Substrate affinity and substrate specificity of proteasomes with RNase activity

We have partially reconstituted 20S proteasome/RNA complexes using oligonucleotides corresponding to ARE (adenosine- and uridine-rich element) (AUUUA)₄ and HIV-TAR (human immunodeficiency virus-Tat transactivation response element), a stem-loop structure in the 5 UTR (untranslated region) of HIV-mRNAs. We demonstrate that these RNAs which associate with proteasomes are degraded by proteasomal endonuclease activity. The formation of these 20S proteasome/RNA substrate complexes is rather specific since 20S proteasomes do not interfere with truncated TAR that is not cleaved by proteasomal endonuclease. In addition, affinity of proteasomes for (AUUUA)₄ is much stronger as it is for HIV-TAR. These results provide further arguments for our hypothesis that proteasomes could be involved in the destabilisation of cytokines mRNAs containing AUUUA sequences as well as viral mRNAs.     

用改进的Mg^＋＋沉淀多聚核糖体法分离胞质mRNA

本文报道一种用改进的Palmiter的方法分离纯化胞质mRNA。即利用镁离子沉淀核糖体,提取细胞质总RNA,进而纯化胞质mRNA的方法。该方法得到的mRNA是正在翻译的成熟的胞质mRNA。所得mRNA得率和质量都优于其他方法,便于常规检测,并可用于cDNA的合成和PCR扩增。     

Detection of mRNAs containing regulatory peptide coding sequences using synthetic oligodeoxynucleotides

To understand the regulation of the production of peptide hormones, it is vital to elucidate their biosynthetic pathways. We chose to study a major regulatory peptide, vasoactive intestinal peptide (VIP), a peptide possessing both neurotransmitter and neurohormone actions. To identify the specific peptide mRNA we are using, as hybridization probes, radiolabeled synthetic oligodcoxynucleotides with sequence complementary to the predicted peptide mRNA sequence. Employing this approach, we identified and partially purified a ～ 1600-base long mRNA containing VIP related sequences which can be translated in vitro into VIP-immunoreactive polypeptides. Such mRNA was detected in normal VIP producing tissue (rat brain), as well as in a tumor producing VIP (human buccal tumor). This mRNA differs in size from a known VIP-mRNA identified in human neuro-blastoma cells, suggesting the possibility of different VIP-mRNAs in different cell types.     

Prospect of circular RNA in osteogenesis: A novel orchestrator of signaling pathways

Circular RNAs (circRNAs) were initially regarded as by-products of aberrant splicing. But now, there are substantial evidence on their various roles in the regulation of genes during the development of organs and diseases. Consistent with these breakthroughs, it is experiencing rapid growth that circRNAs function as the important checkpoints during the osteogenesis. Therefore, characterizing the roles of circRNAs is useful and critical to better understanding the process of osteogenic differentiation, which could provide new avenues for the diagnosis and treatment of bone diseases, such as bone defects and osteoporosis. In this review, we presented a map of the interaction between circRNAs and the molecules of signaling pathways associated with osteogenesis, summarized the current knowledge of the biological functions of circRNAs during the osteogenic differentiation, figured out the limits of existing research works, and provided a novel look on the diagnostic and therapeutic methods of bone diseases based on circRNAs.     

Developmental and nutritional regulation of the messenger RNAs for fatty acid synthase,malic enzyme and albumin in the livers of embryonic and newly-hatched chicks

