79,891 results match your criteria intergenic region

Long-read sequencing reveals the structural complexity of genomic integration of HBV DNA in hepatocellular carcinoma.

NPJ Genom Med 2021 Oct 12;6(1):84. Epub 2021 Oct 12.

Peking University Fifth School of Clinical Medicine, Beijing, China.

The integration of HBV DNA into the human genome can disrupt its structure in hepatocellular carcinoma (HCC), but the complexity of HBV genomic integration remains elusive. Here we applied long-read sequencing to precisely elucidate the HBV integration pattern in the human hepatocellular genome. The DNA library was sequenced using the long-read sequencing on GridION and PacBio Sequel II, respectively. Read More

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October 2021

The CADM1 tumor suppressor gene is a major candidate gene in MDS with deletion of the long arm of chromosome 11.

Blood Adv 2021 Oct 12. Epub 2021 Oct 12.

Belgian Cancer Registry, Brussels, Belgium.

Myelodysplastic syndromes (MDS) represent a heterogeneous group of clonal hematopoietic stem-cell disorders characterized by ineffective hematopoiesis leading to peripheral cytopenias and in a substantial proportion of cases to acute myeloid leukemia. The deletion of the long arm of chromosome 11, del(11q), is a rare but recurrent clonal event in MDS. Here, we detail the largest series of 113 cases of MDS and myelodysplastic syndromes/myeloproliferative neoplasms (MDS/MPN) harboring a del(11q) analyzed at clinical, cytological, cytogenetic and molecular levels. Read More

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October 2021

Plastid phylogenomics of the Gynoxoid group (Senecioneae, Asteraceae) highlights the importance of motif-based sequence alignment amid low genetic distances.

Am J Bot 2021 Oct 12. Epub 2021 Oct 12.

Institut für Biologie, Systematische Botanik und Pflanzengeographie, Freie Universität Berlin, Berlin, 14195, Germany.

Premise: The genus Gynoxys and relatives form a species-rich lineage of Andean shrubs and trees with low genetic distances within the sunflower subtribe Tussilaginineae. Previous molecular phylogenetic investigations of the Tussilaginineae have included few, if any, representatives of this Gynoxoid group or reconstructed ambiguous patterns of relationships for it.

Methods: We sequenced complete plastid genomes of 21 species of the Gynoxoid group and related Tussilaginineae and conducted detailed comparisons of the phylogenetic relationships supported by the gene, intron, and intergenic spacer partitions of these genomes. Read More

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October 2021

Comparative Chloroplast Genomics and Phylogenetic Analysis of (Zygophyllaceae) of China.

Front Plant Sci 2021 24;12:723622. Epub 2021 Sep 24.

College of Life Science, Northwest A&F University, Yangling, China.

The genus comprises over 150 species within the plant family Zygophyllaceae. These species predominantly grow in arid and semiarid areas, and about 20 occur in northwestern China. In this study, we sampled 24 individuals of representing 15 species and sequenced their complete chloroplast (cp) genomes. Read More

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September 2021

[Analysis of pathogenic variants of USH2A gene in a child with Usher syndrome type II].

Zhonghua Yi Xue Yi Chuan Xue Za Zhi 2021 Oct;38(10):966-968

Huzhou Maternity and Child Health Care Hospital, Huzhou, Zhejiang 313000, China.

Objective: To detect pathogenic variant in a child featuring Usher syndrome type II.

Methods: Peripheral blood samples of the child and his parents were collected for the analysis of variants of hearing impairment-related genes. The findings were verified in 100 individuals with normal hearing. Read More

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October 2021

Exon and intron sharing in opposite direction-an undocumented phenomenon in human genome-between Pou5f1 and Tcf19 genes.

BMC Genomics 2021 Oct 5;22(1):718. Epub 2021 Oct 5.

Hematology, Oncology and Stem Cell Transplantation Research Center, Tehran University of Medical Sciences, Tehran, Iran.

