Search our Database of Scientific Publications and Authors

I’m looking for a

    801 results match your criteria BMC Molecular Biology [Journal]

    1 OF 17

    Quantitative profiling of BATF family proteins/JUNB/IRF hetero-trimers using Spec-seq.
    BMC Mol Biol 2018 Mar 27;19(1). Epub 2018 Mar 27.
    Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA.
    Background: BATF family transcription factors (BATF, BATF2 and BATF3) form hetero-trimers with JUNB and either IRF4 or IRF8 to regulate cell fate in T cells and dendritic cells in vivo. While each combination of the hetero-trimer has a distinct role, some degree of cross-compensation was observed. The basis for the differential actions of IRF4 and IRF8 with BATF factors and JUNB is still unknown. Read More

    pH-mediated upregulation of AQP1 gene expression through the Spi-B transcription factor.
    BMC Mol Biol 2018 Mar 20;19(1). Epub 2018 Mar 20.
    Department of Nephrology and Rheumatology, Children's Hospital of Fudan University, No. 399 Wanyuan Road, Shanghai, 201102, China.
    Background: Bicarbonate-based peritoneal dialysis (PD) fluids enhance the migratory capacity and damage-repair ability of human peritoneal mesothelial cells by upregulating AQP1. However, little is known about the underlying molecular mechanisms.

    Results: Here we used HEK-293T cells to investigate the effect of pH on AQP1 gene transcription levels. Read More

    A protocol for custom CRISPR Cas9 donor vector construction to truncate genes in mammalian cells using pcDNA3 backbone.
    BMC Mol Biol 2018 Mar 14;19(1). Epub 2018 Mar 14.
    Department of Biology, University of Texas-Rio Grande Valley, 1201 W. University Dr., Edinburg, TX, 78539, USA.
    Background: Clustered regularly interspaced short palindromic repeat (CRISPR) RNA-guided adaptive immune systems are found in prokaryotes to defend cells from foreign DNA. CRISPR Cas9 systems have been modified and employed as genome editing tools in wide ranging organisms. Here, we provide a detailed protocol to truncate genes in mammalian cells using CRISPR Cas9 editing. Read More

    Recommendations for mRNA analysis of micro-dissected glomerular tufts from paraffin-embedded human kidney biopsy samples.
    BMC Mol Biol 2018 Mar 13;19(1). Epub 2018 Mar 13.
    Department of Nephropathology, Institute of Pathology, Friedrich-Alexander University Erlangen-Nuremberg, Krankenhausstraße 8-10, 91054, Erlangen, Germany.
    Background: Glomeruli are excellent pre-determined natural structures for laser micro-dissection. Compartment-specific glomerular gene expression analysis of formalin-fixed paraffin-embedded renal biopsies could improve research applications. The major challenge for such studies is to obtain good-quality RNA from small amounts of starting material, as applicable for the analysis of glomerular compartments. Read More

    Nutrient depletion and TOR inhibition induce 18S and 25S ribosomal RNAs resistant to a 5'-phosphate-dependent exonuclease in Candida albicans and other yeasts.
    BMC Mol Biol 2018 Jan 19;19(1). Epub 2018 Jan 19.
    Research Division, Greater Los Angeles VA Healthcare System, Los Angeles, CA, USA.
    Background: Messenger RNA (mRNA) represents a small percentage of RNAs in a cell, with ribosomal RNA (rRNA) making up the bulk of it. To isolate mRNA from eukaryotes, typically poly-A selection is carried out. Recently, a 5´-phosphate-dependent, 5´→3´ processive exonuclease called Terminator has become available. Read More

    An optimized rapid bisulfite conversion method with high recovery of cell-free DNA.
    BMC Mol Biol 2017 Dec 19;18(1):24. Epub 2017 Dec 19.
    Department of Forensic medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Rd, Wuhan, 430030, China.
    Background: Methylation analysis of cell-free DNA is a encouraging tool for tumor diagnosis, monitoring and prognosis. Sensitivity of methylation analysis is a very important matter due to the tiny amounts of cell-free DNA available in plasma. Most current methods of DNA methylation analysis are based on the difference of bisulfite-mediated deamination of cytosine between cytosine and 5-methylcytosine. Read More

