scholarly journals DHX36 binding at G-rich sites in mRNA untranslated regions promotes translation

2017 ◽  
Author(s):  
Markus Sauer ◽  
Stefan Juranek ◽  
Hinke G. Kazemier ◽  
Daniel Benhalevy ◽  
Xiantao Wang ◽  
...  
Keyword(s):  
Mrna Stability ◽  
Untranslated Regions ◽  
Translation Efficiency ◽  
Mrna Accumulation ◽  
Target Mrna ◽  
Dna And Rna ◽  
Ribosome Footprinting ◽  
And Function ◽  
Functional Analyses

ABSTRACTTranslation efficiency can be affected by mRNA stability and secondary structures, including so-called G-quadruplex (G4) structures. The highly conserved and essential DEAH-box helicase DHX36/RHAU is able to resolve G4 structures on DNA and RNA in vitro, however a system-wide analysis of DHX36 targets and function is lacking. We globally mapped DHX36 occupancy in human cell lines and found that it preferentially binds to G-rich sequences in the coding sequences (CDS) and 5' and 3' untranslated regions (UTR) of more than 4,500 mRNAs. Functional analyses, including RNA sequencing, ribosome footprinting, and quantitative mass spectrometry revealed that DHX36 decreased target mRNA stability. However, target mRNA accumulation in DHX36 KO cells did not lead to a significant increase in ribosome footprints or protein output indicating that they were translationally incompetent. We hypothesize that DHX36 resolves G4 and other structures that interfere with efficient translation initiation.

scholarly journals Identification of exosome-like nanoparticle-derived microRNAs from 11 edible fruits and vegetables

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5186 ◽  
Author(s):  
Juan Xiao ◽  
Siyuan Feng ◽  
Xun Wang ◽  
Keren Long ◽  
Yi Luo ◽  
...  
Keyword(s):  
Small Rna ◽  
Fruits And Vegetables ◽  
Critical Role ◽  
Target Prediction ◽  
Edible Plant ◽  
Naturally Occurring ◽  
Mirna Species ◽  
And Function ◽  
Functional Analyses

Edible plant-derived exosome-like nanoparticles (EPDELNs) are novel naturally occurring plant ultrastructures that are structurally similar to exosomes. Many EPDELNs have anti-inflammatory properties. MicroRNAs (miRNAs) play a critical role in mediating physiological and pathological processes in animals and plants. Although miRNAs can be selectively encapsulated in extracellular vesicles, little is known about their expression and function in EPDELNs. In this study, we isolated nanovesicles from 11 edible fruits and vegetables and subjected the corresponding EPDELN small RNA libraries to Illumina sequencing. We identified a total of 418 miRNAs—32 to 127 per species—from the 11 EPDELN samples. Target prediction and functional analyses revealed that highly expressed miRNAs were closely associated with the inflammatory response and cancer-related pathways. The 418 miRNAs could be divided into three classes according to their EPDELN distributions: 26 “frequent” miRNAs (FMs), 39 “moderately present” miRNAs (MPMs), and 353 “rare” miRNAs (RMs). FMs were represented by fewer miRNA species than RMs but had a significantly higher cumulative expression level. Taken together, our in vitro results indicate that miRNAs in EPDELNs have the potential to regulate human mRNA.

scholarly journals circITGA7 Functions as an Oncogene by Sponging miR-198 and Upregulating FGFR1 Expression in Thyroid Cancer

2020 ◽  
Vol 2020 ◽  
pp. 1-8 ◽  
Author(s):  
Siqi Li ◽  
Junmei Yang ◽  
Xiaoting Liu ◽  
Rui Guo ◽  
Ruidong Zhang
Keyword(s):  
Thyroid Cancer ◽  
Cell Lines ◽  
Circular Rna ◽  
Clinical Findings ◽  
Circular Rnas ◽  
Potential Marker ◽  
And Function ◽  
Functional Analyses ◽  
Fgfr1 Expression

