Abstract:
:The nuclear receptor vitamin D receptor (VDR) is known to associate with two vitamin D response element (VDRE) containing chromatin regions of the insulin-like growth factor binding protein 3 (IGFBP3) gene. In non-malignant MCF-10A human mammary cells, we show that the natural VDR ligand 1α,25-dihydroxyvitamin D(3) (1α,25(OH)(2)D(3)) causes cyclical IGFBP3 mRNA accumulation with a periodicity of 60 min, while in the presence of the potent VDR agonist Gemini the mRNA is continuously accumulated. Accordingly, VDR also showed cyclical ligand-dependent association with the chromatin regions of both VDREs. Histone deacetylases (HDACs) play an important role both in VDR signalling and in transcriptional cycling. From the 11 HDAC gene family members, only HDAC4 and HDAC6 are up-regulated in a cyclical fashion in response to 1α,25(OH)(2)D(3), while even these two genes do not respond to Gemini. Interestingly, HDAC4 and HDAC6 proteins show cyclical VDR ligand-induced association with both VDRE regions of the IGFBP3 gene, which coincides with histone H4 deacetylation on these regions. Moreover, combined silencing of HDAC4 and HDAC6 abolishes the cycling of the IGFBP3 gene. We assume that due to more efficient VDR interaction, Gemini induces longer lasting chromatin activation and therefore no transcriptional cycling but monotonically increasing IGFBP3 mRNA. In conclusion, 1α,25(OH)(2)D(3) regulates IGFBP3 transcription through short-term cyclical association of VDR, HDAC4 and HDAC6 to both VDRE-containing chromatin regions.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Malinen M,Ryynänen J,Heinäniemi M,Väisänen S,Carlberg Cdoi
10.1093/nar/gkq820subject
Has Abstractpub_date
2011-01-01 00:00:00pages
502-12issue
2eissn
0305-1048issn
1362-4962pii
gkq820journal_volume
39pub_type
杂志文章abstract::The Genomes Online Database (GOLD) (https://gold.jgi.doe.gov) is an open online resource, which maintains an up-to-date catalog of genome and metagenome projects in the context of a comprehensive list of associated metadata. Information in GOLD is organized into four levels: Study, Biosample/Organism, Sequencing Proje...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky977
更新日期:2019-01-08 00:00:00
abstract::As the formation of ribonucleoprotein complexes is a major mechanism of angiotensin II type 1 receptor (AT1R) regulation, we sought to identify novel AT1R mRNA binding proteins. By affinity purification and mass spectroscopy, we identified TIA-1. This interaction was confirmed by colocalization of AT1R mRNA and TIA-1 ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1368
更新日期:2016-04-20 00:00:00
abstract::Optical DNA mapping (ODM) allows visualization of long-range sequence information along single DNA molecules. The data can for example be used for detecting long range structural variations, for aiding DNA sequence assembly of complex genomes and for mapping epigenetic marks and DNA damage across the genome. ODM tradi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz489
更新日期:2019-09-05 00:00:00
abstract::The CRISPR system has become a powerful biological tool with a wide range of applications. However, improving targeting specificity and accurately predicting potential off-targets remains a significant goal. Here, we introduce a web-based CR: ISPR/Cas9 O: ff-target P: rediction and I: dentification T: ool (CROP-IT) th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv575
更新日期:2015-10-15 00:00:00
abstract::HinP1I recognizes and cleaves the palindromic tetranucleotide sequence G downward arrowCGC in DNA. We report three structures of HinP1I-DNA complexes: in the presence of Ca(2+) (pre-reactive complex), in the absence of metal ion (binary complex) and in the presence of Mg(2+) (post-reactive complex). HinP1I forms a bac...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkj484
更新日期:2006-02-09 00:00:00
abstract::RNA-based therapeutics, i.e. the utilization of synthetic RNA molecules to alter cellular functions, have the potential to address targets which are currently out of scope for traditional drug design pipelines. This potential however hinges on the ability to selectively deliver and internalize therapeutic RNAs into ce...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky577
更新日期:2018-09-19 00:00:00
abstract::Understanding interactions between proteins and RNA is key to deciphering the mechanisms of many important biological processes. Here we describe RNABindR, a web-based server that identifies and displays RNA-binding residues in known protein-RNA complexes and predicts RNA-binding residues in proteins of unknown struct...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm294
更新日期:2007-07-01 00:00:00
