42,758 results match your criteria coding regions


Dual RNAseq highlights the kinetics of skin microbiome and fish host responsiveness to bacterial infection.

Anim Microbiome 2021 May 7;3(1):35. Epub 2021 May 7.

Ifremer, IRD, Institut Louis-Malardé, Univ Polynésie Française, EIO, F-98719 Taravao, Tahiti, Polynésie Française.

Background: Tenacibaculum maritimum is a fish pathogen known for causing serious damage to a broad range of wild and farmed marine fish populations worldwide. The recently sequenced genome of T. maritimum strain NCIMB 2154 provided unprecedented information on the possible molecular mechanisms involved in the virulence of this species. Read More

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The RNA Structurome in the Asexual Blood Stages of Malaria Pathogen .

RNA Biol 2021 May 7. Epub 2021 May 7.

Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina 28223.

is a deadly human pathogen responsible for the devastating disease called malaria. In this study, we measured the differential accumulation of RNA secondary structures in coding and noncoding transcripts from the asexual developmental cycle in in human red blood cells. Our comprehensive analysis that combined high-throughput nuclease mapping of RNA structures by duplex RNA-seq, SHAPE-directed RNA structure validation, immunoaffinity purification and characterization of antisense RNAs collectively measured differentially base-paired RNA regions throughout the parasite's asexual RBC cycle. Read More

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Identification and characterization of melon circular RNAs involved in powdery mildew responses through comparative transcriptome analysis.

PeerJ 2021 15;9:e11216. Epub 2021 Apr 15.

Shandong Key Laboratory of Greenhouse Vegetable Biology, Shandong Branch of National Improvement Center for Vegetable, Vegetable Science Observation and Experiment Station in Huang huai District of Ministry of Agriculture (Shandong), Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Jinan, China.

Circular RNAs (circRNAs) are a class of newly discovered non-coding RNAs that are typically derived from a genome's exonic, intronic, and intergenic regions. Recent studies of circRNAs in animals and plants have shown that circRNAs are vital in response to various abiotic and biotic stresses. Powdery mildew disease (PM) is a serious fungal disease threatening the melon industry. Read More

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Extended-representation bisulfite sequencing of gene regulatory elements in multiplexed samples and single cells.

Nat Biotechnol 2021 May 6. Epub 2021 May 6.

Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.

The biological roles of DNA methylation have been elucidated by profiling methods based on whole-genome or reduced-representation bisulfite sequencing, but these approaches do not efficiently survey the vast numbers of non-coding regulatory elements in mammalian genomes. Here we present an extended-representation bisulfite sequencing (XRBS) method for targeted profiling of DNA methylation. Our design strikes a balance between expanding coverage of regulatory elements and reproducibly enriching informative CpG dinucleotides in promoters, enhancers and CTCF binding sites. Read More

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Background Selection Does Not Mimic the Patterns of Genetic Diversity Produced by Selective Sweeps.

Genetics 2020 Oct;216(2):499-519

It is increasingly evident that natural selection plays a prominent role in shaping patterns of diversity across the genome. The most commonly studied modes of natural selection are positive selection and negative selection, which refer to directional selection for and against derived mutations, respectively. Positive selection can result in hitchhiking events, in which a beneficial allele rapidly replaces all others in the population, creating a valley of diversity around the selected site along with characteristic skews in allele frequencies and linkage disequilibrium among linked neutral polymorphisms. Read More

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October 2020

The Paf1 Complex Broadly Impacts the Transcriptome of Saccharomyces cerevisiae.

Genetics 2019 Jul;212(3):711-728

Department of Biological Sciences, University of Pittsburgh, Pennsylvania 15260.

The Polymerase Associated Factor 1 complex (Paf1C) is a multifunctional regulator of eukaryotic gene expression important for the coordination of transcription with chromatin modification and post-transcriptional processes. In this study, we investigated the extent to which the functions of Paf1C combine to regulate the Saccharomyces cerevisiae transcriptome. While previous studies focused on the roles of Paf1C in controlling mRNA levels, here, we took advantage of a genetic background that enriches for unstable transcripts, and demonstrate that deletion of PAF1 affects all classes of Pol II transcripts including multiple classes of noncoding RNAs (ncRNAs). Read More

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The Paf1 Complex Broadly Impacts the Transcriptome of Saccharomyces cerevisiae.

