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Identification of circular rna hsa_circ_0044556 and its effect on the progression of colorectal cancer

CANCER CELL INTErnaTIONAL 2020年第1期20卷 427-427页

作者： Jing, Liang Wu, Junhui Tang, Xiaocheng Ma, Min Long, Fei Tian, Buning Lin, Changwei Cent South Univ Xiangya Hosp 3 Dept Gastrointestinal Surg Changsha Hunan Peoples R China

Background Circular rnas (circrnas) are a novel class of noncoding rnas. Increasing evidence indicates that circrnas play an important role in the occurrence and development of tumors. However, the role of circrna hsa_circ_0044556 in the progression of colorectal cancer (CRC) remains unclear. Methods First, we searched for differentially expressed circrnas using a circrna microarray in paired CRC and adjacent normal tissues. The circrna hsa_circ_0044556 was screened out from the existing CRC circrna microarray in the Gene Expression Omnibus database and our microarray. The clinical significance of hsa_circ_0044556 expression level in CRC patients was then investigated. Finally, the functions of the targets of this circrna were determined in CRC cell lines. Results Hsa_circ_0044556 was highly expressed in CRC patients and was positively correlated with tumor stage and lymph node metastasis. In CRC cell lines, the proliferation, migration, and invasion of cancer cells were inhibited by knocking down hsa_circ_0044556 expression. Conclusion Hsa_circ_0044556 promoted the progression of CRC. It is possible that hsa_circ_0044556 will become a novel biomarker or therapeutic target for CRC.

关键词： noncoding rna Circular rna Colorectal cancer hsa_circ_0044556 Biomarker

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Exosomes-micrornas interacted with gastric cancer and its microenvironment: a mini literature review

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BIOMARKERS IN MEDICINE 2020年第2期14卷 141-150页

作者： Deng, Zhiyong Wu, Jianhong Xu, Song Chen, Fang Zhang, Zhiqing Jin, Anqi Wang, Jianjun Jiangsu Univ Affiliated Kunshan Hosp BioBank Kunshan 215300 Jiangsu Peoples R China Jiangsu Univ Affiliated Kunshan Hosp Dept Clin Lab Kunshan 215300 Jiangsu Peoples R China Jiangsu Univ Affiliated Kunshan Hosp Dept Pathol Kunshan 215300 Jiangsu Peoples R China

Exosomes have appeared as fundamental vehicle-modulated crosstalk among various cells in the tumor microenvironment. The systematic understanding of exosomes in gastric cancer (GC) enhances our comprehension about the tumor growth, metastasis, chemoresistance and diagnosis of cancers. The versatile functions of exosomes provide reasonable explanations about the propensity for GC metastasis. The selectively enriched components, especially some exosomal mirnas, are potential noninvasive biomarkers for sensitive and specific GC diagnosis. Given the characteristics of exosomes, frontier researchers are stimulated to modulate the biogenesis, concentrations or release of exosomes so as to disturb malignant signals between cells. Abnormal expression profiles of exosomal mirnas afford potential GC therapeutic or diagnostic strategies in future.

关键词： biomarkers cancer-associated fibroblasts diagnostic strategies exosomes gastric cancer microarray analysis microenvironment mirnas noncoding rna therapeutic strategies tumor

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noncoding rnas in disease

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FEBS LETTERS 2018年第17期592卷 2884-2900页

作者： Lekka, Evangelia Hall, Jonathan Swiss Fed Inst Technol Inst Pharmaceut Sci Dept Chem & Appl Biosci CH-8093 Zurich Switzerland

noncoding rnas are emerging as potent and multifunctional regulators in all biological processes. In parallel, a rapidly growing number of studies has unravelled associations between aberrant noncoding rna expression and human diseases. These associations have been extensively reviewed, often with the focus on a particular microrna (mirna) (family) or a selected disease/pathology. In this Mini-Review, we highlight a selection of studies in order to demonstrate the wide-scale involvement of mirnas and long noncoding rnas in the pathophysiology of three types of diseases: cancer, cardiovascular and neurological disorders. This research is opening new avenues to novel therapeutic approaches.

