey, mouse, and rat spinal cord axons. Intra-axonal protein synthesis appears to be activated in adult vertebrate spinal cord axons when they are regeneration-competent. Rat spinal cord axons regen- erating into a peripheral nerve graft contain mRNAs and markers of activated translational machinery. Indeed, levels of some growth-associated mRNAs in these spinal cord axons are comparable to the regen- erating sciatic nerve. Markers of active translation tend to decrease when these axons stop growing, but can be reactivated by a second axotomy. These emerging observations raise the possibility that mRNA transport into and translation within axons could be targeted to facilitate regeneration in both the peripheral and central nervous systems.
文摘Background Sam68 plays an important role as a multiple functional RNA binding nuclear protein in cell cycle progress, RNA usage, signal transduction, and tyrosine phosphorylation by Src during mitosis. However, its precise impact on these essential cellular functions remains unclear. The purpose of this study is to further elucidate Sam68 functions in RNA metabolism, signal transduction regulation of cell growth and cell proliferation in DT40 cell line. Methods By using gene targeting method, we isolated a mutation form of Sam68 in DT40 cells and described its effect on cell growth process and signal transduction. Southern, Northern, and Western blot, phosphorylation and flow-cytometric analyses were performed to investigate the Sam68 functions. Results A slower growth rate （2.1 hours growth elongation） and longer S phase （1.7 hours elongation） was observed in the Sam68 mutant cells. Serum depletion resulted in increased amounts of dead cells, and expansion of S phase in mutant cells. Upon B cell cross-linking, the maximal level of tyrosine phosphorylation on BLNK was observed to be significantly lower in mutant cells.Conclusions The proline rich domain of Sam68 is involved in cell growth control by modulating the function of mRNAs in S phase or earlier and the functions as an adaptor molecule in B cell signal transduction pathways.
基金financially supported by the National Natural Science Foundation of China (31171565 and 31371635)
文摘The RNA‐binding glycine‐rich protein（RB‐GRP）family is characterized by the presence of a glycine‐rich domain arranged in（Gly）n‐X repeats and an RNA‐recognition motif（RRM）. RB‐GRPs participate in varied physiological and biochemical processes especially in the stress response of plants. In this study, a total of 23 RB‐GRPs distributed on 10 chromosomes were identified in maize（Zea mays L.）, and they were divided into four subgroups according to their conserved domain architecture. Five pairs of paralogs were identified,while none of them was located on the same chromosomal region, suggesting that segmental duplication is predominant in the duplication events of the RB‐GRPs in maize. Comparative analysis of RB‐GRPs in maize, Arabidopsis（Arabidopsis thaliana L.）, rice（Oryza sativa L.）, and wheat（Triticum aestivum）revealed that two exclusive subgroups were only identified in maize. Expression of eight ZmRB‐GRPs was significantly regulated by at least two kinds of stresses. In addition, cis‐elements predicted in the promoter regions of the ZmRB‐GRPs also indicated that these ZmRB‐GRPs would be involved in stress response of maize. The preliminary genome‐wide analysis of the RB‐GRPs in maize would provide useful information for further study on the function of the ZmRB‐GRPs.
基金supported by grants from the Sanming Project of Medicine in Shenzhen(No.SZSM201612021)Special Foundation for Science and Technology Development of Guangdong Province(No.2017B090904010)+1 种基金Scientific Research Project of Health and Family Planning Commission of Shenzhen Municipality(No.SZXJ2018086)the Science and Technology Development Fund Project of Shenzhen(Nos.JCYJ20190809100217290 and JCYJ20190809095801653)
文摘Background:Long non-coding RNA colon cancer-associated transcript 1(CCAT1)is involved in transforming multiple cancers into malignant cancer types.Previous studies underlining the mechanisms of the functions of CCAT1 primarily focused on its decoy for miRNAs(micro RNAs).However,the regulatory mechanism of CCAT1-protein interaction associated with tumor metastasis is still largely unknown.The present study aimed to identify proteome-wide CCAT1 partners and explored the CCAT1-protein interaction mediated tumor metastasis.Methods:CCAT1-proteins complexes were purified and identified using RNA antisense purification coupled with the mass spectrometry(RAP-MS)method.The database for annotation,visualization,and integrated discovery and database for eukaryotic RNA binding proteins(EuRBPDB)websites were used to bioinformatic analyzing CCAT1 binding proteins.RNA pull-down and RNA immunoprecipitation were used to validate CCAT1-Vimentin interaction.Transwell assay was used to evaluate the migration and invasion abilities of HeLa cells.Results:RAP-MS method worked well by culturing cells with nucleoside analog 4-thiouridine,and cross-linking was performed using 365 nm wavelength ultraviolet.There were 631 proteins identified,out of which about 60%were RNA binding proteins recorded by the EuRBPDB database.Vimentin was one of the CCAT1 binding proteins and participated in the tumor metastasis pathway.Knocked down vimetin(VIM)and rescued the downregulation by overexpressing CCAT1 demonstrated that CCAT1 could enhance tumor migration and invasion abilities by stabilizing Vimentin protein.Conclusion:CCAT1 may bind with and stabilize Vimentin protein,thus enhancing cancer cell migration and invasion abilities.
基金Prinses Beatrix Spierfonds in the Netherlands(Grant No.W.OR.14-13)
文摘Muscle formation is a coordinated process driven by extensive gene expression changes where single cells fuse together to form multinucleated muscle fibers. Newly synthesized m RNAs are then regulated by RNA binding proteins(RBPs), affecting post-transcriptional transcript metabolism. Here, we determined how large-scale gene expression changes affect the catalog of RBPs by studying proliferating and differentiated muscle cells in healthy and dystrophic conditions. Transcriptomic analysis showed that the expression of more than 7000 genes was affected during myogenesis. We identified 769 RBPs, of which 294 were muscle-specific and 49 were uniquely shared with cardiomyocytes. A subset of 32 RBPs(half of which were muscle-specific) was found to be preferentially associated with target mRNAs in either myoblasts(MBs) or myotubes(MTs). A large proportion of catalytic proteins were bound to mRNAs even though they lack classical RNA binding domains. Finally, we showed how the identification of cell-specific RBPs enabled the identification of biomarkers that can separate healthy individuals from dystrophic patients. Our data show how interactome data can shed light on new basic RNA biology as well as provide cell-specific data that can be used for diagnostic purposes.
