Abstract:
:In non-malignant RWPE-1 prostate epithelial cells signaling by the nuclear receptor Vitamin D Receptor (VDR, NR1I1) induces cell cycle arrest through targets including CDKN1A (encodes p21((waf1/cip1))). VDR dynamically induced individual histone modification patterns at three VDR binding sites (R1, 2, 3) on the CDKN1A promoter. The magnitude of these modifications was specific to each phase of the cell cycle. For example, H3K9ac enrichment occurred rapidly only at R2, whereas parallel accumulation of H3K27me3 occurred at R1; these events were significantly enriched in G(1) and S phase cells, respectively. The epigenetic events appeared to allow VDR actions to combine with p53 to enhance p21((waf1/cip1)) activation further. In parallel, VDR binding to the MCM7 gene induced H3K9ac enrichment associated with rapid mRNA up-regulation to generate miR-106b and consequently regulate p21((waf1/cip1)) expression. We conclude that VDR binding site- and promoter-specific patterns of histone modifications combine with miRNA co-regulation to form a VDR-regulated feed-forward loop to control p21((waf1/cip1)) expression and cell cycle arrest. Dissection of this feed-forward loop in a non-malignant prostate cell system illuminates mechanisms of sensitivity and therefore possible resistance in prostate and other VDR responsive cancers.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Thorne JL,Maguire O,Doig CL,Battaglia S,Fehr L,Sucheston LE,Heinaniemi M,O'Neill LP,McCabe CJ,Turner BM,Carlberg C,Campbell MJdoi
10.1093/nar/gkq875subject
Has Abstractpub_date
2011-03-01 00:00:00pages
2045-56issue
6eissn
0305-1048issn
1362-4962pii
gkq875journal_volume
39pub_type
杂志文章abstract::Methylation of the 2'-hydroxyl-group of ribonucleotides is found in all major classes of RNA in eukaryotes and is one of the most abundant posttranscriptional modifications of stable RNAs. In spite of intense studies, the multiple functions of RNA 2'-O-methylation are still not understood. One major obstacle in the fi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw200
更新日期:2016-05-05 00:00:00
abstract::Gene duplication is an important process in evolution. The availability of genome sequences of a number of organisms has made it possible to conduct comprehensive searches for duplicated genes enabling informative studies of their evolution. We have established the FGF (Fishing Gene Family) program to efficiently sear...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm426
更新日期:2007-07-01 00:00:00
abstract::The response to amino acid (AA) limitation of the entire aminoacyl-tRNA synthetase (ARS) gene family revealed that 16/20 of the genes encoding cytoplasmic-localized enzymes are transcriptionally induced by activating transcription factor 4 (Atf4) via C/ebp-Atf-Response-Element (CARE) enhancers. In contrast, only 4/19 ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw667
更新日期:2016-11-16 00:00:00
abstract::Mitochondrial DNA (mtDNA) resides in a high ROS environment and suffers more mutations than its nuclear counterpart. Increasing evidence suggests that mtDNA mutations are not the results of direct oxidative damage, rather are caused, at least in part, by DNA replication errors. To understand how the mtDNA replicase, P...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz1018
更新日期:2020-01-24 00:00:00
abstract::A phage-display library of random peptides is a combinatorial experimental technique that can be harnessed for studying antibody-antigen interactions. In this technique, a phage peptide library is scanned against an antibody molecule to obtain a set of peptides that are bound by the antibody with high affinity. This s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl975
更新日期:2007-01-01 00:00:00
abstract::The DNA damage response is vigorously activated by DNA double-strand breaks (DSBs). The chief mobilizer of the DSB response is the ATM protein kinase. We discovered that the COP9 signalosome (CSN) is a crucial player in the DSB response and an ATM target. CSN is a protein complex that regulates the activity of cullin ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv270
更新日期:2015-05-19 00:00:00
abstract::Oligodeoxyribonucleotides incorporating non-hydrolyzable dialkyl sulfide linked thymidine dimers (TsT) were synthesized chemically by the solid-phase approach. The sulfide dimer TsT was stable to degradation by snake-venom phosphodiesterase, calf spleen phosphodiesterase, Nuclease P1 and Nuclease S1. Thermal denaturat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.6.1473
更新日期:1993-03-25 00:00:00