Summary The mRNAs for fatty acid synthase and malic enzyme were almost undetectable in total RNA extracted from the livers of 16-day old chick embryos. Both mRNAs increased in abundance between the 16th day of incubation and the day of hatching. In neonates, fatty acid synthase mRNA level was dependent on nutritional status, increasing slowly if the chicks were starved and rapidly if they were fed. The abundance of malic enzyme mRNA decreased in starved neonatal chicks and increased in fed ones. When neonates were first fed and then starved, starvation caused a large decrease in the abundance of both mRNAs. Conversely, feeding, after a period of starvation, resulted in a substantial increase in both mRNAs. The relative abundances of fatty acid synthase and malic enzyme mRNAs correlated positively with relative rates of enzyme synthesis. Thus, nutritional and hormonal regulation of the synthesis of these two lipogenic enzymes is exerted primarily at a pre-translational level.The abundance of albumin mRNA decreased significantly between the 16th day of incubation and the day of hatching but did not change thereafter in fed or starved chicks. The relative stability of albumin mRNA levels after hatching attests to the selectivity of the nutritional regulation of fatty acid synthase and malic enzyme mRNAs. The decrease in albumin mRNA which occurred between 16 days of incubation and hatching contrasts with the increase in albumin mRNA sequences which occurred during late gestation in the fetal rat (20). High levels of albumin in the chick embryo may be related to the lack of an analogue of mammalian alpha-fetoprotein in birds.Abbreviations PIPES piperazine-N,N-bis (2 ethanesulfonic acid) - SDS sodium dodecyl sulfate Postdoctoral Fellow of the Medical Research Council of Canada.     

Similar features in the mechanisms of mRNA translation initiation in eukaryotic and prokaryotic systems

Similar features in the mechanisms of mRNA translation initiation on prokaryotic and eukaryotic ribosomes are discussed with examples from mRNAs with nonstandard 5′-untranslated regions (5′-UTRs) and mRNAs lacking 5′-UTR (leaderless mRNAs).     

Murine Vascular Cell Adhesion Molecule-1 (VCAM-1) Proteins Encoded by Alternatively Spliced rnRNAs Are Differentially Targeted in Polarized Cells

VCAM-1 is an immunoglobulin (Ig) superfamily member expressed in endothelial cells that mediates adhesion to a variety of leukocytes in a VLA-4 dependent manner. In the mouse, two distinct forms of VCAM are produced. One form, VCAM(tm), contains seven Ig domains followed by a single transmembrane region and a short cytoplasmic domain. A second form, VCAM^GPI, which is preferentially induced by cytokines and LPS, contains only the first three Ig domains and is attached to the cell surface via a glycosylphosphatidylinositol (GPI) anchor. Both vascular and nonvascular expression of VCAM have been reported in a variety of normal and pathological settings. One possible role for the two VCAM isoforms is to allow for the targeted localization of VCAM to specific cell surface domains of polarized cells. This may be particularly relevant since VCAM is known to be expressed by two different polarized cell types, namely endothelial cells and kidney epithelial cells. In this study, MDCK cells permanently expressing either VCAM(tm) or VCAM^GPI were established and used to examine the targeting of VCAM proteins to different polarized surface domains. VCAM(tm) was primarily located on the basolateral surface while VCAM^GPI was located on the apical surface of polarized MDCK cells. Data is also presented that demonstrates that polarized expression is reversed in endothelial cells where VCAM(tm) was observed primarily on the apical surface. The differential localization of VCAM isoforms on the cell surface has direct implications for the ability of VCAM to mediate cell adhesion and transmigration.     

Identification of a novel glycolysis-related gene signature that can predict the survival of patients with lung adenocarcinoma

Lung cancer is one of the most malignant cancers worldwide, and lung adenocarcinoma (LUAD) is the most common histologic subtype. Thousands of biomarkers related to the survival and prognosis of patients with this cancer type have been investigated through database mining; however, the prediction effect of a single gene biomarker is not satisfactorily specific or sensitive. Thus, the present study aimed to develop a novel gene signature of prognostic values for patients with LUAD. Using a data-mining method, we performed expression profiling of 1145 mRNAs in large cohorts with LUAD (n = 511) from The Cancer Genome Atlas database. Using the Gene Set Enrichment Analysis, we selected 198 genes related to GLYCOLYSIS, which is the most important enrichment gene set. Moreover, these genes were identified using Cox proportional regression modeling. We established a risk score staging system to predict the outcome of patients with LUAD and subsequently identified four genes (AGRN, AKR1A1, DDIT4, and HMMR) that were closely related to the prognosis of patients with LUAD. The identified genes allowed us to classify patients into the high-risk group (with poor outcome) and low-risk group (with better outcome). Compared with other clinical factors, the risk score has a better performance in predicting the outcome of patients with LUAD, particularly in the early stage of LUAD. In conclusion, we developed a four-gene signature related to glycolysis by utilizing the Cox regression model and a risk staging model for LUAD, which might prove valuable for the clinical management of patients with LUAD.     