Background: Overlapping genes share same genomic regions in parallel (sense) or anti-parallel (anti-sense) orientations. These gene pairs seem to occur in all domains of life and are best known from viruses. However, the advantage and biological significance of overlapping genes is still unclear. Read More

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October 2021

Genome-wide association studies of yield-related traits in high-latitude japonica rice.

BMC Genom Data 2021 10 5;22(1):39. Epub 2021 Oct 5.

Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China.

Background: Heilongjiang Province is a high-quality japonica rice cultivation area in China. One in ten bowls of Chinese rice is produced here. Increasing yield is one of the main aims of rice production in this area. Read More

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October 2021

Genome-wide Simple Sequence Repeat Markers in Potato: Abundance, Distribution, Composition, and Polymorphism.

DNA Res 2021 Oct 5. Epub 2021 Oct 5.

Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences; Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China.

Simple sequence repeats (SSRs) are important sources of genetic diversity and are widely used as markers in genetics and molecular breeding. In this study, we examined four potato genomes of DM1-3 516 R44 (DM) from Solanum phureja, RH89039-16 (RH) from Solanum tuberosum, M6 from Solanum chacoense and Solanum commersonii to determine SSR abundance and distribution and develop a larger list of polymorphic markers for a potentially wide range of uses for the potato community. A total of 1 734 619 SSRs were identified across the four genomes with an average of 433 655 SSRs per genome and 2. Read More

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October 2021

Biotyping of isolates of isolated from human infections by RAPD and ERIC-PCR.

Heliyon 2021 Sep 8;7(9):e07967. Epub 2021 Sep 8.

Department of Pathobiology, School of Veterinary Medicine, Shiraz University, Shiraz 71441-11731, Iran.

is a significant mortality factor due to nosocomial infections in humans. has been known with severe infections, high incidence, and multiple drug resistance. The present study aims to rapidly diagnose and biotype the isolates of isolated from human infections in Shiraz hospitals and health centers. Read More

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September 2021

Characterization and comparative analysis of the plastome sequence from (Lamiales: Acanthaceae).

Mitochondrial DNA B Resour 2021 14;6(10):2896-2902. Epub 2021 Sep 14.

Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China.

is a characteristic ethnic herb commonly used to treat Orthopedic pains. Here, to confirm its phylogenetic position and to develop molecular markers that can distinguish different species, we obtained and analyzed the plastome of The plastome was sequenced using the Illumina HiSeq sequencing platform, assembled with NOVOPlasty, and annotated with CPGAVAS2. The genome has a circular structure of 149,700 bp, containing a large single-copy region of 82,324 bp, a small single-copy region of 17,260 bp, and two reverse repeat regions of 25,058 bp each. Read More

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September 2021

Fine Mapping of a New Major QTL- for Gray Leaf Spot Resistance in Maize.

Front Plant Sci 2021 17;12:743869. Epub 2021 Sep 17.

College of Agriculture, Guizhou University, Guiyang, China.

Gray leaf spot (GLS), caused by different species of , is a fungal, non-soil-borne disease that causes serious reductions in maize yield worldwide. The identification of major quantitative trait loci (QTLs) for GLS resistance in maize is essential for developing marker-assisted selection strategies in maize breeding. Previous research found a significant difference ( < 0. Read More

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September 2021

Effects of glufosinate-ammonium on male reproductive health: Focus on epigenome and transcriptome in mouse sperm.

Chemosphere 2021 Sep 28;287(Pt 4):132395. Epub 2021 Sep 28.

State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, 211166, China. Electronic address:

Glufosinate-ammonium (GLA) is a widely used herbicide with emerging concern over its neural and reproductive toxicity. To uncover potential effects of GLA on male reproductive health in mammals, adult male C57BL/6J mice were administered 0.2 mg/kg·d GLA for 5 weeks. Read More

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September 2021

Uncovering and Engineering a Mini-Regulatory Network of the TetR-Family Regulator SACE_0303 for Yield Improvement of Erythromycin in .

Front Bioeng Biotechnol 2021 14;9:692901. Epub 2021 Sep 14.

