Tag: ncRNA

Summary of Genomics and Transcriptomics – DNA sequencing I. Goal II. Methodology A. Sanger DNA

DNA sequencing I. Goal II. Methodology A. Sanger DNA sequencing ● Up to 900 base pairs ● Primer extension with labeled ddNTPs (radioactive or fluorescent) ● Prior knowledge on target needed ● Difficult to detect variation in mixtures ● High accuracy + still in use for genotyping When it is…

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Progress of circRNA/lncRNA-miRNA-mRNA axis in atrial fibrillation [PeerJ]

Introduction The incidence and mortality rates of AF are continuously increasing, leading to serious complications such as heart failure and stroke (Fig. 1) (Sagris et al., 2021). The occurrence and development of AF involve different mechanisms and interactions (Kornej et al., 2020). AF often progresses from paroxysmal to persistent (Nattel…

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Characteristics of Amorphophallus konjac as indicated by its genome

Genome assembly and annotation The DNA sequencing data (1119.58 Gb, average 110× coverage) of the A. konjac sample were obtained using the Illumina Hiseq 2500 sequencer. A summary of the sequence data used for the assembly is presented in Table S1. The estimated genome size is 4,512,012,462 bp using 19-mer frequency distribution based…

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ncRNA | February 2024 – Browse Articles

All articles published by MDPI are made immediately available worldwide under an open access license. No special permission is required to reuse all or part of the article published by MDPI, including figures and tables. For articles published under an open access Creative Common CC BY license, any part of…

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Probing the conformational changes of in vivo overexpressed cell cycle regulator 6S ncRNA

join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Probing the conformational changes of in vivo overexpressed cell cycle regulator 6S ncRNA Makraki, E. ; Miliara, S. ; Pagkalos, M. ; Kokkinidis, M. ; Mylonas, E. (Corresponding author)Extern*EMBL* ; Fadouloglou, V. E. (Corresponding author)Extern*EMBL* 2023Frontiers Lausanne This record in other databases:   Please use a persistent id in citations: doi:10.3389/fmolb.2023.1219668  doi:10.3204/PUBDB-2023-07967 Abstract: The…

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Special Issue : Extracellular Vesicles and ncRNA

Dear Colleagues, Over the past two decades, the biological science arena has witnessed the emergence and rapid advancement of two distinct research domains: noncoding RNA (ncRNA) and extracellular vesicles. Presently, the significance of ncRNA in the biology of virtually all living organisms is beyond dispute, and our comprehension of its…

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An ncRNA transcriptomics-based approach to design siRNA molecules against SARS-CoV-2 double membrane vesicle formation and accessory genes

Background: The corona virus SARS-CoV-2 is the causative agent of recent most global pandemic. Its genome encodes various proteins categorized as non-structural, accessory, and structural proteins. The non-structural proteins, NSP1-16, are located within the ORF1ab. The NSP3, 4, and 6 together are involved in formation of double membrane vesicle (DMV)…

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An ncRNA transcriptomics-based approach to design siRNA molecules against SARS-CoV-2 double membrane vesicle formation and accessory genes | BMC Infectious Diseases

When compared to the genomes of other RNA viruses, coronaviruses have been found to possess largest genome sizes. They are capable of establishing reservoirs in both human and zoonotic populations, enabling their transmission and circulation among a range of animal hosts, including bats, pangolins, civets, cats, mice, pigs, whales, dogs,…

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ncRNA | Free Full-Text | Regulation of Macrophage Polarization in Allergy by Noncoding RNAs

1. Introduction Allergies affect millions of people worldwide and are characterized by an excessive type 2 immune response to normally harmless substances, generally known as antigens or allergens, specifically [1,2]. Consequently, this response leads to the development of various allergic symptoms, including asthma, allergic rhinitis, and atopic dermatitis. In the…

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Nucleolar Pol II interactome reveals TBPL1, PAF1, and Pol I at intergenic rDNA drive rRNA biogenesis

Abstract Nucleolar ribosomal DNA (rDNA) repeats control ribosome manufacturing. rDNA harbors a ribosomal RNA (rRNA) gene and an intergenic spacer (IGS). RNA polymerase (Pol) I transcribes rRNA genes yielding the rRNA components of ribosomes. Pol II at the IGS induces rRNA production by preventing Pol I from excessively synthesizing IGS…

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ASM2462278v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::08/05/2022 10:42:45 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::6.2 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::3,366 CDSs (total)::3,329 Genes (coding)::3,296 CDSs (with protein)::3,296 Genes (RNA)::37 tRNAs::34 ncRNAs::3 Pseudo Genes (total)::33 CDSs (without protein)::33 Pseudo Genes…

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Research progress in the role of non-coding RNAs and embryo implantation

Non-coding RNA (ncRNA) refers to RNA that lack the ability to encode protein. Based on their distinct biological characteristics, ncRNA are mainly classified into microRNA (miRNA), long non-coding RNA (lncRNA), and circular RNA (circRNA). NcRNA plays a crucial regulatory role in various biological processes. Pregnancy is a highly intricate physiological…

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kallisto index build difference according to version

kallisto index build difference according to version 0 Hi all, I’m trying to implement kallisto for a dataset of single-end RNA-seq data, And obviously started with building an index (The files were downloaded from ensembl). Homo_sapiens.GRCh37.ncrna.fa.gz Homo_sapiens.GRCh37.cdna.all.fa.gz using the command kallisto index -i index.idx Homo_sapiens.GRCh37.ncrna.fa.gz Homo_sapiens.GRCh37.cdna.all.fa.gz And although this wasn’t…

