Global miRNA expression analysis identifies novel key regulators of plasma cell differentiation and malignant plasma cell.

abstract：:Reverse transcription of HIV-1 RNA is primed by a tRNA3(Lys) molecule bound at the primer binding site (PBS). Complex intermolecular interactions were proposed between tRNA3(Lys) and the RNA of the HIV-1 Mal isolate. Recently, an alternative interaction was proposed between the TPsiC stem of tRNA3(Lys) and a primer ac...

journal_title：Nucleic acids research

authors： Goldschmidt V,Ehresmann C,Ehresmann B,Marquet R

更新日期：2003-02-01 00:00:00

abstract：:MicroRNAs (miRNAs) are small RNAs ∼22 nt in length that are involved in the regulation of a variety of physiological and pathological processes. Advances in high-throughput small RNA sequencing (smRNA-seq), one of the next-generation sequencing applications, have reshaped the miRNA research landscape. In this study, w...

journal_title：Nucleic acids research

authors： Cheng WC,Chung IF,Huang TS,Chang ST,Sun HJ,Tsai CF,Liang ML,Wong TT,Wang HW

更新日期：2013-01-01 00:00:00

abstract：:The Ensembl project (https://www.ensembl.org) annotates genomes and disseminates genomic data for vertebrate species. We create detailed and comprehensive annotation of gene structures, regulatory elements and variants, and enable comparative genomics by inferring the evolutionary history of genes and genomes. Our int...

journal_title：Nucleic acids research

authors： Howe KL,Achuthan P,Allen J,Allen J,Alvarez-Jarreta J,Amode MR,Armean IM,Azov AG,Bennett R,Bhai J,Billis K,Boddu S,Charkhchi M,Cummins C,Da Rin Fioretto L,Davidson C,Dodiya K,El Houdaigui B,Fatima R,Gall A,Garcia G

更新日期：2021-01-08 00:00:00

abstract：:DEAD, DEAH and DExH proteins are involved in almost every facet of RNA biochemistry. Members of these protein families exhibit an RNA-dependent ATPase activity and some possess an ATP-dependent RNA helicase activity. Although genetic studies have identified specific functions for certain DEx(D)/(H)proteins from which ...

journal_title：Nucleic acids research

authors： Kossen K,Uhlenbeck OC

更新日期：1999-10-01 00:00:00

abstract：:Allosteric nucleic acid ligases have been used previously to transform analyte-binding into the formation of oligonucleotide templates that can be amplified and detected. We have engineered binary deoxyribozyme ligases whose two components are brought together by bridging oligonucleotide effectors. The engineered liga...

journal_title：Nucleic acids research

authors： Tabor JJ,Levy M,Ellington AD

更新日期：2006-04-28 00:00:00

abstract：:The RNA degradosome is a multi-enzyme assembly that contributes to key processes of RNA metabolism, and it engages numerous partners in serving its varied functional roles. Small domains within the assembly recognize collectively a diverse range of macromolecules, including the core protein components, the cytoplasmic...

journal_title：Nucleic acids research

authors： Tsai YC,Du D,Domínguez-Malfavón L,Dimastrogiovanni D,Cross J,Callaghan AJ,García-Mena J,Luisi BF

更新日期：2012-11-01 00:00:00

abstract：:The DINAMelt web server simulates the melting of one or two single-stranded nucleic acids in solution. The goal is to predict not just a melting temperature for a hybridized pair of nucleic acids, but entire equilibrium melting profiles as a function of temperature. The two molecules are not required to be complementa...

journal_title：Nucleic acids research

authors： Markham NR,Zuker M

更新日期：2005-07-01 00:00:00

abstract：:The high-throughput sequencing of nuclease-protected mRNA fragments bound to ribosomes, a technique known as ribosome profiling, quantifies the relative frequencies with which different regions of transcripts are translated. This technique has revealed novel translation initiation sites with unprecedented scope and ha...

journal_title：Nucleic acids research

authors： Martens AT,Taylor J,Hilser VJ

更新日期：2015-04-20 00:00:00

abstract：:Holliday junctions (four-way DNA junctions), formed during homologous recombination, are bound and resolved by junction-specific endonucleases to yield recombinant duplex DNA products. The junction-resolving enzymes are a structurally diverse class of proteins that nevertheless have many properties in common; in parti...

journal_title：Nucleic acids research

authors： White MF,Lilley DM

更新日期：1998-12-15 00:00:00

abstract：:A protein-DNA complex has less gel electrophoretic mobility than the free DNA fragment. One parameter for the degree of retardation of a linear DNA fragment in a protein-DNA complex is the molecular weight of the bound protein(s). The quotient of the migration distances of free DNA (m) and protein-DNA complex (m') is ...