School of Life Sciences, Institute of Physical Science and Information Technology, Anhui University, Hefei, China.

Erythromycins produced by have broad-spectrum antibacterial activities. Recently, several TetR-family transcriptional regulators (TFRs) were identified to control erythromycin production by multiplex control modes; however, their regulatory network remains poorly understood. In this study, we report a novel TFR, SACE_0303, positively correlated with erythromycin production in . Read More

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September 2021

DNA repair inhibition leads to active export of repetitive sequences to the cytoplasm triggering an inflammatory response.

J Neurosci 2021 Sep 28. Epub 2021 Sep 28.

Department of Neurology, Alzheimer's Disease Research Center, University of Pittsburgh, Pittsburgh, PA 15213, USA.

Adult-onset neurodegenerative diseases are often accompanied by evidence of a chronic inflammation that includes activation of microglial cells and altered levels of brain cytokines. Aspects of this response are likely secondary reactions to neurodegeneration, but for many illnesses the inflammation may itself be an early and even causative disease event. In such cases, the inflammation is referred to as "sterile" as it occurs in the absence of an actual bacterial or viral pathogen. Read More

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September 2021

A Novel / Intergenic Region Fusion Responded Well to Alectinib in a Patient With Lung Adenocarcinoma.

JTO Clin Res Rep 2021 Jan 17;2(1):100112. Epub 2020 Oct 17.

Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China.

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January 2021

ERα determines the chemo-resistant function of mutant p53 involving the switch between lincRNA-p21 and DDB2 expressions.

Mol Ther Nucleic Acids 2021 Sep 8;25:536-553. Epub 2021 Aug 8.

The PhD Program for Cancer Biology and Drug Discovery, China Medical University and Academia Sinica, Taichung 40402, Taiwan.

Mutant p53 (mutp53) commonly loses its DNA binding affinity to p53 response elements (p53REs) and fails to induce apoptosis fully. However, the p53 mutation does not predict chemoresistance in all subtypes of breast cancers, and the critical determinants remain to be identified. In this study, mutp53 was found to mediate chemotherapy-induced long intergenic noncoding RNA-p21 (lincRNA-p21) expression by targeting the G-quadruplex structure rather than the p53RE on its promoter to promote chemosensitivity. Read More

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September 2021

An assessment of the epidemiology and socioeconomic impact of the 2019 African swine fever outbreak in Ngara district, western Tanzania.

Vet Anim Sci 2021 Dec 24;14:100198. Epub 2021 Aug 24.

Department of Veterinary Microbiology, Parasitology and Biotechnology, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania.

African swine fever (ASF) is a contagious viral transboundary animal disease affecting domestic pigs caused by ASF virus (ASFV). This study was conducted in order to determine the genetic characteristics, risk factors and socioeconomic impact of an ASF outbreak in 2019 in Ngara, western Tanzania. Tissue samples from dead domestic pigs with clinical picture suggestive of ASF infection were collected for ASF confirmation and genetic characterization of ASFV. Read More

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December 2021

Detection and Complete Genome Analysis of Circoviruses and Cycloviruses in the Small Indian Mongoose (): Identification of Novel Species.

Viruses 2021 Aug 27;13(9). Epub 2021 Aug 27.

Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre P.O. Box 334, Saint Kitts and Nevis, West Indies.

Fecal samples from 76 of 83 apparently healthy small Indian mongooses () were PCR positive with circovirus/cyclovirus pan- (replicase gene) primers. In this case, 30 samples yielded high quality partial rep sequences (~400 bp), of which 26 sequences shared maximum homology with cycloviruses from an arthropod, bats, humans or a sheep. Three sequences exhibited maximum identities with a bat circovirus, whilst a single sequence could not be assigned to either genus. Read More

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Infections in Cats and Cat Fleas in Lithuania.

Pathogens 2021 Sep 17;10(9). Epub 2021 Sep 17.

