High-resolution profiling of the LEDGF/p75 chromatin interaction in the ENCODE region.

abstract：:Biological networks play increasingly important roles in omics data integration and systems biology. Over the past decade, many excellent tools have been developed to support creation, analysis and visualization of biological networks. However, important limitations remain: most tools are standalone programs, the majo...

journal_title：Nucleic acids research

authors： Zhou G,Xia J

更新日期：2018-07-02 00:00:00

abstract：:Highly repetitive Hind III restriction fragments of 0.72-0.76 KBP from total Xenopus laevis genomic DNA are organized in a tandem like arrangement. Cloning of these fragments in pBR 322 with subsequent restriction site mapping and nucleotide sequence analysis of some selected clones showed two different types of seque...

journal_title：Nucleic acids research

authors： Meyerhof W,Tappeser B,Korge E,Knöchel W

更新日期：1983-10-25 00:00:00

abstract：:A crucial step in analyzing mRNA-Seq data is to accurately and efficiently map hundreds of millions of reads to the reference genome and exon junctions. Here we present OLego, an algorithm specifically designed for de novo mapping of spliced mRNA-Seq reads. OLego adopts a multiple-seed-and-extend scheme, and does not ...

journal_title：Nucleic acids research

authors： Wu J,Anczuków O,Krainer AR,Zhang MQ,Zhang C

更新日期：2013-05-01 00:00:00

abstract：:Transcription termination defines accurate transcript 3'-ends and ensures programmed transcriptomes, making it critical to life. However, transcription termination mechanisms remain largely unknown in Archaea. Here, we reported the physiological significance of the newly identified general transcription termination fa...

journal_title：Nucleic acids research

authors： Yue L,Li J,Zhang B,Qi L,Li Z,Zhao F,Li L,Zheng X,Dong X

更新日期：2020-09-25 00:00:00

abstract：:Quantitative real-time PCR has revolutionized many aspects of genetic research, biomedical diagnostics and pathogen detection. Nevertheless, the full potential of this technology has yet to be realized, primarily due to the limitations of the threshold-based methodologies that are currently used for quantitative analy...

journal_title：Nucleic acids research

authors： Rutledge RG

更新日期：2004-12-15 00:00:00

abstract：:Conventional approaches to predict transcriptional regulatory interactions usually rely on the definition of a shared motif sequence on the target genes of a transcription factor (TF). These efforts have been frustrated by the limited availability and accuracy of TF binding site motifs, usually represented as position...

journal_title：Nucleic acids research

authors： Elati M,Nicolle R,Junier I,Fernández D,Fekih R,Font J,Képès F

更新日期：2013-02-01 00:00:00

abstract：:Post-transcriptional regulation and the formation of mRNA 3' ends are crucial for gene expression in eukaryotes. Interspecies conservation of many sequences within 3'UTRs reveals selective constraint due to similar function. To study the pattern of conservation within 3'UTRs, we compiled and aligned 50 sets of complet...

journal_title：Nucleic acids research

authors： Shabalina SA,Ogurtsov AY,Lipman DJ,Kondrashov AS

更新日期：2003-09-15 00:00:00

abstract：:Tcf/Lef family transcription factors are the downstream effectors of the Wingless/Wnt signal transduction pathway. Upon Wingless/Wnt signalling, beta-catenin translocates to the nucleus, interacts with Tcf (1-3) and thus activates transcription of target genes (4,5). Tcf factors also interact with members of the Grouc...

journal_title：Nucleic acids research

authors： Brantjes H,Roose J,van De Wetering M,Clevers H

更新日期：2001-04-01 00:00:00

abstract：:Restriction endonucleases HindII and TaqI, but not SalI, were found to efficiently cleave synthetic hexadecanucleotide duplexes which contained either an A/C or a G/T mismatch within their respective restriction sites. Double-stranded M13 DNAs with identical mismatches were also cleaved under the assay conditions. The...

journal_title：Nucleic acids research

authors： Jiricny J,Martin D

更新日期：1986-03-11 00:00:00

abstract：:Scalable multiplexed amplification technologies are needed for cost-effective large-scale genotyping of genetic markers such as single nucleotide polymorphisms (SNPs). We present SNPWave, a novel SNP genotyping technology to detect various subsets of sequences in a flexible fashion in a fixed detection format. SNPWave...

journal_title：Nucleic acids research

authors： van Eijk MJ,Broekhof JL,van der Poel HJ,Hogers RC,Schneiders H,Kamerbeek J,Verstege E,van Aart JW,Geerlings H,Buntjer JB,van Oeveren AJ,Vos P

更新日期：2004-03-05 00:00:00

abstract：:Mechanisms that preserve genome integrity are highly important during the normal life cycle of human cells. Loss of genome protective mechanisms can lead to the development of diseases such as cancer. Checkpoint kinases function in the cellular surveillance pathways that help cells to cope with DNA damage. Importantly...