关键词： long noncoding rna microrna noncoding rna

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Small rna-Sequencing Library Preparation for the Halophilic Archaeon

Small RNA-Sequencing Library Preparation for the Halophilic ...

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作者： Diego Rivera Gelsinger Jocelyne DiRuggiero

Posttranscriptional regulation actuated by small rnas (srnas) plays essential roles in a wide variety of cellular processes, especially in stress responses and environmental signaling. Hundreds of srnas have recently been discovered in archaea using genome-wide approaches but the molecular mechanisms of only a few have been characterized experimentally. Here, we describe how to build srna sequencing libraries using size-selected total rna in the model archaeon, Haloferax volcanii, to provide a tool to further characterize srnas in archaea. less

关键词： rna-seq Library Preparation Total rna Extraction PAGE PCR Illumina Sequencing Snap Freeze Nucleic Acid Microarray Small rna-seq Gel Electrophoresis Saccharomyces cerevisiae Transcription Small rna noncoding rna Sequencing libraries Haloarchaea

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Quantitative, Convenient, and Efficient Genome-Wide R-Loop Profiling by ssDRIP-Seq in Multiple Organisms

Quantitative, Convenient, and Efficient Genome-Wide R-Loop P...

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作者： Wei Xu Kuan Li Qin Li Shuai Li Jincong Zhou Qianwen Sun

R-loop is a three-stranded chromatin structure, comprising one single-stranded DNA and another DNA:rna hybrid strand, plays various and essential biological functions in many organisms. Developing a precise, efficient, faithful, and unbiased genome-wide R-loop detection method with extensive adaptability in all organisms is at the top priority for R-loop biology. Here, we provide a straightforward and highly efficient protocol for genome-wide strand-specific R-loop profiling in various organisms. In brief, genomic DNA is extracted and fragmented by the cocktail of restriction enzymes, and then the DNA:rna hybrids are immunoprecipitated, following by the single-stranded DNA adaptor ligation and next-generation sequencing (named as ssDRIP-seq). Coupling with a straightforward and step-by-step bioinformatic pipeline, this method can provide high resolution and comprehensive strand-specific information for R-loop formation. ssDRIP-seq has been successfully applied for detecting R-loops from prokaryotes such as E. coli, to eukaryotes such as S. cerevisiae, mammalian cell culture and tissues, as well as plants Arabidopsis and rice, with high reproducibility and sensitivity. less

关键词： PCR Immunoprecipitation DNA Ligation Cell And Tissue Culture Electrophoresis EMSA Native PAGE DNA Extraction Bowtie bedtools Real-time PCR Genomics Next-generation sequencing Genome Nucleic acid noncoding rna R-loop

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The CCR4-NOT Complex Maintains Stability and Transcription of rrna Genes by Repressing Antisense Transcripts

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MOLECULAR AND CELLULAR BIOLOGY 2020年第1期40卷 1-15页

作者： Hosoyamada, Shun Sasaki, Mariko Kobayashi, Takehiko IQB Tokyo Japan Univ Tokyo Grad Sch Sci Dept Biol Sci Tokyo Japan Univ Tokyo Collaborat Res Inst Innovat Microbiol Tokyo Japan