Specific roles for the Ccr4-Not complex subunits in expression of the genome

In this work we used micro-array experiments to determine the role of each nonessential subunit of the conserved Ccr4-Not complex in the control of gene expression in the yeast Saccharomyces cerevisiae. The study was performed with cells growing exponentially in high glucose and with cells grown to glucose depletion. Specific patterns of gene deregulation were observed upon deletion of any given subunit, revealing the specificity of each subunit''s function. Consistently, the purification of the Ccr4-Not complex through Caf40p by tandem affinity purification from wild-type cells or cells lacking individual subunits of the Ccr4-Not complex revealed that each subunit had a particular impact on complex integrity. Furthermore, the micro-arrays revealed that the role of each subunit was specific to the growth conditions. From the study of only two different growth conditions, revealing an impact of the Ccr4-Not complex on more than 85% of all studied genes, we can infer that the Ccr4-Not complex is important for expression of most of the yeast genome.     

Murine Vascular Cell Adhesion Molecule-1 (VCAM-1) Proteins Encoded by Alternatively Spliced rnRNAs Are Differentially Targeted in Polarized Cells

VCAM-1 is an immunoglobulin (Ig) superfamily member expressed in endothelial cells that mediates adhesion to a variety of leukocytes in a VLA-4 dependent manner. In the mouse, two distinct forms of VCAM are produced. One form, VCAM(tm), contains seven Ig domains followed by a single transmembrane region and a short cytoplasmic domain. A second form, VCAM^GPI, which is preferentially induced by cytokines and LPS, contains only the first three Ig domains and is attached to the cell surface via a glycosylphosphatidylinositol (GPI) anchor. Both vascular and nonvascular expression of VCAM have been reported in a variety of normal and pathological settings. One possible role for the two VCAM isoforms is to allow for the targeted localization of VCAM to specific cell surface domains of polarized cells. This may be particularly relevant since VCAM is known to be expressed by two different polarized cell types, namely endothelial cells and kidney epithelial cells. In this study, MDCK cells permanently expressing either VCAM(tm) or VCAM^GPI were established and used to examine the targeting of VCAM proteins to different polarized surface domains. VCAM(tm) was primarily located on the basolateral surface while VCAM^GPI was located on the apical surface of polarized MDCK cells. Data is also presented that demonstrates that polarized expression is reversed in endothelial cells where VCAM(tm) was observed primarily on the apical surface. The differential localization of VCAM isoforms on the cell surface has direct implications for the ability of VCAM to mediate cell adhesion and transmigration.     

Improved Screening of cDNAs Generated by mRNA Differential Display Enables the Selection of True Positives and the Isolation of Weakly Expressed Messages

The high percentage of false positives generated by differential display (as high as 85%) has previously limited the potential of the method. This report describes an efficient methodology that enables false positives to be discarded prior to cloning, via reverse Northern analysis. This first step of the screening also allows the detection of putative low abundance differential clones. Following cloning, a second reverse Northern combined with partial DNA sequencing and RT-PCR detection allows isolation of all differential cDNAs including very low abundance clones. Use of the sequential screening procedure described here led to the isolation of novel tomato genes responding to the plant hormone ethylene while minimising labor and materials input.     

Identification of a novel cell cycle-related gene signature predicting survival in patients with gastric cancer

