2,574,892 results match your criteria gene function

Global RNA profiles show target selectivity and physiological effects of peptide-delivered antisense antibiotics.

Nucleic Acids Res 2021 Apr 13. Epub 2021 Apr 13.

Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany.

Antisense peptide nucleic acids (PNAs) inhibiting mRNAs of essential genes provide a straight-forward way to repurpose our knowledge of bacterial regulatory RNAs for development of programmable species-specific antibiotics. While there is ample proof of PNA efficacy, their target selectivity and impact on bacterial physiology are poorly understood. Moreover, while antibacterial PNAs are typically designed to block mRNA translation, effects on target mRNA levels are not well-investigated. Read More

View Article and Full-Text PDF

Bimodal regulation of the PRC2 complex by USP7 underlies tumorigenesis.

Nucleic Acids Res 2021 Apr 13. Epub 2021 Apr 13.

Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China.

Although overexpression of EZH2, a catalytic subunit of the polycomb repressive complex 2 (PRC2), is an eminent feature of various cancers, the regulation of its abundance and function remains insufficiently understood. We report here that the PRC2 complex is physically associated with ubiquitin-specific protease USP7 in cancer cells where USP7 acts to deubiquitinate and stabilize EZH2. Interestingly, we found that USP7-catalyzed H2BK120ub1 deubiquitination is a prerequisite for chromatin loading of PRC2 thus H3K27 trimethylation, and this process is not affected by H2AK119 ubiquitination catalyzed by PRC1. Read More

View Article and Full-Text PDF

Genome-wide characterization of human minisatellite VNTRs: population-specific alleles and gene expression differences.

Nucleic Acids Res 2021 Apr 13. Epub 2021 Apr 13.

Graduate Program in Bioinformatics, Boston University, Boston, MA 02215, USA.

Variable Number Tandem Repeats (VNTRs) are tandem repeat (TR) loci that vary in copy number across a population. Using our program, VNTRseek, we analyzed human whole genome sequencing datasets from 2770 individuals in order to detect minisatellite VNTRs, i.e. Read More

View Article and Full-Text PDF

Cistrome analysis of YY1 uncovers a regulatory axis of YY1:BRD2/4-PFKP during tumorigenesis of advanced prostate cancer.

Nucleic Acids Res 2021 Apr 13. Epub 2021 Apr 13.

Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA.

Castration-resistant prostate cancer (CRPC) is a terminal disease and the molecular underpinnings of CRPC development need to be better understood in order to improve its treatment. Here, we report that a transcription factor Yin Yang 1 (YY1) is significantly overexpressed during prostate cancer progression. Functional and cistrome studies of YY1 uncover its roles in promoting prostate oncogenesis in vitro and in vivo, as well as sustaining tumor metabolism including the Warburg effect and mitochondria respiration. Read More

View Article and Full-Text PDF

Reproductive performance, expression of TRAP6 and TGF-β4 genes in utero-vaginal junction mucosa, and indicators of liver function in female Chukar partridge (Alectoris chukar) breeders fed with fish oil and calcitriol during the egg-laying period.

Theriogenology 2021 Mar 30;168:50-58. Epub 2021 Mar 30.

Department of Animal Science, Sari Agricultural Science and Natural Resources University, Sari, 48177- 36781, Iran.

Reproductive attributes, expression of TRAP6 and TGF-β mRNA in the mucosa of the utero-vaginal junction (UVJ) of oviduct, and liver function were evaluated in Chukar partridge (Alectoris chukar) breeders subjected to long-term oral administration of fish oil (FO) and/or calcitriol (CT). A total of forty-eight 1.5-year-old laying Chukar partridges and 16 age-matched males (female:male ratio of 3:1) were randomly allocated to four groups (4 replicates of 3 female birds and one male bird each). Read More

View Article and Full-Text PDF

The role of SYT-SSX fusion gene in tumorigenesis of synovial sarcoma.

Pathol Res Pract 2021 Mar 24;222:153416. Epub 2021 Mar 24.

Department of Pathology, Shihezi University School of Medicine & the First Affiliated Hospital to Shihezi University School of Medicine, Shihezi, 832002, Xinjiang, China; Department of Pathology, Central People's Hospital of Zhanjiang and Zhanjiang Central Hospital, Guangdong Medical University, Zhanjiang, China. Electronic address:

Synovial sarcoma (SS) is an aggressive malignancy of an unknown tissue origin that is characterized by biphasic differentiation. A possible basis of the pathogenesis of SS is pathognomonic t(X;18) (p11.2; q11. Read More

View Article and Full-Text PDF

Analysis of Populus glycosyl hydrolase family I members and their potential role in the ABA treatment and drought stress response.

