Abstract：
:Histone modifications are fundamental to chromatin structure and transcriptional regulation, and are recognized by a limited number of protein folds. Among these folds are PHD fingers, which are present in most chromatin modification complexes. To date, about 15 PHD finger domains have been structurally characterized, whereas hundreds of different sequences have been identified. Consequently, an important open problem is to predict structural features of a PHD finger knowing only its sequence. Here, we classify PHD fingers into different groups based on the analysis of residue-residue co-evolution in their sequences. We measure the degree to which fixing the amino acid type at one position modifies the frequencies of amino acids at other positions. We then detect those position/amino acid combinations, or 'conditions', which have the strongest impact on other sequence positions. Clustering these strong conditions yields four families, providing informative labels for PHD finger sequences. Existing experimental results, as well as docking calculations performed here, reveal that these families indeed show discrepancies at the functional level. Our method should facilitate the functional characterization of new PHD fingers, as well as other protein families, solely based on sequence information.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Slama P,Geman Ddoi
10.1093/nar/gkq947subject
Has Abstractpub_date
2011-03-01 00:00:00pages
1666-79issue
5eissn
0305-1048issn
1362-4962pii
gkq947journal_volume
39pub_type
杂志文章abstract：:Escherichia coli Exonuclease I (ExoI) digests single-stranded DNA (ssDNA) in the 3'-5' direction in a highly processive manner. The crystal structure of ExoI, determined previously in the absence of DNA, revealed a C-shaped molecule with three domains that form a central positively charged groove. The active site is a...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt278
更新日期：2013-06-01 00:00:00
abstract：:Human cells are, in general, poor recipients of foreign DNA, which has severely hampered the cloning of genes by direct phenotypic correction of deficient human cell lines after DNA mediated gene transfer. In this communication a methodology is presented which largely circumvents this problems. The method relies on th...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.18.4861
更新日期：1991-09-25 00:00:00
abstract：:Lateral ribosomal stalk is responsible for binding and recruiting translation factors during protein synthesis. The eukaryotic stalk consists of one P0 protein with two copies of P1•P2 heterodimers to form a P0(P1•P2)₂ pentameric P-complex. Here, we have solved the structure of full-length P1•P2 by nuclear magnetic re...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt636
更新日期：2013-10-01 00:00:00
abstract：:Mitochondrial-DNA diseases have no effective treatments. Allotopic expression-synthesis of a wild-type version of the mutated protein in the nuclear-cytosolic compartment and its importation into mitochondria-has been proposed as a gene-therapy approach. Allotopic expression has been successfully demonstrated in yeast...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq769
更新日期：2011-01-01 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
pub_type： 杂志文章
doi：10.1093/nar/gkt216
更新日期：2013-05-01 00:00:00
abstract：:Recently published alignments of available 5 S rRNA sequences have shown that a rigid base pairing pattern, pointing to the existence of a universal five-helix secondary structure for all 5 S RNAs, can be superimposed on such alignments. For a few species, the alignment and the base pairing pattern show distortions wi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.5.1245
更新日期：1983-03-11 00:00:00
abstract：:Daunomycin is one of the most important agents used in anticancer chemotherapy. It interacts with DNA through intercalation of its planar chromophore between successive base pairs. The effect of intercalation on structure, dynamics and energetics is the topic of a wealth of scientific studies. In the present study, we...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh788
更新日期：2004-09-01 00:00:00
abstract：:The task of gene identification frequently confronting researchers working with both novel and well studied genomes can be conveniently and reliably solved with the help of the GeneMark web software (http://opal.biology.gatech.edu/GeneMark/). The website provides interfaces to the GeneMark family of programs designed ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki487
更新日期：2005-07-01 00:00:00
abstract：:The frequencies of occurrence of four bases in the first, second and third codon positions and in the total coding sequences have been calculated by the codon usage table published in 1990 by Ikemura et al. The distribution of frequencies are further analysed in detail by a graphic technique presented recently by us. ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.22.6313
更新日期：1991-11-25 00:00:00
abstract：:Alternative splicing of pre-mRNA generates protein diversity. Dysfunction of splicing machinery and expression of specific transcripts has been linked to cancer progression and drug response. Exon microarray technology enables genome-wide quantification of expression levels of the majority of exons and facilitates the...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr513
更新日期：2011-10-01 00:00:00
abstract：:MobA protein, encoded by the broad host-range plasmid R1162, is required for conjugal mobilization of this plasmid. The protein is an essential part of the relaxosome, and is also necessary for the termination of strand transfer. In vitro, MobA is a nuclease specific for one of the two DNA strands of the origin of tra...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.19.4563
更新日期：1993-09-25 00:00:00
abstract：:Proteins that catalyse homologous recombination have been identified in all living organisms and are essential for the repair of damaged DNA as well as for the generation of genetic diversity. In bacteria homologous recombination is performed by the RecA protein, whereas in the eukarya a related protein called Rad51 i...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.22.4509
更新日期：2001-11-15 00:00:00
abstract：:The replication origin region of the Escherichia coli K-12 chromosome has been cloned, and a region of 245 base-pairs has been shown to contain all the information for autonomous replication (defined ori). In order to obtain further information on the sequence organization in the defined ori stretch, various types of ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.12.3745
更新日期：1982-06-25 00:00:00