The rrna genes (rDNA) in eukaryotes are organized into highly repetitive gene clusters. Each organism maintains a particular number of copies, suggesting that the rDNA is actively stabilized. We previously identified about 700 Saccharomyces cerevisiae genes that could contribute to rDNA maintenance. Here, we further analyzed these deletion mutants with unstable rDNA by measuring the amounts of extrachromosomal rDNA circles (ERCs) that are released as by-products of intrachromosomal recombination. We found that extremely high levels of ERCs were formed in the absence of Pop2 (Caf1), which is a subunit of the CCR4-NOT complex, important for the regulation of all stages of gene expression. In the pop2 mutant, transcripts from the noncoding promoter E-pro in the rDNA accumulated, and the amounts of cohesin and condensin were reduced, which could promote recombination events. Moreover, we discovered that the amount of rrna was decreased in the pop2 mutant. Similar phenotypes were observed in the absence of subunits Ccr4 and Not4 that, like Pop2, convey enzymatic activity to the complex. These findings indicate that lack of any CCR4-NOT-associated enzymatic activity resulted in a severe unstable rDNA phenotype related to the accumulation of noncoding rna from E-pro.

关键词： CCR4-NOT complex rna degradation genome instability noncoding rna ribosomal rna gene

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A Conserved noncoding Locus Regulates Random Monoallelic Xist Expression across a Topological Boundary

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MOLECULAR CELL 2020年第2期77卷 352-+页

作者： Galupa, Rafael Nora, Elphege Pierre Worsley-Hunt, Rebecca Picard, Christel Gard, Chris van Bemmel, Joke Gerarda Servant, Nicolas Zhan, Yinxiu El Marjou, Fatima Johanneau, Colin Diabangouaya, Patricia Le Saux, Agnes Lameiras, Sonia da Fonseca, Juliana Pipoli Loos, Friedemann Gribnau, Joost Baulande, Sylvain Ohler, Uwe Giorgetti, Luca Heard, Edith PSL Res Univ Inst Curie CNRSGenet & Dev Biol Unit UMR3215INSERMU934Mammalian Dev Epigenet Grp Paris France Berlin Inst Med Syst Biol Max Delbruck Ctr Mol Med Helmholtz Assoc Berlin Germany PSL Res Univ Bioinformat Biostat Epidemiol & Computat Syst Uni INSERM U900Inst Curie Paris France PSL Res Univ Ctr Computat Biol CBIO MINES ParisTech Paris France Friedrich Miescher Inst Biomed Res Basel Switzerland Univ Basel Basel Switzerland Inst Curie Transgenesis Facil Paris France Inst Curie Inst Curie Genom Excellence ICGex Paris France Erasmus MC Univ Med Ctr Dept Dev Biol Rotterdam Netherlands Humboldt Univ Dept Biol Berlin Germany Coll France Paris France European Mol Biol Lab Heidelberg Germany Gladstone Inst Cardiovasc Dis San Francisco CA USA Univ Calif San Francisco Cardiovasc Res Inst San Francisco CA 94143 USA Univ Calif San Francisco Dept Biochem & Biophys San Francisco CA USA

cis-Regulatory communication is crucial in mammalian development and is thought to be restricted by the spatial partitioning of the genome in topologically associating domains (TADs). Here, we discovered that the Xist locus is regulated by sequences in the neighboring TAD. In particular, the promoter of the noncoding rna Linx (LinxP) acts as a long-range silencer and influences the choice of X chromosome to be inactivated. This is independent of Linx transcription and independent of any effect on Tsix, the antisense regulator of Xist that shares the same TAD as Linx. Unlike Tsix, LinxP is well conserved across mammals, suggesting an ancestral mechanism for random monoallelic Xist regulation. When introduced in the same TAD as Xist, LinxP switches from a silencer to an enhancer. Our study uncovers an unsuspected regulatory axis for X chromosome inactivation and a class of cis-regulatory effects that may exploit TAD partitioning to modulate developmental decisions.

