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

authors： Michel AM,Kiniry SJ,O'Connor PBF,Mullan JP,Baranov PV

更新日期：2018-01-04 00:00:00

abstract：:The Ensembl project has been aggregating, processing, integrating and redistributing genomic datasets since the initial releases of the draft human genome, with the aim of accelerating genomics research through rapid open distribution of public data. Large amounts of raw data are thus transformed into knowledge, which...

journal_title：Nucleic acids research

authors： Zerbino DR,Achuthan P,Akanni W,Amode MR,Barrell D,Bhai J,Billis K,Cummins C,Gall A,Girón CG,Gil L,Gordon L,Haggerty L,Haskell E,Hourlier T,Izuogu OG,Janacek SH,Juettemann T,To JK,Laird MR,Lavidas I,Liu Z,Lovel

更新日期：2018-01-04 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

authors： Lefkowitz EJ,Dempsey DM,Hendrickson RC,Orton RJ,Siddell SG,Smith DB

更新日期：2018-01-04 00:00:00

abstract：:Since 2010, the Genomicus web server is available online at http://genomicus.biologie.ens.fr/genomicus. This graphical browser provides access to comparative genomic analyses in four different phyla (Vertebrate, Plants, Fungi, and non vertebrate Metazoans). Users can analyse genomic information from extant species, as...

journal_title：Nucleic acids research

authors： Nguyen NTT,Vincens P,Roest Crollius H,Louis A

更新日期：2018-01-04 00:00:00

abstract：:The European Bioinformatics Institute (EMBL-EBI) supports life-science research throughout the world by providing open data, open-source software and analytical tools, and technical infrastructure (https://www.ebi.ac.uk). We accommodate an increasingly diverse range of data types and integrate them, so that biologists...

journal_title：Nucleic acids research

authors： Cook CE,Bergman MT,Cochrane G,Apweiler R,Birney E

更新日期：2018-01-04 00:00:00

abstract：:Recent evidence indicates a link between Parkinson's Disease (PD) and the expression of a-synuclein (SNCA) isoforms with different 3' untranslated regions (3'UTRs). Yet, the post-transcriptional mechanisms regulating SNCA expression are unknown. Using a large-scale in vitro /in silico screening we identified RNA-bindi...

journal_title：Nucleic acids research

authors： Marchese D,Botta-Orfila T,Cirillo D,Rodriguez JA,Livi CM,Fernández-Santiago R,Ezquerra M,Martí MJ,Bechara E,Tartaglia GG,Catalan MSA Registry (CMSAR).

更新日期：2017-12-15 00:00:00

abstract：:By successively assembling genetic parts such as BioBrick according to grammatical models, complex genetic constructs composed of dozens of functional blocks can be built. However, usually every category of genetic parts includes a few or many parts. With increasing quantity of genetic parts, the process of assembling...

journal_title：Nucleic acids research

authors： Fang G,Zhang S,Dong Y

更新日期：2017-12-15 00:00:00

abstract：:High-throughput chromosome conformation capture (3C) technologies, such as Hi-C, have made it possible to survey 3D genome structure. However, obtaining 3D profiles at kilobase resolution at low cost remains a major challenge. Therefore, we herein present an algorithm for precise identification of chromatin interactio...

journal_title：Nucleic acids research

authors： Zhang H,Li F,Jia Y,Xu B,Zhang Y,Li X,Zhang Z

更新日期：2017-12-15 00:00:00

abstract：:Nucleotide excision repair is initiated by two different damage recognition subpathways, global genome repair (GGR) and transcription-coupled repair (TCR). In GGR, XPC detects DNA lesions and recruits TFIIH via interaction with the pleckstrin homology (PH) domain of TFIIH subunit p62. In TCR, an elongating form of RNA...

journal_title：Nucleic acids research

authors： Okuda M,Nakazawa Y,Guo C,Ogi T,Nishimura Y

更新日期：2017-12-15 00:00:00

abstract：:A molecular rotor thioflavin T (ThT) is usually used as a fluorescent ligand specific for G-quadruplexes. Here, we demonstrate that ThT can tightly bind non-G-quadruplex DNAs with several GA motifs and dimerize them in a parallel double-stranded mode, accompanied by over 100-fold enhancement in the fluorescence emissi...

journal_title：Nucleic acids research

authors： Liu S,Peng P,Wang H,Shi L,Li T

更新日期：2017-12-01 00:00:00

abstract：:Although many tools have been developed to analyze small RNA sequencing (sRNA-Seq) data, it remains challenging to accurately analyze the small RNA population, mainly due to multiple sequence ID assignment caused by short read length. Additional issues in small RNA analysis include low consistency of microRNA (miRNA) ...

