Abstract:
:The spatio-temporal organization of chromatin in the eukaryotic cell nucleus is of vital importance for transcription, DNA replication and genome maintenance. Each of these activities is tightly regulated in both time and space. While we have a good understanding of chromatin organization in space, for example in fixed snapshots as a result of techniques like FISH and Hi-C, little is known about chromatin dynamics in living cells. The rapid development of flexible genomic loci imaging approaches can address fundamental questions on chromatin dynamics in a range of model organisms. Moreover, it is now possible to visualize not only single genomic loci but the whole genome simultaneously. These advances have opened many doors leading to insight into several nuclear processes including transcription and DNA repair. In this review, we discuss new chromatin imaging methods and how they have been applied to study transcription.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Shaban HA,Seeber Adoi
10.1093/nar/gkaa135subject
Has Abstractpub_date
2020-04-17 00:00:00pages
3423-3434issue
7eissn
0305-1048issn
1362-4962pii
5775307journal_volume
48pub_type
杂志文章,评审abstract::PUF proteins, named for Drosophila Pumilio (PUM) and Caenorhabditis elegans fem-3-binding factor (FBF), recognize specific sequences in the mRNAs they bind and control. RNA binding by classical PUF proteins is mediated by a characteristic PUM homology domain (PUM-HD). The Puf1 and Puf2 proteins possess a distinct arch...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz583
更新日期:2019-09-19 00:00:00
abstract::The sequence of the 356 nucleotide residues of chrysanthemum stunt viroid (CSV) has been determined. Overlapping linear viroid fragments were obtained by partial ribonuclease digestion, radiolabelled in vitro at their 5'-ends, and sequenced using partial enzymic cleavage methods. Of the CSV sequence, 69% is contained ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.12.2741
更新日期:1981-06-25 00:00:00
abstract::Transcription termination defines accurate transcript 3'-ends and ensures programmed transcriptomes, making it critical to life. However, transcription termination mechanisms remain largely unknown in Archaea. Here, we reported the physiological significance of the newly identified general transcription termination fa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa702
更新日期:2020-09-25 00:00:00
abstract::Extensive efforts have been directed at the discovery, investigation and clinical monitoring of targeted therapeutics. These efforts may be facilitated by the convenient access of the genetic, proteomic, interactive and other aspects of the therapeutic targets. Here, we describe an update of the Therapeutic target dat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1076
更新日期:2018-01-04 00:00:00
abstract::Originally identified as an RNA polymerase II interactor, Che-1/AATF (Che-1) has now been recognized as a multifunctional protein involved in cell-cycle regulation and cancer progression, as well as apoptosis inhibition and response to stress. This protein displays a peculiar nucleolar localization and it has recently...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa344
更新日期:2020-06-19 00:00:00
abstract::In bacteria, promoter identification by RNA polymerase is mediated by a dissociable σ factor. The housekeeping σ(70) factor of Escherichia coli recognizes two well characterized DNA sequence elements, known as the '-10' and '-35' hexamers. These elements are separated by 'spacer' DNA, the sequence of which is generall...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr080
更新日期:2011-07-01 00:00:00
abstract::A terminator of transcription with bidirectional activity has been located between the translation termination codons of the genes tetA and orfL on Tn10. These genes are transcribed towards each other. Each orientation of the intervening sequence is shown to reduce the expression of the lacZ and galK genes when cloned...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.12.4227
更新日期:1985-06-25 00:00:00
abstract::Ribosome biogenesis is a dynamic multistep process, many features of which are still incompletely documented. Here, we show that changes in this pathway can be captured and annotated by means of a graphic set of pre-rRNA ratios, a technique we call Ratio Analysis of Multiple Precursors (RAMP). We find that knocking do...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku787
更新日期:2014-01-01 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::Uridylation-dependent RNA decay is a widespread eukaryotic pathway modulating RNA homeostasis. Terminal uridylyltransferases (Tutases) add untemplated uridyl residues to RNA 3'-ends, marking them for degradation by the U-specific exonuclease Dis3L2. In Schizosaccharomyces pombe, Cid1 uridylates a variety of RNAs. In t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz043
更新日期:2019-04-08 00:00:00
abstract:UNLABELLED:Synonymous codon usage biases are associated with various biological factors, such as gene expression level, gene length, gene translation initiation signal, protein amino acid composition, protein structure, tRNA abundance, mutation frequency and patterns, and GC compositions. Quantification of codon usage ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm392
更新日期:2007-07-01 00:00:00
abstract::The ability of the tumor suppressor protein, p53, to recognize certain types of DNA lesions may represent one of the mechanisms by which this protein modulates cellular response to DNA damage. p53 DNA binding properties are regulated by several factors, such as post-translational modifications including phosphorylatio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.11.2427
更新日期:2002-06-01 00:00:00