关键词： TADs X-inactivation cis-regulatory landscape gene regulation noncoding rna silencer enhancer Xist Linx 5C

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Opposing roles of C/EBPα and eEF1A1 in Sp1-regulated miR-122 transcription

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rna BIOLOGY 2020年第2期17卷 202-210页

作者： Zeng, Chunxian Sang, Ye Wang, Feng-Yi Zhuang, Shi-Mei Sun Yat Sen Univ MOE Key Lab Gene Funct & Regulat State Key Lab Biocontrol Sch Life SciInnovat Ctr Canc Med Guangzhou Peoples R China Sun Yat Sen Univ Key Lab Liver Dis Guangdong Prov Affiliated Hosp 3 Guangzhou Peoples R China

We previously showed that miR- 122 was frequently downregulated in hepatocellular carcinoma (HCC) and C/EBP alpha transactivated miR-122 expression. In this study, we found that Sp1 bound to the miR-122 promoter at two different sites. Interestingly, either inhibition or overexpression of Sp1 could decrease the miR-122 promoter activity and the cellular miR-122 level in hepatoma cells. Further investigations disclosed that Sp1 cooperated with C/EBP alpha to induce miR- 122 transcription by binding to the positive regulatory site D in the miR-122 promoter, whereas eEF1A1 interacted with Sp1 to bind to the negative regulatory site E and inhibit miR-122 transcription. Significantly, both Sp1 and eEF1A1 levels were enhanced, but C/EBP alpha and miR-122 expression were reduced in HCC tissues. Knockdown of eEF1A1 enhanced miR-122 level and inhibited cell growth, and these effects were abrogated when Sp1 was silenced. Consistently, the promoter activity enhanced by site E deletion was attenuated by silencing Sp1. Moreover, reduction of miR-122 resulted from Sp1 overexpression was rescued by coexpressing C/EBP alpha. These data suggest that C/EBP alpha and eEF1A1 may play opposing roles in Sp1-regulating miR-122 transcription, and the eEF1A1 upregulation accompanied by C/EBP alpha downregulation in HCC may switch the regulatory functions of Sp1 and led to reduced miR-122 transcription. These findings highlight the complex regulatory network of miR- 122 expression and its significance in hepatocarcinogenesis.

关键词： noncoding rna mirna miR-122 Sp1 C/EBP alpha eEF1A1

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Role of epigenetics andmirnasin orofacial clefts

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BIRTH DEFECTS RESEARCH 2020年第19期112卷 1635-1659页

作者： Garland, Michael A. Sun, Bo Zhang, Shuwen Reynolds, Kurt Ji, Yu Zhou, Chengji J. Univ Calif Davis Sch Med Dept Biochem & Mol Med Sacramento CA 95817 USA Univ Calif Davis Sch Med Shriners Hosp Children Inst Pediat Regenerat Med Sacramento CA 95817 USA Univ Calif Davis Biochem Mol Cellular & Dev Biol BMCDB Grad Grp Davis CA 95616 USA

Orofacial clefts (OFCs) have multiple etiologies and likely result from an interplay between genetic and environmental factors. Within the last decade, studies have implicated specific epigenetic modifications and noncoding rnas as additional facets of OFC etiology. Altered gene expression through DNA methylation and histone modification offer novel insights into how specific genes contribute to distinct OFC subtypes. Epigenetics research has also provided further evidence that cleft lip only (CLO) is a cleft subtype with distinct etiology. Polymorphisms or misexpression of genes encoding micrornas, as well as their targets, contribute to OFC risk. The ability to experimentally manipulate epigenetic changes and noncoding rnas in animal models, such as zebrafish,Xenopus, mice, and rats, has offered novel insights into the mechanisms of various OFC subtypes. Although much remains to be understood, recent advancements in our understanding of OFC etiology may advise future strategies of research and preventive care.