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Senior Bioinformatics Scientist Job in Bencos Research Solutions Pvt. Ltd. at Other Karnataka -Job Description #13526332

Job Details The Job Position We are looking for motivated Senior Bioinformatics Analyst with skills in Next Generation Sequence analysis who is able to work independently and meet deadlines. Strong programming background and machine learnning skills will be a plus. Qualification PhD or MS/M.Tech/MSc. in Bioinformatics/Biotechnology/Computer Science/Life Sciences with equivalent…

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RNA Pol II Assembly Affects ncRNA Expression[v1]

Preprint Article Version 1 This version is not peer-reviewed Version 1 : Received: 30 November 2023 / Approved: 1 December 2023 / Online: 1 December 2023 (10:10:30 CET) Garrido-Godino, A.I.; Gupta, I.; Pelechano, V.; Navarro, F. RNA Pol II Assembly Affects ncRNA Expression. Preprints 2023, 2023120065. doi.org/10.20944/preprints202312.0065.v1 Garrido-Godino, A.I.; Gupta,…

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issue in RNA -seq analysis

Forum:issue in RNA -seq analysis 0 hello all. i am working on RNA seq analysis. i would like to know following things: first i downloaded genome fasta file for non-coding rna from ensembl and got the gtf file for hg38 from there itself. performed hist2 and got 17% alignment for…

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Evaluating 17 methods incorporating biological function with GWAS summary statistics to accelerate discovery demonstrates a tradeoff between high sensitivity and high positive predictive value

Method selection We reviewed the published literature through February 2020 to identify methods that met the following criteria: i. Descriptively categorized as (a) annotation-based; (b) pleiotropy-based; or (c) eQTL-based. ii. Utilized GWAS summary statistics, as opposed to individual-level genotype data. iii. Implemented using freely-available software or packages. iv. Provided either…

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ncRNA | Free Full-Text | Ethanol

Received: 14 July 2023 / Revised: 23 October 2023 / Accepted: 3 November 2023 / Published: 17 November 2023 Round 1 Reviewer 1 Report Comments and Suggestions for Authors Rizavi and colleagues present a study describing the effects of alcohol and PARP inhibitor on the lncRNA ribosomal binding. The study…

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Partners hope to regenerate heart tissue using ncRNA

Ethris and Heqet Therapeutics have revealed plans to collaborate on RNA-based therapeutics for heart attack and heart failure, using non coding RNAs (ncRNAs) in regenerating heart tissue. Under the terms of the agreement, Heqet Therapeutics will lead the development of the programme, while Ethris will provide its proprietary Stabilized NanoParticle…

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ncRNA | Free Full-Text | LADON, a Natural Antisense Transcript of NODAL, Promotes Tumour Progression and Metastasis in Melanoma

Received: 10 October 2023 / Revised: 2 November 2023 / Accepted: 10 November 2023 / Published: 15 November 2023 Round 1 Reviewer 1 Report Comments and Suggestions for Authors The manuscript by Dutriaux et al. is of moderate to high significance to ncRNA readership. The model and techniques used are…

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Ethris, Heqet Partner On RNA-based Heart Disease Therapeutics

Ethris GmbH, a biotechnology company pioneering next-generation RNA therapeutics and vaccines, and Heqet Therapeutics, a biotechnology spin-out company from King’s College London active in the field of regenerative medicine, entered into a collaboration agreement to harness the potential of ncRNA for heart tissue regeneration following acute myocardial infarction (heart attack)…

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Ethris and Heqet Therapeutics Announce Collaboration to

Collaboration will harness the potential of non coding RNAs (ncRNAs) in regenerating heart tissue Ethris will contribute its proprietary SNaP LNP platform for precise ncRNA delivery while Heqet Therapeutics will lead preclinical and clinical development Ethris to receive milestone and royalty payments, highlighting the commitment of both companies to advance…

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What are the functions of long ncRNA in bacteriophages?

Does the herpes simplex virus cause Parkinson’s disease? 5 answers How does the herpes simplex virus cause parkinson’s disease? 3 answers How does 5-HTP work in the body? 5 answers Maturation of tibia tuberosity in osgood schlatter? 5 answers What mRNA would promote citrulline production in human? 4 answers What…

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When will RNA get its AlphaFold moment? | Nucleic Acids Research

Abstract The protein structure prediction problem has been solved for many types of proteins by AlphaFold. Recently, there has been considerable excitement to build off the success of AlphaFold and predict the 3D structures of RNAs. RNA prediction methods use a variety of techniques, from physics-based to machine learning approaches….

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ncRNA | Free Full-Text | An Overview of the Immune Modulatory Properties of Long Non-Coding RNAs and Their Potential Use as Therapeutic Targets in Cancer

Non-Coding RNA 2023, 9(6), 70; doi.org/10.3390/ncrna9060070 (registering DOI) Non-Coding RNA 2023, 9(6), 70; doi.org/10.3390/ncrna9060070 (registering DOI) Received: 27 June 2023 / Revised: 25 October 2023 / Accepted: 8 November 2023 / Published: 11 November 2023 Round 1 Reviewer 1 Report Comments and Suggestions for Authors In the current manuscript, Moises et al….

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Why am I getting different results with kallisto?