journal_title：Nucleic acids research

authors： Wu X,Kim TK,Baxter D,Scherler K,Gordon A,Fong O,Etheridge A,Galas DJ,Wang K

更新日期：2017-12-01 00:00:00

abstract：:Protein-DNA binding is a fundamental component of gene regulatory processes, but it is still not completely understood how proteins recognize their target sites in the genome. Besides hydrogen bonding in the major groove (base readout), proteins recognize minor-groove geometry using positively charged amino acids (sha...

journal_title：Nucleic acids research

authors： Chiu TP,Rao S,Mann RS,Honig B,Rohs R

更新日期：2017-12-01 00:00:00

abstract：:RNase III enzymes cleave double stranded (ds)RNA. This is an essential step for regulating the processing of mRNA, rRNA, snoRNA and other small RNAs, including siRNA and miRNA. Arabidopsis thaliana encodes nine RNase III: four DICER-LIKE (DCL) and five RNASE THREE LIKE (RTL). To better understand the molecular functio...

journal_title：Nucleic acids research

authors： Charbonnel C,Niazi AK,Elvira-Matelot E,Nowak E,Zytnicki M,de Bures A,Jobet E,Opsomer A,Shamandi N,Nowotny M,Carapito C,Reichheld JP,Vaucheret H,Sáez-Vásquez J

更新日期：2017-11-16 00:00:00

abstract：:The HIRA histone chaperone complex deposits histone H3.3 into nucleosomes in a DNA replication- and sequence-independent manner. As herpesvirus genomes enter the nucleus as naked DNA, we asked whether the HIRA chaperone complex affects herpesvirus infection. After infection of primary cells with HSV or CMV, or transie...

journal_title：Nucleic acids research

authors： Rai TS,Glass M,Cole JJ,Rather MI,Marsden M,Neilson M,Brock C,Humphreys IR,Everett RD,Adams PD

更新日期：2017-11-16 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

abstract：:Light-inducible systems allow spatiotemporal control of a variety of biological activities. Here, we report newly optimized optogenetic tools to induce transcription with light in mammalian cells, using the Arabidopsis photoreceptor Flavin Kelch-repeat F-box 1 (FKF1) and its binding partner GIGANTEA (GI) as well as CR...

journal_title：Nucleic acids research

authors： Quejada JR,Park SE,Awari DW,Shi F,Yamamoto HE,Kawano F,Jung JC,Yazawa M

更新日期：2017-11-16 00:00:00

abstract：:HBV genotypes differ in pathogenicity. In addition, genotype-specific differences in the regulation of transcription and virus replication exist in HBV, but the underlying mechanisms are unknown. Here, we show the presence of a G-quadruplex motif in the promoter of the preS2/S gene; this G-quadruplex is highly conserv...

journal_title：Nucleic acids research

authors： Biswas B,Kandpal M,Vivekanandan P

更新日期：2017-11-02 00:00:00

abstract：:We observed overexpression and increased intra-nuclear accumulation of the PRMT5/WDR77 in breast cancer cell lines relative to immortalized breast epithelial cells. Utilizing mass spectrometry and biochemistry approaches we identified the Zn-finger protein ZNF326, as a novel interaction partner and substrate of the nu...

journal_title：Nucleic acids research

authors： Rengasamy M,Zhang F,Vashisht A,Song WM,Aguilo F,Sun Y,Li S,Zhang W,Zhang B,Wohlschlegel JA,Walsh MJ

更新日期：2017-11-02 00:00:00

abstract：:Sequence heterogeneity is a common characteristic of RNA viruses that is often referred to as sub-populations or quasispecies. Traditional techniques used for assembly of short sequence reads produced by deep sequencing, such as de-novo assemblers, ignore the underlying diversity. Here, we introduce a novel algorithm ...

journal_title：Nucleic acids research

authors： Karagiannis K,Simonyan V,Chumakov K,Mazumder R

更新日期：2017-11-02 00:00:00

abstract：:Cpf1 nucleases were recently reported to be highly specific and programmable nucleases with efficiencies comparable to those of SpCas9. AsCpf1 and LbCpf1 require a single crRNA and recognize a 5'-TTTN-3' protospacer adjacent motif (PAM) at the 5' end of the protospacer for genome editing. For widespread application in...

journal_title：Nucleic acids research

authors： Tu M,Lin L,Cheng Y,He X,Sun H,Xie H,Fu J,Liu C,Li J,Chen D,Xi H,Xue D,Liu Q,Zhao J,Gao C,Song Z,Qu J,Gu F