abstract：:We have used a polymerase chain reaction (PCR) procedure to analyse low abundance complementary sense RNAs of Digitaria streak virus (DSV) from infected leaves of Digitaria setigera. This study has confirmed that both spliced and unspliced RNAs are synthesised by the same transcription unit. The position of the intron...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.24.7259
更新日期：1990-12-25 00:00:00
abstract：:The RNA of a deleted strain (lacking Src gene) of an avian sarcoma virus (ASV) was examined by a newly developed immunoelectron microscopic procedure which uses anti-nucleotide antibodies as probes. After denaturation of the RNA and reaction with a high affinity, highly specific anti-7-methylguanosine-5'-phosphate (an...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/8.19.4485
更新日期：1980-10-10 00:00:00
abstract：:TcruziDB (http://TcruziDB.org) is an integrated genome database for the parasitic organism Trypanosoma cruzi, the causative agent of Chagas' disease. The database currently incorporates all available sequence data (Genomic, BAC, EST) in a single user-friendly location. The database contains a variety of tools specific...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh049
更新日期：2004-01-01 00:00:00
abstract：:Here we describe a two-stepped photobiotin-based procedure to enrich a target (canine retinal) cDNA library for tissue specific clones without removing those containing repetitive ( SINE ) elements, despite the presence of these elements in the driver population. In a first hybridization excess SINE elements were hybr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.21.4427
更新日期：1997-11-01 00:00:00
abstract：:Virulence factor database (VFDB) was set up in 2004 dedicated for providing current knowledge of virulence factors (VFs) from various medical significant bacterial pathogens to facilitate pathogenomic research. Nowadays, complete genome sequences of almost all the major pathogenic microbes have been determined, which ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm951
更新日期：2008-01-01 00:00:00
abstract：:Site-specific DNA double-strand breaks have been used to generate knock-in through the homology-dependent or -independent pathway. However, low efficiency and accompanying negative impacts such as undesirable indels or tumorigenic potential remain problematic. In this study, we present an enhanced reduced-risk genome ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa195
更新日期：2020-06-04 00:00:00
abstract：:Protein species interacting with newly replicated DNA were analyzed using a photo cross-linking technique. Nascent DNA was labeled in vitro with [alpha-32P]dCTP and BrdUTP in SV40-infected CV-1 cells made permeable with saponin. The labeled cells were then irradiated with UV light (254 nm) and were treated extensively...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.14.4793
更新日期：1983-07-25 00:00:00
abstract：:Explicit solvent molecular dynamics (MD) was used to describe the intrinsic flexibility of the helix 42-44 portion of the 23S rRNA (abbreviated as Kt-42+rGAC; kink-turn 42 and GTPase-associated center rRNA). The bottom part of this molecule consists of alternating rigid and flexible segments. The first flexible segmen...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm245
更新日期：2007-01-01 00:00:00
abstract：:A positive cis-acting DNA element in the near 5'-upstream region of the CYP2B1/B2 genes in rat liver was found to play an important role in the transcription of these genes. An oligonucleotide covering -69 to -98 nt mimicked the gel mobility shift pattern given by the fragment -179 to +29 nt, which was earlier found a...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.3.557
更新日期：1992-02-11 00:00:00
abstract：:Differential scanning microcalorimetry (DSC), UV absorption and circular dichroism (CD) have been used to study structure and stability of linear (lin), open circular (oc), supercoiled (cd) and relaxed circular duplex (rd) DNA and calf thymus (CT) DNA. Investigations were made in low salt buffer and in the presence of...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.24.11737
更新日期：1988-12-23 00:00:00
abstract：:In this report, we provide an update on the services and content which are available on the web server of IBM's Bioinformatics and Pattern Discovery group. The server, which is operational around the clock, provides access to a large number of methods that have been developed and published by the group's members. Ther...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh367
更新日期：2004-07-01 00:00:00
abstract：:The leaf senescence database (LSD) is a comprehensive resource of senescence-associated genes (SAGs) and their corresponding mutants. Through manual curation and extensive annotation, we updated the LSD to a new version LSD 3.0, which contains 5853 genes and 617 mutants from 68 species. To provide sustainable and reli...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz898
更新日期：2020-01-08 00:00:00
abstract：:Detecting recombinations in the genome sequence of human immunodeficiency virus (HIV-1) is crucial for epidemiological studies and for vaccine development. Herein, we present a web server for subtyping and localization of phylogenetic breakpoints in HIV-1. Our software is based on a jumping profile Hidden Markov Model...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl255
更新日期：2006-07-01 00:00:00
abstract：:Differential melting profiles and denaturation maps are calculated for fdDNA whose sequence of nucleotides has been determined recently. The melting profiles for the total DNA and a number of its restriction fragments are compared with experimental data taken from literature. The comparison enables one to correlate a ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/5.7.2547
更新日期：1978-07-01 00:00:00
abstract：:The mode of action of regulated promoters is largely determined by kinetic parameters which govern the interaction between promoters and proteins involved in induction and repression of transcription. To gain insight into the interplay between positively and negatively acting transcriptional regulators, in this case A...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.18.3873
更新日期：2001-09-15 00:00:00
abstract：:GenBank (R) is a comprehensive database that contains publicly available nucleotide sequences for more than 260 000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the web-based BankIt or st...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm929
更新日期：2008-01-01 00:00:00
abstract：:Influenza viruses have a segmented viral RNA (vRNA) genome, which is replicated by the viral RNA-dependent RNA polymerase (RNAP). Replication initiates on the vRNA 3' terminus, producing a complementary RNA (cRNA) intermediate, which serves as a template for the synthesis of new vRNA. RNAP structures show the 3' termi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw884
更新日期：2016-12-01 00:00:00