Why am I getting different results with kallisto? 1 Hello, I created a reference for my species of interest using the cDNA file from ensembl and then aligned my data to it using kallisto. Then, i was asked to add the ncRNA to the reference and a egfp sequence. I…

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Targeting nucleic acid phase transitions as a mechanism of action for antimicrobial peptides

Phase separation propensity of AMPs We retrieved the sequences of previously identified AMPs deposited into the Database of Antimicrobial Activity and Structure of Peptides (DBAASP)40 and in the APD3 antimicrobial peptide database41 to analyse their predicted propensities to undergo phase separation. Interestingly, we find that some AMPs possess features42,43,44 that…

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ncRNA | Free Full-Text | Dysregulation of Non-Coding RNAs: Roles of miRNAs and lncRNAs in the Pathogenesis of Multiple Myeloma

4. Dysregulation of lncRNAs in MM In recent years, numerous studies have focused on the role of lncRNAs in MM pathogenesis. Since then, the role of aberrantly expressed lncRNAs in MM has been reported, highlighting the potential in clinical applications. For instance, lncRNAs participate in the differentiation of erythroid, myeloid,…

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ncRNA | Free Full-Text | Downregulation of Exosomal hsa-miR-551b-3p in Obesity and Its Link to Type 2 Diabetes Mellitus

Non-Coding RNA 2023, 9(6), 67; doi.org/10.3390/ncrna9060067 (registering DOI) Non-Coding RNA 2023, 9(6), 67; doi.org/10.3390/ncrna9060067 (registering DOI) Received: 31 August 2023 / Revised: 6 October 2023 / Accepted: 24 October 2023 / Published: 2 November 2023 Round 1 Reviewer 1 Report Comments and Suggestions for Authors The study by Kseniia V. Dracheva and…

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Revolutionizing Genomic Research: Introducing GERONIMO, The User-Friendly ncRNA Discovery Tool | CEITEC

31. Oct. 2023 The idea of creating a user-friendly tool for biologists to discover novel non-coding RNAs (ncRNA) was born in Agata Kilar’s head, a researcher in Jiří Fajkus research group based at CEITEC Masaryk University in Brno. She developed GERONIMO, a bioinformatics tool that simplifies the identification of ncRNA…

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Diet-induced rewiring of the Wnt gene regulatory network connects aberrant splicing to fatty liver and liver cancer in DIAMOND mice

DIAMOND mice develop HCC in the context of obesity and insulin resistance To investigate in depth the genome-wide transcriptional and epigenetic changes that occur during development of MAFLD and obesity-related hepatocellular carcinoma (HCC), we performed RNA-sequencing (RNA-seq) and Chromatin ImmunoPrecipitation-sequencing (ChIP-seq) of liver tumours (HCC) and liver control tissue (FL)…

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Roles of SNORD115 and SNORD116 ncRNA clusters in neuronal differentiation

Abstract Prader-Willi syndrome shows features linked to brain development and hypothalamus-related endocrine abnormalities. The smallest clinical deletions fall within the large (~650Kb) SNHG14 gene, removing 29 consecutive introns that each generate SNORD116. SNHG14 also includes 48 tandem introns encoding SNORD115 and generates multiple, extended snoRNA-related species. SNORD115 and SNORD116 resemble…

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ncRNA | Free Full-Text | Discovery of Novel miRNAs in Colorectal Cancer: Potential Biological Roles and Clinical Utility

1. Introduction Colorectal cancer (CRC) is the third most common cancer and the second leading cause of cancer-related deaths [1]. In Brazil, CRC is the second most common cancer in both men and women, with an estimated 45,630 new cases nationwide by the year 2023 [2]. CRC is a heterogeneous…

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Computational Methods for Predicting ncRNA-protein Interactions

Title:Computational Methods for Predicting ncRNA-protein Interactions Volume: 13 Issue: 6 Author(s): Shao-Wu Zhang*Xiao-Nan Fan Affiliation: Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, Xi’an, 710072,China Keywords: ncRNA-protein interaction, prediction, dataset construction, feature representation, machine learning, RNA purification. Abstract: Background: RNA-protein interactions (RPIs)…

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How do I write a correctly formatted gff3 file in R?

Dear all, I am trying to annotate non-coding RNA in a small RNA-seq dataset. The RNACentral gff3 file that I am using has different chromosome identifiers than the genome assembly. I have loaded the gff3 file in R where I changed the chromosome identifiers using the the assembly report and…

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RNA Targeting Small Molecule Drug Discovery Market Size, Share And Growth Analysis For 2023-2032

(MENAFN– EIN Presswire) RNA Targeting Small Molecule Drug Discovery Global Market Report 2023 – Market Size, Trends, And Market Forecast 2023-2032 The Business Research Company’s RNA Targeting Small Molecule Drug Discovery Global Market Report 2023 – Market Size, Trends, And Market Forecast 2023-2032 The Business Research Company’s global market reports…

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Epitranscriptomic Modifications and How to Detect Them

What is epitranscriptomic modification? RNA modifications, not limited to purine or pyrimidine bases, including N6-methyladenosine (m6A), 1-methyladenosine (m1A), 5-methylcytidine (m5C), 5-hydroxymethylcytidine (hm5C), 5-formylcytidine (f5C), 5-carboxycytidine (ca5C), inosine (I), pseudouridine (Ψ), and 2′-O-methylation (Nm). RNA modifications can structurally alter the pairing of nucleobases, leading to structural rearrangements of RNA and thus…

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Pseudogene MAPK6P4-encoded functional peptide promotes glioblastoma vasculogenic mimicry development

Gusyatiner, O. & Hegi, M. E. Glioma epigenetics: from subclassification to novel treatment options. Semin. Cancer Biol. 51, 50–58 (2018). Article  PubMed  Google Scholar  Kunnakkat, S. & Narayana, A. Bevacizumab in the treatment of high-grade gliomas: an overview. Angiogenesis 14, 423–430 (2011). Article  PubMed  Google Scholar  Luo, Q. et al….

