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Detection of microrna-335-5p on an Interdigitated Electrode Surface for Determination of the Severity of Abdominal Aortic Aneurysms

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NANOSCALE RESEARCH LETTERS 2020年第1期15卷 105-105页

作者： Lu, Bei Liu, Leiting Wang, Jingrui Chen, Yuan Li, Zhijiang Gopinath, Subash C. B. Lakshmipriya, Thangavel Huo, Zongwei Zhejiang Univ Affiliated Hangzhou First Peoples Hosp Sch Med Dept Hepatopancreatobiliaty Surg Hangzhou 310006 Zhejiang Peoples R China Wuhan 1 Hosp Dept Gen Thorac & Vasc Surg Wuhan 430022 Hubei Peoples R China First Peoples Hosp Zunyi Dept Endocrinol Zunyi 563000 Guizhou Peoples R China Jingmen 1 Peoples Hosp Dept Gallbladder Pancreas & Vasc Surg Jingmen 448000 Hubei Peoples R China Univ Malaysia Perlis Sch Bioproc Engn Arau 02600 Perlis Malaysia Univ Malaysia Perlis Inst Nano Elect Engn Kangar 01000 Perlis Malaysia Shandong First Med Univ & Shandong Acad Med Sci Shandong Canc Hosp & Inst Dept Nucl Med Jinan 250117 Shandong Peoples R China

Abdominal aortic aneurysm (AAA) refers to the enlargement of the lower artery of the abdominal aorta, and identification of an early detection tool is urgently needed for diagnosis. In the current study, an interdigitated electrode (IDE) sensing surface was used to identify mirna-335-5p, which reflects the formation of AAAs. The uniformity of the silica material was observed by 3D profilometry, and the chemically modified highly conductive surface improved the detection via the I-V mode. The targeted mirna-335-5p was detected in a dose-dependent manner and based on linear regression and 3 sigma analyses, the sensitivity was determined to be 1 fM with a biotinylated probe. The high specificity was shown by discriminating the target sequence from noncomplementary and single- and triple-mismatched sequences. These outputs demonstrated the high-performance detection of mirna-335-5p with good reproducibility for determination of the severity of AAA.

关键词： Biosensor noncoding rna Bulging aorta Early diagnosis Streptavidin-biotin

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Discovery of a large-scale, cell-state-responsive allosteric switch in the 7SK rna using DANCE-MaP

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MOLECULAR CELL 2022年第9期82卷 1708-+页

作者： Olson, Samuel W. Turner, Anne-Marie W. Arney, J. Winston Saleem, Irfana Weidmann, Chase A. Margolis, David M. Weeks, Kevin M. Mustoe, Anthony M. Univ N Carolina Dept Chem Chapel Hill NC 27599 USA Univ N Carolina Dept Med Chapel Hill NC 27599 USA Univ N Carolina UNC HIV Cure Ctr Chapel Hill NC 27599 USA Baylor Coll Med Verna & Marrs McClean Dept Biochem & Mol Biol Therapeut Innovat Ctr THINC Houston TX 77030 USA Baylor Coll Med Dept Mol & Human Genet Houston TX 77030 USA

7SK is a conserved noncoding rna that regulates transcription by sequestering the transcription factor PTEFb. 7SK function entails complex changes in rna structure, but characterizing rna dynamics in cells remains an unsolved challenge. We developed a single-molecule chemical probing strategy, DANCE-MaP (deconvolution and annotation of ribonucleic conformational ensembles), that defines per-nucleotide reactivity, direct base pairing interactions, tertiary interactions, and thermodynamic populations for each state in rna structural ensembles from a single experiment. DANCE-MaP reveals that 7SK rna encodes a large-scale structural switch that couples dissolution of the P-TEFb binding site to structural remodeling at distal release factor binding sites. The 7SK structural equilibrium shifts in response to cell growth and stress and can be targeted to modulate expression of P-TEFbresponsive genes. Our study reveals that rna structural dynamics underlie 7SK function as an integrator of diverse cellular signals to control transcription and establishes the power of DANCE-MaP to define rna dynamics in cells.

关键词： DANCE-MaP ensemble deconvolution noncoding rna transcriptional regulation cancer HIV

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Maintenance of epigenetic information: a noncoding rna perspective

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CHROMOSOME RESEARCH 2013年第6-7期21卷 615-625页

作者： Mondal, Tanmoy Kanduri, Chandrasekhar Gothenburg Univ Sahlgrenska Acad Inst Biomed Dept Med Genet S-40530 Gothenburg Sweden

Along the lines of established players like chromatin modifiers and transcription factors, noncoding rna (ncrna) are now widely accepted as one of the key regulatory molecules in epigenetic regulation of transcription. With increasing evidence of ncrnas in the establishment of gene silencing through their ability to interact with major chromatin modifiers, in the current review, we discuss their prospective role in the area of inheritance and maintenance of these established silenced states which can be reversible or irreversible in nature. In addition, we attempt to understand and speculate how these rna dependent or independent maintenance mechanisms differ between each other in a developmental stage, tissue, and gene-specific manner in different biological contexts by utilizing known/unknown regulatory factors.

