The structure of the yeast ribosomal RNA genes. I. The complete nucleotide sequence of the 18S ribosomal RNA gene from Saccharomyces cerevisiae.

abstract：:Despite the increasing wealth of available data, the structure of cancer transcriptional space remains largely unknown. Analysis of this space would provide novel insights into the complexity of cancer, assess relative implications in complex biological processes and responses, evaluate the effectiveness of cancer mod...

journal_title：Nucleic acids research

authors： Gadaleta E,Cutts RJ,Kelly GP,Crnogorac-Jurcevic T,Kocher HM,Lemoine NR,Chelala C

更新日期：2011-10-01 00:00:00

abstract：:During S phase, the entire genome must be precisely duplicated, with no sections of DNA left unreplicated. Here, we develop a simple mathematical model to describe the probability of replication failing due to the irreversible stalling of replication forks. We show that the probability of complete genome replication i...

journal_title：Nucleic acids research

authors： Newman TJ,Mamun MA,Nieduszynski CA,Blow JJ

更新日期：2013-11-01 00:00:00

abstract：:We have exploited properties of photosensitizers to study an aspect of the packing of chromatin in the cell nucleus. The fluorescent photosensitizers mesotetra(3-hydroxyphenyl) porphyrin and Photofrin II were both localized in the nuclear membrane and other membrane structures, but could not be found inside the nuclei...

journal_title：Nucleic acids research

authors： Kvam E,Stokke T,Moan J,Steen HB

更新日期：1992-12-25 00:00:00

abstract：:The genome-wide identification of microRNA transcription start sites (miRNA TSSs) is essential for understanding how miRNAs are regulated in development and disease. In this study, we developed mirSTP (mirna transcription Start sites Tracking Program), a probabilistic model for identifying active miRNA TSSs from nasce...

journal_title：Nucleic acids research

authors： Liu Q,Wang J,Zhao Y,Li CI,Stengel KR,Acharya P,Johnston G,Hiebert SW,Shyr Y

更新日期：2017-07-27 00:00:00

abstract：:The putative role of double-strand breaks (DSBs) created in vitro by restriction enzyme cleavage in or near CGG*CCG or CTG*CAG repeat tracts on their genetic instabilities, both within the repeats and in their flanking sequences, was investigated in an Escherichia coli plasmid system. DSBs at TRS junctions with the ve...

journal_title：Nucleic acids research

authors： Kosmider B,Wells RD

更新日期：2006-01-01 00:00:00

abstract：:We have determined the genomic structure of the fosB gene and shown that it consists of 4 exons and 3 introns at positions also found in the c-fos gene. By deletion analysis we have characterized a region upstream of the TATA box which is the promoter region of the gene. Several consensus sequences have been identifie...

journal_title：Nucleic acids research

authors： Lazo PS,Dorfman K,Noguchi T,Mattéi MG,Bravo R

更新日期：1992-01-25 00:00:00

abstract：:Using a powerful computer-assisted analysis strategy, a large-scale search of small nucleolar RNA (snoRNA) genes in the recently released draft sequence of the rice genome was carried out. This analysis identified 120 different box C/D snoRNA genes with a total of 346 gene variants, which were predicted to guide 135 2...

journal_title：Nucleic acids research

authors： Chen CL,Liang D,Zhou H,Zhuo M,Chen YQ,Qu LH

更新日期：2003-05-15 00:00:00

abstract：:Cells respond to DNA damage by activating both cellular growth arrest and DNA repair processes. In Saccharomyces cerevesiae the RAD9 gene controls DNA damage-mediated cell cycle arrest that is known to allow efficient repair. To ascertain whether RAD9 plays a role in DNA repair per se, the removal of UV-induced photol...

journal_title：Nucleic acids research

authors： Al-Moghrabi NM,Al-Sharif IS,Aboussekhra A

更新日期：2001-05-15 00:00:00

abstract：:This article presents W-IQ-TREE, an intuitive and user-friendly web interface and server for IQ-TREE, an efficient phylogenetic software for maximum likelihood analysis. W-IQ-TREE supports multiple sequence types (DNA, protein, codon, binary and morphology) in common alignment formats and a wide range of evolutionary ...

journal_title：Nucleic acids research

authors： Trifinopoulos J,Nguyen LT,von Haeseler A,Minh BQ

更新日期：2016-07-08 00:00:00

abstract：:The National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB), provides a suite of database resources to support worldwide research activities in both academia and industry. With the explosive growth of multi-omics data, CNCB-NGDC is continually expanding, updating and enriching...

journal_title：Nucleic acids research

authors： CNCB-NGDC Members and Partners.