Background. Emerging evidence has indicated that circular RNAs (circRNAs), recognized as functional noncoding transcripts in eukaryotic cells, may be involved in regulating many physiological or pathological processes. However, the regulation and function of circular RNA circITGA7 in thyroid cancer (TC) remains unknown. Methods. In this study, we found that circITGA7 is upregulated in TC cell lines. We then performed functional analyses in the cell lines to support clinical findings. Mechanistically, we demonstrated that circITGA7 can directly bind to miR-198 and reduce the inhibition effect of miR-198 on target FGFR1 expression. Results. We reported an upregulation of circITGA7 in patients with TC. Silencing of circITGA7 inhibits metastasis and proliferation of TC cell lines in vitro. In addition, in the TC cell lines, the knockdown of circITGA7 or overexpression of miR-198 significantly suppressed FGFR1 levels. Mechanistically, we found that circITGA7 acts as miR-198 competitive endogenous RNA (ceRNA) to regulate FGFR1 expression. Conclusions. In summary, circRNA circITGA7 may play a regulatory role in TC and may be a potential marker for TC diagnosis or progression.

scholarly journals Functional diversification of a basic helix–loop–helix protein due to alternative transcription during generation of amphidiploidy in tobacco plants

2007 ◽  
Vol 403 (3) ◽  
pp. 493-499 ◽  
Author(s):  
Yutaka Kodama ◽  
Hiroshi Sano
Keyword(s):  
Nicotiana Sylvestris ◽  
In Vitro Translation ◽  
Untranslated Regions ◽  
Translation Efficiency ◽  
Functional Diversification ◽  
Basic Helix Loop Helix ◽  
Helix Loop Helix ◽  
Alternative Transcription ◽  
Initiation Frequency

A plastid-resident basic helix–loop–helix protein, previously identified in Nicotiana tabacum and designated as NtWIN4 (N. tabacum wound-induced clone 4), has been converted from a nuclear transcription repressor into a plastid-resident regulatory factor through replacement of the DNA-binding domain with a plastid transit sequence during evolution. N. tabacum is a natural amphidiploid plant derived from Nicotiana tomentosiformis and Nicotiana sylvestris and immunoblot staining using anti-NtWIN4 antibodies identified two protein species, a 26 kDa form and a 17 kDa form, in N. sylvestris, whereas only the 17 kDa form was found in N. tabacum. The 26 kDa protein is produced when translation starts from the first AUG codon of the mRNA and is predominantly localized in the cytoplasm and nucleus, whereas the 17 kDa protein is derived from a 24 kDa precursor protein, synthesized from the second AUG codon, and localizes only to plastids. Subsequent analyses revealed that the lengths of the mRNAs vary in the two plant species. One major form lacks the first AUG, while minor populations possess variable 5′-untranslated regions prior to the first AUG codon. Translation of the two types produces the 24 kDa and 26 kDa proteins respectively. In vitro translation assays indicated that initiation frequency from the first AUG codon is higher in mRNAs from N. sylvestris than from N. tabacum. In contrast, initiation from the second AUG codon was found to be equally efficient in mRNAs from both species. These results suggest that both mRNA populations and translation efficiency changed during the amphidiploidization responsible for generation of N. tabacum. This scheme could reflect a molecular mechanism of protein evolution in plants.

scholarly journals Macrophage Plasticity and Function in the Lung Tumour Microenvironment Revealed in 3D Heterotypic Spheroid and Explant Models

Biomedicines ◽  
2021 ◽  
Vol 9 (3) ◽  
pp. 302
Author(s):  
Lauren Evans ◽  
Kate Milward ◽  
Richard Attanoos ◽  
Aled Clayton ◽  
Rachel Errington ◽  
...  
Keyword(s):  
Ex Vivo ◽  
Tumour Microenvironment ◽  
Therapeutic Interventions ◽  
Lung Tumour ◽  
Cell Responses ◽  
Dual Analysis ◽  
Macrophage Plasticity ◽  
And Function ◽  
Functional Analyses