journal_title：Nucleic acids research

authors： Bading H

更新日期：1988-06-24 00:00:00

abstract：:An important problem in genomics is automatically clustering homologous proteins when only sequence information is available. Most methods for clustering proteins are local, and are based on simply thresholding a measure related to sequence distance. We first show how locality limits the performance of such methods by...

journal_title：Nucleic acids research

authors： Paccanaro A,Casbon JA,Saqi MA

更新日期：2006-03-17 00:00:00

abstract：:Wybutine (Ywye), situated next to the 3'-side of the anticodon of tRNAPhe from Saccharomyces cerevisiae, can be photo-crosslinked to mRNA when bound to Escherichia coli ribosomes. Crosslinking can be obtained with poly(U) as well as with oligonucleotides such as pAUGUUU or p(U)6. In order to identify the site of react...

journal_title：Nucleic acids research

authors： Steiner G,Lührmann R,Kuechler E

更新日期：1984-11-12 00:00:00

abstract：:A pan-genome is the union of the gene sets of all the individuals of a clade or a species and it provides a new dimension of genome complexity with the presence/absence variations (PAVs) of genes among these genomes. With the progress of sequencing technologies, pan-genome study is becoming affordable for eukaryotes w...

journal_title：Nucleic acids research

authors： Sun C,Hu Z,Zheng T,Lu K,Zhao Y,Wang W,Shi J,Wang C,Lu J,Zhang D,Li Z,Wei C

更新日期：2017-01-25 00:00:00

abstract：:RNA:5-methylcytosine (m5C) methyltransferases are currently the focus of intense research following a series of high-profile reports documenting their physiological links to several diseases. However, no methods exist which permit the specific analysis of RNA:m5C methyltransferases in cells. Herein, we described how a...

journal_title：Nucleic acids research

authors： Yang T,Low JJA,Woon ECY

更新日期：2020-01-10 00:00:00

abstract：:A straightforward enzymatic protocol for converting regular DNA into pseudo-complementary DNA could improve the performance of oligonucleotide microarrays by generating readily hybridizable structure-free targets. Here we screened several highly destabilizing analogs of G and C for one that could be used with 2-aminoa...

journal_title：Nucleic acids research

authors： Lahoud G,Timoshchuk V,Lebedev A,Arar K,Hou YM,Gamper H

更新日期：2008-12-01 00:00:00

abstract：:Dinucleoside diphosphates of the general type pGpN have been prepared enzymatically using ribonuclease N1. Alkylated uridines or cytidines, which are products of carcinogens acting on nucleic acids, were tested in dinucleoside diphosphates for their ability to stimulate the binding of Ala- or Val-tRNA to ribosomes. O2...

journal_title：Nucleic acids research

authors： Singer B,Pergolizzi RG,Grunberger D

更新日期：1979-04-01 00:00:00

abstract：:In prokaryotes and archaea transfer ribonucleic acid (tRNA) stability as well as cellular UV protection relies on the post-transcriptional modification of uracil at position 8 (U8) of tRNAs by the 4-thiouridine synthetase ThiI. Here, we report three crystal structures of ThiI from Thermotoga maritima in complex with a...

journal_title：Nucleic acids research

authors： Neumann P,Lakomek K,Naumann PT,Erwin WM,Lauhon CT,Ficner R

更新日期：2014-06-01 00:00:00

abstract：:Proteins that bind to DNA are found in all areas of genetic activity within the cell. To help understand how these proteins perform their various functions, it is useful to analyse which residues are involved in binding to the DNA and how they interact with the bases and sugar-phosphate backbone of nucleic acids. Here...

journal_title：Nucleic acids research

authors： Luscombe NM,Laskowski RA,Thornton JM

更新日期：1997-12-15 00:00:00

abstract：:Inability of T7 RNA polymerase to processively transcribe higher eukaryotic chromatin is interpreted as a correlate of its reported inhibition by nucleosomes on reconstituted templates in vitro . We used chromosomally integrated reporter cassettes to examine features of T7 transcription in a lower eukaryotic system. L...

journal_title：Nucleic acids research

authors： Wirtz E,Hoek M,Cross GA

更新日期：1998-10-15 00:00:00

abstract：:Mutations in the gene of human RNase T2 are associated with white matter disease of the human brain. Although brain abnormalities (bilateral temporal lobe cysts and multifocal white matter lesions) and clinical symptoms (psychomotor impairments, spasticity and epilepsy) are well characterized, the pathomechanism of RN...

journal_title：Nucleic acids research

authors： Thorn A,Steinfeld R,Ziegenbein M,Grapp M,Hsiao HH,Urlaub H,Sheldrick GM,Gärtner J,Krätzner R