Faculty of Natural Sciences, Vytautas Magnus University, K. Donelaičio Str. 58, LT-44248 Kaunas, Lithuania.

are vector-borne parasitic bacteria that cause zoonotic infections in humans. One of the most common infections is cat-scratch disease caused by and . Cats are the major reservoir for these two species of bacteria, while cat fleas are vectors for the transmission of infection agents among cats. Read More

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September 2021

Potential Therapeutic Effect of Micrornas in Extracellular Vesicles from Mesenchymal Stem Cells against SARS-CoV-2.

Cells 2021 09 12;10(9). Epub 2021 Sep 12.

Department of Biotechnology, College of Life Science, CHA University, Seongnam 13488, Korea.

Extracellular vesicles (EVs) are cell-released, nanometer-scaled, membrane-bound materials and contain diverse contents including proteins, small peptides, and nucleic acids. Once released, EVs can alter the microenvironment and regulate a myriad of cellular physiology components, including cell-cell communication, proliferation, differentiation, and immune responses against viral infection. Among the cargoes in the vesicles, small non-coding micro-RNAs (miRNAs) have received attention in that they can regulate the expression of a variety of human genes as well as external viral genes via binding to the complementary mRNAs. Read More

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September 2021

Longitudinal change in blood DNA epigenetic signature after smoking cessation.

Epigenetics 2021 Oct 6:1-12. Epub 2021 Oct 6.

Pulmonary Center, Boston University School of Medicine, Boston, MA, USA.

Cigarette smoking is associated with epigenetic changes that may be reversible following smoking cessation. Whole blood DNA methylation was evaluated in Framingham Heart Study Offspring (n = 169) and Third Generation (n = 30) cohort participants at two study visits 6 years apart and in Atherosclerosis Risk in Communities (ARIC) study (n = 222) participants at two study visits 20 years apart. Changes in DNA methylation (delta β values) at 483,565 cytosine-phosphate-guanine (CpG) sites and differentially methylated regions (DMRs) were compared between participants who were current, former, or never smokers at both visits (current-current, former-former, never-never, respectively), versus those who quit in the interim (current-former). Read More

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October 2021

New PCR-based assay for the identification of causing potato soft rot.

Plant Dis 2021 Sep 27. Epub 2021 Sep 27.

Centro Regional de Diagnóstico de Aldearrubia, 557793, Salamanca, Castilla y León, Spain;

Soft rot on potato tuber is a destructive disease caused by pathogenic bacterial species of the genera and . Accurate identification of the causal agent is necessary to ensure adequate disease management, since different species may have distinct levels of aggressiveness and host range. One of the most important potato pathogens is , a highly heterogeneous species capable of infecting multiple hosts. Read More

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September 2021

MtDNA Analysis Indicates Human-Induced Temporal Changes of Serbian Honey Bees Diversity.

Insects 2021 Aug 27;12(9). Epub 2021 Aug 27.

Department of Genetics of Populations and Ecogenotoxicology, Institute for Biological Research "Siniša Stanković"-National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia.

Local populations of are rapidly changing by modern beekeeping through the introduction of nonnative queens, selection and migratory beekeeping. To assess the genetic diversity of contemporary managed honey bees in Serbia, we sequenced mitochondrial intergenic region of 241 worker bees from 46 apiaries at eight localities. Nine haplotypes were observed in our samples, with C2d being the most common and widespread. Read More

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Black raspberries attenuate colonic adenoma development in mice: Relationship to hypomethylation of promoters and gene bodies.

Food Front 2020 Sep 9;1(3):234-242. Epub 2020 Sep 9.

Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin.

Recent studies have suggested that in addition to promoter region, DNA methylation in intragenic and intergenic regions also changes during physiological processes and disease. The current study showed that feeding of black raspberries (BRBs) to mice suppressed colon and intestinal tumors. MBDCap-seq suggested that dietary BRBs hypomethylated promoter, intragenic, and intergenic regions. Read More

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September 2020

Complete mitochondrial genome of and its phylogenetic implication to subfamily Satyrinae (Lepidoptera: Nymphalidae).