Plant Physiol Biochem 2021 Apr 5;163:178-188. Epub 2021 Apr 5.

State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, Guangdong, 510520, China. Electronic address:

Glycoside hydrolase family 1 (GH1) β-glucosidases (BGLUs) are encoded by a large number of genes and are involved in many developmental processes and stress responses in plants. Due to their importance in plant growth and development, genome-wide analyses have been conducted in the model plant species Arabidopsis thaliana, rice and maize but not in woody plant species, which have important economic and ecological value. In this study, we systematically analyzed Populus BGLUs (PtBGLUs) and demonstrated the involvement of several genes under stress conditions. Read More

View Article and Full-Text PDF

Chronic chlorpyrifos exposure induces oxidative stress, apoptosis and immune dysfunction in largemouth bass (Micropterus salmoides).

Environ Pollut 2021 Mar 24;282:117010. Epub 2021 Mar 24.

College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China. Electronic address:

This study was undertaken to (a) evaluate the destructive effects of chronic exposure to low-dose of chlorpyrifos (CPF) on antioxidant system and immune function in largemouth bass (Micropterus salmoides), and (b) to examine whether dietary supplementation of curcumin can mitigate the adverse effects induced by CPF contamination. The experiment consisted of three groups (with three replicates, 30 fish per replicate) which lasted for 60 days: A control group (without CPF exposure or CU application), CP group (exposed to 0.004 mg/L of CPF), and CU group (exposed to 0. Read More

View Article and Full-Text PDF

New insights into restoring microbial communities by side-stream supersaturated oxygenation to improve the resilience of rivers affected by combined sewer overflows.

Sci Total Environ 2021 Apr 6;782:146903. Epub 2021 Apr 6.

State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China. Electronic address:

Combined sewer overflows (CSOs) are a dominant contributor to urban river pollution. Therefore, reducing the environmental impacts of CSOs and improving the self-purification capacity of water bodies are essential. In this study, the side-stream supersaturation (SSS) oxygenation was applied to restore microbial function of rivers which are affected by CSOs to improve the self-purification capacity. Read More

View Article and Full-Text PDF

G-CSF promotes alloregulatory function of MDSCs through a c-Kit dependent mechanism.

Cell Immunol 2021 Mar 26;364:104346. Epub 2021 Mar 26.

Department of Surgery, University of Maryland School of Medicine, Baltimore, United States; Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, United States; Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, United States. Electronic address:

Myeloid-derived suppressor cells (MDSC) are a heterogeneous population of immature myeloid cells that expand in inflammatory conditions including transplantation. MDSCs may be capable of controlling rejection. The critical mechanisms underlying MDSC mediated alloregulation remain unexplored. Read More

View Article and Full-Text PDF

Common variants in CREB1 gene confer risk for bipolar disorder in Han Chinese.

Asian J Psychiatr 2021 Apr 6;59:102648. Epub 2021 Apr 6.

Division of Mood Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China. Electronic address:

Recently, we have identified involvement of the gene encoding cAMP responsive element-binding 1 (CREB1) in risk of BD in European ancestry. CREB1 has significant genetic diversity between Europeans and Chinese, thereby resulting in diverged CREB1 genetic backgrounds. In this study, we aimed to determine whether CREB1 confers susceptibility to BD and cognitive dysfunction in Han Chinese. Read More

View Article and Full-Text PDF

An induced pluripotent stem cell line (GZHMCi004-A) derived from a fetus with heterozygous G380R mutation in FGFR3 gene causing achondroplasia.

Stem Cell Res 2021 Apr 5;53:102322. Epub 2021 Apr 5.