    Sumoylation in p27kip1 via RanBP2 promotes cancer cell growth in cholangiocarcinoma cell line QBC939.
    BMC Mol Biol 2017 Sep 7;18(1):23. Epub 2017 Sep 7.
    Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, Hubei, People's Republic of China.
    Background: Cholangiocarcinoma is one of the deadly disease with poor 5-year survival and poor response to conventional therapies. Previously, we found that p27kip1 nuclear-cytoplasmic translocation confers proliferation potential to cholangiocarcinoma cell line QBC939 and this process is mediated by crm-1. However, no other post-transcriptional regulation was found in this process including sumoylation in cholangiocarcinoma. Read More

    An optimised protocol for isolation of RNA from small sections of laser-capture microdissected FFPE tissue amenable for next-generation sequencing.
    BMC Mol Biol 2017 Aug 23;18(1):22. Epub 2017 Aug 23.
    Institute of Veterinary Pharmacology and Toxicology, Vetsuisse Faculty, University of Zürich, Winterthurerstr. 260, 8057, Zurich, Switzerland.
    Background: Formalin-fixed paraffin embedded (FFPE) tissue constitutes a vast treasury of samples for biomedical research. Thus far however, extraction of RNA from FFPE tissue has proved challenging due to chemical RNA-protein crosslinking and RNA fragmentation, both of which heavily impact on RNA quantity and quality for downstream analysis. With very small sample sizes, e. Read More

    Physical shearing imparts biological activity to DNA and ability to transmit itself horizontally across species and kingdom boundaries.
    BMC Mol Biol 2017 Aug 9;18(1):21. Epub 2017 Aug 9.
    Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India.
    Background: We have recently reported that cell-free DNA (cfDNA) fragments derived from dying cells that circulate in blood are biologically active molecules and can readily enter into healthy cells to activate DNA damage and apoptotic responses in the recipients. However, DNA is not conventionally known to spontaneously enter into cells or to have any intrinsic biological activity. We hypothesized that cellular entry and acquisition of biological properties are functions of the size of DNA. Read More

    Interaction between NFATc2 and the transcription factor Sp1 in pancreatic carcinoma cells PaTu 8988t.
    BMC Mol Biol 2017 Aug 3;18(1):20. Epub 2017 Aug 3.
    Department of Obstetrics and Gynecology, University Hospital Mainz, Mainz, Germany.
    Background: Nuclear factors of activated T-cells (NFATs) have been mainly characterized in the context of immune response regulation because, as transcription factors, they have the ability to induce gene transcription. NFAT proteins are found in several types of tumors, for instance, pancreatic carcinoma. The role of NFATs in carcinogenesis is regulating central genes in cell differentiation and cell growth. Read More

    Splicing arrays reveal novel RBM10 targets, including SMN2 pre-mRNA.
    BMC Mol Biol 2017 Jul 20;18(1):19. Epub 2017 Jul 20.
    Département de Microbiologie et d'infectiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada.
    Background: RBM10 is an RNA binding protein involved in message stabilization and alternative splicing regulation. The objective of the research described herein was to identify novel targets of RBM10-regulated splicing. To accomplish this, we downregulated RBM10 in human cell lines, using small interfering RNAs, then monitored alternative splicing, using a reverse transcription-PCR screening platform. Read More

    Growth arrest specific gene 2 in tilapia (Oreochromis niloticus): molecular characterization and functional analysis under low-temperature stress.
    BMC Mol Biol 2017 Jul 17;18(1):18. Epub 2017 Jul 17.
    Key Laboratory of Freshwater Biodiversity Conservation and Utilization of Ministry of Agriculture, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, China.
    Background: Growth arrest specific 2 (gas2) gene is a component of the microfilament system that plays a major role in the cell cycle, regulation of microfilaments, and cell morphology during apoptotic processes. However, little information is available on fish gas2. In this study, the tilapia (Oreochromis niloticus) gas2 gene was cloned and characterized for the first time. Read More