In non-small cell lung cancer (NSCLC), stroma-resident and tumour-infiltrating macrophages may facilitate an immunosuppressive tumour microenvironment (TME) and hamper immunotherapeutic responses. Analysis of tumour-associated macrophage (TAM) plasticity in NSCLC is largely lacking. We established a novel, multi-marker, dual analysis approach for assessing monocyte-derived macrophage (Mf polarisation and M1/M2 phenotypic plasticity. We developed a flow cytometry-based, two-marker analysis (CD64 and CD206) of CD14+ cells. The phenotype and immune function of in vitro-induced TAMs was studied in a heterotypic spheroid and tumour-derived explant model of NSCLC. Heterotypic spheroids and NSCLC explants skewed Mfs from an M1- (CD206loCD64hi) to M2-like (CD206hiCD64lo) phenotype. Lipopolysaccharide (LPS) and IFNg treatment reversed M2-like Mf polarisation, indicating the plasticity of Mfs. Importantly, antigen-specific CD8+ T cell responses were reduced in the presence of tumour explant-conditioned Mfs, but not spheroid-conditioned Mfs, suggesting explants are likely a more relevant model of the immune TME than cell line-derived spheroids. Our data indicates the importance of multi-marker, functional analyses within Mf subsets and the advantages of the ex vivo NSCLC explant model in immunomodulation studies. We highlight the plasticity of the M1/M2 phenotype using the explant model and provide a tool for studying therapeutic interventions designed to reprogram M2-like Mf-induced immunosuppression.

Differences in the translation efficiency and mRNA stability mediated by 5′-UTR splice variants of human SP-A1 and SP-A2 genes

2005 ◽  
Vol 289 (3) ◽  
pp. L497-L508 ◽  
Author(s):  
Guirong Wang ◽  
Xiaoxuan Guo ◽  
Joanna Floros
Keyword(s):  
Gene Expression ◽  
Mrna Stability ◽  
Mrna Decay ◽  
Molecular Mechanisms ◽  
Luciferase Activity ◽  
Splice Variants ◽  
Translational Efficiency ◽  
Translation Efficiency ◽  
Control Vector

Surfactant protein A (SP-A) plays an important role in host defense, modulation of inflammatory processes, and surfactant-related functions of the lung. The human SP-A (hSP-A) locus consists of two functional genes, SP-A1 and SP-A2. Several hSP-A 5′-untranslated region (UTR) splice variants for each gene have been characterized and shown to be translated in vitro and in vivo. In this report, we investigated the role of hSP-A 5′-UTR splice variants on SP-A production and molecular mechanisms involved. We used in vitro transient expression of hSP-A 5′-UTR constructs containing luciferase as the reporter gene and quantitative real-time PCR to study hSP-A 5′-UTR-mediated gene expression. We found that 1) the four (A′D′, ABD, AB′D′, and A′CD′) 5′-UTR splice variants under study enhanced gene expression, by increasing luciferase activity from 2.5- to 19.5-fold and luciferase mRNA from 4.3- to 8.8-fold compared with the control vector that lacked hSP-A 5′-UTR; 2) all four 5′-UTR splice variants studied regulated mRNA stability. The ABD variant exhibited the lowest rate of mRNA decay compared with the other three constructs (A′D′, AB′D′, and A′CD′). These three constructs also exhibited significantly lower rate of mRNA decay compared with the control vector; 3) based on the indexes of translational efficiency (luciferase activity/mRNA), ABD and AB′D′ exhibited higher translational efficiency compared with the control vector, whereas the translational efficiency of each A′D′ and A′CD′ was lower than that of the control vector. These findings indicate that the hSP-A 5′-UTR splice variants play an important role in both SP-A translation and mRNA stability.