Department of Obstetrics and Gynecology, Department of Fetal Medicine and Prenatal Diagnosis, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China. Electronic address:

Achondroplasia (ACH; MIM #100800) is an autosomal dominant genetic disease caused by gain-of-function mutations in FGFR3 gene and results in short-limb dwarfism. Here, we generated an induced pluripotent stem cell line GZHMCi004-A derived from umbilical cord blood mononuclear cells (UCBMCs) of a fetus with heterozygous G380R mutation in FGFR3 gene. This iPSC line is a valuable in vitro model to study the pathological mechanism and the treatment of ACH. Read More

View Article and Full-Text PDF

Arsenic accumulation and speciation in two cultivars of Pteris cretica L. and characterization of arsenate reductase PcACR2 and arsenite transporter PcACR3 genes in the hyperaccumulating cv. Albo-lineata.

Ecotoxicol Environ Saf 2021 Apr 10;216:112196. Epub 2021 Apr 10.

Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Technická 3, 166 28 Prague, Czech Republic. Electronic address:

Pollution and poisoning with carcinogenic arsenic (As) is of major concern globally. Interestingly, there are ferns that can naturally tolerate remarkably high As concentrations in soils while hyperaccumulating this metalloid in their fronds. Besides Pteris vittata in which As-related traits and molecular determinants have been studied in detail, the As hyperaccumulation status has been attributed also to Pteris cretica. Read More

View Article and Full-Text PDF

Characterization of monomeric and soluble aggregated Aβ in Down's syndrome and Alzheimer's disease brains.

Neurosci Lett 2021 Apr 10:135894. Epub 2021 Apr 10.

Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden; Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden.

The major characteristics of Alzheimer's disease (AD) are amyloid plaques, consisting of aggregated beta amyloid (Aβ) peptides, together with tau pathology (tangles, neuropil treads and dystrophic neurites surrounding the plaques), in the brain. Down's syndrome (DS) individuals are at increased risk to develop AD-type pathology; most DS individuals have developed substantial pathology already at the age of 40. DS individuals have an extra copy of chromosome 21, harbouring the amyloid precursor protein gene (APP). Read More

View Article and Full-Text PDF

The brominated flame retardants TBECH and DPTE alter prostate growth, histology and gene expression patterns in the mouse.

Reprod Toxicol 2021 Apr 10. Epub 2021 Apr 10.

Biology, The Life Science Center, School of Science and Technology, Örebro University, SE-701 82, Örebro, Sweden. Electronic address:

The brominated flame retardants (BFRs), 1,2-dibromo-4-(1,2 dibromoethyl)cyclohexane (TBECH) and 2,3-dibromopropyl-2,4,6-tribromophenyl ether (DPTE) bind to the androgen receptor (AR). In vitro bioassays have shown that TBECH is a potent androgen agonist while DPTE is a potent AR antagonist. Both TBECH and DPTE alter gene expression associated with AR regulation. Read More

View Article and Full-Text PDF

Synergistic effects of green tea extract and Paclitaxel in the induction of mitochondrial apoptosis in ovarian cancer cell lines.

Gene 2021 Apr 10:145638. Epub 2021 Apr 10.

Department of Medical Radiation, Faculty of Engineering, Islamic Azad University, Science and Research Branch, Tehran, Iran. Electronic address:

Background: Green tea is a natural compound with anti-neoplastic properties. Paclitaxel (PTX) is a natural anti-tumor medication used to manage patients with advanced ovarian cancer. This manuscript evaluated the cytotoxic effects of green tea extract combined with PTX drug in two human ovarian cancer cell lines (p53-negative cell line, SKOV-3; and mutant type p53 cell line, OVCAR-3) and underlying mechanisms. Read More

View Article and Full-Text PDF

Identification of the trehalose-6-phosphate synthase gene family in Medicago truncatula and expression analysis under abiotic stresses.

Gene 2021 Apr 10:145641. Epub 2021 Apr 10.

College of Biological Sciences and Engineering, Jiangxi Agricultural University, Nanchang, 330045, PR China. Electronic address:

Trehalose-6-phosphate synthase (TPS) exerts important functions related to plant desiccation tolerance and responses to environmental stimuli. However, in Medicago truncatula, the TPS family has not been reported to date. This study found 11 MtTPS genes in the genome of M. Read More

View Article and Full-Text PDF

Genome-wide characterization and expression profiling of the PDR gene family in N. tabacum.

Gene 2021 Apr 10:145637. Epub 2021 Apr 10.