    Identification of G-quadruplex structures that possess transcriptional regulating functions in the Dele and Cdc6 CpG islands.
    BMC Mol Biol 2017 Jun 27;18(1):17. Epub 2017 Jun 27.
    School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakuramachi, Hachioji, Tokyo, 192-0982, Japan.
    Background: G-quadruplex is a DNA secondary structure that has been shown to play an important role in biological systems. In a previous study, we identified 1998 G-quadruplex-forming sequences using a mouse CpG islands DNA microarray with a fluorescent-labeled G-quadruplex ligand. Among these putative G-quadruplex-forming sequences, G-quadruplex formation was verified for 10 randomly selected sequences by CD spectroscopy and DMS footprinting analysis. Read More

    Mitochondrial RNA processing in absence of tRNA punctuations in octocorals.
    BMC Mol Biol 2017 Jun 17;18(1):16. Epub 2017 Jun 17.
    Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner Str. 10, 80333, Munich, Germany.
    Background: Mitogenome diversity is staggering among early branching animals with respect to size, gene density, content and order, and number of tRNA genes, especially in cnidarians. This last point is of special interest as tRNA cleavage drives the maturation of mitochondrial mRNAs and is a primary mechanism for mt-RNA processing in animals. Mitochondrial RNA processing in non-bilaterian metazoans, some of which possess a single tRNA gene in their mitogenomes, is essentially unstudied despite its importance in understanding the evolution of mitochondrial transcription in animals. Read More

    Microarray expression profiling in the denervated hippocampus identifies long noncoding RNAs functionally involved in neurogenesis.
    BMC Mol Biol 2017 Jun 6;18(1):15. Epub 2017 Jun 6.
    Department of Anatomy and Neurobiology, The Jiangsu Key Laboratory of Neuroregeneration, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, Jiangsu, People's Republic of China.
    Background: The denervated hippocampus provides a proper microenvironment for the survival and neuronal differentiation of neural progenitors. While thousands of lncRNAs were identified, only a few lncRNAs that regulate neurogenesis in the hippocampus are reported. The present study aimed to perform microarray expression profiling to identify long noncoding RNAs (lncRNAs) that might participate in the hippocampal neurogenesis, and investigate the potential roles of identified lncRNAs in the hippocampal neurogenesis. Read More

    Early growth response protein 1 regulates promoter activity of α-plasma membrane calcium ATPase 2, a major calcium pump in the brain and auditory system.
    BMC Mol Biol 2017 May 22;18(1):14. Epub 2017 May 22.
    Department of Pharmacology, School of Medicine, University of Washington, Seattle, WA, 98195, USA.
    Background: Along with sodium/calcium (Ca) exchangers, plasma membrane Ca ATPases (ATP2Bs) are main regulators of intracellular Ca levels. There are four ATP2B paralogs encoded by four different genes. Atp2b2 encodes the protein pump with the fastest activation, ATP2B2. Read More

    hSSB1 associates with and promotes stability of the BLM helicase.
    BMC Mol Biol 2017 May 15;18(1):13. Epub 2017 May 15.
    School of Biomedical Research, Institute of Health and Biomedical Innovation at the Translational Research Institute, Queensland University of Technology, 37 Kent Street, Woolloongabba, QLD, 4102, Australia.
    Background: Maintenance of genome stability is critical in human cells. Mutations in or loss of genome stability pathways can lead to a number of pathologies including cancer. hSSB1 is a critical DNA repair protein functioning in the repair and signalling of stalled DNA replication forks, double strand DNA breaks and oxidised DNA lesions. Read More

    Selective measurement of α smooth muscle actin: why β-actin can not be used as a housekeeping gene when tissue fibrosis occurs.
    BMC Mol Biol 2017 Apr 27;18(1):12. Epub 2017 Apr 27.
    MTA-SE Pediatrics and Nephrology Research Group, Budapest, Hungary.
    Background: Prevalence of fibroproliferative diseases, including chronic kidney disease is rapidly increasing and has become a major public health problem worldwide. Fibroproliferative diseases are characterized by increased expression of α smooth muscle actin (α-SMA) that belongs to the family of the six conserved actin isoforms showing high degree homology. The aim of the present study was to develop real-time PCRs that clearly discriminate α-SMA and ß-actin from other actin isoforms. Read More

