NEpiC: a network-assisted algorithm for epigenetic studies using mean and variance combined signals.

abstract：:CeR-2 RNA is one of the newly identified Caenorhabditis elegans noncoding RNAs (ncRNAs). The characterization of CeR-2 by RNomic studies has failed to classify it into any known ncRNA family. In this study, we examined the spatiotemporal expression patterns of CeR-2 to gain insight into its function. CeR-2 is expresse...

journal_title：Nucleic acids research

authors： Hokii Y,Sasano Y,Sato M,Sakamoto H,Sakata K,Shingai R,Taneda A,Oka S,Himeno H,Muto A,Fujiwara T,Ushida C

更新日期：2010-09-01 00:00:00

abstract：:Yeast Dna2 helicase/nuclease is essential for DNA replication and assists FEN1 nuclease in processing a subset of Okazaki fragments that have long single-stranded 5' flaps. It is also involved in the maintenance of telomeres. DNA2 is a gene conserved in eukaryotes, and a putative human ortholog of yeast DNA2 (ScDNA2) ...

journal_title：Nucleic acids research

authors： Masuda-Sasa T,Imamura O,Campbell JL

更新日期：2006-04-04 00:00:00

abstract：:The 80S ribosome from Saccharomyces cerevisiae has been reconstructed from cryo electron micrographs to a resolution of 35 A. It is strikingly similar to the 70S ribosome from Escherichia coli, while displaying the characteristic eukaryotic features familiar from reconstructions of ribosomes from higher eukaryotes. As...

journal_title：Nucleic acids research

authors： Verschoor A,Warner JR,Srivastava S,Grassucci RA,Frank J

更新日期：1998-01-15 00:00:00

abstract：:In conditions that mimic those of the living cell, where various biomolecules and other components are present, DNA strands can adopt many structures in addition to the canonical B-form duplex. Previous studies in the presence of cosolutes that induce molecular crowding showed that thermal stabilities of DNA structure...

journal_title：Nucleic acids research

authors： Nakano M,Tateishi-Karimata H,Tanaka S,Tama F,Miyashita O,Nakano S,Sugimoto N

更新日期：2015-12-02 00:00:00

abstract：:Sequence-dependent variation in structure and dynamics of a DNA duplex, collectively referred to as 'DNA shape', critically impacts interactions between DNA and proteins. Here, a method based on the technique of site-directed spin labeling was developed to experimentally map shapes of two DNA duplexes that contain res...

journal_title：Nucleic acids research

authors： Ding Y,Zhang X,Tham KW,Qin PZ

更新日期：2014-10-01 00:00:00

abstract：:Nucleosomes are the most abundant protein-DNA complexes in eukaryotes that provide compaction of genomic DNA and are implicated in regulation of transcription, DNA replication and repair. The details of DNA positioning on the nucleosome and the DNA conformation can provide key regulatory signals. Hydroxyl-radical foot...

journal_title：Nucleic acids research

authors： Shaytan AK,Xiao H,Armeev GA,Wu C,Landsman D,Panchenko AR

更新日期：2017-09-19 00:00:00

abstract：:Differential expression analysis of RNA sequencing (RNA-seq) data typically relies on reconstructing transcripts or counting reads that overlap known gene structures. We previously introduced an intermediate statistical approach called differentially expressed region (DER) finder that seeks to identify contiguous regi...

journal_title：Nucleic acids research

authors： Collado-Torres L,Nellore A,Frazee AC,Wilks C,Love MI,Langmead B,Irizarry RA,Leek JT,Jaffe AE

更新日期：2017-01-25 00:00:00

abstract：:The cDNA-chip technology is a highly versatile tool for the comprehensive analysis of gene expression at the transcript level. Although it has been applied successfully in expression profiling projects, there is an ongoing dispute concerning the quality of such expression data. The latter critically depends on the spe...

journal_title：Nucleic acids research

authors： Drobyshev AL,Machka C,Horsch M,Seltmann M,Liebscher V,Hrabé de Angelis M,Beckers J

更新日期：2003-01-15 00:00:00

abstract：:DNA polymerase beta (polbeta), a member of the X family of DNA polymerases, is the major polymerase in the base excision repair pathway. Using in vitro selection, we obtained RNA aptamers for polbeta from a variable pool of 8 x 10(12) individual RNA sequences containing 30 random nucleotides. A total of 60 individual ...