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Non-coding RNAs in inflammation induced cancer; from mechanisms to therapy

Overview Project ID: SST_SHiMR_2 Chronic intestinal inflammation contributes to the development of colorectal carcinoma and population-based studies demonstrate higher mortality rates for patients with chronic inflammation-associated colorectal cancer. Non-coding RNAs (ncRNAs), transcripts without coding potential, have emerged as a new crucial layer of gene regulation at the epigenetic level….

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ncRNA | Free Full-Text | The Potential Role of Circulating Long Miscellaneous RNAs in the Diagnosis and Prognosis of Hepatitis C Related Hepatocellular Carcinoma

All articles published by MDPI are made immediately available worldwide under an open access license. No special permission is required to reuse all or part of the article published by MDPI, including figures and tables. For articles published under an open access Creative Common CC BY license, any part of…

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ncRNA | Free Full-Text | A Small De Novo CNV Deletion of the Paternal Copy of FOXF1, Leaving lncRNA FENDRR Intact, Provides Insight into Their Bidirectional Promoter Region

Received: 28 August 2023 / Revised: 3 October 2023 / Accepted: 6 October 2023 / Published: 9 October 2023 Round 1 Reviewer 1 Report Dear authors, After consideration, I have some recommendations and concerns that I believe will improve the quality and impact of your manuscript. While the manuscript provides…

Continue Reading ncRNA | Free Full-Text | A Small De Novo CNV Deletion of the Paternal Copy of FOXF1, Leaving lncRNA FENDRR Intact, Provides Insight into Their Bidirectional Promoter Region

ncRNA | Free Full-Text | Altered Expression of Vitamin D Metabolism Genes and Circulating MicroRNAs in PBMCs of Patients with Type 1 Diabetes: Their Association with Vitamin D Status and Ongoing Islet Autoimmunity

1. Introduction Type 1 diabetes mellitus (T1DM) is a chronic autoimmune disease characterized by the degeneration of beta cells, resulting in insulin deficiency [1]. T1DM incidence is strongly associated with vitamin D deficiency, and 1,25(OH)2D3 can potentially prevent islet cell death and enhance insulin production. Several studies suggest that low…

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Functional analysis of differentially expressed circular RNAs in sheep subcutaneous fat | BMC Genomics

Chikwanha, O. C., P. Vahmani, V. Muchenje, M. E. R. Dugan and C. Mapiye (2018). Nutritional enhancement of sheep meat fatty acid profile for human health and wellbeing. Food research international (Ottawa, Ont.) 104: 25–38. doi.org/10.1016/j.foodres.2017.05.005. Khan R, Raza SHA, Schreurs N, Xiaoyu W, Hongbao W, Ullah I, et al….

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Virulence Characteristics of Salmonella Enteritidis

Introduction As an important zoonosis pathogen, Salmonella is widely distributed in nature and one of the four major pathogens causing global diarrhea diseases.1 Salmonella has six subspecies and 2659 serotypes, among which Salmonella Enteritidis (S. Enteritidis) are the most common serotypes causing Salmonella outbreaks.1 S. Enteritidis has a wide variety…

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Progress and challenges in completing the human gene catalogue

In a recent review published in Nature, a group of authors reviewed the progress and challenges in annotating the human genome, including protein-coding genes, isoforms, and non-coding ribonucleic acids (RNAs), and advocated for a universal annotation standard for clinical use. Study: The status of the human gene catalogue. Image Credit:…

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RefSeq: XP_024590519

LOCUS XP_024590519 142 aa linear MAM 18-APR-2018 DEFINITION glia maturation factor beta isoform X2 [Neophocaena asiaeorientalis asiaeorientalis]. ACCESSION XP_024590519 VERSION XP_024590519.1 DBLINK BioProject: PRJNA449518 DBSOURCE REFSEQ: accession XM_024734751.1 KEYWORDS RefSeq. SOURCE Neophocaena asiaeorientalis asiaeorientalis (Yangtze finless porpoise) ORGANISM Neophocaena asiaeorientalis asiaeorientalis Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria;…

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RefSeq: XP_033346483

LOCUS XP_033346483 290 aa linear INV 16-APR-2020 DEFINITION COP9 signalosome complex subunit 7b isoform X1 [Bombus vosnesenskii]. ACCESSION XP_033346483 VERSION XP_033346483.1 DBLINK BioProject: PRJNA623919 DBSOURCE REFSEQ: accession XM_033490592.1 KEYWORDS RefSeq. SOURCE Bombus vosnesenskii ORGANISM Bombus vosnesenskii Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Apoidea; Anthophila;…

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Global mapping of RNA-chromatin contacts reveals a proximity-dominated connectivity model for ncRNA-gene interactions

. 2023 Sep 28;14(1):6073. doi: 10.1038/s41467-023-41848-9. Affiliations Expand Affiliations 1 Department of Biochemistry, Stanford University, Stanford, California, USA. 2 Department of Chemical and Systems Biology, Stanford University, Stanford, California, USA. 3 Department of Genetics, Stanford University, Stanford, California, USA. 4 Department of Biochemistry, Stanford University, Stanford, California, USA. astraigh@stanford.edu. Item…

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ncRNA | Free Full-Text | The Intergenic Type lncRNA (LINC RNA) Faces in Cancer with In Silico Scope and a Directed Lens to LINC00511: A Step toward ncRNA Precision

CRC Upregulated 153-5p HIF-1 activates LINC00511, targeting HIF-1’s 3-UTR and +ve feedback loop [78] Oncogene Human CRC tissues vs. paired adjacent non-tumor and CRC cell lines HT29, LOVO, SW620, SW480 vs. normal colon epithelial FHC cell line and athymic BALB/c nude mice for implantation – HNF4 promotes LINC00511 transcription, interaction…