    Identification of suitable reference genes for real-time quantitative PCR analysis of hydrogen peroxide-treated human umbilical vein endothelial cells.
    BMC Mol Biol 2017 04 5;18(1):10. Epub 2017 Apr 5.
    Department of Cardiology, The Second Hospital of Jilin University, Changchun, 130041, Jilin, China.
    Background: Oxidative stress can induce cell injury in vascular endothelial cells, which is the initial event in the development of atherosclerosis. Although quantitative real-time polymerase chain reaction (qRT-PCR) has been widely used in gene expression studies in oxidative stress injuries, using carefully validated reference genes has not received sufficient attention in related studies. The objective of this study, therefore, was to select a set of stably expressed reference genes for use in qRT-PCR normalization in oxidative stress injuries in human umbilical vein endothelial cells (HUVECs) induced by hydrogen peroxide (HO). Read More

    RUNX1 induces DNA replication independent active DNA demethylation at SPI1 regulatory regions.
    BMC Mol Biol 2017 04 4;18(1). Epub 2017 Apr 4.
    Division of Genomic Technologies, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
    Background: SPI1 is an essential transcription factor (TF) for the hematopoietic lineage, in which its expression is tightly controlled through a -17-kb upstream regulatory region and a promoter region. Both regulatory regions are demethylated during hematopoietic development, although how the change of DNA methylation status is performed is still unknown.

    Results: We found that the ectopic overexpression of RUNX1 (another key TF in hematopoiesis) in HEK-293T cells induces almost complete DNA demethylation at the -17-kb upstream regulatory region and partial but significant DNA demethylation at the proximal promoter region. Read More

    Immunoglobulin T from sea bass (Dicentrarchus labrax L.): molecular characterization, tissue localization and expression after nodavirus infection.
    BMC Mol Biol 2017 03 15;18(1). Epub 2017 Mar 15.
    Department for Innovation in Biological, Agro-food and Forest Systems, University of Tuscia, Largo dell'Università snc, 05100, Viterbo, VT, Italy.
    Background: Immunoglobulins (Igs) are fundamental components of the adaptive immune system of vertebrates, with the IgT/IgZ isotype specific of Teleosts. In this paper we describe the identification of an IgT heavy chain from the European sea bass (Dicentrarchus labrax L.), its molecular characterization and tissue mRNA localization by in situ hybridization. Read More

    Methylated site display (MSD)-AFLP, a sensitive and affordable method for analysis of CpG methylation profiles.
    BMC Mol Biol 2017 03 9;18(1). Epub 2017 Mar 9.
    Laboratory of Environmental Health Sciences, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
    Background: It has been pointed out that environmental factors or chemicals can cause diseases that are developmental in origin. To detect abnormal epigenetic alterations in DNA methylation, convenient and cost-effective methods are required for such research, in which multiple samples are processed simultaneously. We here present methylated site display (MSD), a unique technique for the preparation of DNA libraries. Read More

    Properties of STAT1 and IRF1 enhancers and the influence of SNPs.
    BMC Mol Biol 2017 03 9;18(1). Epub 2017 Mar 9.
    Lunenfeld Tanenbaum Research Institute, Mt Sinai Hospital, Toronto, ON, Canada.
    Background: STAT1 and IRF1 collaborate to induce interferon-γ (IFNγ) stimulated genes (ISGs), but the extent to which they act alone or together is unclear. The effect of single nucleotide polymorphisms (SNPs) on in vivo binding is also largely unknown.

    Results: We show that IRF1 binds at proximal or distant ISG sites twice as often as STAT1, increasing to sixfold at the MHC class I locus. Read More

    Identification of microRNAs and their response to the stress of plant allelochemicals in Aphis gossypii (Hemiptera: Aphididae).
    BMC Mol Biol 2017 02 16;18(1). Epub 2017 Feb 16.
    China Agricultural University, Beijing, China.
    Background: MicroRNAs (miRNAs) are a group of short non-coding RNAs involved in the inhibition of protein translation or in mRNA degradation. Although the regulatory roles of miRNAs in various biological processes have been investigated, there is as yet an absence of studies about the regulatory roles of miRNAs involved in the metabolism of plant allelochemicals in insects.

    Results: We constructed five small RNA libraries from apterous Aphis gossypii adults that had fed on an artificial diet containing various allelochemicals. Read More

    Binding affinity of five PBPs to Ostrinia sex pheromones.
    BMC Mol Biol 2017 02 7;18(1). Epub 2017 Feb 7.
    State Key Laboratory for the Biology of the Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Beijing, 100193, China.
    Background: Pheromone binding proteins (PBPs) of male Lepidoptera function in chemical communication, mate attraction and recognition. Directional selection was previously predicted between PBP3 orthologs of Ostrinia furnacalis and Ostrinia nubilalis were interpreted as being involved in sexual isolation.