journal_title：Nucleic acids research

authors： Gening LV,Klincheva SA,Reshetnjak A,Grollman AP,Miller H

更新日期：2006-05-17 00:00:00

abstract：:The unknown modified nucleotide G*, isolated from both Schizosaccharomyces pombe and Torulopsis utilis initiator tRNAs(Met), has been identified as an O-ribosyl-(1"----2')-guanosine-5"-phosphate, called Gr(p), by means of HPLC, UV-absorption, mass spectrometry and periodate oxidation procedures. By comparison with the...

journal_title：Nucleic acids research

authors： Glasser AL,Desgres J,Heitzler J,Gehrke CW,Keith G

更新日期：1991-10-11 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：:MODPROPEP is a web server for knowledge-based modeling of protein-peptide complexes, specifically peptides in complex with major histocompatibility complex (MHC) proteins and kinases. The available crystal structures of protein-peptide complexes in PDB are used as templates for modeling peptides of desired sequence in...

journal_title：Nucleic acids research

authors： Kumar N,Mohanty D

更新日期：2007-07-01 00:00:00

abstract：:The type I insulin-like growth factor receptor (IGF-IR) is an integral component in the control of cell proliferation, differentiation and apoptosis. The IGF-IR mRNA contains an extraordinarily long (1038 nt) 5'-untranslated region (5'-UTR), and we have characterized a diverse series of proteins interacting with this ...

journal_title：Nucleic acids research

authors： Meng Z,King PH,Nabors LB,Jackson NL,Chen CY,Emanuel PD,Blume SW

更新日期：2005-05-24 00:00:00

abstract：:A simple and efficient gene replacement method, based on the recombination and repair activities of the cell, was developed. The method permits the targeted construction of markerless deletions, insertions and point mutations in the Escherichia coli chromosome. A suicide plasmid, carrying the mutant allele and the rec...

journal_title：Nucleic acids research

authors： Pósfai G,Kolisnychenko V,Bereczki Z,Blattner FR

更新日期：1999-11-15 00:00:00

abstract：:Using two primers corresponding to helix 1 and helix 3 regions in the homeodomain, we subjected genomic DNA from Caenorhabditis elegans to amplification by the polymerase chain reaction. Sequence analysis of the amplified products revealed a new homeobox-containing gene, designated ceh-19. This gene was located betwee...

journal_title：Nucleic acids research

authors： Naito M,Kohara Y,Kurosawa Y

更新日期：1992-06-25 00:00:00

abstract：:GC content bias describes the dependence between fragment count (read coverage) and GC content found in Illumina sequencing data. This bias can dominate the signal of interest for analyses that focus on measuring fragment abundance within a genome, such as copy number estimation (DNA-seq). The bias is not consistent b...

journal_title：Nucleic acids research

authors： Benjamini Y,Speed TP

更新日期：2012-05-01 00:00:00

abstract：:High-throughput experimental technologies gradually shift the paradigm of biological research from hypothesis-validation toward hypothesis-generation science. Translating diverse types of large-scale experimental data into testable hypotheses, however, remains a daunting task. We previously demonstrated that heterogen...

journal_title：Nucleic acids research

authors： Cho A,Shin J,Hwang S,Kim C,Shim H,Kim H,Kim H,Lee I

更新日期：2014-07-01 00:00:00

abstract：:We identify a new subgroup of Type I Restriction-Modification enzymes that modify cytosine in one DNA strand and adenine in the opposite strand for host protection. Recognition specificity has been determined for ten systems using SMRT sequencing and each recognizes a novel DNA sequence motif. Previously characterized...

journal_title：Nucleic acids research

authors： Morgan RD,Luyten YA,Johnson SA,Clough EM,Clark TA,Roberts RJ

更新日期：2016-11-02 00:00:00

abstract：:Molecules of single-stranded ribosomal RNA and double-stranded replicative form of phage f2 RNA (dsRNA) adopt a compact form in solutions, containing sufficiently high concentrations of salt (NaCl) and polymer (PEG). However, only in the cases of native dsRNA molecules the compact particles are characterized by a regu...

journal_title：Nucleic acids research

authors： Evdokimov YM,Pyatigorskaya TL,Kadikov VA,Polyvtsev OF,Doskocil J,Koudelka J,Varshavsky YM

更新日期：1976-06-01 00:00:00

abstract：:Gene trap mutagenesis of mouse embryonic stem cells generates random loss-of-function mutations, which can be identified by a sequence tag and can often report the endogenous expression of the mutated gene. The Centre for Modeling Human Disease is performing expression- and sequence-based screens of gene trap insertio...