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ncRNA | Free Full-Text | Discovery and Comprehensive Characterization of Novel Circular RNAs of the Apoptosis-Related BOK Gene in Human Ovarian and Prostate Cancer Cells, Using Nanopore Sequencing

1. Introduction Cancers of the reproductive organs, including human ovarian and prostate cancer, account for a big percentage of cancer morbidity and mortality worldwide, while their incidences have gradually increased in many countries [1]. According to the American Cancer Society, an estimated 268,490 men and 19,880 women were diagnosed with…

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Non-coding RNAs in cancer immunotherapy: Predictive biomarkers and targets

Background: To date, standardising clinical predictive biomarkers for assessing the response to immunotherapy remains challenging due to variations in personal genetic signatures, tumour microenvironment complexities and epigenetic onco-mechanisms. Main body: Early monitoring of key non-coding RNA (ncRNA) biomarkers may help in predicting the clinical efficacy of cancer immunotherapy and come…

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Bioengineered non-coding RNA agent (BERA) in action.

Abstract Non-coding RNAs (ncRNAs) including microRNAs (miRNAs) and small interfering RNAs (siRNAs) are important players in the control of gene regulation and represent novel promising therapeutic targets or agents for the treatment of various diseases. While synthetic ncRNAs are predominately utilized, the effects of excessive artificial modifications on higher-order structures,…

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ncRNA | Free Full-Text | Long Non-Coding RNA TUG1 Gene Polymorphism and TUG1 Expression Level as Molecular Biomarkers of Systemic Lupus Erythematosus and Lupus Nephritis

1. Introduction Systemic lupus erythematosus (SLE) is a chronic autoimmune disease with a wide variety of manifestations ranging from mild cutaneous to organ failure as lupus nephritis (LN) and cardiopulmonary complications [1]. SLE is mainly present among young women, with a greater incidence in certain ethnic groups, such as Asian,…

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Integrated meta-omics approaches reveal Saccharopolyspora as the core functional genus in huangjiu fermentations

Saccharopolyspora is abundant in the wheat qu and HJFM microbiota To uncover the variation curve of microorganisms during fermentation, microbial DNA copy numbers and community structure were analyzed using quantitative real-time PCR (qPCR) and metagenomic analyses. DNA copy numbers of total bacteria and fungi in wheat qu were 11.2 ± 0.2 log10…

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Profiling a ncRNA in Breast Cancer

The project focused on identifying and characterizing novel non-coding RNAs (ncRNAs) and miRNAs that are misregulated in different cancer subtypes, focusing on breast cancer cells. The project aims to explore the regulatory roles of ncRNAs in cancer cells and identify potential therapeutic targets for breast cancer treatment. RNA1 was used…

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ncRNA | Free Full-Text | Novel Insights into Circular RNAs in Metastasis in Breast Cancer: An Update

Non-Coding RNA 2023, 9(5), 55; doi.org/10.3390/ncrna9050055 (registering DOI) Non-Coding RNA 2023, 9(5), 55; doi.org/10.3390/ncrna9050055 (registering DOI) Received: 23 July 2023 / Revised: 26 August 2023 / Accepted: 28 August 2023 / Published: 16 September 2023 Round 1 Reviewer 1 Report   This manuscript by Zepeda-Enríquez et. al. sets out to review repertoire…

Continue Reading ncRNA | Free Full-Text | Novel Insights into Circular RNAs in Metastasis in Breast Cancer: An Update

ncRNA | Free Full-Text | The Potential microRNA Prognostic Signature in HNSCCs: A Systematic Review

Jung et al., 2012 [24] USA RT 17 OSCC (Tongue base 6, Tongue anterior 3, Tongue border 2, Tongue ventral, Mouth 1, Oropharynx 1, Tongue unspecified 2) miR-7, miR-21, miR-424 180 17 Ma 34–81 \ \ HPV +10, −7 pTNM stage I 1, II 5, IV 8, 3 N\A Kawakita…

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Integrated bioinformatics analysis of noncoding RNAs with tumor immune microenvironment in gastric cancer

Sung, H. et al. Global Cancer Statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J. Clin. 71, 209–249. doi.org/10.3322/caac.21660 (2021). Article  PubMed  Google Scholar  Siegel, R. L., Miller, K. D., Fuchs, H. E. & Jemal, A. Cancer statistics, 2022. CA A…

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Genome sequence and annotation of Periconia digitata a hopeful biocontrol agent of phytopathogenic oomycetes

Strain identification The strain Phoma sp. CNCM I-4278 was previously isolated from the rhizosphere of Nicotiana tabacum (cv Xanthi, Solanaceae) grown under controlled conditions17. The fungus was identified according to the closest similarity of its 18 S rRNA sequence (HM16174323) with those present in GenBank by that time and it was…

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Genome-wide analysis identifies novel loci influencing plasma apolipoprotein E concentration and Alzheimer’s disease risk

The details of study participants, plasma ApoE measurement, genotyping and imputation, statistical analyses, and functional annotations are given in Online Methods. Association of plasma ApoE concentration with incident dementia and cognition function Whole plasma ApoE concentration at baseline was determined in 3031 participants, of which 2893 were European Americans (EAs),…

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Whole genome analysis and cold adaptation strategies of Pseudomonas sivasensis W-6 isolated from the Napahai plateau wetland