关键词： noncoding rna Long noncoding rna Chromatin Histone modifications DNA methylation Genomic imprinting X chromosome inactivation Kcnq1ot1 Xist Replication PRC1 PRC2

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Regulation of epigenetic homeostasis in uveal melanoma and retinoblastoma

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PROGRESS IN RETINAL AND EYE RESEARCH 2022年 89卷 101030页

作者： Chai, Peiwei Jia, Ruobing Li, Yongyun Zhou, Chuandi Gu, Xiang Yang, Ludi Shi, Hanhan Tian, Hao Lin, Huimin Yu, Jie Zhuang, Ai Ge, Shengfang Jia, Renbing Fan, Xianqun Shanghai Jiao Tong Univ Sch Med Peoples Hosp 9 Dept Ophthalmol Shanghai 200025 Peoples R China Shanghai Key Lab Orbital Dis & Ocular Oncol Shanghai 200025 Peoples R China Shanghai Jiao Tong Univ Shanghai Gen Hosp Dept Ophthalmol Shanghai Peoples R China

Uveal melanoma (UM) and retinoblastoma (RB), which cause blindness and even death, are the most frequently observed primary intraocular malignancies in adults and children, respectively. Epigenetic studies have shown that changes in the epigenome contribute to the rapid progression of both UM and RB following classic genetic changes. The loss of epigenetic homeostasis plays an important role in oncogenesis by disrupting the normal patterns of gene expression. The targetable nature of epigenetic modifications provides a unique opportunity to optimize treatment paradigms and establish new therapeutic options for both UM and RB with these aberrant epigenetic modifications. We aimed to review the research findings regarding relevant epigenetic changes in UM and RB. Herein, we 1) summarize the literature, with an emphasis on epigenetic alterations, including DNA methylation, histone modifications, rna modifications, noncoding rnas and an abnormal chromosomal architecture;2) elaborate on the regulatory role of epigenetic modifications in biological processes during tumorigenesis;and 3) propose promising therapeutic candidates for epigenetic targets and update the list of epigenetic drugs for the treatment of UM and RB. In summary, we endeavour to depict the epigenetic landscape of primary intraocular malignancy tumorigenesis and provide potential epigenetic targets in the treatment of these tumours.

关键词： Epigenetics Uveal melanoma Retinoblastoma noncoding rna Chromosome conformation rna Modifications

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Pervasive rna Regulation of Metabolism Enhances the Root Colonization Ability of Nitrogen-Fixing Symbiotic alpha-Rhizobia

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MBIO 2022年第1期13卷 e0357621页

作者： Garcia-Tomsig, Natalia, I Robledo, Marta diCenzo, George C. Mengoni, Alessio Millan, Vicenta Peregrina, Alexandra Uceta, Alejandro Jimenez-Zurdo, Jose, I CSIC Struct Dynam & Funct Rhizobacterial Genomes Grp Ecol Genet Rizosfera Estn Expt Zaidin Granada Spain Queens Univ Dept Biol Kingston ON Canada Univ Florence Dept Biol Sesto Fiorentino Italy Univ Cantabria Sodercan Intergen Grp Dept Biol Mol Inst Biomed & Biotecnol CantabriaCSIC Santander Spain Univ Nova Lisboa Control Gene Express Lab Inst Tecnol Quim & Biol Antonio Xavier Oeiras Portugal

The rhizosphere and rhizoplane are nutrient-rich but selective environments for the root microbiome. Here, we deciphered a posttranscriptional network regulated by the homologous trans-small rnas (srnas) AbcR1 and AbcR2, which rewire the metabolism of the nitrogen-fixing a-rhizobium Sinorhizobium meliloti during preinfection stages of symbiosis with its legume host alfalfa. The LysR-type regulator LsrB, which transduces the cell redox state, is indispensable for AbcR1 expression in actively dividing bacteria, whereas the stress-induced transcription of AbcR2 depends on the alternative o factor RpoH1. MS2 affinity purification coupled with rna sequencing unveiled exceptionally large and overlapping AbcR1/2 mrna interactomes, jointly representing similar to 6% of the S. meliloti protein-coding genes. Most mrnas encode transport/metabolic proteins whose translation is silenced by base pairing to two distinct anti-Shine Dalgarno motifs that function independently in both srnas. A metabolic model-aided analysis of the targetomes predicted changes in AbcR1/2 expression driven by shifts in carbon/nitrogen sources, which were confirmed experimentally. Low AbcR1/2 levels in some defined media anticipated overexpression growth phenotypes linked to the silencing of specific mrnas. As a proof of principle, we confirmed AbcR1/2-mediated downregulation of the L-amino acid AapQ permease. AbcR1/2 interactomes are well represented in rhizosphere-related S. meliloti transcriptomic signatures. Remarkably, a lack of AbcR1 specifically compromised the ability of S. meliloti to colonize the root rhizoplane. The AbcR1 regulon likely ranks the utilization of available substrates to optimize metabolism, thus conferring on S. meliloti an advantage for efficient rhizosphere/rhizoplane colonization. AbcR1 regulation is predicted to be conserved in related alpha-rhizobia, which opens unprecedented possibilities for engineering highly competitive biofertilizers. IMPORTANCE Nitrogen-fixing root n