更新日期：2017-11-02 00:00:00

abstract：:The 'sandwich' binding format, which uses two reagents that can bind simultaneously to a given analyte, is the gold standard in diagnostics and many biochemical techniques. One of the bottlenecks in creating a sandwich assay is identifying pairs of reagents that bind non-competitively to the target. To bridge this gap...

journal_title：Nucleic acids research

authors： Gorman KT,Roby LC,Giuffre A,Huang R,Kay BK

更新日期：2017-10-13 00:00:00

abstract：:Ribosomal protein (RP) genes must be coordinately expressed for proper assembly of the ribosome yet the mechanisms that control expression of RP genes in metazoans are poorly understood. Recently, TATA-binding protein-related factor 2 (TRF2) rather than the TATA-binding protein (TBP) was found to function in transcrip...

journal_title：Nucleic acids research

authors： Baumann DG,Gilmour DS

更新日期：2017-10-13 00:00:00

abstract：:DNA primases recognize single-stranded DNA (ssDNA) sequences to synthesize RNA primers during lagging-strand replication. Arabidopsis thaliana encodes an ortholog of the DNA primase-helicase from bacteriophage T7, dubbed AtTwinkle, that localizes in chloroplasts and mitochondria. Herein, we report that AtTwinkle synth...

journal_title：Nucleic acids research

authors： Peralta-Castro A,Baruch-Torres N,Brieba LG

更新日期：2017-10-13 00:00:00

abstract：:While proteins are highly biochemically competent, DNA offers the ability to program, both reactions and the assembly of nanostructures, with a control that is unprecedented by any other molecule. Their joining: DNA-protein conjugates - offer the ability to combine the programmability of DNA with the competence of pro...

journal_title：Nucleic acids research

authors： Bernardinelli G,Högberg B

更新日期：2017-10-13 00:00:00

abstract：:The polyadenylate binding protein 1 (PABPN1) is a ubiquitously expressed RNA binding protein vital for multiple steps in RNA metabolism. Although PABPN1 plays a critical role in the regulation of RNA processing, mutation of the gene encoding this ubiquitously expressed RNA binding protein causes a specific form of mus...

journal_title：Nucleic acids research

authors： Banerjee A,Vest KE,Pavlath GK,Corbett AH

更新日期：2017-10-13 00:00:00

abstract：:Pluripotency, the ability of embryonic stem cells to differentiate into specialized cell types, is determined by ESC-specific gene regulators such as transcription factors and chromatin modification factors. It is not well understood how ESCs are poised for differentiation, however, and methods are needed for prognosi...

journal_title：Nucleic acids research

authors： Ha M,Hong S

更新日期：2017-10-13 00:00:00

abstract：:An R-loop is a DNA:RNA hybrid formed during transcription when a DNA duplex is invaded by a nascent RNA transcript. R-loops accumulate in nucleoli during RNA polymerase I (RNAP I) transcription. Here, we report that mammalian RNase H1 enriches in nucleoli and co-localizes with R-loops in cultured human cells. Co-migra...

journal_title：Nucleic acids research

authors： Shen W,Sun H,De Hoyos CL,Bailey JK,Liang XH,Crooke ST

更新日期：2017-10-13 00:00:00

abstract：:Single-molecule force spectroscopy provides insight into how proteins bind to and move along DNA. Such studies often embed a single-stranded (ss) DNA region within a longer double-stranded (ds) DNA molecule. Yet, producing these substrates remains laborious and inefficient, particularly when using the traditional thre...

journal_title：Nucleic acids research

authors： Okoniewski SR,Uyetake L,Perkins TT

更新日期：2017-10-13 00:00:00

abstract：:The nucleoplasm is not homogenous; it consists of many types of nuclear bodies, also known as nuclear domains or nuclear subcompartments. These self-organizing structures gather machinery involved in various nuclear activities. Nuclear speckles (NSs) or splicing speckles, also called interchromatin granule clusters, w...

journal_title：Nucleic acids research

authors： Galganski L,Urbanek MO,Krzyzosiak WJ

更新日期：2017-10-13 00:00:00

abstract：:Most E2F-binding sites repress transcription through the recruitment of Retinoblastoma (RB) family members until the end of the G1 cell-cycle phase. Although the MYB promoter contains an E2F-binding site, its transcription is activated shortly after the exit from quiescence, before RB family members inactivation, by u...

journal_title：Nucleic acids research

authors： Álvaro-Blanco J,Urso K,Chiodo Y,Martín-Cortázar C,Kourani O,Arco PG,Rodríguez-Martínez M,Calonge E,Alcamí J,Redondo JM,Iglesias T,Campanero MR

