Abstract：
:The recent publication of the Caenorhabditis elegans cisRED database has provided an extensive catalog of upstream elements that are conserved between nematode genomes. We have performed a secondary analysis to determine which subsequences of the cisRED motifs are found in multiple locations throughout the C. elegans genome. We used the word-counting motif discovery algorithm DME to form the motifs into groups based on sequence similarity. We then examined the genes associated with each motif group using DAVID and Ontologizer to determine which groups are associated with genes that also have significant functional associations in the Gene Ontology and other gene annotation sources. Of the 3265 motif groups formed, 612 (19%) had significant functional associations with respect to GO terms. Eight of the first 20 motif groups based on frequent dodecamers among the cisRED motif sequences were specifically associated with ribosomal protein genes; two of these were similar to mouse EBP-45, rat HNF3-family and Drosophila Zeste transcription factor binding sites. Additionally, seven motif groups were extensions of the canonical C. elegans trans-splice acceptor site. One motif group was tested for regulatory function in a series of green fluorescent protein expression experiments and was shown to be involved in pharyngeal expression.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Sleumer MC,Mah AK,Baillie DL,Jones SJdoi
10.1093/nar/gkq003subject
Has Abstractpub_date
2010-05-01 00:00:00pages
2990-3004issue
9eissn
0305-1048issn
1362-4962pii
gkq003journal_volume
38pub_type
杂志文章abstract：:A flow-injection (FI) device is combined, through the use of a low-volume (4 microl) flow cell, with an ultrasensitive surface plasmon resonance (SPR) spectrometer equipped with a bi-cell photodiode detector. The application of this novel FI-SPR device for sequence-specific ultratrace analysis of oligodeoxynucleotides...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gnf072
更新日期：2002-07-15 00:00:00
abstract：:The database of 3D interacting domains (3did) is a collection of protein interactions for which high-resolution 3D structures are known. 3did exploits structural information to provide the crucial molecular details necessary for understanding how protein interactions occur. Besides interactions between globular domain...
journal_title：Nucleic acids research
pub_type： 杂志文章
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更新日期：2009-01-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.7.1600
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki919
更新日期：2005-10-24 00:00:00
abstract：:The major immediate early regulatory region of human cytomegalovirus (HCMV) has a complex set of DNA sites through which both cellular and viral factors coordinately regulate immediate early gene expression. In undifferentiated human teratocarcinoma (T2) cells we have previously shown that major immediate early gene e...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.8.1767
更新日期：1991-04-25 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky519
更新日期：2019-02-20 00:00:00
abstract：:Archaeal family-B DNA polymerases bind tightly to deaminated bases and stall replication on encountering uracil in template strands, four bases ahead of the primer-template junction. Should the polymerase progress further towards the uracil, for example, to position uracil only two bases in front of the junction, 3'-5...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks1364
更新日期：2013-02-01 00:00:00
abstract：:Members of the basic helix-loop-helix (bHLH) family of transcription factors regulate a wide array of developmental processes in many cell types, including cell fate specification, differentiation and morphogenesis. Our studies describe the cloning of a gene from the nematode Caenorhabditis elegans that is closely rel...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.21.4423
更新日期：2001-11-01 00:00:00
abstract：:A linear method for the search of eukaryotic nuclear tRNA genes in DNA databases is described. Based on a modified version of the general weight matrix procedure, our algorithm relies on the recognition of two intragenic control regions known as A and B boxes, a transcription termination signal, and on the evaluation ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.7.1247
更新日期：1994-04-11 00:00:00
abstract：:We present the preparation of an ion exchange paper which can be used as a solid carrier in the transfer of RNA from gels. In addition to detection by blot hybridization to specific probes, transferred RNA can be characterized by cell-free translation in situ. Preparation of the paper is simple, inexpensive and reprod...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.16.4831
更新日期：1982-08-25 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.1.373
更新日期：1989-01-11 00:00:00
abstract：:We have investigated the mechanism of the electrophoresis-driven chromatin aggregation which had been described by Weintraub (1984, Cell 38, 17-27) as a putative mean for propagation of genetic repression in eukaryotes. We show that the oligonucleosome aggregates are assembled de novo at the starting zone of DNP elect...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.24.7397
更新日期：1990-12-25 00:00:00
abstract：:The ASTRAL compendium provides several databases and tools to aid in the analysis of protein structures, particularly through the use of their sequences. It is partially derived from the SCOP database of protein domains, and it includes sequences for each domain as well as other resources useful for studying these seq...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/30.1.260
更新日期：2002-01-01 00:00:00
abstract：:A repeat sequence 682 base pairs (bp) long produced by cleavage of human DNA with Xba I restriction enzyme is composed of four tandemly arranged subunits with lengths of 171, 170, 171, and 170 bp each. The sequence organization of the 682 bp Xba I repeat bears a striking resemblance to other complex satellite DNAs of ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/13.2.521