更新日期：2021-01-08 00:00:00

abstract：:Recent advances in next-generation sequencing technologies and genome assembly algorithms have enabled the accumulation of a huge volume of genome sequences from various species. This has provided new opportunities for large-scale comparative genomics studies. Identifying and utilizing synteny blocks, which are genomi...

journal_title：Nucleic acids research

authors： Lee J,Hong WY,Cho M,Sim M,Lee D,Ko Y,Kim J

更新日期：2016-07-08 00:00:00

abstract：:During DNA double-strand break and replication fork repair by homologous recombination, the RAD51 recombinase catalyzes the DNA strand exchange reaction via a helical polymer assembled on single-stranded DNA, termed the presynaptic filament. Our published work has demonstrated a dual function of the SWI5-SFR1 complex ...

journal_title：Nucleic acids research

authors： Su GC,Yeh HY,Lin SW,Chung CI,Huang YS,Liu YC,Lyu PC,Chi P

更新日期：2016-07-27 00:00:00

abstract：:Two types of different repetitive DNA sequences called RepMP1 and RepMP2 were identified in the genome of Mycoplasma pneumoniae. The number of these repeated elements, their nucleotide sequence and their localization on a physical map of the M. pneumoniae genome were determined. The results show that RepMP1 appears at...

journal_title：Nucleic acids research

authors： Wenzel R,Herrmann R

更新日期：1988-09-12 00:00:00

abstract：:Analysis of large-scale gene expression studies usually begins with gene clustering. A ubiquitous problem is that different algorithms applied to the same data inevitably give different results, and the differences are often substantial, involving a quarter or more of the genes analyzed. This raises a series of import...

journal_title：Nucleic acids research

authors： Hart CE,Sharenbroich L,Bornstein BJ,Trout D,King B,Mjolsness E,Wold BJ

更新日期：2005-05-10 00:00:00

abstract：:Here, we describe the development of WikiPathways (http://www.wikipathways.org), a public wiki for pathway curation, since it was first published in 2008. New features are discussed, as well as developments in the community of contributors. New features include a zoomable pathway viewer, support for pathway ontology a...

journal_title：Nucleic acids research

authors： Kelder T,van Iersel MP,Hanspers K,Kutmon M,Conklin BR,Evelo CT,Pico AR

更新日期：2012-01-01 00:00:00

abstract：:A circular denaturation and restriction map of mitochondrial DNA from Neurospora crassa is presented. The map shows the position of all twelve fragments produced by restriction endonuclease Eco R I and the position of the largest Hin III fragment along the previously established map of AT-rich sequences. The two wild ...

journal_title：Nucleic acids research

authors： Bernard U,Goldthwaite C,Küntzel H

更新日期：1976-11-01 00:00:00

abstract：:Copy number variants (CNVs) are currently defined as genomic sequences that are polymorphic in copy number and range in length from 1000 to several million base pairs. Among current array-based CNV detection platforms, long-oligonucleotide arrays promise the highest resolution. However, the performance of currently av...

journal_title：Nucleic acids research

authors： Cahan P,Godfrey LE,Eis PS,Richmond TA,Selzer RR,Brent M,McLeod HL,Ley TJ,Graubert TA

更新日期：2008-04-01 00:00:00

abstract：:The integrases are a diverse family of tyrosine recombinases which rearrange DNA duplexes by means of conservative site-specific recombination reactions. Members of this family, of which the well-studied lambda Int protein is the prototype, were previously found to share four strongly conserved residues, including an ...

journal_title：Nucleic acids research

authors： Esposito D,Scocca JJ

更新日期：1997-09-15 00:00:00

abstract：:The crystal structure of d(CATGGGCCCATG)(2) shows unique stacking patterns of a stable B<-->A-DNA intermediate. We evaluated intrinsic base stacking energies in this crystal structure using an ab initio quantum mechanical method. We found that all crystal base pair steps have stacking energies close to their values in...

journal_title：Nucleic acids research

authors： Poner J,Florián J,Ng HL,Poner JE,Packová N

更新日期：2000-12-15 00:00:00

abstract：:We used the high resolution and accuracy of the Cambridge Structural Database (CSD) to provide detailed information regarding base pairing interactions of selected nucleobases. We searched for base pairs in which nucleobases interact with each other through two or more hydrogen bonds and form more or less planar struc...