关键词： Sinorhizobium meliloti alphaproteobacteria noncoding rna riboregulation

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Analysis of Eukaryotic lincrna Sequences Indicates Signatures of Hindered Translation Linked to Selection Pressure

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MOLECULAR BIOLOGY AND EVOLUTION 2022年第2期39卷 msab356-msab356页

作者： Brummer, Anneke Dreos, Rene Marques, Ana Claudia Bergmann, Sven Univ Lausanne Dept Computat Biol DBC Lausanne Switzerland Swiss Inst Bioinformat SIB Lausanne Switzerland Univ Lausanne Ctr Integrat Genom CIG Lausanne Switzerland Univ Cape Town Dept Integrat Biomed Sci Cape Town South Africa

Long intergenic noncoding rnas (lincrnas) represent a large fraction of transcribed loci in eukaryotic genomes. Although classified as noncoding, most lincrnas contain open reading frames (ORFs), and it remains unclear why cytoplasmic lincrnas are not or very inefficiently translated. Here, we analyzed signatures of hindered translation in lincrna sequences from five eukaryotes, covering a range of natural selection pressures. In fission yeast and Caenorhabditis elegans, that is, species under strong selection, we detected significantly shorter ORFs, a suboptimal sequence context around start codons for translation initiation, and trinucleotides ("codons") corresponding to less abundant trnas than for neutrally evolving control sequences, likely impeding translation elongation. For human, we detected signatures for cell-type-specific hindrance of lincrna translation, in particular codons in abundant cytoplasmic lincrnas corresponding to lower expressed trnas than control codons, in three out of five human cell lines. We verified that varying trna expression levels between cell lines are reflected in the amount of ribosomes bound to cytoplasmic lincrnas in each cell line. We further propose that codons at ORF starts are particularly important for reducing ribosome-binding to cytoplasmic lincrna ORFs. Altogether, our analyses indicate that in species under stronger selection lincrnas evolved sequence features generally hindering translation and support cell-type-specific hindrance of translation efficiency in human lincrnas. The sequence signatures we have identified may improve predicting peptide-coding and genuine noncoding lincrnas in a cell type.

关键词： noncoding rna computational sequence analysis codon usage trna abundance ribosome binding evolutionary selection pressure

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Death by lipids: The role of small nucleolar rnas in metabolic stress

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JOUrnaL OF BIOLOGICAL CHEMISTRY 2020年第25期295卷 8628-8635页

作者： Schaffer, Jean E. Harvard Med Sch Joslin Diabet Ctr Boston MA 02115 USA

Excess fatty acid accumulation in nonadipose tissues leads to cell dysfunction and cell death that is linked to the pathogenesis of inherited and acquired human diseases. Study of this process, known as lipotoxicity, has provided new insights into the regulation of lipid homeostasis and has revealed new molecular pathways involved in lipid-induced cellular stress. The discovery that disruption of specific small nucleolar rnas protects against fatty acid?induced cell death and remodels metabolismin vivoopens new opportunities for understanding how nutrient signals influence cellular and systemic metabolic homeostasis through rna biology.

关键词： lipotoxicity noncoding rna snornas diabetes complications genetic screens rna diabetes fatty acid triacylglycerol noncoding rnas

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Protocols for Northern Analysis of Exosome Substrates and Other noncoding rnas

Protocols for Northern Analysis of Exosome Substrates and Ot...