Growth conditions and identification The growth of the strain W-6 was measured at different temperatures of 4, 10, 15, 20, 25, 30, and 37 °C. It can be seen that strain W-6 could grow at the range from 4 to 30 °C with the optimal growth temperature 15 °C. Then, the growth curve of…

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ncRNA | Free Full-Text | Non-Coding RNAs: Foes or Friends for Targeting Tumor Microenvironment

Received: 27 June 2023 / Revised: 17 August 2023 / Accepted: 22 August 2023 / Published: 28 August 2023 Round 1 Reviewer 1 Report This is a very comprehensive treatment of the topic of ncRNAs in cancer therapy. There is definitely a need for this work to be published but…

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RefSeq: XP_007448290

LOCUS XP_007448290 260 aa linear MAM 01-APR-2014 DEFINITION PREDICTED: alpha-ketoglutarate-dependent dioxygenase alkB homolog 2 isoform X1 [Lipotes vexillifer]. ACCESSION XP_007448290 VERSION XP_007448290.1 DBLINK BioProject: PRJNA232751 DBSOURCE REFSEQ: accession XM_007448228.1 KEYWORDS RefSeq. SOURCE Lipotes vexillifer (Yangtze River dolphin) ORGANISM Lipotes vexillifer Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Artiodactyla;…

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MFPred: prediction of ncRNA families based on multi-feature fusion

doi: 10.1093/bib/bbad303. Online ahead of print. Affiliations Expand Affiliations 1 College of Software, jilin University, Changchun, 130012, China. 2 Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, jilin University, Changchun, 130012, China. 3 College of Computer Science and Technology, jilin University, Changchun, 130012, China. Item in…

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ncRNA | Free Full-Text | Inverse-Folding Design of Yeast Telomerase RNA Increases Activity In Vitro

Non-Coding RNA 2023, 9(5), 51; doi.org/10.3390/ncrna9050051 (registering DOI) Non-Coding RNA 2023, 9(5), 51; doi.org/10.3390/ncrna9050051 (registering DOI) Received: 24 July 2023 / Revised: 19 August 2023 / Accepted: 24 August 2023 / Published: 28 August 2023 Round 1 Reviewer 1 Report The authors report on newly designed variants of yeast telomerase RNA that…

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RefSeq: XP_026912832

LOCUS XP_026912832 160 aa linear MAM 04-APR-2023 DEFINITION protein FAM162B isoform X3 [Acinonyx jubatus]. ACCESSION XP_026912832 VERSION XP_026912832.1 DBLINK BioProject: PRJNA923316 DBSOURCE REFSEQ: accession XM_027057031.2 KEYWORDS RefSeq. SOURCE Acinonyx jubatus (cheetah) ORGANISM Acinonyx jubatus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Carnivora; Feliformia; Felidae; Acinonychinae; Acinonyx. COMMENT MODEL…

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ncRNA | Free Full-Text | Systematic Analysis of Long Non-Coding RNAs in Inflammasome Activation in Monocytes/Macrophages

Received: 7 August 2023 / Revised: 21 August 2023 / Accepted: 23 August 2023 / Published: 25 August 2023 Round 1 Reviewer 1 Report There are a few errors that must be corrected before the manuscript is accepted.   1) In Figure 1C the green ovals are mislabeled. They should…

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RefSeq: XP_007166569

LOCUS XP_007166569 140 aa linear MAM 27-JUN-2023 DEFINITION profilin-1 [Balaenoptera acutorostrata]. ACCESSION XP_007166569 VERSION XP_007166569.1 DBLINK BioProject: PRJNA986088 DBSOURCE REFSEQ: accession XM_007166507.3 KEYWORDS RefSeq. SOURCE Balaenoptera acutorostrata (minke whale) ORGANISM Balaenoptera acutorostrata Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Artiodactyla; Whippomorpha; Cetacea; Mysticeti; Balaenopteridae; Balaenoptera. COMMENT MODEL REFSEQ:…

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RefSeq: XP_024597028

LOCUS XP_024597028 208 aa linear MAM 18-APR-2018 DEFINITION protein THEM6 [Neophocaena asiaeorientalis asiaeorientalis]. ACCESSION XP_024597028 VERSION XP_024597028.1 DBLINK BioProject: PRJNA449518 DBSOURCE REFSEQ: accession XM_024741260.1 KEYWORDS RefSeq. SOURCE Neophocaena asiaeorientalis asiaeorientalis (Yangtze finless porpoise) ORGANISM Neophocaena asiaeorientalis asiaeorientalis Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Artiodactyla; Whippomorpha; Cetacea; Odontoceti;…

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GSVIVT01038180001 details

Home Species Vitis vinifera Sequence GSVIVT01038180001 Description : RNA processing.RNA splicing.U2-type-intron-specific major spliceosome.U5 small nuclear ribonucleoprotein particle (snRNP).snRNP40/U5-40kDa snRNP component Expression Profile Note:Only the main profile, including all conditions, is shown. Additional statistics and tissue specific profiles are available here. Co-expression Networks Type Description Actions Neighborhood HRR: GSVIVT01038180001 Cluster HCCA:…

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RefSeq: XP_013985108

LOCUS XP_013985108 229 aa linear VRT 07-JAN-2022 DEFINITION esterase OVCA2 isoform X1 [Salmo salar]. ACCESSION XP_013985108 VERSION XP_013985108.1 DBLINK BioProject: PRJNA788898 DBSOURCE REFSEQ: accession XM_014129633.2 KEYWORDS RefSeq. SOURCE Salmo salar (Atlantic salmon) ORGANISM Salmo salar Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Protacanthopterygii; Salmoniformes; Salmonidae; Salmoninae; Salmo. COMMENT…

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ncRNA | October 2023 – Browse Articles

All articles published by MDPI are made immediately available worldwide under an open access license. No special permission is required to reuse all or part of the article published by MDPI, including figures and tables. For articles published under an open access Creative Common CC BY license, any part of…

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RefSeq: XP_018454631

LOCUS XP_018454631 269 aa linear PLN 08-JUN-2023 DEFINITION disease resistance protein ADR2 [Raphanus sativus]. ACCESSION XP_018454631 VERSION XP_018454631.1 DBLINK BioProject: PRJNA344915 DBSOURCE REFSEQ: accession XM_018599129.2 KEYWORDS RefSeq. SOURCE Raphanus sativus (radish) ORGANISM Raphanus sativus Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus….