更新日期：2012-09-01 00:00:00

abstract：:The human mitochondrial translation apparatus, which synthesizes the core subunits of the oxidative phosphorylation system, is of central interest as mutations in several genes encoding for mitoribosomal proteins or translation factors cause severe human diseases. Little is known, how this complex machinery assembles ...

journal_title：Nucleic acids research

authors： Lavdovskaia E,Kolander E,Steube E,Mai MM,Urlaub H,Richter-Dennerlein R

更新日期：2018-09-19 00:00:00

abstract：:MolProbity is a general-purpose web server offering quality validation for 3D structures of proteins, nucleic acids and complexes. It provides detailed all-atom contact analysis of any steric problems within the molecules as well as updated dihedral-angle diagnostics, and it can calculate and display the H-bond and va...

journal_title：Nucleic acids research

authors： Davis IW,Leaver-Fay A,Chen VB,Block JN,Kapral GJ,Wang X,Murray LW,Arendall WB 3rd,Snoeyink J,Richardson JS,Richardson DC

更新日期：2007-07-01 00:00:00

abstract：:A minor tRNA-Glu1 constituent of a preparation of E. coli B tRNA-Glu (Oak Ridge) has a guanosine residue at position 66 rather than an adenosine as in the tRNA-Glu2 described by Ohashi et al. (3). Automated sequential degradation was used to sequence this region. ...

journal_title：Nucleic acids research

authors： Uziel M,Weinberger AJ

更新日期：1975-04-01 00:00:00

abstract：:The Orthologous Matrix (OMA) is a leading resource to relate genes across many species from all of life. In this update paper, we review the recent algorithmic improvements in the OMA pipeline, describe increases in species coverage (particularly in plants and early-branching eukaryotes) and introduce several new feat...

journal_title：Nucleic acids research

authors： Altenhoff AM,Glover NM,Train CM,Kaleb K,Warwick Vesztrocy A,Dylus D,de Farias TM,Zile K,Stevenson C,Long J,Redestig H,Gonnet GH,Dessimoz C

更新日期：2018-01-04 00:00:00

abstract：:The X chromosome-linked inhibitor of apoptosis protein (XIAP) is the most potent intrinsic caspase inhibitor and plays an important role in the maintenance of intestinal epithelial integrity. The RNA binding protein, HuR, regulates the stability and translation of many target transcripts. Here, we report that HuR asso...

journal_title：Nucleic acids research

authors： Zhang X,Zou T,Rao JN,Liu L,Xiao L,Wang PY,Cui YH,Gorospe M,Wang JY

更新日期：2009-12-01 00:00:00

abstract：:A unique 52mer oligonucleotide deduced from the amino acid sequence of bovine Factor IX was synthesized and used as a probe to screen a human liver cDNA bank. The Factor IX clone isolated shows 5 differences in nucleotide and deduced amino acid sequence as compared to a previously isolated clone. In addition, precisel...

journal_title：Nucleic acids research

authors： Jaye M,de la Salle H,Schamber F,Balland A,Kohli V,Findeli A,Tolstoshev P,Lecocq JP

更新日期：1983-04-25 00:00:00

abstract：:The advent of jellyfish green fluorescent protein and its spectral variants, together with promising new fluorescent proteins from other classes of the Cnidarian phylum (coral and anemones), has greatly enhanced and promises to further boost the detection and localization of proteins in cell biology. It has been less ...

journal_title：Nucleic acids research

authors： Pederson T

更新日期：2001-03-01 00:00:00

abstract：:A novel method to measure mRNA levels has been developed by combining the detection capabilities of RNase protection (RPA) with the quantification advantages of scintillation proximity assay (SPA) technology. Sample processing is reduced to the addition of a single reagent post RNase digestion. As a model system, the ...

journal_title：Nucleic acids research

authors： Kenrick MK,Jiang L,Potts CL,Owen PJ,Shuey DJ,Econome JG,Anson JG,Quinet EM

更新日期：1997-07-15 00:00:00

abstract：:A reporter assay was developed to detect and quantify nonsense codon suppression by chemically aminoacylated tRNAs in mammalian cells. It is based on the cellular expression of the enhanced green fluorescent protein (EGFP) as a reporter for the site-specific amino acid incorporation in its sequence using an orthogonal...

journal_title：Nucleic acids research

authors： Ilegems E,Pick HM,Vogel H

更新日期：2002-12-01 00:00:00

abstract：:This paper presents TurboFold II, an extension of the TurboFold algorithm for predicting secondary structures for multiple RNA homologs. TurboFold II augments the structure prediction capabilities of TurboFold by additionally providing multiple sequence alignments. Probabilities for alignment of nucleotide positions b...

journal_title：Nucleic acids research

authors： Tan Z,Fu Y,Sharma G,Mathews DH

更新日期：2017-11-16 00:00:00