China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China. Electronic address:

The pleiotropic drug resistance (PDR) proteins of the ATP-binding cassette (ABC) family play essential roles in physiological processes and have been characterized in many plant species. However, no comprehensive investigation of tobacco (Nicotiana tabacum), an important economic crop and a useful model plant for scientific research, has been presented. We identified 32 PDR genes in the tobacco genome and explored their domain organization, chromosomal distribution and evolution, promoter cis-elements, and expression profiles. Read More

View Article and Full-Text PDF

Impact of chromatin context on Cas9-induced DNA double-strand break repair pathway balance.

Mol Cell 2021 Apr 6. Epub 2021 Apr 6.

Oncode Institute, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands; Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands; Department of Cell Biology, Erasmus University Medical Centre, 3015 CN, Rotterdam, the Netherlands. Electronic address:

DNA double-strand break (DSB) repair is mediated by multiple pathways. It is thought that the local chromatin context affects the pathway choice, but the underlying principles are poorly understood. Using a multiplexed reporter assay in combination with Cas9 cutting, we systematically measure the relative activities of three DSB repair pathways as a function of chromatin context in >1,000 genomic locations. Read More

View Article and Full-Text PDF

UV-induced activation of ATR is mediated by UHRF2.

Genes Cells 2021 Apr 13. Epub 2021 Apr 13.

Department of Veterinary Biochemistry, Yamaguchi University, 1677-1 Yoshida, Yamaguchi City, Yamaguchi Prefecture, 753-8511, Japan.

UHRF1 (Ubiquitin-like with PHD and ring finger domains 1) regulates DNA methylation and histone modifications, and plays a key role in cell proliferation and the DNA damage response. However, the function of UHRF2, a paralog of UHRF1, in the DNA damage response remains largely unknown. Here, we show that UHRF2 is essential for maintaining cell viability after UV irradiation, as well as for the proliferation of cancer cells. Read More

View Article and Full-Text PDF

Recent advances in the pathophysiology of PIEZO1-related hereditary xerocytosis.

Am J Hematol 2021 Apr 13. Epub 2021 Apr 13.

UR4666 HEMATIM, Université Picardie Jules Verne, Amiens, France.

Hereditary xerocytosis is a rare red blood cell disease related to gain-of-function mutations in the FAM38A gene, encoding PIEZO1, in 90% of cases. PIEZO1 is a broadly expressed mechano-transducer that plays a major role in many cell systems and tissues that respond to mechanical stress. In erythrocytes, PIEZO1 adapts the intracellular ionic content and cell hydration status to the mechanical constraints induced by the environment. Read More

View Article and Full-Text PDF

Calmodulin-Binding Protein 60b is a central transcriptional activator of immunity.

Plant Physiol 2021 Apr 12. Epub 2021 Apr 12.

State Key laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China.

Plants use a dual defense system to cope with microbial pathogens. The first involves pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) which is conferred by membrane receptors, and the second involves effector-triggered immunity (ETI), which is conferred by disease-resistance proteins (nucleotide-binding leucine-rich repeat containing proteins; NLRs). Calmodulin-Binding Protein 60 (CBP60) family transcription factors are crucial for pathogen defense: CBP60g and Systemic Acquired Resistance Deficient 1 (SARD1) positively regulate immunity, whereas CBP60a negatively regulates immunity. Read More

View Article and Full-Text PDF

Multiplexing Mutation Rate Assessment: Determining Pathogenicity of Msh2 Variants in S. cerevisiae.

Genetics 2021 Apr 12. Epub 2021 Apr 12.

Genome Sciences Department, University of Washington, Seattle, WA 98195, USA.

Despite the fundamental importance of mutation rate as a driving force in evolution and disease risk, common methods to assay mutation rate are time consuming and tedious. Established methods such as fluctuation tests and mutation accumulation experiments are low-throughput and often require significant optimization to ensure accuracy. We established a new method to determine the mutation rate of many strains simultaneously by tracking mutation events in a chemostat continuous culture device and applying deep sequencing to link mutations to alleles of a DNA-repair gene. Read More

View Article and Full-Text PDF

Lack of collagen α6(IV) chain in mice does not cause severe-to-profound hearing loss or cochlear malformation, a distinct phenotype from nonsyndromic hearing loss with COL4A6 missense mutation.

PLoS One 2021 13;16(4):e0249909. Epub 2021 Apr 13.

Department of Molecular Biology and Biochemistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan.