abstract::Monocrotaline is a pyrrolizidine alkaloid known to cause toxicity in humans and animals. Its mechanism of biological action is still unclear although DNA crosslinking has been suggested to a play a role in its activity. In this study we found that an active metabolite of monocrotaline, dehydromonocrotaline (DHM), alky...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.23.5441
更新日期:1998-12-01 00:00:00
abstract::The rat beta-casein gene is a member of a small gene family, encoding the principal milk proteins. In order to understand the mechanisms by which its stage- and tissue-specific expression are regulated, initially, a 14 kb genomic clone containing the entire 7.5 kb rat beta-casein gene with 3.5 kb of 5' and 3.0 kb of 3...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.3.1027
更新日期:1988-02-11 00:00:00
abstract::The Mouse Genome Database (MGD, http://www.informatics.jax.org/), integrates genetic, genomic and phenotypic information about the laboratory mouse, a primary animal model for studying human biology and disease. Information in MGD is obtained from diverse sources, including the scientific literature and external datab...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn886
更新日期:2009-01-01 00:00:00
abstract::Methionyl-tRNA synthetase belongs to the class I aminoacyl-tRNA synthetase family characterized both by a catalytic center built around a Rossmann Fold and by the presence of the two peptidic marker sequences HIGH and KMSKS. In this study, the role of the 21HLGH24 motif of Escherichia coli methionyl-tRNA synthetase wa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.23.4793
更新日期:1995-12-11 00:00:00
abstract::We describe Protogene, a server that can turn a protein multiple sequence alignment into the equivalent alignment of the original gene coding DNA. Protogene relies on a pipeline where every initial protein sequence is BLASTed against RefSeq or NR. The annotation associated with potential matches is used to identify th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl170
更新日期:2006-07-01 00:00:00
abstract::Sequencing by hybridization (SBH) approaches to DNA sequencing face two conflicting constraints. First, in order to ensure that the target DNA binds reliably, the oligonucleotide probes that are attached to the chip array must be >15 bp in length. Secondly, the total number of possible 15 bp oligonucleotides is too la...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh210
更新日期:2004-02-18 00:00:00
abstract::Addition of thiol compounds containing an anionic group to the 3'-terminal unsaturated sugar of the 5' fragment obtained from an oligonucleotide containing an AP site cleaved by beta-elimination, can be followed by gel electrophoresis. The technique enables to distinguish between two mechanisms of cleavage of the C3'-...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.20.9489
更新日期:1988-10-25 00:00:00
abstract::TIGRFAMs is a collection of protein family definitions built to aid in high-throughput annotation of specific protein functions. Each family is based on a hidden Markov model (HMM), where both cutoff scores and membership in the seed alignment are chosen so that the HMMs can classify numerous proteins according to the...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl1043
更新日期:2007-01-01 00:00:00
abstract::IGF2 mRNA-binding protein 1 (IMP1) is a key regulator of messenger RNA (mRNA) metabolism and transport in organismal development and, in cancer, its mis-regulation is an important component of tumour metastasis. IMP1 function relies on the recognition of a diverse set of mRNA targets that is mediated by the combinator...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz136
更新日期:2019-05-07 00:00:00
abstract::One of the greatest challenges that modern molecular biology is facing is the understanding of the complex mechanisms regulating gene expression. A fundamental step in this process requires the characterization of regulatory motifs playing key roles in the regulation of gene expression at transcriptional and post-tran...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh465
更新日期:2004-07-01 00:00:00
abstract::Many DNA modification and repair enzymes require access to DNA bases and therefore flip nucleotides. Restriction endonucleases (REases) hydrolyze the phosphodiester backbone within or in the vicinity of the target recognition site and do not require base extrusion for the sequence readout and catalysis. Therefore, the...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm513
更新日期:2007-01-01 00:00:00
abstract::Members of several classes of proto-oncogenes replicate during the first third of S-phase in two human (K562 erythroleukemia and HeLa), one Chinese hamster (CHO) and eight mouse cell lines. These cell lines exhibit a variety of specialized functions characteristic of pre-B and B cells, T cells and erythroid cells. The...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.1.87