abstract::Single-stranded DNA-binding proteins (SSBs) support DNA replication by protecting single-stranded DNA from nucleolytic attack, preventing intra-strand pairing events and playing many other regulatory roles within the replisome. Recent developments in single-molecule approaches have led to a revised picture of the repl...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz090
更新日期:2019-05-07 00:00:00
abstract::In the process of establishing more and more complete annotations of eukaryotic genomes, a constantly growing number of alternative splicing (AS) events has been reported over the last decade. Consequently, the increasing transcript coverage also revealed the real complexity of some variations in the exon-intron struc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm311
更新日期:2007-07-01 00:00:00
abstract::Nuclear factors NF90 and NF45 form a complex involved in a variety of cellular processes and are thought to affect gene expression both at the transcriptional and translational level. In addition, this complex affects the replication of several viruses through direct interactions with viral RNA. NF90 and NF45 dimerize...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks696
更新日期:2012-10-01 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
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl665
更新日期:2006-01-01 00:00:00
abstract::Here we describe a method of labelling short oligonucleotide probes with enzyme without purification or chemical modifications. Biotinylated oligonucleotides as short as 10 nt are coupled with streptavidin-conjugated enzyme, hybridised and detected with enzyme-triggered chemiluminescence. The detection of hybridisatio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.2.703
更新日期:1999-01-15 00:00:00
abstract::Peptides of defined length carrying a diazirine photoaffinity label attached either to the alpha-NH2 group of the N-terminal methionine residue, or to the epsilon-NH2 group of an immediately adjacent lysine residue, were prepared in situ on Escherichia coli ribosomes in the presence of a synthetic mRNA analogue. Pepti...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.8.1394
更新日期:1994-04-25 00:00:00
abstract::Bacillus subtilis OhrR is a dimeric repressor that senses organic peroxides and regulates the expression of the OhrA peroxiredoxin. Derepression results from oxidation of an active site cysteine which ultimately results in formation of a mixed disulfide with a low molecular weight thiol, a cyclic sulfenamide, or overo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn1052
更新日期:2009-03-01 00:00:00
abstract::Approaches to characterize the nucleic acid-binding properties of drugs and druglike small molecules are crucial to understanding the behavior of these compounds in cellular systems. Here, we use a Small Molecule Microarray (SMM) profiling approach to identify the preferential interaction between chlorhexidine, a wide...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky084
更新日期:2018-04-06 00:00:00
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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
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.14.6617
更新日期:1988-07-25 00:00:00
abstract::In order to direct antisense oligonucleotides to specific tissues or cell types in vivo, we are exploring the possibility to utilize lipoproteins as transport vehicles. A 16-mer oligonucleotide (ODN) was derivatized at the 5' prime through a 32P phosphate spacer with cholesterol, yielding a 32P-labeled amphiphatic cho...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.17.4695
更新日期:1991-09-11 00:00:00
abstract::The DNA sequence was determined for the narL gene of Escherichia coli. This gene is involved in global regulation of a number of nitrate controlled genes including frdABCD, tor, narGHJI, and adhE which are associated with bacterial respiration and fermentation. Comparison of the deduced amino acid sequence of narL to ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.5.1965
更新日期:1989-03-11 00:00:00
abstract::Retroviral particles contain a dimeric RNA genome, which serves as template for the generation of double-stranded DNA by reverse transcription. Transfer between RNA strands during DNA synthesis is governed by both sequence similarity between templates and structural features of the dimeric RNA. A kissing hairpin, beli...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh159
更新日期:2004-01-09 00:00:00
abstract::A cDNA clone covering the whole coding region for a glycinin subunit precursor containing the A1a acidic subunit, one of the A2 family, has been identified from a library of soybean cotyledonary cDNA clones using a mixed oligonucleotide probe. Analysis of the cDNA insert revealed that it contained 1746 nucleotides of ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.18.6719
更新日期:1985-09-25 00:00:00
abstract::Tunable induction of gene expression is an essential tool in biology and biotechnology. In spite of that, current induction systems often exhibit unpredictable behavior and performance shortcomings, including high sensitivity to transactivator dosage and plasmid take-up variation, and excessive consumption of cellular...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky795
更新日期:2018-10-12 00:00:00
abstract::The availability of protein fluorophores with appropriate spectral properties has made it possible to employ fluorescence resonance energy transfer (FRET) to assess interactions between three proteins microscopically. Flow cytometry offers excellent sensitivity, effective signal separation and the capacity to assess a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gni057
更新日期:2005-04-01 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.1.95
更新日期:1999-01-01 00:00:00