Congenital hearing loss affects 1 in every 1000 births, with genetic mutations contributing to more than 50% of all cases. X-linked nonsyndromic hereditary hearing loss is associated with six loci (DFNX1-6) and five genes. Recently, the missense mutation (c. Read More

View Article and Full-Text PDF

Base editing repairs an SGCA mutation in human primary muscle stem cells.

JCI Insight 2021 Apr 13. Epub 2021 Apr 13.

Muscle Research Unit, Charité University Hospital Berlin, Berlin, Germany.

Skeletal muscle can regenerate from muscle stem cells and their myogenic precursor cell progeny, myoblasts. However, precise gene editing in human muscle stem cells for autologous cell replacement therapies of untreatable genetic muscle diseases has not yet been reported. Loss-of-function mutations in SGCA, encoding α-sarcoglycan, cause limb-girdle muscular dystrophy 2D/R3, an early onset, severe and rapidly progressive form of muscular dystrophy affecting equally girls and boys. Read More

View Article and Full-Text PDF

MAPLE: A Microbiome Analysis Pipeline Enabling Optimal Peptide Search and Comparative Taxonomic and Functional Analysis.

J Proteome Res 2021 Apr 13. Epub 2021 Apr 13.

Department of Pharmaceutical Sciences, University of Maryland, School of Pharmacy, Baltimore, Maryland 21201, United States.

Metaproteomics by mass spectrometry (MS) is a powerful approach to profile a large number of proteins expressed by all organisms in a highly complex biological or ecological sample, which is able to provide a direct and quantitative assessment of the functional makeup of a microbiota. The human gastrointestinal microbiota has been found playing important roles in human physiology and health, and metaproteomics has been shown to shed light on multiple novel associations between microbiota and diseases. MS-powered proteomics generally relies on genome data to define search space. Read More

View Article and Full-Text PDF

Silicon induces metallochaperone-driven Cd binding to the cell wall and restores redox status through elevated glutathione in Cd-toxic sugar beet.

Physiol Plant 2021 Apr 13. Epub 2021 Apr 13.

Grassland and Forage Division, National Institute of Animal Science, Rural Development Administration, Cheonan, Republic of Korea.

Cadmium (Cd) is toxic; however, whether silicon (Si) alleviates Cd toxicity was never studied in sugar beet. The study was conducted on two weeks old sugar beet cultivated in the presence or absence of Cd (10 μM CdSO ) and Si (1 mM Na SiO ) in hydroponic conditions. The morphological impairment and cellular damages observed in sugar beet upon Cd toxicity were entirely reversed due to Si. Read More

View Article and Full-Text PDF

Age-Related Macular Degeneration: From Epigenetics to Therapeutic Implications.

Adv Exp Med Biol 2021 ;1256:221-235

Department of Ophthalmology, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA.

Aberrant regulation of epigenetic mechanisms, including the two most common types; DNA methylation and histone modification have been implicated in common chronic progressive conditions, including Alzheimer disease, cardiovascular disease, and age-related macular degeneration (AMD). All these conditions are complex, meaning that environmental factors, genetic factors, and their interactions play a role in disease pathophysiology. Although genome wide association studies (GWAS), and studies on twins demonstrate the genetic/hereditary component to these complex diseases, including AMD, this contribution is much less than 100%. Read More

View Article and Full-Text PDF
January 2021

Making Biological Sense of Genetic Studies of Age-Related Macular Degeneration.

Adv Exp Med Biol 2021 ;1256:201-219

Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA.

Age-related macular degeneration (AMD) is a major cause of blindness in older individuals worldwide. The disease is characterized by deposition of drusen between the retinal pigment epithelium (RPE) and Bruch's membrane, RPE atrophy and death of photoreceptors. AMD is a complex disease with multiple genetic and non-genetic risk factors. Read More

View Article and Full-Text PDF
January 2021

Guide RNA Design for Genome-Wide CRISPR Screens in Yarrowia lipolytica.

Methods Mol Biol 2021 ;2307:123-137

Chemical and Environmental Engineering, University of California Riverside, Riverside, CA, USA.

Genome-wide functional genomic screens are essential to determining the genetic underpinning of a biological process. Novel and powerful tools for perturbing gene function, with the help of genetic and epigenetic information, have made it possible to systematically investigate the contribution of every gene to evolved and engineered phenotypes. Functional genomics and screening for enhanced phenotypes become ever more important when dealing with nonconventional hosts. Read More

View Article and Full-Text PDF
January 2021