journal_title：Nucleic acids research

authors： To C,Epp T,Reid T,Lan Q,Yu M,Li CY,Ohishi M,Hant P,Tsao N,Casallo G,Rossant J,Osborne LR,Stanford WL

更新日期：2004-01-01 00:00:00

abstract：:Prokaryotic genomic DNA is generally negatively supercoiled in vivo. Many regulatory processes, including the initiation of transcription, are known to depend on the superhelical state of the DNA substrate. The stresses induced within DNA by negative superhelicity can destabilize the DNA duplex at specific sites. Vari...

journal_title：Nucleic acids research

authors： Wang H,Kaloper M,Benham CJ

更新日期：2006-01-01 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：:The thyroid hormone receptor alpha (THRA or c-erbA-1) gene belongs to a family of genes which encode nuclear receptors for various hydrophobic ligands such as steroids, vitamin D, retinoic acid and thyroid hormones. These receptors are composed of several domains important for hormone-binding, DNA-binding, dimerizatio...

journal_title：Nucleic acids research

authors： Laudet V,Begue A,Henry-Duthoit C,Joubel A,Martin P,Stehelin D,Saule S

更新日期：1991-03-11 00:00:00

abstract：:The transcription activator-like effectors (TALEs) and the RNA-guided clustered regularly interspaced short palindromic repeat (CRISPR) associated protein (Cas9) utlilize distinct molecular mechanisms in targeting site recognition. The two proteins can be modified to carry additional functional domains to regulate exp...

journal_title：Nucleic acids research

authors： Gao X,Tsang JC,Gaba F,Wu D,Lu L,Liu P

更新日期：2014-11-10 00:00:00

abstract：:Recent studies have employed cross-species comparisons of transcription factor binding, reporting significant regulatory network 'rewiring' between species. Here, we address how a transcriptional repressor targets and regulates neural genes differentially between human and mouse embryonic stem cells (ESCs). We find th...

journal_title：Nucleic acids research

authors： Rockowitz S,Zheng D

更新日期：2015-07-13 00:00:00

abstract：:Non-coding RNA regulatory elements are important for viral replication, making them promising targets for therapeutic intervention. However, regulatory RNA is challenging to detect and characterise using classical structure-function assays. Here, we present in cell Mutational Interference Mapping Experiment (in cell M...

journal_title：Nucleic acids research

authors： Smyth RP,Smith MR,Jousset AC,Despons L,Laumond G,Decoville T,Cattenoz P,Moog C,Jossinet F,Mougel M,Paillart JC,von Kleist M,Marquet R

更新日期：2018-05-18 00:00:00

abstract：:The synthesis of ribosomal precursor RNA in Novikoff hepatoma (N1S1) cells is very sensitive to cordycepin (3'-dA). The synthesis of hnRNA, however, is resistant to inhibition concentrations of 3'-dA that completely block the synthesis of 45S ribosomal RNA precursor. We have examined the RNA polymerases present in the...

journal_title：Nucleic acids research

authors： Desrosiers RC,Rottman FM,Boezi JA,Towle HC

更新日期：1976-02-01 00:00:00

abstract：:A small library of 49 peptide-oligonucleotide conjugates were synthesized to explore the influence of various peptide side chains on the hybridization properties of the DNA. An invariant 8mer oligonucleotide was coupled to a peptide portion that contained a five residue variable region composed of the cationic amino a...

journal_title：Nucleic acids research

authors： Harrison JG,Balasubramanian S

更新日期：1998-07-01 00:00:00

abstract：:DNA restriction fragments located 5' to the human c-myc gene display anomalous electrophoretic mobility on polyacrylamide gels. Computer modeling of the c-myc flanking DNA suggests that the slow-moving DNA fragments spanning nucleotides -1690 to -1054 (relative to c-myc promoter P1) and -718 to -452 form large left ha...

journal_title：Nucleic acids research

authors： Kumar S,Leffak M

更新日期：1989-04-11 00:00:00

abstract：:It has been postulated that a myriad of long noncoding RNAs (lncRNAs) contribute to gene regulation. In fission yeast, glucose starvation triggers lncRNA transcription across promoter regions of stress-responsive genes including fbp1 (fructose-1,6-bisphosphatase1). At the fbp1 promoter, this transcription promotes chr...

journal_title：Nucleic acids research

authors： Takemata N,Oda A,Yamada T,Galipon J,Miyoshi T,Suzuki Y,Sugano S,Hoffman CS,Hirota K,Ohta K

更新日期：2016-06-20 00:00:00