Gastric cancer (GC) is one of the most fatal cancers in the world. Thousands of biomarkers have been explored that might be related to survival and prognosis via database mining. However, the prediction effect of single gene biomarkers is not specific enough. Increasing evidence suggests that gene signatures are emerging as a possible better alternative. We aimed to develop a novel gene signature to improve the prognosis prediction of GC. Using the messenger RNA (mRNA)-mining approach, we performed mRNA expression profiling in a large GC cohort (n = 375) from The Cancer Genome Atlas (TCGA) database. Gene Set Enrichment Analysis (GSEA) was performed, and we recovered genes related to the G2/M checkpoint, which we identified with a Cox proportional regression model. We identified a set of five genes (MARCKS, CCNF, MAPK14, INCENP, and CHAF1A), which were significantly associated with overall survival (OS) in the test series. Based on this five-gene signature, the test series patients could be classified into high-risk or low-risk subgroups. Multivariate Cox regression analysis indicated that the prognostic power of this five-gene signature was independent of clinical features. In conclusion, we developed a five-gene signature related to the cell cycle that can predict survival for GC. Our findings provide novel insight that is useful for understanding cell cycle mechanisms and for identifying patients with GC with poor prognoses.     

Genome-wide identification of mRNAs associated with the protein SMN whose depletion decreases their axonal localization

Spinal muscular atrophy is a neuromuscular disease resulting from mutations in the SMN1 gene, which encodes the survival motor neuron (SMN) protein. SMN is part of a large complex that is essential for the biogenesis of spliceosomal small nuclear RNPs. SMN also colocalizes with mRNAs in granules that are actively transported in neuronal processes, supporting the hypothesis that SMN is involved in axonal trafficking of mRNPs. Here, we have performed a genome-wide analysis of RNAs present in complexes containing the SMN protein and identified more than 200 mRNAs associated with SMN in differentiated NSC-34 motor neuron-like cells. Remarkably, ∼30% are described to localize in axons of different neuron types. In situ hybridization and immuno-fluorescence experiments performed on several candidates indicate that these mRNAs colocalize with the SMN protein in neurites and axons of differentiated NSC-34 cells. Moreover, they localize in cell processes in an SMN-dependent manner. Thus, low SMN levels might result in localization deficiencies of mRNAs required for axonogenesis.     

The expression of cholinesterases in human renal tumours varies according to their histological types

The change in the expression of acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) activities in neoplastic colon and lung prompted us to study the possible effect of cancer on the expression of cholinesterases (ChEs) in kidney. Samples of papillary renal cell carcinoma (pRCC), conventional RCC (cRCC), chromophobe RCC (chRCC) and renal oncocytoma (RON), beside adjacent non-cancerous tissues, were analyzed. In pRCC both AChE and BuChE activities were statistically increased; in cRCC and chRCC only AChE activity increased and in RON neither AChE nor BuChE activities were affected. Abundant amphiphilic AChE dimers (G(2)(A)) and fewer monomers (G(1)(A)) were identified in healthy kidney as well as in all tumour classes. Incubation with PIPLC revealed glycosylphosphatidylinositol in AChE forms. BuChE is distributed between principal G(4)(H), fewer G(1)(H), and much fewer G(4)(A) and G(1)(A) species. RT-PCR showed similar amounts of AChE-H, AChE-T and BuChE mRNAs in healthy kidney. Their levels increased in pRCC but not in the other tumour types. The data support the idea that, as in lung tumours, in renal carcinomas expression of ChE mRNAs, biosynthesis of molecular components and level of enzyme activity change according to the specific kind of cell from which tumours arise.     

The role of alternative translation start sites in the generation of human protein diversity

According to the scanning model, 40S ribosomal subunits initiate translation at the first (5 proximal) AUG codon they encounter. However, if the first AUG is in a suboptimal context, it may not be recognized, and translation can then initiate at downstream AUG(s). In this way, a single RNA can produce several variant products. Earlier experiments suggested that some of these additional protein variants might be functionally important. We have analysed human mRNAs that have AUG triplets in 5 untranslated regions and mRNAs in which the annotated translational start codon is located in a suboptimal context. It was found that 3% of human mRNAs have the potential to encode N-terminally extended variants of the annotated proteins and 12% could code for N-truncated variants. The predicted subcellular localizations of these protein variants were compared: 31% of the N-extended proteins and 30% of the N-truncated proteins were predicted to localize to subcellular compartments that differed from those targeted by the annotated protein forms. These results suggest that additional AUGs may frequently be exploited for the synthesis of proteins that possess novel functional properties.Electronic Supplementary Material Supplementary material is available for this article at