    Results: In vitro assays show that recombinant male OfurPBP3 bound O. Read More

    Positive selection and functional divergence of farnesyl pyrophosphate synthase genes in plants.
    BMC Mol Biol 2017 02 4;18(1). Epub 2017 Feb 4.
    Key Laboratory of Biological Molecular Medicine Research of Guangxi Higher Education, Department of Biochemistry and Molecular Biology, Guangxi Medical University, Nanning, Guangxi, People's Republic of China.
    Background: Farnesyl pyrophosphate synthase (FPS) belongs to the short-chain prenyltransferase family, and it performs a conserved and essential role in the terpenoid biosynthesis pathway. However, its classification, evolutionary history, and the forces driving the evolution of FPS genes in plants remain poorly understood.

    Results: Phylogeny and positive selection analysis was used to identify the evolutionary forces that led to the functional divergence of FPS in plants, and recombinant detection was undertaken using the Genetic Algorithm for Recombination Detection (GARD) method. Read More

    Transcriptional regulation of human sperm-associated antigen 16 gene by S-SOX5.
    BMC Mol Biol 2017 01 31;18(1). Epub 2017 Jan 31.
    Department of Obstetrics and Gynecology, Virginia Commonwealth University, Richmond, VA, 23298, USA.
    Background: The mammalian sperm-associated antigen 16 gene (Spag16) uses alternative promoters to produce two major transcript isoforms (Spag16L and Spag16S) and encode proteins that are involved in the cilia/flagella formation and motility. In silico analysis of both mouse and human SPAG16L promoters reveals the existence of multiple putative SOX5 binding sites. Given that the SOX5 gene encodes a 48-kDa transcription factor (S-SOX5) and the presence of putative SOX5 binding sites at the SPAG16L promoter, regulation of SPAG16L expression by S-SOX5 was studied in the present work. Read More

    Heterogeneous pattern of DNA methylation in developmentally important genes correlates with its chromatin conformation.
    BMC Mol Biol 2017 01 11;18(1). Epub 2017 Jan 11.
    Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, 211004, India.
    Background: DNA methylation is a major epigenetic modification, playing a crucial role in the development and differentiation of higher organisms. DNA methylation is also known to regulate transcription by gene repression. Various developmental genes such as c-mos, HoxB5, Sox11, and Sry show tissue-specific gene expression that was shown to be regulated by promoter DNA methylation. Read More

    Novel insight into the composition of human single-stranded DNA-binding protein 1 (hSSB1)-containing protein complexes.
    BMC Mol Biol 2016 12 9;17(1):24. Epub 2016 Dec 9.
    School of Biomedical Research, Institute of Health and Biomedical Innovation, Queensland University of Technology, Translational Research Institute, 37 Kent Street, Woolloongabba, QLD, 4102, Australia.
    Background: Single-stranded DNA-binding proteins are essential cellular components required for the protection, metabolism and processing of single-stranded DNA. Human single-stranded DNA-binding protein 1 (hSSB1) is one such protein, with described roles in genome stability maintenance and transcriptional regulation. As yet, however, the mechanisms through which hSSB1 functions and the binding partners with which it interacts remain poorly understood. Read More

    3C-digital PCR for quantification of chromatin interactions.
    BMC Mol Biol 2016 12 6;17(1):23. Epub 2016 Dec 6.
    Department of Pathology and MCW Cancer Center, Medical College of Wisconsin, Milwaukee, WI, 53226, USA.
    Background: Chromosome conformation capture (3C) is a powerful and widely used technique for detecting the physical interactions between chromatin regions in vivo. The principle of 3C is to convert physical chromatin interactions into specific DNA ligation products, which are then detected by quantitative polymerase chain reaction (qPCR). However, 3C-qPCR assays are often complicated by the necessity of normalization controls to correct for amplification biases. Read More