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作者： Cristina Cruz Jonathan Houseley

Over the past decade a plethora of noncoding rnas (ncrnas) have been identified, initiating an explosion in rna research. Although rna sequencing methods provide unsurpassed insights into ncrna distribution and expression, detailed information on structure and processing are harder to extract from sequence data. In contrast, northern blotting methods provide uniquely detailed insights into complex rna populations but are rarely employed outside specialist rna research groups. Such techniques are generally considered difficult for nonspecialists, which is unfortunate as substantial technical advances in the past few decades have solved the major challenges. Here we present simple, reproducible and highly robust protocols for separating glyoxylated rna on agarose gels and heat denatured rna on polyacrylamide–urea gels using standard laboratory electrophoresis equipment. We also provide reliable transfer and hybridization protocols that do not require optimization for most applications. Together, these should allow any molecular biology lab to elucidate the structure and processing of ncrnas of interest. less

关键词： rna Electrophoresis Northern Blot rna-seq Electrophoresis Dissection Gel Imaging Chromatography Exosome noncoding rna Glyoxal

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rna thermometers and other regulatory elements: Diversity and importance in bacterial pathogenesis

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WILEY INTERDISCIPLINARY REVIEWS-rna 2022年第5期13卷 e1711-e1711页

作者： Sharma, Akanksha Alajangi, Hema Kumari Pisignano, Giuseppina Sood, Vikas Singh, Gurpal Barnwal, Ravi Pratap Panjab Univ Dept Biophys Chandigarh 160014 India Panjab Univ Univ Inst Pharmaceut Sci Chandigarh India Univ Bath Dept Biol & Biochem Bath Avon England Jamia Hamdard Dept Biochem New Delhi India

Survival of microorganisms depends to a large extent on environmental conditions and the occupied host. By adopting specific strategies, microorganisms can thrive in the surrounding environment and, at the same time, preserve their viability. Evading the host defenses requires several mechanisms compatible with the host survival which include the production of rna thermometers to regulate the expression of genes responsible for heat or cold shock as well as of those involved in virulence. Microorganisms have developed a variety of molecules in response to the environmental changes in temperature and even more specifically to the host they invade. Among all, rna-based regulatory mechanisms are the most common ones, highlighting the importance of such molecules in gene expression control and novel drug development by suitable structure-based alterations. This article is categorized under: rna Structure and Dynamics > rna Structure, Dynamics and Chemistry rna in Disease and Development > rna in Disease rna Structure and Dynamics > Influence of rna Structure in Biological Systems

关键词： heat shock noncoding rna pathogenesis riboswitches rna thermometer temperature virulence

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Low levels of miR-34c in nasal washings as a candidate marker of aggressive disease in wood and leather exposed workers with sinonasal intestinal-type adenocarcinomas (ITACs)

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TRANSLATIONAL ONCOLOGY 2022年 25卷 101507-101507页

作者： Bigagli, Elisabetta Maggiore, Giandomenico Cinci, Lorenzo D'Ambrosio, Mario Locatello, Luca Giovanni Nardi, Cosimo Palomba, Annarita Leopardi, Gianluca Orlando, Pietro Licci, Giuseppe Gallo, Oreste Luceri, Cristina Univ Florence Dept Neurosci Psychol Drug Res & Child Hlth NEUROF Sect Pharmacol & Toxicol Florence Italy Univ Florence Careggi Univ Hosp Dept Otorhinolaryngol Florence Italy Careggi Univ Hosp Dept Expt & Clin Biomed Sci Radiodiagnost Unit 2 Florence Italy Univ Florence Dept Hlth Sci Sect Pathol Anat Azienda Ospedaliero Univ Careggi Florence Italy Osped S Giuseppe Empoli Empoli Italy

Introduction: Sinonasal intestinal-type adenocarcinomas (ITACs) are rare and aggressive tumors, closely related to professional exposure to wood dusts or leather. Here we explored the role of non-coding rnas controlling MUC2 in liquid biopsies and tumors from ITAC patients with the aim of identifying biomarkers and molecular mechanisms to improve early diagnosis, prognosis, and therapeutic approaches for this rare cancer. Methods: MiR-34c-3p, lncrna AF147447 and MUC2 were measured in tumors and normal mucosa, in nasal washings (NW) from the affected and non-affected nostril and in plasma from 17 ITAC patients. The Apparent Diffusion Coefficient (ADC) was also evaluated by Magnetic Resonance Imaging. Results: MiR-34c was higher in ITACs compared to the corresponding normal mucosa (p = 0.021). Differentiated tumors exhibited higher miR-34c levels (p = 0.025) and lower ADC values (p<0.001) compared to mucinous ones and these parameters were also inversely correlated (r = 0.87;p = 0.001). High MUC2 tumor expression was associated with orbital extension (p = 0.010). Low miR-34c levels in NW were associated with orbital (p = 0.009) and intracranial (p = 0.031) extension and with advanced TNM stage (p = 0.054). Functional analysis identified Wnt, Focal adhesion, MAPK and inflammatory signalings among the pathways most enriched in mir34c targets. Discussion: Our results suggest measuring miR-34c in NW as a biomarker for early diagnosis and monitoring of ITAC patients and for the surveillance of wood and leather exposed workers. Further research on the involvement of miR-34c regulated pathways in ITAC tumorigenesis may also allow the development of new therapeutic approaches for this rare cancer.

关键词： Intestinal -type sinonasal adenocarcinomas ITAC Microrna noncoding rna Biomarkers

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