更新日期：2017-09-29 00:00:00

abstract：:Mitochondrial aprataxin (APTX) protects the mitochondrial genome from the consequence of ligase failure by removing the abortive ligation product, i.e. the 5'-adenylate (5'-AMP) group, during DNA replication and repair. In the absence of APTX activity, blocked base excision repair (BER) intermediates containing the 5'...

journal_title：Nucleic acids research

authors： Çaglayan M,Prasad R,Krasich R,Longley MJ,Kadoda K,Tsuda M,Sasanuma H,Takeda S,Tano K,Copeland WC,Wilson SH

更新日期：2017-09-29 00:00:00

abstract：:New transcripts generated by RNA polymerase II (RNAPII) are generally processed in order to form mature mRNAs. Two key processing steps include a precise cleavage within the 3' end of the pre-mRNA, and the subsequent polymerization of adenosines to produce the poly(A) tail. In yeast, these two functions are performed ...

journal_title：Nucleic acids research

authors： Guéguéniat J,Dupin AF,Stojko J,Beaurepaire L,Cianférani S,Mackereth CD,Minvielle-Sébastia L,Fribourg S

更新日期：2017-09-29 00:00:00

abstract：:Synthesis of HIV GagPol involves a proportion of ribosomes translating a U6A shift site at the distal end of the gag gene performing a programmed -1 ribosomal frameshift event to enter the overlapping pol gene. In vitro studies here show that at the same shift motif HIV reverse transcriptase generates -1 and +1 indels...

journal_title：Nucleic acids research

authors： Penno C,Kumari R,Baranov PV,van Sinderen D,Atkins JF

更新日期：2017-09-29 00:00:00

abstract：:An essential coordinator of all DNA metabolic processes is Replication Protein A (RPA). RPA orchestrates these processes by binding to single-stranded DNA (ssDNA) and interacting with several other DNA binding proteins. Determining the real-time kinetics of single players such as RPA in the presence of multiple DNA pr...

journal_title：Nucleic acids research

authors： Pokhrel N,Origanti S,Davenport EP,Gandhi D,Kaniecki K,Mehl RA,Greene EC,Dockendorff C,Antony E

更新日期：2017-09-19 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：:Although the involvement of Ser/Arg-rich (SR) proteins in RNA metabolism is well documented, their role in vertebrate development remains elusive. We, therefore, elected to take advantage of the zebrafish model organism to study the SR genes' functions using the splicing morpholino (sMO) microinjection and the program...

journal_title：Nucleic acids research

authors： Joris M,Schloesser M,Baurain D,Hanikenne M,Muller M,Motte P

更新日期：2017-09-19 00:00:00

abstract：:Targeted differentiation of human induced pluripotent stem cells (hiPSCs) using only chemicals would have value-added clinical potential in the regeneration of complex cell types including cardiomyocytes. Despite the availability of several chemical inhibitors targeting proteins involved in signaling pathways, no bioa...

journal_title：Nucleic acids research

authors： Taniguchi J,Pandian GN,Hidaka T,Hashiya K,Bando T,Kim KK,Sugiyama H

更新日期：2017-09-19 00:00:00

abstract：:Influenza A virus (IAV) genomes are composed of eight single-stranded RNA segments that are coated by viral nucleoprotein (NP) molecules. Classically, the interaction between NP and viral RNA (vRNA) is depicted as a uniform pattern of 'beads on a string'. Using high-throughput sequencing of RNA isolated by crosslinkin...

journal_title：Nucleic acids research

authors： Lee N,Le Sage V,Nanni AV,Snyder DJ,Cooper VS,Lakdawala SS

更新日期：2017-09-06 00:00:00

abstract：:MicroRNAs are a class of small non-coding RNAs that serve as important regulators of gene expression at the posttranscriptional level. They are stable in body fluids and pose great potential to serve as biomarkers. Here, we present a highly specific, sensitive and cost-effective system to quantify miRNA expression bas...

journal_title：Nucleic acids research

authors： Androvic P,Valihrach L,Elling J,Sjoback R,Kubista M

更新日期：2017-09-06 00:00:00

abstract：:Highly regulated induction systems enabling dose-dependent and reversible fine-tuning of protein expression output are beneficial for engineering complex biosynthetic pathways. To address this, we developed PhiReX, a novel red/far-red light-regulated protein expression system for use in Saccharomyces cerevisiae. PhiRe...

journal_title：Nucleic acids research

authors： Hochrein L,Machens F,Messerschmidt K,Mueller-Roeber B

更新日期：2017-09-06 00:00:00