更新日期：1985-01-25 00:00:00
abstract：:The CD spectra of twelve DNA restriction fragments ranging in size from 12 to 360 base pairs are reported. Since the sequences of these fragments are known, it is possible to calculate their CD spectra from a set of nearest neighbor contributions derived from a combination of synthetic polydeoxyribonucleotides. While ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.13.3029
更新日期：1981-07-10 00:00:00
abstract：:The enterovirus 71 (EV71) 3Dpol is an RNA-dependent RNA polymerase (RdRP) that plays the central role in the viral genome replication, and is an important target in antiviral studies. Here, we report a crystal structure of EV71 3Dpol elongation complex (EC) at 1.8 Å resolution. The structure reveals that the 5'-end gu...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz1170
更新日期：2020-02-20 00:00:00
abstract：:VA RNA(I) is a non-coding adenoviral transcript that counteracts the host cell anti-viral defenses such as immune responses mediated via PKR. We investigated potential alternate secondary structure conformations within the PKR-binding domain of VA RNA(I) using site-directed mutagenesis, RNA UV-melting analysis and enz...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp595
更新日期：2009-09-01 00:00:00
abstract：:We examined the 3'-flanking regions required for accurate 3'-end formation of wheat histone H3 mRNA using gene expression in transformed sunflower cells. The introduction of mutations into the conserved sequence AATGGAAATG in the 3'-flanking region of plant histone genes, located 22 bp upstream from the polyadenylatio...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.6.1052
更新日期：1994-03-25 00:00:00
abstract：:mRNA deadenylation is under the control of cis-acting regulatory elements, which include AU-rich elements (AREs) and microRNA (miRNA) targeting sites, within the 3' untranslated region (3' UTRs) of eukaryotic mRNAs. Deadenylases promote miRNA-induced mRNA decay through their interaction with miRNA-induced silencing co...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv959
更新日期：2015-12-15 00:00:00
abstract：:Sequential chromatin immunoprecipitation (SeqChIP) is a procedure in which formaldehyde-crosslinked, protein-DNA complexes from living cells are subjected to two sequential immunoprecipitations with antibodies of different specificity. SeqChIP has been used to address, in a qualitative manner, whether two proteins can...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gnh148
更新日期：2004-11-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky199
更新日期：2018-04-20 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky386
更新日期：2018-06-20 00:00:00
abstract：:A number of cysteine-rich proteins have recently been isolated by homology screening, differential library screens, and association with other proteins. In this report, we describe the isolation of the rat cysteine-rich protein from a rat brain library during a search for clones with homology to the delta-opioid recep...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.24.5477
更新日期：1994-12-11 00:00:00
abstract：:Direct visualization of DNA and proteins allows researchers to investigate DNA-protein interactions with great detail. Much progress has been made in this area as a result of increasingly sensitive single-molecule fluorescence techniques. At the same time, methods that control the conformation of DNA molecules have be...
journal_title：Nucleic acids research
pub_type： 杂志文章,评审
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更新日期：2008-08-01 00:00:00
abstract：:Heteroduplexes between the viral DNA of phiX174 and DNA from the replicative form (RF) of phage G4 were examined by electron microscopy. The single Eco RI site of G4-RF was utilized as a physical marker by preparing the heteroduplexes from the denatured, linear DNA obtained by restricting G4-RF with Eco RI endonucleas...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/6.5.1979
更新日期：1979-01-01 00:00:00
abstract：:Primase synthesizes decaribonucleotides for priming of lagging and possibly leading strand synthesis at a replication fork. The sites of initiation by purified mouse primase were shown to be highly specific within the SV40 origin of replication. This study further examines the role of the 27-bp inverted repeat in the ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.5.1953
更新日期：1989-03-11 00:00:00
abstract：:The Integrated Microbial Genomes (IMG) system serves as a community resource for comparative analysis of publicly available genomes in a comprehensive integrated context. IMG integrates publicly available draft and complete genomes from all three domains of life with a large number of plasmids and viruses. IMG provide...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr1044
更新日期：2012-01-01 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
pub_type： 杂志文章
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更新日期：2017-11-16 00:00:00
abstract：:The InParanoid eukaryotic ortholog database (http://InParanoid.sbc.su.se/) has been updated to version 6 and is now based on 35 species. We collected all available 'complete' eukaryotic proteomes and Escherichia coli, and calculated ortholog groups for all 595 species pairs using the InParanoid program. This resulted ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm1020
更新日期：2008-01-01 00:00:00
abstract：:We have used DNase I footprinting to examine the association kinetics of GA-, GT- and CT-containing oligonucleotides with the target sequence (GGA)5GG. (CCT)5CC. These reactions are slow yielding bimolecular association rate constants between 50 and 2000 M-1s-1. We find that GT-containing oligonucleotides bind much fa...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.16.3269
更新日期：1997-08-15 00:00:00