abstract::The HAMSTeRS WWW site was set up in 1996 in order to facilitate easy access to, and aid understanding of, the causes of haemophilia A at the molecular level; previously, the first and second text editions of the database have been published in Nucleic Acids Research. This report describes the facilities originally ava...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.1.128
更新日期:1997-01-01 00:00:00
abstract::Toscana virus (TOSV) is an arthropod-borne human pathogen responsible for seasonal outbreaks of fever and meningoencephalitis in the Mediterranean basin. TOSV is a segmented negative-strand RNA virus (sNSV) that belongs to the genus phlebovirus (family Phenuiviridae, order Bunyavirales), encompassing other important h...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz838
更新日期:2019-11-18 00:00:00
abstract::We have synthesized the tetradecamer GAGCXGATAACAAG containing a part of the sequence of the lactose operator. A guanine base in the sequence is replaced by the adduct of the carcinogen 2-acetylaminofluorene with guanine. Under the standard conditions of de-protection, the fluorene moiety is lost, leaving behind a gua...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.15.5093
更新日期:1983-08-11 00:00:00
abstract::In previous studies, we reported that fractionation of HeLa cell nuclear extracts on glycerol gradients revealed an endogenous ∼10S particle that contained galectin-3 and U1 snRNP and this particle was sufficient to load the galectin polypeptide onto a pre-mRNA substrate. We now document that this interaction between ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw303
更新日期:2016-07-27 00:00:00
abstract::Stabilization of stalled replication forks prevents excessive fork reversal or degradation, which can undermine genome integrity. The WRN protein is unique among the other human RecQ family members to possess exonuclease activity. However, the biological role of the WRN exonuclease is poorly defined. Recently, the WRN...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz431
更新日期:2019-07-26 00:00:00
abstract::Biological networks are a topic of great current interest, particularly with the publication of a number of large genome-wide interaction datasets. They are globally characterized by a variety of graph-theoretic statistics, such as the degree distribution, clustering coefficient, characteristic path length and diamete...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh164
更新日期:2004-01-14 00:00:00
abstract::Influenza A viruses are hosted by numerous avian and mammalian species, which have shaped their evolution into distinct lineages worldwide. The viral genome consists of eight RNA segments that are frequently exchanged between different viruses via a process known as genetic reassortment. A complete genotype nomenclatu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm365
更新日期:2007-07-01 00:00:00
abstract::The 34-nucleotide trans-activator (TA) located within the RNA-2 of Red clover necrotic mosaic virus folds into a simple hairpin. The eight-nucleotide TA loop base pairs with eight complementary nucleotides in the TA binding sequence (TABS) of the capsid protein subgenomic promoter on RNA-1 and trans-activates subgenom...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh585
更新日期:2004-05-20 00:00:00
abstract::Cisplatin analogues were synthesised that consisted of platinum(II) diamine complexes tethered via a polymethylene chain ( n = 3, 5, 8 and 10) to a phenanthridinium cation. Both chloro and iodo leaving groups were examined. DNA adduct formation was quantitatively analysed using a linear amplification system with the p...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.17.3933
更新日期:1998-09-01 00:00:00
abstract::The Agrobacterium tumefaciens Ti plasmid contains at least six transcriptional units (designated vir loci) which are essential for efficient crown gall tumorigenesis. Mutations in one of these loci, virE, result in a sharply attenuated virulence phenotype. In the present communication, we have analyzed the virE operon...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.2.825
更新日期:1987-01-26 00:00:00
abstract::The primary structures of two overlapping novel alpha-tubulin cDNA clones isolated from a Macaca fascicularis testis cDNA library and the corresponding human gene are presented. Although the general structure of the human gene conforms to that of previously described mammalian alpha-tubulin genes, there is a surprisin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.1.199
更新日期:1987-01-12 00:00:00
abstract::Modification of chromatin and related transcription factors by histone deacetylases (HDACs) is one of the major strategies for controlling gene expression in eukaryotes. The HDAC domains of class IIa HDACs repress the respective target genes by interacting with the C-terminal region of the silencing mediator for retin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky926