Genetics 2019 Jul;212(3):711-728

Department of Biological Sciences, University of Pittsburgh, Pennsylvania 15260.

The Polymerase Associated Factor 1 complex (Paf1C) is a multifunctional regulator of eukaryotic gene expression important for the coordination of transcription with chromatin modification and post-transcriptional processes. In this study, we investigated the extent to which the functions of Paf1C combine to regulate the Saccharomyces cerevisiae transcriptome. While previous studies focused on the roles of Paf1C in controlling mRNA levels, here, we took advantage of a genetic background that enriches for unstable transcripts, and demonstrate that deletion of PAF1 affects all classes of Pol II transcripts including multiple classes of noncoding RNAs (ncRNAs). Read More

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-regulatory elements in conserved non-coding sequences of nuclear receptor genes indicate for crosstalk between endocrine systems.

Open Med (Wars) 2021 12;16(1):640-650. Epub 2021 Apr 12.

Sahlgrenska University Hospital, Gothia Forum for Clinical Research, Gothenburg, Sweden.

Nuclear receptors (NRs) are ligand-activated transcription factors that regulate gene expression when bound to specific DNA sequences. Crosstalk between steroid NR systems has been studied for understanding the development of hormone-driven cancers but not to an extent at a genetic level. This study aimed to investigate crosstalk between steroid NRs in conserved intron and exon sequences, with a focus on steroid NRs involved in prostate cancer etiology. Read More

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Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas.

Leukemia 2021 May 5. Epub 2021 May 5.

University of Duesseldorf, Medical Faculty, Department of Pediatric Oncology, Hematology and Clinical Immunology, Center for Child and Adolescent Health, Düsseldorf, Germany.

B cells have the unique property to somatically alter their immunoglobulin (IG) genes by V(D)J recombination, somatic hypermutation (SHM) and class-switch recombination (CSR). Aberrant targeting of these mechanisms is implicated in lymphomagenesis, but the mutational processes are poorly understood. By performing whole genome and transcriptome sequencing of 181 germinal center derived B-cell lymphomas (gcBCL) we identified distinct mutational signatures linked to SHM and CSR. Read More

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Intergenic RNA mainly derives from nascent transcripts of known genes.

Genome Biol 2021 May 5;22(1):136. Epub 2021 May 5.

The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.

Background: Eukaryotic genomes undergo pervasive transcription, leading to the production of many types of stable and unstable RNAs. Transcription is not restricted to regions with annotated gene features but includes almost any genomic context. Currently, the source and function of most RNAs originating from intergenic regions in the human genome remain unclear. Read More

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Distinct expression of select and transcriptome-wide isolated 3'UTRs suggests critical roles in development and transition states.

PLoS One 2021 5;16(5):e0250669. Epub 2021 May 5.

Dept. of Biology, Stanford University, Stanford, CA, United States of America.

Mature mRNA molecules are expected to be comprised of a 5'UTR, a 3'UTR and a coding region (CDS). Unexpectedly, however, there have been multiple recent reports of widespread differential expression of mRNA 3'UTRs and their cognate coding regions (CDS), reflecting the expression of isolated 3'UTRs (i3'UTRs); these i3'UTRs can be highly expressed, often in reciprocal patterns to their cognate CDS. As with other long non-coding (lncRNAs), isolated 3'UTRs are likely to play an important role in gene regulation, but little is known about the contexts in which they are deployed. Read More

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Absence of CG methylation alters the long non-coding transcriptome landscape in multiple species.

FEBS Lett 2021 May 5. Epub 2021 May 5.

Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.