journal_title：Nucleic acids research

authors： Sørensen CS,Syljuåsen RG

更新日期：2012-01-01 00:00:00

abstract：:p53 is thought to function in the maintenance of genomic stability by modulating transcription and interacting with cellular proteins to influence the cell cycle, DNA repair and apoptosis. p53 mutations occur in >50% of human cancers, and cells which lack wild type p53 accumulate karyotypic abnormalities such as ampli...

journal_title：Nucleic acids research

authors： Buchhop S,Gibson MK,Wang XW,Wagner P,Stürzbecher HW,Harris CC

更新日期：1997-10-01 00:00:00

abstract：:Telomerase is a ribonucleoprotein reverse transcriptase that synthesizes and maintains telomeric DNA. Studies of telomeres and telomerase are facilitated by the large number of linear DNA molecules found in ciliated protozoa, such as Tetrahymena thermophila. To examine the expression of telomerase, we investigated the...

journal_title：Nucleic acids research

authors： Hargrove BW,Bhattacharyya A,Domitrovich AM,Kapler GM,Kirk K,Shippen DE,Kunkel GR

更新日期：1999-11-01 00:00:00

abstract：:Mitotic chromosome structure is pivotal to cell division but difficult to observe in fine detail using conventional methods. DNA catenation has been implicated in both sister chromatid cohesion and chromosome condensation, but has never been observed directly. We have used a lab-on-a-chip microfluidic device and fluor...

journal_title：Nucleic acids research

authors： Bauer DL,Marie R,Rasmussen KH,Kristensen A,Mir KU

更新日期：2012-12-01 00:00:00

abstract：:We have investigated the response of the filamentous fungus Aspergillus nidulans to low, non-killing, doses of the alkylating agent MNNG (N-methyl-N'-nitro-N-nitrosoguanidine). Such treatment causes a substantial induction of DNA alkyltransferase activity, with the specific activity in treated cells increasing up to o...

journal_title：Nucleic acids research

authors： Baker SM,Margison GP,Strike P

更新日期：1992-02-25 00:00:00

abstract：:The influence of an upstream small open reading frame (URF) on the translation of two consecutive coding regions on an eukaryotic mRNA was studied. The cis effects of leader length, URF length, the sequences of the URF and neighboring regions, and the trans effects of the Cauliflower mosaic virus transactivator (TAV) ...

journal_title：Nucleic acids research

authors： Fütterer J,Hohn T

更新日期：1992-08-11 00:00:00

abstract：:Over the past 10 years, fluorescent end-labeling of DNA fragments has evolved into the preferred method of DNA detection for a wide variety of applications, including DNA sequencing and PCR fragment analysis. One of the advantages inherent in fluorescent detection methods is the ability to perform multi-color analyses...

journal_title：Nucleic acids research

authors： Tu O,Knott T,Marsh M,Bechtol K,Harris D,Barker D,Bashkin J

更新日期：1998-06-01 00:00:00

abstract：:Two of the tRNA's found in rabbit reticulocytes are substrates for a post-transcriptional modification leading to the incorporation of guanine into the polynucleotide chain. The major guanylated tRNA was previously identified as tRNA (His). In the present report we show that the minor guanylated tRNA is tRNA (Asn), an...

journal_title：Nucleic acids research

authors： Farkas WR,Chernoff D

更新日期：1976-10-01 00:00:00

abstract：:GGRNA (http://GGRNA.dbcls.jp/) is a Google-like, ultrafast search engine for genes and transcripts. The web server accepts arbitrary words and phrases, such as gene names, IDs, gene descriptions, annotations of gene and even nucleotide/amino acid sequences through one simple search box, and quickly returns relevant Re...

journal_title：Nucleic acids research

authors： Naito Y,Bono H

更新日期：2012-07-01 00:00:00

abstract：:Replication of the promiscuous plasmid pMV158 requires expression of the initiator repB gene, which is controlled by the repressor CopG. Genes repB and copG are co-transcribed from promoter P(cr). We have studied the interactions between RNA polymerase, CopG and the promoter to elucidate the mechanism of repression by...

journal_title：Nucleic acids research

authors： Hernández-Arriaga AM,Rubio-Lepe TS,Espinosa M,del Solar G

更新日期：2009-08-01 00:00:00

abstract：:Interactions between proteins bound to distant sites along a DNA molecule require bending and twisting deformations in the intervening DNA. In certain systems, the sterically allowed protein-DNA and protein-protein interactions are hypothesized to produce loops with distinct geometries that may also be thermodynamical...