更新日期:1987-01-12 00:00:00
abstract::Allostery is the most direct, rapid and efficient way of regulating protein function, ranging from the control of metabolic mechanisms to signal-transduction pathways. However, an enormous amount of unsystematic allostery information has deterred scientists who could benefit from this field. Here, we present the AlloS...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq1022
更新日期:2011-01-01 00:00:00
abstract::Primer Design Assistant (PDA) is a web interface primer design service combined with thermodynamic theory to evaluate the fitness of primers. It runs in a Linux-Apache-MySQL-PHP structure on a PC equipped with dual CPU (Intel Pentium III 1.4 GHz) and 512 Mb of RAM. A succinct user interface of PDA is accomplished by b...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg560
更新日期:2003-07-01 00:00:00
abstract::We have investigated the distribution of mitochondrial DNA polymorphisms in a rare maternally transmitted genetic trait that causes hypersensitivity to aminoglycoside antibiotics, in the hope that a characterization of its molecular basis might provide a molecular and cellular understanding of aminoglycoside-induced d...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.18.4174
更新日期:1993-09-11 00:00:00
abstract::Myocyte enhancer binding factor 2 (MEF2) proteins belong to the MADS box family of transcription factors and four MEF2 proteins, MEF2A, MEF2B, MEF2C and MEF2D, have been found. MEF2 proteins have been shown to play critical roles in differentiation of muscles and neuronal tissues. How transactivational activity of MEF...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.13.2836
更新日期:2001-07-01 00:00:00
abstract::The transcription of ribosomal genes in a cell line (Kc) derived from female D.melanogaster, has been investigated using hybridization probes prepared from restriction fragments of a cloned rDNA repeat with a 5 kb type I [Wellauer et al. (1978) Cell 14, 269-278] intron. Gels, of nuclear RNA that have been transferred ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.1.67
更新日期:1980-01-11 00:00:00
abstract::Bacillus stearothermophilus large ribosomal subunits were reconstituted in the presence of 5S rRNAs from different origins and tested for their biological activities. The results obtained have shown that eubacterial and archaebacterial 5S rRNAs can easily substitute for B. stearothermophilus 5S rRNA in the reconstitut...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.8.3511
更新日期:1988-04-25 00:00:00
abstract::Recently, prokaryotic riboswitches have been identified that regulate transcription in response to change of the concentration of secondary messengers. The ZMP (5-Aminoimidazole-4-carboxamide ribonucleotide (AICAR))-sensing riboswitch from Thermosinus carboxydivorans is a transcriptional ON-switch that is involved in ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa427
更新日期:2020-07-09 00:00:00
abstract::Human T-cell leukemia virus type 1 (HTLV-1) is the etiological agent of adult T-cell leukemia (ATL). The HTLV-1 basic leucine zipper protein (HBZ) is expressed in all cases of ATL and is directly associated with virus pathogenicity. The two isoforms of the HBZ protein are synthesized from antisense messenger RNAs (mRN...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky802
更新日期:2018-11-16 00:00:00
abstract::U1-snRNA is an integral part of the U1 ribonucleoprotein pivotal for pre-mRNA splicing. Toll-like receptor (TLR) signaling has recently been associated with immunoregulatory capacities of U1-snRNA. Using lung A549 epithelial/carcinoma cells, we report for the first time on interferon regulatory factor (IRF)-3 activati...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp525
更新日期:2009-08-01 00:00:00
abstract::The gene for the thymidine kinase (TK) of Herpes simplex virus type 1 (HSV-1) is located in the KpnI m and BamHI p fragments of the genome (Wigler et al., Cell 11, 223-232 (1977)). These fragments have been inserted into the EcoRI and BamHI sites, respectively, of plasmid pBR322, and propagated in E.coli. The TK gene ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/7.4.859
更新日期:1979-10-25 00:00:00
abstract::FASTQ has emerged as a common file format for sharing sequencing read data combining both the sequence and an associated per base quality score, despite lacking any formal definition to date, and existing in at least three incompatible variants. This article defines the FASTQ format, covering the original Sanger stand...
journal_title:Nucleic acids research
pub_type: 历史文章,杂志文章,评审
doi:10.1093/nar/gkp1137
更新日期:2010-04-01 00:00:00