Abstract：
:Elucidating the dynamic organization of nuclear RNA foci is important for understanding and manipulating these functional sites of gene expression in both physiological and pathological states. However, such studies have been difficult to establish in vivo as a result of the absence of suitable RNA imaging methods. Here, we describe a high-resolution fluorescence RNA imaging method, ECHO-liveFISH, to label endogenous nuclear RNA in living mice and chicks. Upon in vivo electroporation, exciton-controlled sequence-specific oligonucleotide probes revealed focally concentrated endogenous 28S rRNA and U3 snoRNA at nucleoli and poly(A) RNA at nuclear speckles. Time-lapse imaging reveals steady-state stability of these RNA foci and dynamic dissipation of 28S rRNA concentrations upon polymerase I inhibition in native brain tissue. Confirming the validity of this technique in a physiological context, the in vivo RNA labeling did not interfere with the function of target RNA nor cause noticeable cytotoxicity or perturbation of cellular behavior.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Oomoto I,Suzuki-Hirano A,Umeshima H,Han YW,Yanagisawa H,Carlton P,Harada Y,Kengaku M,Okamoto A,Shimogori T,Wang DOdoi
10.1093/nar/gkv614subject
Has Abstractpub_date
2015-10-30 00:00:00pages
e126issue
19eissn
0305-1048issn
1362-4962pii
gkv614journal_volume
43pub_type
杂志文章abstract：:The crystal structure of the DNA dodecamer duplex CATGGGCCCATG lies on a structural continuum along the transition between A- and B-DNA. The dodecamer possesses the normal vector plot and inclination values typical of B-DNA, but has the crystal packing, helical twist, groove width, sugar pucker, slide and x-displaceme...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkf515
更新日期：2002-09-15 00:00:00
abstract：:Histone post-translational modifications have been shown to contribute to DNA damage repair. Prior studies have suggested that specific H3K79 methylation states play distinct roles in the response to UV-induced DNA damage. To evaluate these observations, we examined the effect of altered H3K79 methylation patterns on ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku242
更新日期：2014-06-01 00:00:00
abstract：:The high similarity of tunicates and vertebrates during their development coupled with the transparency of tunicate larvae, their well-studied cell lineages and the availability of simple and efficient transgenesis methods makes of this subphylum an ideal system for the investigation of vertebrate physiological and de...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkj064
更新日期：2006-01-01 00:00:00
abstract：:Short interfering RNAs (siRNAs) are valuable reagents for sequence-specific inhibition of gene expression via the RNA interference (RNAi) pathway. Although it has been proposed that the relative thermodynamic stability at the 5'-ends of siRNAs plays a crucial role in siRNA strand selection, we demonstrate here that a ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn584
更新日期：2008-10-01 00:00:00
abstract：:Two dimensional (2D) NMR and molecular dynamics simulations have been used to determine the three dimensional (3D) structure of a hairpin DNA, d-CTA-GAGGATCC-TUTT-GGATCCT (22mer; abbreviated as U2-hairpin), which has uracil at the second position from the 5' end of the tetraloop. The(1)H resonances of this hairpin hav...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.9.1906
更新日期：2000-05-01 00:00:00
abstract：:DNA breaks occur during many processes in mammalian cells, including recombination, repair, mutagenesis and apoptosis. Here we report a simple and rapid method for assaying DNA breaks and identifying DNA breaksites. Breaksites are first tagged and amplified by ligation-mediated PCR (LM-PCR), using nested PCR primers t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.6.e33
更新日期：2001-03-15 00:00:00
abstract：:Fundamental aspects of the biochemistry of Type III restriction endonucleases remain unresolved despite being characterized by numerous research groups in the past decades. One such feature is the subunit stoichiometry of these hetero-oligomeric enzyme complexes, which has important implications for the reaction mecha...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku122
更新日期：2014-04-01 00:00:00
abstract：:In Eukaryotes, DNA is wound around the histone octamer forming the basic chromatin unit, the nucleosome. Atomic structures have been obtained from crystallography and single particle cryo-electron microscopy (cryoEM) of identical engineered particles. But native nucleosomes are dynamical entities with diverse DNA sequ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky670