    Ataxia telangiectasia mutated (ATM) interacts with p400 ATPase for an efficient DNA damage response.
    BMC Mol Biol 2016 11 4;17(1):22. Epub 2016 Nov 4.
    Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand.
    Background: Ataxia telangiectasia mutated (ATM) and TRRAP proteins belong to the phosphatidylinositol 3-kinase-related kinase family and are involved in DNA damage repair and chromatin remodeling. ATM is a checkpoint kinase that is recruited to sites of DNA double-strand breaks where it phosphorylates a diverse range of proteins that are part of the chromatin and DNA repair machinery. As an integral subunit of the TRRAP-TIP60 complexes, p400 ATPase is a chromatin remodeler that is also targeted to DNA double-strand break sites. Read More

    RNA polymerase II depletion promotes transcription of alternative mRNA species.
    BMC Mol Biol 2016 08 30;17(1):20. Epub 2016 Aug 30.
    Microbiological and Physiological Systems, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA, 01655, USA.
    Background: Cells respond to numerous internal and external stresses, such as heat, cold, oxidative stress, DNA damage, and osmotic pressure changes. In most cases, the primary response to stress is transcriptional induction of genes that assist the cells in tolerating the stress and facilitate the repair of the cellular damage. However, when the transcription machinery itself is stressed, responding by such standard mechanisms may not be possible. Read More

    Distinct recruitment of human eIF4E isoforms to processing bodies and stress granules.
    BMC Mol Biol 2016 08 30;17(1):21. Epub 2016 Aug 30.
    Laboratory of RNA Biochemistry, Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Viničná 5, 128 00, Prague 2, Czech Republic.
    Background: Eukaryotic translation initiation factor 4E (eIF4E) plays a pivotal role in the control of cap-dependent translation initiation, modulates the fate of specific mRNAs, occurs in processing bodies (PBs) and is required for formation of stress granules (SGs). In this study, we focused on the subcellular localization of a representative compendium of eIF4E protein isoforms, particularly on the less studied members of the human eIF4E protein family, eIF4E2 and eIF4E3.

    Results: We showed that unlike eIF4E1, its less studied isoform eIF4E3_A, encoded by human chromosome 3, localized to stress granules but not PBs upon both heat shock and arsenite stress. Read More

    Nucleophosmin: from structure and function to disease development.
    BMC Mol Biol 2016 08 24;17(1):19. Epub 2016 Aug 24.
    School of Biomedical Research, Institute of Health and Biomedical Innovation at the Translational Research Institute, Queensland University of Technology, Brisbane, QLD, Australia.
    Nucleophosmin (NPM1) is a critical cellular protein that has been implicated in a number of pathways including mRNA transport, chromatin remodeling, apoptosis and genome stability. NPM1 function is a critical requirement for normal cellular biology as is underlined in cancer where NPM1 is commonly overexpressed, mutated, rearranged and sporadically deleted. Consistent with a multifunctional role within the cell, NPM1 can function not only as a proto-oncogene but also as a tumor suppressor. Read More

    Myelodysplasia-associated mutations in serine/arginine-rich splicing factor SRSF2 lead to alternative splicing of CDC25C.
    BMC Mol Biol 2016 08 23;17(1):18. Epub 2016 Aug 23.
    Department of Molecular and Cellular Biology, Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA, 91010, USA.
    Background: Serine-arginine rich splicing factor 2 (SRSF2) is a protein known for its role in RNA splicing and genome stability. It has been recently discovered that SRSF2, along with other splicing regulators, is frequently mutated in patients with myelodysplastic syndrome (MDS). The most common MDS mutations in SRSF2 occur at proline 95; the mutant proteins are shown to have different RNA binding preferences, which may contribute to splicing changes detected in mutant cells. Read More

    MicroRNA 433 regulates nonsense-mediated mRNA decay by targeting SMG5 mRNA.
    BMC Mol Biol 2016 07 29;17(1):17. Epub 2016 Jul 29.
    Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture & Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China.
    Background: Nonsense-mediated mRNA decay (NMD) is a RNA quality surveillance system for eukaryotes. It prevents cells from generating deleterious truncated proteins by degrading abnormal mRNAs that harbor premature termination codon (PTC). However, little is known about the molecular regulation mechanism underlying the inhibition of NMD by microRNAs. Read More