journal_title：Nucleic acids research

authors： Cabaj MK,Dominiak PM

更新日期：2020-09-04 00:00:00

abstract：:The nature of mammalian origins of DNA replication remains controversial and this is primarily because two-dimensional gel replicon mapping techniques have identified broad zones of replication initiation whereas several other techniques, such as quantitative PCR, have disclosed more discrete sites of initiation at th...

journal_title：Nucleic acids research

authors： Toledo F,Baron B,Fernandez MA,Lachagès AM,Mayau V,Buttin G,Debatisse M

更新日期：1998-05-15 00:00:00

abstract：:Previous work has demonstrated that the yeast SPT3 gene is required for transcription from delta sequences, the long terminal repeats that flank yeast Ty elements. In spt3 null mutants, transcription fails to initiate in delta sequences and instead initiates farther downstream. Null mutations in SPT3 cause other mutan...

journal_title：Nucleic acids research

authors： Winston F,Minehart PL

更新日期：1986-09-11 00:00:00

abstract：:The mouse is widely used as system to study human genetic mechanisms. However, extensive rewiring of transcriptional regulatory networks often confounds translation of findings between human and mouse. Site-specific gain and loss of individual transcription factor binding sites (TFBS) has caused functional divergence ...

journal_title：Nucleic acids research

authors： Diehl AG,Boyle AP

更新日期：2018-02-28 00:00:00

abstract：:Controllable gene delivery via vector-based systems remains a formidable challenge in mammalian synthetic biology and a desirable asset in gene therapy applications. Here, we introduce a methodology to control the copies and residence time of a gene product delivered in host human cells but also selectively disrupt fr...

journal_title：Nucleic acids research

authors： Moore R,Spinhirne A,Lai MJ,Preisser S,Li Y,Kang T,Bleris L

更新日期：2015-01-01 00:00:00

abstract：:By in vivo DMS footprint and reporter gene analyses we identified two transcription factor binding sites in the human c-sis/PDGF B gene promoter. The low basal activity of the PDGF B promoter in HeLa and undifferentiated K562 cells, which express low PDGF B mRNA levels, and in PC3 cells, which express a high PDGF B mR...

journal_title：Nucleic acids research

authors： Dirks RP,Jansen HJ,van Gerven B,Onnekink C,Bloemers HP

更新日期：1995-04-11 00:00:00

abstract：:Gene trapping is a method of generating murine embryonic stem (ES) cell lines containing insertional mutations in known and novel genes. A number of international groups have used this approach to create sizeable public cell line repositories available to the scientific community for the generation of mutant mouse str...

journal_title：Nucleic acids research

authors： Nord AS,Chang PJ,Conklin BR,Cox AV,Harper CA,Hicks GG,Huang CC,Johns SJ,Kawamoto M,Liu S,Meng EC,Morris JH,Rossant J,Ruiz P,Skarnes WC,Soriano P,Stanford WL,Stryke D,von Melchner H,Wurst W,Yamamura K,Young SG,

更新日期：2006-01-01 00:00:00

abstract：:Chromatin footprinting in Drosophila tissue culture cells has detected the binding of a non-histone protein at +8 of the distal Adh RNA start site, on a 10-bp direct repeat motif abutting a nucleosome positioned over the inactive Adh distal promoter. Alternatively the active promoter is bound by a transcription initia...

journal_title：Nucleic acids research

authors： Benyajati C,Ewel A,McKeon J,Chovav M,Juan E

更新日期：1992-09-11 00:00:00

abstract：:Fluorescence anisotropy and fluorescence correlation spectroscopy measurements of rhodamine-labeled DNA oligonucleotide duplexes have been used to determine equilibrium binding constants for DNA binding of the prokaryotic transcription activator protein NtrC. Measurements were made with wild-type NtrC from Escherichia...

journal_title：Nucleic acids research

authors： Sevenich FW,Langowski J,Weiss V,Rippe K

更新日期：1998-03-15 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：:Four pseudorevertants of a -10 region lacP mutation were isolated. Three of these mutations were found to activate nascent promoters. These mutations were: a -2 G/C----A/T change (-2A) promoting transcription at position +11, a +1 A/T----T/A change (+1T) promoting transcription initiation at position +13, and a +10 C/...

journal_title：Nucleic acids research

authors： Karls R,Schulz V,Jovanovich SB,Flynn S,Pak A,Reznikoff WS

更新日期：1989-05-25 00:00:00