更新日期：2018-09-28 00:00:00
abstract：:The small proline-rich protein genes ( SPRRs ) code for precursors of the cornified cell envelope, and are specifically expressed during keratinocyte terminal differentiation. The single intron of SPRR2A enhanced the activity of the SPRR2A promoter in transient transfection assays. This enhancement was position depend...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.23.5288
更新日期：1998-12-01 00:00:00
abstract：:The International Committee on Taxonomy of Viruses (ICTV) is charged with the task of developing, refining, and maintaining a universal virus taxonomy. This task encompasses the classification of virus species and higher-level taxa according to the genetic and biological properties of their members; naming virus taxa;...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx932
更新日期：2018-01-04 00:00:00
abstract：:Increased cytochrome P450 2E1 (CYP2E1) expression is the main cause of oxidative stress, which exacerbates alcoholic liver diseases (ALDs). Estrogen-related receptor gamma (ERRγ) induces CYP2E1 expression and contributes to enhancing alcohol-induced liver injury. Retinoic acid-related orphan receptor alpha (RORα) has ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv1034
更新日期：2016-02-18 00:00:00
abstract：:The ribosomal proteins L4 and L22 form part of the peptide exit tunnel in the large ribosomal subunit. In Escherichia coli, alterations in either of these proteins can confer resistance to the macrolide antibiotic, erythromycin. The structures of the 30S as well as the 50S subunits from each antibiotic resistant mutan...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh913
更新日期：2004-10-27 00:00:00
abstract：:We recently identified a region of preferential replication initiation, oriGNAI3, near the 3' end of the Chinese hamster GNAI3 gene. oriGNAI3 is co-amplified in mutants selected for AMPD2 amplification, a process generating chromosomal rearrangements. In this report we have taken advantage of cell lines with truncated...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.7.1600
更新日期：1999-04-01 00:00:00
abstract：:Radioactive iodine has been used to probe the relative reactivities of nucleosomal H4 tyrosine residues under various conditions of subphysiological ionic strength. We observe that tyrosine 72 of H4, which is not reactive over the range 20-150 mM NaCl, becomes the predominant site of iodination within H4 when nucleoso...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.17.4367
更新日期：1981-09-11 00:00:00
abstract：:The method employed to determine the sequence of a T1 RNase fragment, A-A-A-A-A-U-A-A-C-A-A-U-A-C-A-Gp, from Novikoff rat hepatoma 18S ribosomal RNA is described. This method is applicable to any oligoribonucleotide produced by specific endonucleases that leave the newly cleaved 5'-end free for labeling with polynucle...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/4.2.339
更新日期：1977-02-01 00:00:00
abstract：:The C-terminal domain (CTD) of the large subunit of RNA polymerase II plays a role in transcription and RNA processing. Yeast ESS1, a peptidyl-prolyl cis/trans isomerase, is involved in RNA processing and can associate with the CTD. Using several types of assays we could not find any evidence of an effect of Pin1, the...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.3.767
更新日期：2001-02-01 00:00:00
abstract：:PUF proteins, named for Drosophila Pumilio (PUM) and Caenorhabditis elegans fem-3-binding factor (FBF), recognize specific sequences in the mRNAs they bind and control. RNA binding by classical PUF proteins is mediated by a characteristic PUM homology domain (PUM-HD). The Puf1 and Puf2 proteins possess a distinct arch...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz583
更新日期：2019-09-19 00:00:00
abstract：:In this paper we develop a new method for genotyping Affymetrix single nucleotide polymorphism (SNP) array. The method is based on (i) using multiple arrays at the same time to determine the genotypes and (ii) a model that relates intensities of individual SNPs to each other. The latter point allows us to annotate SNP...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl475
更新日期：2006-01-01 00:00:00
abstract：:The sequence of the 1173 nt 12S kinetoplast ribosomal RNA from Leishmania tarentolae was determined from the maxicircle DNA sequence, and the 5' and 3' ends localized by primer runoff and S1 nuclease protection experiments. The gene was shown to be free of introns by S1 nuclease analysis. A partial secondary structure...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/13.7.2337