The non-coding regions throughout the genome are in large part comprised of transposable elements (TEs), some of which are functionalized with long intergenic non-coding RNAs (lincRNAs). DNA methylation is predominantly associated with TEs, but little is known about its contribution to the transcription of lincRNAs. Here, we examine the lincRNA profiles of DNA methylation-related mutants of five species, Arabidopsis, rice, tomato, maize, and mouse, to elucidate patterns in lincRNA regulation under altered DNA methylation status. Read More

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MicroRNA in Multiple Myeloma - A Role in Pathogenesis and Prognostic Significance.

Curr Med Chem 2021 May 3. Epub 2021 May 3.

Department of Hematology, Medical University of Lodz, Copernicus Memorial Hospital, 93-510 Lodz Ul. Ciolkowskiego 2. Poland.

Multiple myeloma (MM) is a common malignant hematological malignancy. Recently, interest has grown in the role of non-coding regions in disease pathogenesis. MicroRNAs (miRNAs) are small non-coding RNAs containing 19-25 bases that play a crucial role in messenger RNA silencing and post-transcriptional regulation of gene expression. Read More

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Molecular tools confirm natural Leishmania (Viannia) guyanensis/L. (V.) shawi hybrids causing cutaneous leishmaniasis in the Amazon region of Brazil.

Genet Mol Biol 2021 30;44(2):e20200123. Epub 2021 Apr 30.

Universidade de São Paulo, Instituto de Biociências, Departamento de Fisiologia, São Paulo, SP, Brazil.

Seven isolates from patients with American cutaneous leishmaniasis in the Amazon region of Brazil were phenotypically suggestive of Leishmania (Viannia) guyanensis/L. (V.) shawi hybrids. Read More

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Complete chloroplast genome sequencing of Job's tears ( L.): genome structure, comparative analysis, and phylogenetic relationships.

Mitochondrial DNA B Resour 2021 Apr 15;6(4):1399-1405. Epub 2021 Apr 15.

Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.

Job's tears, also known as adlay, is a valuable plant that has commonly been used in traditional Chinese medicine, as well as an edible food. Due to the lack of knowledge of its genetics and gaps in its evolutionary analysis, breeding of adlay has been hindered. Here, we report five complete chloroplast genomes of various species and varieties in the genus by Illumina sequencing, while their genome structure, comparative analysis, and phylogenetic relationships were conducted. Read More

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The complete chloroplast genome sequence of S. M. Hwang (Styracaceae) from Jiangxi Province, China.

Mitochondrial DNA B Resour 2021 Apr 15;6(4):1395-1396. Epub 2021 Apr 15.

College of Forestry, Jiangxi Agricultural University, Nanchang, PR China.

S. M. Hwang is an endemic species distributed in China. Read More

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The Lost Neural Hierarchy of the Autistic Self-Locked-Out of the Mental Self and Its Default-Mode Network.

Brain Sci 2021 Apr 29;11(5). Epub 2021 Apr 29.

Institute of Mental Health Research, University of Ottawa, Ottawa, ON K1Z 7K4, Canada.

Autism spectrum disorder (ASD) is characterized by a fundamental change in self-awareness including seemingly paradoxical features like increased ego-centeredness and weakened self-referentiality. What is the neural basis of this so-called "self-paradox"? Conducting a meta-analytic review of fMRI rest and task studies, we show that ASD exhibits consistent hypofunction in anterior and posterior midline regions of the default-mode network (DMN) in both rest and task with decreased self-non-self differentiation. Relying on a multilayered nested hierarchical model of self, as recently established (Qin et al. Read More

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Sequence Length of HIV-1 Subtype B Increases over Time: Analysis of a Cohort of Patients with Hemophilia over 30 Years.

Viruses 2021 04 30;13(5). Epub 2021 Apr 30.

HIV Databases, Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87544, USA.

We aimed to investigate whether the sequence length of HIV-1 increases over time. We performed a longitudinal analysis of full-length coding region sequences (FLs) during an HIV-1 outbreak among patients with hemophilia and local controls infected with the Korean subclade B of HIV-1 (KSB). Genes were amplified by overlapping RT-PCR or nested PCR and subjected to direct sequencing. Read More

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An overview of from the Neotropics, including four new species.