scholarly journals N6-methyladenosine (m6A) methyltransferase KIAA1429 accelerates the gefitinib resistance of non-small-cell lung cancer

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Jun Tang ◽  
Tianci Han ◽  
Wei Tong ◽  
Jian Zhao ◽  
Wei Wang
Keyword(s):  
Lung Cancer ◽  
Mrna Stability ◽  
Therapeutic Target ◽  
Human Cancer ◽  
Small Cell ◽  
Untranslated Regions ◽  
Small Cell Lung ◽  
Gefitinib Resistance

AbstractN6-methyladenosine (m6A) modification has been convincingly identified to be a critical regulator in human cancer. However, the contribution of m6A to NSCLC gefitinib resistance is still largely unknown. Here, we screened and identified that m6A methyltransferase KIAA1429 was highly expressed in gefitinib-resistant NSCLC cells (PC9-GR), tissues, and closely related to unfavorable survival. Functionally, KIAA1429 accelerated the gefitinib resistance of NSCLC in vitro. Depletion of KIAA1429 repressed the tumor growth of PC9-GR cells in vivo. Mechanistically, KIAA1429 enhanced the mRNA stability of HOXA1 through targeting its 3′-untranslated regions (3′-UTR). Overall, our findings indicate that KIAA1429 plays essential oncogenic roles in NSCLC gefitinib resistance, which may provide a feasible therapeutic target for NSCLC.

scholarly journals Higher-Level Production of Volatile Fatty AcidsIn Vitroby Chicken Gut Microbiotas than by Human Gut Microbiotas as Determined by Functional Analyses

2012 ◽  
Vol 78 (16) ◽  
pp. 5763-5772 ◽  
Author(s):  
Fang Lei ◽  
Yeshi Yin ◽  
Yuezhu Wang ◽  
Bo Deng ◽  
Hongwei David Yu ◽  
...  
Keyword(s):  
Volatile Fatty Acids ◽  
Rrna Gene ◽  
And Function ◽  
Functional Analyses ◽  
The Relationship ◽  
Level Production ◽  
V3 Region ◽  
Chicken Cecum ◽  
Selection Of

ABSTRACTThe aim of this study was to determine the relationship between the composition and function of gut microbiota. Here, we compared the bacterial compositions and fermentation metabolites of human and chicken gut microbiotas. Results generated by quantitative PCR (qPCR) and 454 pyrosequencing of the 16S rRNA gene V3 region showed the compositions of human and chicken microbiotas to be markedly different, with chicken cecal microbiotas displaying more diversity than human fecal microbiotas. The nutrient requirements of each microbiota growing under batch and chemostat conditions were analyzed. The results showed that chicken cecal microbiotas required simple sugars and peptides to maintain balanced growthin vitrobut that human fecal microbiotas preferred polysaccharides and proteins. Chicken microbiotas also produced higher concentrations of volatile fatty acids than did human microbiotas. Our data suggest that the availability of different fermentable substrates in the chicken cecum, which exist due to the unique anatomical structure of the cecum, may provide an environment favorable to the nourishment of microbiotas suited to the production of the higher-energy metabolites required by the bird. Therefore, gut structure, nutrition, immunity, and life-style all contribute to the selection of an exclusive bacterial community that produces types of metabolites beneficial to the host.

scholarly journals AUF1 and HuR Proteins Stabilize Interleukin-8 mRNA in Human Saliva

2008 ◽  
Vol 87 (8) ◽  
pp. 772-776 ◽  
Author(s):  
V. Palanisamy ◽  
N.J. Park ◽  
J. Wang ◽  
D.T. Wong
Keyword(s):  
Mrna Stability ◽  
Binding Proteins ◽  
Human Saliva ◽  
Salivary Protein ◽  
Untranslated Regions ◽  
Cross Linking ◽  
Rna Turnover ◽  
In Vitro Degradation ◽  
The Stability