journal_title：Nucleic acids research

authors： Lia G,Semsey S,Lewis DE,Adhya S,Bensimon D,Dunlap D,Finzi L

更新日期：2008-07-01 00:00:00

abstract：:Small RNA (sRNA) Sequencing technology has revealed that microRNAs (miRNAs) are capable of exhibiting frequent variations from their canonical sequences, generating multiple variants: the isoforms of miRNAs (isomiRs). However, integrated tool to precisely detect and systematically annotate isomiRs from sRNA sequencing...

journal_title：Nucleic acids research

authors： Zhang Y,Zang Q,Zhang H,Ban R,Yang Y,Iqbal F,Li A,Shi Q

更新日期：2016-07-08 00:00:00

abstract：:We have developed a novel method of genetic library construction on magnetic microbeads based on solid-phase single-molecule PCR in a fine and robust water-phase compartment formed in water-in-oil (w/o) emulsions. In this method, critically diluted DNA fragments were distributed over the emulsion as templates, where b...

journal_title：Nucleic acids research

authors： Kojima T,Takei Y,Ohtsuka M,Kawarasaki Y,Yamane T,Nakano H

更新日期：2005-10-06 00:00:00

abstract：:Therapeutic small interfering RNAs (siRNAs) are composed of chemically modified nucleotides, which enhance RNA stability and increase affinity in Watson-Crick base pairing. However, the precise fate of such modified nucleotides once the siRNA is degraded within the cell is unknown. Previously, we demonstrated that deo...

journal_title：Nucleic acids research

authors： Wu SY,Chen TM,Gmeiner WH,Chu E,Schmitz JC

更新日期：2013-04-01 00:00:00

abstract：:The intron 2 of the murine thymidine kinase (TK) gene was observed to contain two DNase hypersensitive site. In vitro footprinting experiments indicated specific binding sites for nuclear proteins which were characterized within the sequence of intron 2. Two GC boxes (binding sites for transcription factor SP1) and tw...

journal_title：Nucleic acids research

authors： Rotheneder H,Grabner M,Wintersberger E

更新日期：1991-12-25 00:00:00

abstract：:As shown in the accompanying paper (5), the oligonucleotide composition of the E. coli genome is highly asymmetric for sequences up to 6 bp in length when ranked from highest to lowest abundance. We show here that this largely reflects codon usage because heavily used codons were found in the highly abundant oligomers...

journal_title：Nucleic acids research

authors： Phillips GJ,Arnold J,Ivarie R

更新日期：1987-03-25 00:00:00

abstract：:IMGT, the international ImMunoGeneTics database (http://imgt.cines. fr:8104 ), is a high-quality integrated database specialising in Immunoglobulins (Ig), T cell Receptors (TcR) and Major Histocompatibility Complex (MHC) molecules of all vertebrate species, created in 1989 by Marie-Paule Lefranc, Université Montpellie...

journal_title：Nucleic acids research

authors： Ruiz M,Giudicelli V,Ginestoux C,Stoehr P,Robinson J,Bodmer J,Marsh SG,Bontrop R,Lemaitre M,Lefranc G,Chaume D,Lefranc MP

更新日期：2000-01-01 00:00:00

abstract：:1,10-Phenanthroline-platinum(II)-ethylenediamine ( PEPt ) forms a crystalline complex with cytidine-3'-phosphate (3'-CMP) and its structure has been determined by X-ray crystallography. 3'-CMP molecules are hemiprotonated and form hydrogen-bonded pairs that stack above and below the phenanthroline-platinum(II) drug mo...

journal_title：Nucleic acids research

authors： Vijay-Kumar S,Sakore TD,Sobell HM

更新日期：1984-04-25 00:00:00

abstract：:It has been inferred from DNA sequence analyses that in echinoderm mitochondria not only the usual asparagine codons AAU and AAC, but also the usual lysine codon AAA, are translated as asparagine by a single mitochondrial (mt) tRNAAsn with the anticodon GUU. Nucleotide sequencing of starfish mt tRNAAsn revealed that t...

journal_title：Nucleic acids research

authors： Tomita K,Ueda T,Watanabe K

更新日期：1999-04-01 00:00:00

abstract：:ArrayExpress is a public repository for microarray data that supports the MIAME (Minimum Information About a Microarray Experiment) requirements and stores well-annotated raw and normalized data. As of November 2004, ArrayExpress contains data from approximately 12,000 hybridizations covering 35 species. Data can be s...

journal_title：Nucleic acids research

authors： Parkinson H,Sarkans U,Shojatalab M,Abeygunawardena N,Contrino S,Coulson R,Farne A,Lara GG,Holloway E,Kapushesky M,Lilja P,Mukherjee G,Oezcimen A,Rayner T,Rocca-Serra P,Sharma A,Sansone S,Brazma A

更新日期：2005-01-01 00:00:00