更新日期：1985-04-11 00:00:00
abstract：:Gene duplications are a major source of evolutionary innovations. Understanding the functional divergence of duplicates and their role in genetic robustness is an important challenge in biology. Previously, analyses of genetic robustness were primarily focused on duplicates essentiality and epistasis in several labora...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt1200
更新日期：2014-02-01 00:00:00
abstract：:The three dimensional structures for representatives of nearly half of all protein families are now available in public databases. Thus, no matter which protein one investigates, it is increasingly likely that the 3D structure of a homolog will be known and may reveal unsuspected structure-function relationships. The ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.1.240
更新日期：1999-01-01 00:00:00
abstract：:Exposure to genotoxic agents, such as ionizing radiation (IR), produces double-strand breaks, repaired predominantly in mammalian cells by non-homologous end-joining (NHEJ). Ku70 was identified as an interacting partner of a proteolytic Cyclin E (CycE) fragment, p18CycE. p18CycE endogenous generation during IR-induced...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt812
更新日期：2013-12-01 00:00:00
abstract：:Virtually the whole region of the mobile dispersed genetic element mdg1 including the direct repeats that frame mdg1 /1/ is transcribed. The end of the transcriptional unit is located within the direct repeat. Although the transcription of mdg1 is symmetric, one direction is transcribed preferentially and is a full-le...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/8.22.5347
更新日期：1980-11-25 00:00:00
abstract：:The nucleotide sequence of Drosophila melanogaster methionine tRNAi was determined to be: pA-G-C-A-G-A-G-U-m1G-m2G-C-G-C-A-G-U-G-G-A-A-G-C-G-U-m2G-C-U-G-G-G-C-C-C-A-U-t6A-A-C-C-C-A-G-A-G-m7G-D-m5C-C-C-G-A-G-G-A-U-C-G-m1A-A-A-C-C-U-U-G-C-U-C-U-G-C-U-A-C-C-A(OH). It differs from vertebrate initiator tRNAs in only 6 out ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/6.2.421
更新日期：1979-02-01 00:00:00
abstract：:CSP41 is a ubiquitous chloroplast endoribonuclease belonging to the short chain dehydrogenase/reductase (SDR) superfamily. To help elucidate the role of CSP41 in chloroplast gene regulation, the mechanisms that determine its substrate recognition and catalytic activity were investigated. A divalent metal is required f...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg640
更新日期：2003-08-01 00:00:00
abstract：:The current release of ProTherm, Thermodynamic Database for Proteins and Mutants, contains more than 10 000 numerical data (300% of the first version) of several thermodynamic parameters, experimental methods and conditions, reversibility of folding, details about the surrounding residues in space for all mutants, str...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/30.1.301
更新日期：2002-01-01 00:00:00
abstract：:We have studied the coil-to-helix transition of the DNA oligomer d(C4A4T4C4), using circular dichroism measurements to monitor the formation of A.T base pairs within the central self-complementary A4T4 region and the formation of protonated C.C+ base pairs at the ends of the oligomer. We found that both A.T and C.C+ b...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.19.7565
更新日期：1984-10-11 00:00:00
abstract：:We describe a new exonuclease-based method for joining and/or constructing two or more DNA molecules. DNA fragments containing ends complementary to those of a vector or another independent molecules were generated by the polymerase chain reaction. The 3' ends of these molecules as well as the vector DNA were then rec...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.8.1889
更新日期：1993-04-25 00:00:00
abstract：:IStrons are chimeric genetic elements composed of a group I intron associated with an insertion sequence (IS). The group I intron is a catalytic RNA providing the IStron with self-splicing ability, which renders IStron insertions harmless to the host genome. The IS element is a DNA transposon conferring mobility, and ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku939
更新日期：2014-11-10 00:00:00
abstract：:Cadmium (Cd2+) is a known carcinogen that inactivates the DNA mismatch repair (MMR) pathway. In this study, we have tested the effect of Cd2+ exposure on the enzymatic activity of the mismatch binding complex MSH2-MSH6. Our results indicate that Cd2+ is highly inhibitory to the ATP binding and hydrolysis activities of...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki291
更新日期：2005-03-03 00:00:00