Mycologia 2021 May 4:1-17. Epub 2021 May 4.

Departamento de Botânica, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9500, Prédio 43.433, Campus do Vale, Agronomia, 91501-970, Porto Alegre, Rio Grande do Sul, Brazil.

is a monophyletic genus of polypores that causes white rot of various woody plants. The genus has a worldwide distribution and is ecologically and economically important. Several taxa have been described or reported from the Neotropics, and , described originally from Brazil, is the type species for the genus. Read More

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The role of NOTCH3 variants in Alzheimer's disease and subcortical vascular dementia in the Chinese population.

CNS Neurosci Ther 2021 May 4. Epub 2021 May 4.

Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.

Aims: NOTCH3 gene mutations predominantly cause cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy, a common etiology of subcortical vascular dementia (SVaD). Besides, there may be a pathogenic link between NOTCH3 variants and Alzheimer's disease (AD). We aimed to study the role of NOTCH3 variants in AD and SVaD patients. Read More

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Environmental and sex-specific molecular signatures of glioma causation.

Neuro Oncol 2021 May 4. Epub 2021 May 4.

Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut.

Background: The relative importance of genetic and environmental risk factors in gliomagenesis remains uncertain.

Methods: Using whole-exome sequencing data from 1105 adult gliomas, we evaluate the relative contribution to cancer cell lineage proliferation and survival of single-nucleotide mutations in tumors by IDH mutation subtype and sex. We also quantify the contributions of COSMIC cancer mutational signatures to these tumors, identifying possible risk exposures. Read More

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A nonsynonymous polymorphism (rs117179004, T392M) of hyaluronidase 1 (HYAL1) is associated with increased risk of idiopathic pulmonary fibrosis in Southern Han Chinese.

J Clin Lab Anal 2021 May 4:e23782. Epub 2021 May 4.

Department of Internal Medicine and Genetic Diagnosis Center, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China.

Background: Idiopathic pulmonary fibrosis (IPF) is a genetic heterogeneous disease with high mortality and poor prognosis. Hyaluronidase 1 (HYAL1) was found to be upregulated in fibroblasts from IPF patients, and overexpression of HYAL1 could prevent human fetal lung fibroblast proliferation. However, the genetic correlation between the HYAL1 and IPF or connective tissue diseases related interstitial lung disease (CTD-ILD) has not been determined. Read More

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Frequency-Dependent Cortical Interactions during Semantic Processing: An Electrocorticogram Cross-spectrum Analysis Using a Semantic Space Model.

Cereb Cortex 2021 May 4. Epub 2021 May 4.

Department of Epilepsy, Movement Disorders and Physiology, Kyoto University Graduate School of Medicine, Sakyo, Kyoto 606-8507, Japan.

Convergent evidence has demonstrated that semantics are represented by the interaction between a multimodal semantic hub at the anterior temporal lobe (ATL) and other modality-specific association cortical areas. Electrocorticogram (ECoG) recording with high spatiotemporal resolutions is efficient in evaluating such cortical interactions; however, this has not been a focus of preceding studies. The present study evaluated cortical interactions during picture naming using a novel ECoG cross-spectrum analysis, which was formulated from a computational simulation of neuronal networks and combined with a vector space model of semantics. Read More

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The genetic variability, phylogeny and functional significance of E6, E7 and LCR in human papillomavirus type 52 isolates in Sichuan, China.

Virol J 2021 May 3;18(1):94. Epub 2021 May 3.

Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China.

Background: Variations in human papillomavirus (HPV) E6 and E7 have been shown to be closely related to the persistence of the virus and the occurrence and development of cervical cancer. Long control region (LCR) of HPV has been shown multiple functions on regulating viral transcription. In recent years, there have been reports on E6/E7/LCR of HPV-16 and HPV-58, but there are few studies on HPV-52, especially for LCR. Read More

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A PCR-Based Technique to Track the Geographic Origin of With 23-SNP Barcode Analysis.