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Heimdall, an alternative protein issued from a ncRNA related to kappa light chain variable region of immunoglobulins from astrocytes: a new player in neural proteome

The dogma “One gene, one protein” is clearly obsolete since cells use alternative splicing and generate multiple transcripts which are translated into protein isoforms, but also use alternative translation initiation sites (TISs) and termination sites on a given transcript. Alternative open reading frames for individual transcripts give proteins originate from…

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ApolloRNA main page

ApolloRNA main page Apollo for non protein coding RNA (ncRNA) identification ApolloRNA is an extension for ncRNA identification of the Apollo environment [1], a genome annotation viewer and editor. ApolloRNA is developed by the Biometry and Artificial Intelligence Laboratory of INRA Toulouse, France. Source code is available on the Forge…

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circRNA: a promising all-around star in the future

Review doi: 10.2217/epi-2023-0141. Online ahead of print. Affiliations Expand Affiliation 1 Tianjin Institute of Urology, the Second Hospital of Tianjin Medical University, Tianjin, 300211, China. Item in Clipboard Review Hanlin Li. Epigenomics. 2023. Show details Display options Display options Format AbstractPubMedPMID doi: 10.2217/epi-2023-0141. Online ahead of print. Affiliation 1 Tianjin…

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Using RNAcentral to explore and investigate non-coding RNA sequences

Non-coding RNAs (ncRNAs) are a key molecule for life. They are involved in many complex biological processes, from gene regulation to translation. This complexity has led to an explosion of many different databases with specialised focuses and data. RNAcentral provides users a single entry point into the complexity of ncRNA…

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ncRNA | Free Full-Text | Investigation into the Role of Long-Non-Coding RNA MIAT in Leukemia

1. Introduction Recent advances in RNA-based approaches and Next Generation Technologies have unveiled the existence of non-coding RNAs (ncRNA), transcripts that lack the ability to code for proteins [1,2]. ncRNAs typically lack an open reading frame (ORF) and are subdivided into housekeeping and regulatory transcripts. Housekeeping ncRNAs are usually 50–500…

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LncRNA FENDRR suppresses melanoma growth

Introduction Cutaneous melanoma is a kind of highly aggressive and metastatic cancer.1 It only occurs in 5% of all skin cancers but causes more than 75% of deaths.2,3 Melanoma can be cured by surgical removal at an early stage.4 However, when the disease progresses to an advanced stage (stage IV),…

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ASM361163v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::09/28/2018 18:16:55 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline Annotation Method::Best-placed reference protein set; GeneMarkS+ Annotation Software revision::4.6 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::8,506 CDS (total)::8,444 Genes (coding)::8,247 CDS (coding)::8,247 Genes (RNA)::62 rRNAs::1, 1, 1 (5S, 16S, 23S) complete rRNAs::1, 1, 1 (5S, 16S,…

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ASM491215v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::04/19/2019 21:15:33 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::4.8 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::5,008 CDSs (total)::4,951 Genes (coding)::4,808 CDSs (with protein)::4,808 Genes (RNA)::57 rRNAs::3, 1, 1 (5S, 16S, 23S) complete rRNAs::3 (5S) partial…

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ASM969558v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::09/10/2019 03:25:17 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::4.9 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::2,851 CDSs (total)::2,768 Genes (coding)::2,716 CDSs (with protein)::2,716 Genes (RNA)::83 rRNAs::5, 4, 5 (5S, 16S, 23S) complete rRNAs::5 (5S) partial…

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ncRNA | Free Full-Text | Effects of Controlled Ozone Exposure on Circulating microRNAs and Vascular and Coagulation Biomarkers: A Mediation Analysis

1. Introduction Tropospheric ozone (O3) is a ubiquitous, highly reactive oxidant pollutant produced by photochemical reactions between nitrogen oxides and volatile organic compounds in the presence of ultraviolet light [1]. Ambient O3 levels are regulated by the U.S. Environmental Protection Agency under the Clean Air Act, with the current National…

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ncRNA | Free Full-Text | Long Non-Coding RNA Signatures in Lymphopoiesis and Lymphoid Malignancies

The most common types of B-cell lymphomas include chronic lymphocytic leukemia (CLL), mantle-cell lymphoma (MCL), Burkitt’s lymphoma (BL), follicular lymphoma (FL), and diffuse large B-cell lymphoma (DLBCL). Several studies have identified differently expressed lncRNAs in B-cell NHLs by using datasets that confirm the findings in tissue samples or cell lines…

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ncRNA | Free Full-Text | Crosstalk between Long Non-Coding RNA and Spliceosomal microRNA as a Novel Biomarker for Cancer

3.1.1. HAGLR (HOXD Antisense Growth-Associated Long Non-Coding RNA) HAGLR, known also as HOXD-AS1, is located between the HOXD1 and HOXD3 genes on chromosome 2q31.1 (Figure 1A) and has been reported to play a critical role in the development and progression of different human cancers, including bladder, cervical, colorectal, gastric, ovarian,…