Mitochondrial DNA B Resour 2021 15;6(10):2943-2945. Epub 2021 Sep 15.

College of Life Science, Huaibei Normal University, Huaibei, P.R. China.

Eversmann taxonomically belongs to lepidopteran family Nymphalidae Rafinesque, 1815. The Complete mitochondrial genome (mitogenome) of the insect had been sequenced, with 15,244 bp of total length that has 81.12% AT content and contains a typical set of genes (13 protein-coding genes (PCGs), 22 tRNA genes and 2 rRNA genes) and a 417 bp AT-rich region. Read More

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September 2021

Complete mitochondrial genome of Scopoli, 1763 and its phylogenetic position within family Geometridae.

Mitochondrial DNA B Resour 2021 15;6(10):2910-2912. Epub 2021 Sep 15.

College of Life Science, Huaibei Normal University, Huaibei, PR China.

Scopoli, 1763 belongs to the Lepidopteran family Geometridae. We sequenced the complete mitochondrial genome (mitogenome) of . The mitogenome is 15,648 bp long and contains a typical set of genes (13 protein-coding genes (PCGs), 22 tRNA genes, and two rRNA genes) and a 484 bp AT-rich region. Read More

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September 2021

Phylogenetic analysis and development of molecular markers for five medicinal Alpinia species based on complete plastome sequences.

BMC Plant Biol 2021 Sep 22;21(1):431. Epub 2021 Sep 22.

Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, 100193, Beijing, People's Republic of China.

Background: Alpinia species are widely used as medicinal herbs. To understand the taxonomic classification and plastome evolution of the medicinal Alpinia species and correctly identify medicinal products derived from Alpinia species, we systematically analyzed the plastome sequences from five Alpinia species. Four of the Alpinia species: Alpinia galanga (L. Read More

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September 2021

Evaluating Methylation of the Oxytocin Receptor Gene and the Oxytocin Intergenic Region.

Methods Mol Biol 2022 ;2384:81-103

Jewish General Hospital, Lady Davis Institute for Medical Research and Department of Psychiatry, McGill University, Montreal, QC, Canada.

Oxytocin and its paralogue, vasopressin, are widely studied biomarkers in relation to pregnancy and birth, maternal and social behavior, and mental health. Epigenetics is a biological mechanism that mediates the link between environmental influences and behavioral patterns. In a candidate gene approach, we describe here a DNA methylation assay of two regions within the oxytocin system, using human buccal cells and next-generation sequencing. Read More

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January 2022

SON drives oncogenic RNA splicing in glioblastoma by regulating PTBP1/PTBP2 switching and RBFOX2 activity.

Nat Commun 2021 09 21;12(1):5551. Epub 2021 Sep 21.

Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA.

While dysregulation of RNA splicing has been recognized as an emerging target for cancer therapy, the functional significance of RNA splicing and individual splicing factors in brain tumors is poorly understood. Here, we identify SON as a master regulator that activates PTBP1-mediated oncogenic splicing while suppressing RBFOX2-mediated non-oncogenic neuronal splicing in glioblastoma multiforme (GBM). SON is overexpressed in GBM patients and SON knockdown causes failure in intron removal from the PTBP1 transcript, resulting in PTBP1 downregulation and inhibition of its downstream oncogenic splicing. Read More

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September 2021

Differential analysis of chromatin accessibility and gene expression profiles identifies cis-regulatory elements in rat adipose and muscle.

Genomics 2021 Sep 20;113(6):3827-3841. Epub 2021 Sep 20.

Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.

Chromatin accessibility is a key factor influencing gene expression. We optimized the Omni-ATAC-seq protocol and used it together with RNA-seq to investigate cis-regulatory elements in rat white adipose and skeletal muscle, two tissues with contrasting metabolic functions. While promoter accessibility correlated with RNA expression, integration of the two datasets identified tissue-specific differentially accessible regions (DARs) that predominantly localized in intergenic and intron regions. Read More

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September 2021