    Stearoyl-CoA desaturase 1 expression is downregulated in liver and udder during E. coli mastitis through enhanced expression of repressive C/EBP factors and reduced expression of the inducer SREBP1A.
    BMC Mol Biol 2016 07 20;17(1):16. Epub 2016 Jul 20.
    Leibniz Institute for Farm Animal Biology, Institute for Genome Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany.
    Background: Stearoyl-CoA desaturase 1 (SCD1) desaturates long chain fatty acids and is therefore a key enzyme in fat catabolism. Its synthesis is downregulated in liver during illnesses caused by high levels of circulating lipopolysaccharide (LPS). SCD1 expression is known to be stimulated under adipogenic conditions through a variety of transcription factors, notably SREBP1 and C/EBPα and -β. Read More

    Confirmation of translatability and functionality certifies the dual endothelin1/VEGFsp receptor (DEspR) protein.
    BMC Mol Biol 2016 06 14;17(1):15. Epub 2016 Jun 14.
    Whitaker Cardiovascular Institute, Boston University School of Medicine, 700 Albany Street, Boston, MA, 02118, USA.
    Background: In contrast to rat and mouse databases, the NCBI gene database lists the human dual-endothelin1/VEGFsp receptor (DEspR, formerly Dear) as a unitary transcribed pseudogene due to a stop [TGA]-codon at codon#14 in automated DNA and RNA sequences. However, re-analysis is needed given prior single gene studies detected a tryptophan [TGG]-codon#14 by manual Sanger sequencing, demonstrated DEspR translatability and functionality, and since the demonstration of actual non-translatability through expression studies, the standard-of-excellence for pseudogene designation, has not been performed. Re-analysis must meet UNIPROT criteria for demonstration of a protein's existence at the highest (protein) level, which a priori, would override DNA- or RNA-based deductions. Read More

    Strong preference of BRCA1 protein to topologically constrained non-B DNA structures.
    BMC Mol Biol 2016 06 8;17(1):14. Epub 2016 Jun 8.
    Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 65, Brno, Czech Republic.
    Background: The breast and ovarian cancer susceptibility gene BRCA1 encodes a multifunctional tumor suppressor protein BRCA1, which is involved in regulating cellular processes such as cell cycle, transcription, DNA repair, DNA damage response and chromatin remodeling. BRCA1 protein, located primarily in cell nuclei, interacts with multiple proteins and various DNA targets. It has been demonstrated that BRCA1 protein binds to damaged DNA and plays a role in the transcriptional regulation of downstream target genes. Read More

    A potential role for protein palmitoylation and zDHHC16 in DNA damage response.
    BMC Mol Biol 2016 05 10;17(1):12. Epub 2016 May 10.
    Department of Ophthalmology, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
    Background: Cells respond to DNA damage by activating the phosphatidylinositol-3 kinase-related kinases, p53 and other pathways to promote cell cycle arrest, apoptosis, and/or DNA repair. Here we report that protein palmitoylation, a modification carried out by protein acyltransferases with zinc-finger and Asp-His-His-Cys domains (zDHHC), is required for proper DNA damage responses.

    Results: Inhibition of protein palmitoylation compromised DNA damage-induced activation of Atm, induction and activation of p53, cell cycle arrest at G2/M phase, and DNA damage foci assembly/disassembly in primary mouse embryonic fibroblasts. Read More

    Mice lacking microRNAs in Pax8-expressing cells develop hypothyroidism and end-stage renal failure.
    BMC Mol Biol 2016 Apr 18;17:11. Epub 2016 Apr 18.
    Department II of Internal Medicine and Center for Molecular Medicine, University of Cologne, Kerpener Str. 62, 50937, Cologne, Germany.
    Background: Non-coding RNAs have gained increasing attention during the last decade. The first large group of non-coding RNAs to be characterized systematically starting at the beginning of the 21st century were small oligonucleotides--the so-called microRNAs (miRNAs). By now we have learnt that microRNAs are indispensable for most biological processes including organogenesis and maintenance of organ structure and function. Read More

    Signal transducer and activator of transcription STAT5 is recruited to c-Myc super-enhancer.
    BMC Mol Biol 2016 Apr 14;17:10. Epub 2016 Apr 14.
    Stat5 Signaling Research Group, Institute of Immunology, University of Regensburg, 93053, Regensburg, Germany.
    Background: c-Myc has been proposed as a putative target gene of signal transducer and activator of transcription 5 (STAT5). No functional STAT5 binding site has been identified so far within the c-Myc gene locus, therefore a direct transcriptional regulation by STAT5 remains uncertain. c-Myc super-enhancer, located 1. Read More