Front Public Health 2021 16;9:649170. Epub 2021 Apr 16.

Jiangsu Key Laboratory of Experimental and Translational Non-coding RNA Research, School of Medicine, Yangzhou University, Yangzhou, China.

Increased population movement has increased the risk of reintroducing parasites to elimination areas and also dispersing drug-resistant parasites to new regions. Therefore, reliable and repeatable methods to trace back to the source of imported infections are essential. The recently developed 23-single-nucleotide polymorphism (SNP) barcode from organellar genomes of mitochondrion () and apicoplast () provides a valuable tool to locate the geographic origin of . Read More

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Germline Structural Variations in Cancer Predisposition Genes.

Front Genet 2021 14;12:634217. Epub 2021 Apr 14.

Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary.

In addition to single nucleotide variations and small-scale indels, structural variations (SVs) also contribute to the genetic diversity of the genome. SVs, such as deletions, duplications, amplifications, or inversions may also affect coding regions of cancer-predisposing genes. These rearrangements may abrogate the open reading frame of these genes or adversely affect their expression and may thus act as germline mutations in hereditary cancer syndromes. Read More

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Central Nervous System Barriers Impact Distribution and Expression of iNOS and Arginase-1 in Infiltrating Macrophages During Neuroinflammation.

Front Immunol 2021 15;12:666961. Epub 2021 Apr 15.

Theodor Kocher Institute, University Bern, Bern, Switzerland.

In multiple sclerosis (MS) and other neuroinflammatory diseases, monocyte-derived cells (MoCs) traffic through distinct central nervous system (CNS) barriers and gain access to the organ parenchyma exerting detrimental or beneficial functions. How and where these MoCs acquire their different functional commitments during CNS invasion remains however unclear, thus hindering the design of MS treatments specifically blocking detrimental MoC actions. To clarify this issue, we investigated the distribution of iNOS pro-inflammatory and arginase-1 anti-inflammatory MoCs at the distinct border regions of the CNS in a mouse model of MS. Read More

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RNA-Mediated Control in : Insights Into Regulatory Mechanisms and Roles in Metabolism and Virulence.

Front Microbiol 2021 14;12:622829. Epub 2021 Apr 14.

Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.

is an intracellular pathogen that is well known for its adaptability to life in a broad spectrum of different niches. RNA-mediated regulatory mechanisms in play important roles in successful adaptation providing fast and versatile responses to a changing environment. Recent findings indicate that non-coding RNAs (ncRNAs) regulate a variety of processes in this bacterium, such as environmental sensing, metabolism and virulence, as well as immune responses in eukaryotic cells. Read More

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Sequencing of the coding regions of GNBIL on chromosome 22q11.2 as a risk gene of schizophrenia.

Psychiatry Res 2021 Apr 18;300:113943. Epub 2021 Apr 18.

Department of Psychiatry, Yuli Branch, Taipei Veterans General Hospital, Hualien County, Taiwan. Electronic address:

GNB1L haploinsufficiency caused by 22q11.2 deletion syndrome may contribute to schizophrenia pathophysiology. We resequenced the protein-coding sequences of GNB1L in 553 patients with schizophrenia and 535 controls from Taiwan. Read More

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Multilocus sequence typing (MLST) of Entamoeba histolytica identifies kerp2 as a genetic marker associated with disease outcomes.

Parasitol Int 2021 Apr 29;83:102370. Epub 2021 Apr 29.

Division of Parasitology, ICMR-National Institute of Cholera and Enteric Diseases, P-33 CIT Road, Scheme XM, Beliaghata, Kolkata 700010, West Bengal, India. Electronic address:

Amoebiasis caused by protozoan parasite Entamoeba histolytica has diverse infection outcomes. The relationship between parasite genotypes and outcome of amoebic infection is still a paradox and needs to be explored. Genome information of infecting strains from endemic areas throughout the world is essential to explore this relation. Read More

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