关键词： cleft lip palate DNA methylation epigenetics histone modification noncoding rna

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A systems approach delivers a functional microrna catalog and expanded targets for seizure suppression in temporal lobe epilepsy

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PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 2020年第27期117卷 15977-15988页

作者： Veno, Morten T. Reschke, Cristina R. Morris, Gareth Connolly, Niamh M. C. Su, Junyi Yan, Yan Engel, Tobias Jimenez-Mateos, Eva M. Harder, Lea M. Pultz, Dennis Haunsberger, Stefan J. Pal, Ajay Heller, Janosch P. Campbell, Aoife Langa, Elena Brennan, Gary P. Conboy, Karen Richardson, Amy Norwood, Braxton A. Costard, Lara S. Neubert, Valentin Del Gallo, Federico Salvetti, Beatrice Vangoor, Vamshidhar R. Sanz-Rodriguez, Amaya Muilu, Juha Fabene, Paolo F. Pasterkamp, R. Jeroen Prehn, Jochen H. M. Schorge, Stephanie Andersen, Jens S. Rosenow, Felix Bauer, Sebastian Kjems, Jorgen Henshall, David C. Aarhus Univ Interdisciplinary Nanosci Ctr Dept Mol Biol & Genet DK-8000 Aarhus C Denmark Royal Coll Surgeons Ireland Dept Physiol & Med Phys Dublin D02 YN77 Ireland Royal Coll Surgeons Ireland FutureNeuro Sci Fdn Ireland Res Ctr Chron & Rare Neurol Dis Dublin D02 YN77 Ireland UCL Inst Neurol Dept Clin & Expt Epilepsy London WC1N 3BG England Univ Southern Denmark Ctr Expt Bioinformat DK-5230 Odense M Denmark Expesicor Inc Dept Neurosci Kalispell MT 59901 USA FYR Diagnost Diagnost Dev Missoula MT 59801 USA Philipps Univ Marburg Epilepsy Ctr Dept Neurol D-35043 Marburg Germany Univ Hosp Frankfurt Epilepsy Ctr Frankfurt Rhine Main Neuroctr D-60528 Frankfurt Germany Goethe Univ Frankfurt Ctr Personalized Translat Epilepsy Res D-60528 Frankfurt Germany Rostock Univ Oscar Langendorff Inst Physiol Med Ctr D-18051 Rostock Germany Univ Verona Dept Neurosci Biomed & Movement Sci I-837134 Verona Italy Univ Utrecht Affiliated Partner European Reference Network Epi Dept Translat Neurosci Univ Med Ctr UtrechtBrain Ctr NL-3584 CG Utrecht Netherlands BC Platforms Res & Dev FI-02130 Espoo Finland UCL UCL Sch Pharm London WC1N 1AX England

Temporal lobe epilepsy is the most common drug-resistant form of epilepsy in adults. The reorganization of neural networks and the gene expression landscape underlying pathophysiologic network behavior in brain structures such as the hippocampus has been suggested to be controlled, in part, by micrornas. To systemati-cally assess their significance, we sequenced Argonaute-loaded micrornas to define functionally engaged micrornas in the hip-pocampus of three different animal models in two species and at six time points between the initial precipitating insult through to the establishment of chronic epilepsy. We then selected commonly up-regulated micrornas for a functional in vivo therapeutic screen using oligonucleotide inhibitors. Argonaute sequencing generated 1.44 billion small rna reads of which up to 82% were micrornas, with over 400 unique micrornas detected per model. Approximately half of the detected micrornas were dysregulated in each epilepsy model. We prioritized commonly up-regulated micrornas that were fully conserved in humans and designed custom antisense oligonu-cleotides for these candidate targets. Antiseizure phenotypes were observed upon knockdown of miR-10a-5p, miR-21a-5p, and miR-142a-5p and electrophysiological analyses indicated broad safety of this approach. Combined inhibition of these three micrornas reduced spontaneous seizures in epileptic mice. Proteomic data, rna sequenc-ing, and pathway analysis on predicted and validated targets of these micrornas implicated derepressed TGF-beta signaling as a shared seizure-modifying mechanism. Correspondingly, inhibition of TGF-beta signaling occluded the antiseizure effects of the antagomirs. To-gether, these results identify shared, dysregulated, and functionally active micrornas during the pathogenesis of epilepsy which repre-sent therapeutic antiseizure targets.

关键词： antisense oligonucleotide biomarker epigenetic epilepsy noncoding rna

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