更新日期:2018-12-14 00:00:00
abstract::Computational modelling of mammalian cell cycle regulation is a challenging task, which requires comprehensive knowledge on many interrelated processes in the cell. We have developed a web-based integrated database on cell cycle regulation in mammals in normal and pathological states (Cyclonet database). It integrates...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl912
更新日期:2007-01-01 00:00:00
abstract::The Moloney murine leukemia virus (MLV) is a prototype gammaretrovirus requiring nuclear disassembly before DNA integration. In the nucleus, integration site selection towards promoter/enhancer elements is mediated by the host factor bromo- and extraterminal domain (BET) proteins (bromodomain (Brd) proteins 2, 3 and 4...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1157
更新日期:2019-02-20 00:00:00
abstract::The three-dimensional structures of two DNA duplexes d(CATGAGTAC). d(GTACXCATG) (1) and d(CATGAGTAC).d(GTACTCATG) (2), where X represents 1-(2'-deoxy-beta-D-ribofuranosyl)-3-nitropyrrole, were solved using high resolution nuclear magnetic resonance spectroscopy and restrained molecular dynamics. Good convergence was o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.22.4514
更新日期:2000-11-15 00:00:00
abstract::While it has been long recognized that genes are not randomly positioned along the genome, the degree to which its 3D structure influences the arrangement of genes has remained elusive. In particular, several lines of evidence suggest that actively transcribed genes are spatially co-localized, forming transcription fa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks1360
更新日期:2013-02-01 00:00:00
abstract::From gene expression to nanotechnology, understanding and controlling DNA requires a detailed knowledge of its higher order structure and dynamics. Here we take advantage of the environment-sensitive photoisomerization of cyanine dyes to probe local and global changes in DNA structure. We report that a covalently atta...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky887
更新日期:2018-11-30 00:00:00
abstract::The alternative proliferating-cell nuclear antigen (PCNA)-loader CTF18-RFC forms a stable complex with DNA polymerase ε (Polε). We observed that, under near-physiological conditions, CTF18-RFC alone loaded PCNA inefficiently, but loaded it efficiently when complexed with Polε. During efficient PCNA loading, CTF18-RFC ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx096
更新日期:2017-05-05 00:00:00
abstract::The GWIPS-viz browser (http://gwips.ucc.ie/) is an on-line genome browser which is tailored for exploring ribosome profiling (Ribo-seq) data. Since its publication in 2014, GWIPS-viz provides Ribo-seq data for an additional 14 genomes bringing the current total to 23. The integration of new Ribo-seq data has been auto...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx790
更新日期:2018-01-04 00:00:00
abstract::Post-transcriptional modifications in archaeal RNA are known to be phylogenetically distinct but relatively little is known of tRNA from the Methanococci, a lineage of methanogenic marine euryarchaea that grow over an unusually broad temperature range. Transfer RNAs from Methanococcus vannielii, Methanococcus maripalu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.22.4699
更新日期:2001-11-15 00:00:00
abstract::Regulation of gene expression influences almost all biological processes in an organism; sequence-specific DNA-binding transcription factors are critical to this control. For most genomes, the repertoire of transcription factors is only partially known. Hitherto transcription factor identification has been largely bas...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkj131
更新日期:2006-01-01 00:00:00
abstract::As proteomics initiatives mature, the need will arise for the multiple visualization of proteins and supramolecular complexes within their true context, in situ. Single-stranded DNA and RNA aptamers can be used for low resolution imaging of cellular receptors and cytoplasmic proteins by light microscopy (LM). These te...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gnh164
更新日期:2004-11-23 00:00:00
abstract::MicroArray Gene expression and Network Evaluation Toolkit (MAGNET) is a web-based application that provides tools to generate and score both protein-protein interaction networks and coexpression networks. MAGNET integrates user-provided experimental measurements with high-throughput proteomic datasets, generating weig...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks526
更新日期:2012-07-01 00:00:00