Human saliva contains thousands of mRNAs, some of which have translational value as diagnostic markers for human diseases. We have found that more than 30% of the mRNAs detected in human saliva contain AU-rich elements (ARE) in their 3′ untranslated regions (3′UTR). Since AREs are known to contribute to RNA turnover by forming complexes with ARE-binding proteins, we hypothesized that salivary mRNA stability is mediated by ARE-binding proteins in human saliva. To test this hypothesis, we monitored the in vitro degradation of a radiolabeled ARE-containing salivary mRNA (IL-8) in salivary protein extracts. The degradation of IL-8 mRNA was accelerated by competition for saliva ARE-binding proteins through the addition of excess unlabeled IL-8 mRNA fragments containing 4 tandem AREs. UV cross-linking and immunoprecipitation experiments revealed 2 ARE-binding proteins, AUF1 and HuR, associated with IL-8 mRNA in saliva. These results demonstrate that ARE-binding proteins contribute to the stability of ARE mRNAs in human saliva.

Scanning tunneling microscopy (STM) of DNA and RNA

1989 ◽  
Vol 47 ◽  
pp. 34-35
Author(s):  
Patricia G. Arscott ◽  
Gil Lee ◽  
Victor A. Bloomfield ◽  
D. Fennell Evans
Keyword(s):  
Molecular Structures ◽  
Inorganic Materials ◽  
Resolving Power ◽  
Scanning Tunneling ◽  
Tunneling Microscopy ◽  
Form And Function ◽  
Dna And Rna ◽  
Calf Thymus ◽  
And Function ◽  
The Relationship

STM is one of the most promising techniques available for visualizing the fine details of biomolecular structure. It has been used to map the surface topography of inorganic materials in atomic dimensions, and thus has the resolving power not only to determine the conformation of small molecules but to distinguish site-specific features within a molecule. That level of detail is of critical importance in understanding the relationship between form and function in biological systems. The size, shape, and accessibility of molecular structures can be determined much more accurately by STM than by electron microscopy since no staining, shadowing or labeling with heavy metals is required, and there is no exposure to damaging radiation by electrons. Crystallography and most other physical techniques do not give information about individual molecules.We have obtained striking images of DNA and RNA, using calf thymus DNA and two synthetic polynucleotides, poly(dG-me5dC)·poly(dG-me5dC) and poly(rA)·poly(rU).

Molecular architecture and functions of the neuronal cytoskeleton

1990 ◽  
Vol 48 (3) ◽  
pp. 2-3
Author(s):  
Nobutaka Hirokawa
Keyword(s):  
Major Elements ◽  
Molecular Structures ◽  
Organelle Transport ◽  
Molecular Architecture ◽  
Neuronal Morphogenesis ◽  
Microtubule Associated Proteins ◽  
Associated Proteins ◽  
And Function ◽  
Small Clusters

In this symposium I will present our studies about the molecular architecture and function of the cytomatrix of the nerve cells. The nerve cell is a highly polarized cell composed of highly branched dendrites, cell body, and a single long axon along the direction of the impulse propagation. Each part of the neuron takes characteristic shapes for which the cytoskeleton provides the framework. The neuronal cytoskeletons play important roles on neuronal morphogenesis, organelle transport and the synaptic transmission. In the axon neurofilaments (NF) form dense arrays, while microtubules (MT) are arranged as small clusters among the NFs. On the other hand, MTs are distributed uniformly, whereas NFs tend to run solitarily or form small fascicles in the dendrites Quick freeze deep etch electron microscopy revealed various kinds of strands among MTs, NFs and membranous organelles (MO). These structures form major elements of the cytomatrix in the neuron. To investigate molecular nature and function of these filaments first we studied molecular structures of microtubule associated proteins (MAP1A, MAP1B, MAP2, MAP2C and tau), and microtubules reconstituted from MAPs and tubulin in vitro. These MAPs were all fibrous molecules with different length and formed arm like projections from the microtubule surface.

Sign in / Sign up

Export Citation Format

Share Document