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ASM2078331v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::10/07/2022 02:25:48 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::6.3 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::2,910 CDSs (total)::2,860 Genes (coding)::2,857 CDSs (with protein)::2,857 Genes (RNA)::50 rRNAs::1, 1, 1 (5S, 16S, 23S) complete rRNAs::1, 1,…

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ncRNA | Free Full-Text | Conservation and Targets of miR-71: A Systematic Review and Meta-Analysis

Non-Coding RNA 2023, 9(4), 41; doi.org/10.3390/ncrna9040041 (registering DOI) Non-Coding RNA 2023, 9(4), 41; doi.org/10.3390/ncrna9040041 (registering DOI) Received: 26 June 2023 / Revised: 17 July 2023 / Accepted: 24 July 2023 / Published: 26 July 2023 Round 1 Reviewer 1 Report I compliment the authors for following a rigorous approach in preparing a…

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DataSheet1_Probing the conformational changes of in vivo overexpressed cell cycle regulator 6S ncRNA.pdf

The non-coding 6S RNA is a master regulator of the cell cycle in bacteria which binds to the RNA polymerase-σ70 holoenzyme during the stationary phase to inhibit transcription from the primary σ factor. Inhibition is reversed upon outgrowth from the stationary phase by synthesis of small product RNA transcripts (pRNAs)….

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ncRNA | Free Full-Text | Phosphate Deficiency: A Tale from the End of PILNCR2

Since PILNCR2 protects ZmPHT1s from miRNA-mediated degradation and showed inducible expression under Pi-deficient conditions, one questions remain to be answered: is it involved in low-Pi tolerance? To answer this question, Wang et al. [7] generated overexpression (OE), knock-down (KD), and knock-out (KO) lines for PILNCR2 in the maize plants and…

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a hub of information for non-coding RNA sequences

RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences, collating information on ncRNA sequences of all types from a broad range of organisms. We have recently added a new genome mapping pipeline that identifies genomic locations for ncRNA sequences in 296 species. We have also added several new types…

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ASM1313180v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::05/19/2020 07:11:15 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::4.11 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::7,496 CDSs (total)::7,428 Genes (coding)::7,326 CDSs (with protein)::7,326 Genes (RNA)::68 rRNAs::4, 5, 3 (5S, 16S, 23S) complete rRNAs::1, 1 (5S,…

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Cryomorphaceae_CECT30217 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::09/04/2022 11:55:32 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::6.2 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::3,569 CDSs (total)::3,527 Genes (coding)::3,502 CDSs (with protein)::3,502 Genes (RNA)::42 rRNAs::1, 1, 1 (5S, 16S, 23S) complete rRNAs::1, 1,…

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ASM2328384v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::01/20/2022 16:35:44 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::5.3 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::4,276 CDSs (total)::4,140 Genes (coding)::4,114 CDSs (with protein)::4,114 Genes (RNA)::136 rRNAs::8, 6, 5 (5S, 16S, 23S) complete rRNAs::3, 1 (5S,…

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C. ramosum in immunocompetent patient with SARS-CoV-2

Introduction Clostridium ramosum was first identified and characterized in 1898 following its isolation from a patient with pulmonary gangrene and appendicitis.1 This species, initially identified as Bacillus ramosum and later referred to as C. ramosum, was renamed Erysipelatoclostridium ramosum in 2013.2 However, its taxonomic name has not been legally published…

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Is reciprocal best hit method applicable for non-coding RNA to find orthologs?

The reciprocal best hit (RBH) method is primarily used to identify orthologous genes in coding sequences or protein sequences. It relies on the assumption that orthologous genes, which have evolved from a common ancestral gene, are likely to be each other’s best match in different species. For non-coding RNA (ncRNA),…

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a rising star in leukemia [PeerJ]

Basic reporting Li et al. summarized the circRNAs related to leukemia in this short review manuscript. The authors start with an introduction of leukemia and circRNAs and then illustrate the abnormal circRNAs in four different classes of leukemia. In the following, the related circRNAs are extended to chemoresistance, immune modulation,…

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ASM528147v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI RefSeq Annotation Date::10/06/2022 04:12:32 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::6.3 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::4,755 CDSs (total)::4,698 Genes (coding)::4,670 CDSs (with protein)::4,670 Genes (RNA)::57 rRNAs::4, 4, 4 (5S, 16S, 23S) complete rRNAs::4, 4,…

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Why did Darwin’s 20th-century followers get evolution so wrong?

Since 1859, when Charles Darwin’s On the Origin of Species was first published, the theory of natural selection has dominated our conceptions of evolution. As Darwin understood it, natural selection is a slow and gradual process that takes place across multiple generations through successive random hereditary variations. In the short…

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ASM1988058v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::08/31/2021 18:47:03 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::5.2 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::5,924 CDSs (total)::5,867 Genes (coding)::5,840 CDSs (with protein)::5,840 Genes (RNA)::57 rRNAs::1, 1, 1 (5S, 16S, 23S) complete rRNAs::1, 1, 1…

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ASM362665v1 – Genome – Assembly

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::10/01/2018 17:55:31 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline Annotation Method::Best-placed reference protein set; GeneMarkS+ Annotation Software revision::4.6 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::6,630 CDS (total)::6,537 Genes (coding)::6,350 CDS (coding)::6,350 Genes (RNA)::93 rRNAs::3, 3, 1 (5S, 16S, 23S) complete rRNAs::3, 1, 1 (5S, 16S,…

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