    Immunoblot screening of CRISPR/Cas9-mediated gene knockouts without selection.
    BMC Mol Biol 2016 Apr 2;17. Epub 2016 Apr 2.
    Department of Cell Biology and Neuroscience, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA.
    Background: Targeted genomic editing using the CRISPR/Cas9 methodology has opened exciting new avenues in probing gene function in virtually any model system, including cultured mammalian cells. Depending on the desired mutation, several experimental options exist in the isolation of clonal lines, such as selection with introduced markers, or screening by PCR amplification of genomic DNA. However, streamlined approaches to establishing deletion and tagging mutants with minimal genomic perturbation are of interest in applying this methodology. Read More

    A reliable method for quantification of splice variants using RT-qPCR.
    BMC Mol Biol 2016 Mar 15;17. Epub 2016 Mar 15.
    Experimentelle und Klinische Pharmakologie und Toxikologie, Universität des Saarlandes, 66421, Homburg, Germany.
    Background: The majority of protein isoforms arise from alternative splicing of the encoding primary RNA transcripts. To understand the significance of single splicing events, reliable techniques are needed to determine their incidence. However, existing methods are labour-intensive, error-prone or of limited use. Read More

    Gene expression profiling of the venom gland from the Venezuelan mapanare (Bothrops colombiensis) using expressed sequence tags (ESTs).
    BMC Mol Biol 2016 Mar 5;17. Epub 2016 Mar 5.
    Laboratorio de Inmunoquímica y Ultraestructura, Instituto Anatómico de la Universidad Central de Venezuela, Caracas, Venezuela.
    Background: Bothrops colombiensis is a highly dangerous pit viper and responsible for over 70% of snakebites in Venezuela. Although the composition in B. colombiensis venom has been identified using a proteome analysis, the venom gland transcriptome is currently lacking. Read More

    Knockdown of SALL4 inhibits the proliferation and reverses the resistance of MCF-7/ADR cells to doxorubicin hydrochloride.
    BMC Mol Biol 2016 Mar 2;17. Epub 2016 Mar 2.
    Department of General Surgery and Laboratory of General Surgery, Xinhua Hospital, Affiliated with Shanghai Jiao Tong University, School of Medicine, No. 1665 Kong Jiang Road, 200092, Shanghai, China.
    Background: Breast cancer is the most frequent malignancy in women and drug resistance is the major obstacle for its successful chemotherapy. In the present study, we analyzed the involvement of an oncofetal gene, sal-like 4 (SALL4), in the tumor proliferation and drug resistance of human breast cancer.

    Results: Our study showed that SALL4 was up-regulated in the drug resistant breast cancer cell line, MCF-7/ADR, compared to the other five cell lines. Read More

    What is normal? Next generation sequencing-driven analysis of the human circulating miRNAOme.
    BMC Mol Biol 2016 Feb 9;17. Epub 2016 Feb 9.
    Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Harwell Science and Innovation Campus, Didcot, OX11 0RQ, UK.
    Background: MicroRNAs (miRNAs) are short non-protein-coding RNA species that have a regulatory function in modulating protein translation and degradation of specific mRNAs. MicroRNAs are estimated to target approximately 60% of all human mRNAs and are associated with the regulation of all physiological processes. Similar to many messenger RNAs (mRNA), miRNAs exhibit marked tissue specificity, and appear to be dysregulated in response to specific pathological conditions. Read More

    TLK1B mediated phosphorylation of Rad9 regulates its nuclear/cytoplasmic localization and cell cycle checkpoint.
    BMC Mol Biol 2016 Feb 9;17. Epub 2016 Feb 9.
    Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, 1501 Kings Highway, Shreveport, LA, 71130, USA.
    Background: The Tousled like kinase 1B (TLK1B) is critical for DNA repair and survival of cells. Upon DNA damage, Chk1 phosphorylates TLK1B at S457 leading to its transient inhibition. Once TLK1B regains its kinase activity it phosphorylates Rad9 at S328. Read More

    1 OF 17