Abstract：
:Chromosome conformation-capture technologies are widely used in 3D genomics; however, experimentally, such methods have high-noise limitations and, therefore, require significant bioinformatics efforts to extract reliable distal interactions. Miscellaneous undesired linear DNAs, present during proximity-ligation, represent a main noise source, which needs to be minimized or eliminated. In this study, different exonuclease combinations were tested to remove linear DNA fragments from a circularized DNA preparation. This method efficiently removed linear DNAs, raised the proportion of annulation and increased the valid-pairs ratio from ∼40% to ∼80% for enhanced interaction detection in standard Hi-C. This strategy is applicable for development of various 3D genomics technologies, or optimization of Hi-C sequencing efficiency.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Kong S,Li Q,Zhang G,Li Q,Huang Q,Huang L,Zhang H,Huang Y,Peng Y,Qin B,Zhang Ydoi
10.1093/nar/gkaa106subject
Has Abstractpub_date
2020-05-07 00:00:00pages
e44issue
8eissn
0305-1048issn
1362-4962pii
5780087journal_volume
48pub_type
杂志文章abstract：:Analysis of phylogenetically conserved secondary structure has been important in the development of models for the secondary structure of structural RNAs. In this paper, we apply this type of analysis to several families of informational RNAs to evaluate its usefulness in developing secondary structure models for mRNA...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/13.23.8645
更新日期：1985-12-09 00:00:00
abstract：:The development of biosensors based on DNA hybridization requires a more precise knowledge of the thermodynamics of the hybridization at a solid interface. In particular, the selectivity of hybridization can be affected by a lot of parameters such as the single-strand (ss)DNA density, the pH, the ionic strength or the...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gng150
更新日期：2003-12-01 00:00:00
abstract：:Oxoguanine DNA glycosylase (OGG1) initiates the repair of 8-oxoguanine (8-oxoG), a major oxidative DNA base modification that has been directly implicated in cancer and aging. OGG1 functions in the base excision repair pathway, for which a molecular hand-off mechanism has been proposed. To date, only one functional an...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki636
更新日期：2005-06-07 00:00:00
abstract：:VL30 genetic elements constitute a murine multicopy gene family that is retrovirus-like, despite the lack of sequence homology with any known retrovirus. Over one hundred copies of VL30 units are dispersed throughout the mouse genome. We report here that the mouse genome also contains 'solo' VL30 long terminal repeats...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.5.2273
更新日期：1984-03-12 00:00:00
abstract：:Structural information on interacting proteins is important for understanding life processes at the molecular level. Genome-wide docking database is an integrated resource for structural studies of protein-protein interactions on the genome scale, which combines the available experimental data with models obtained by ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp944
更新日期：2010-01-01 00:00:00
abstract：:The "ovalbumin Y" gene, one of three which constitute the ovalbumin gene family in chicken has been completely sequenced. The exact location of exons can be derived from the comparison with the ovalbumin gene sequence and from the map previously established by electron microscopy analysis. During evolution of the Y ge...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.14.4363
更新日期：1982-07-24 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：:DNA damage tolerance (DDT) is responsible for genomic stability and cell viability by bypassing the replication block. In Saccharomyces cerevisiae DDT employs two parallel branch pathways to bypass the DNA lesion, namely translesion DNA synthesis (TLS) and error-free lesion bypass, which are mediated by sequential mod...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw183
更新日期：2016-06-20 00:00:00
abstract：:Reagents for proteome research must of necessity be generated by high throughput methods. Aptamers are potentially useful as reagents to identify and quantitate individual proteins, yet are currently produced for the most part by manual selection procedures. We have developed automated selection methods, but must stil...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gnf107
更新日期：2002-10-15 00:00:00
abstract：:Unmodified tRNA molecules are useful for many purposes in cell-free protein biosynthesis, but there is little information about how the lack of tRNA post-transcriptional modifications affects the coding specificity for synonymous codons. In the present study, we prepared an unmodified form of Escherichia coli tRNA1Ser...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.15.2894
更新日期：1996-08-01 00:00:00
abstract：:The chromatin structure of a germ-line specific gene, the TPG-3 gene, one of the rainbow trout protamine genes was analyzed in various tissues. The protamine genes are expressed in early stage testis but not in late stage testis, liver or erythrocyte. Five potential CpG methylation sites in the coding and flanking reg...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.8.3385
更新日期：1987-04-24 00:00:00
abstract：:With the improved rapid sequencing techniques, the earlier sequence of U2 RNA of Novikoff hepatoma (Shibata et al, J. Biol. Chem. 250, 3909-3920, 1975) was reanalyzed and modified. The improved sequence of U2 RNA is 188 (or 189) nucleotides long and is in register with a characterized U2 RNA pseudogene (Denison et al,...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.21.5645
更新日期：1981-11-11 00:00:00
abstract：:Eukaryotic cells use numerous pathways to regulate RNA production, localization and stability. Several of these pathways are controlled by ribonucleases. The essential ribonuclease, Dis3, plays important roles in distinct RNA metabolic pathways. Despite much progress in understanding general characteristics of the Dis...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq295
更新日期：2010-09-01 00:00:00
abstract：:A small family of DNA sequences is rearranged during the development of the somatic nucleus in Tetrahymena. The family is defined by 266 bp of highly conserved sequence which restriction mapping, hybridization and sequence analysis have shown is shared by a cloned micronuclear fragment and three sequences which consti...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.20.8007
更新日期：1986-10-24 00:00:00
abstract：:Arylsulfatase, produced by Chlamydomonas reinhardtii during sulfur-limited growth, is secreted into the periplasmic space and is readily assayed using a chromogenic substrate. To assess the usefulness of the gene encoding arylsulfatase (ars) as a reporter gene in C. reinhardtii, we have fused the promoter region of th...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.12.2959
更新日期：1992-06-25 00:00:00
abstract：:A sixty base pair DNA duplex containing the nucleotide sequence of the bacteriophage T5 early (T5P25) promoter has been constructed using a combination of chemical synthesis and enzymatic methods. Subsequent to cloning into pBR322, the promoter has been demonstrated to be biologically active being capable of directing...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.17.5921
更新日期：1983-09-10 00:00:00
abstract：:We have used computer assisted dot matrix and oligonucleotide frequency analyses to identify highly recurring sequence elements of 7-11 base pairs in eukaryotic genes and viral DNAs. Such elements are found much more frequently than expected, often with an average spacing of a few hundred base pairs. Furthermore, the ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.4.1835
更新日期：1987-02-25 00:00:00
abstract：:Telomeres play a central role in human cancer, cardiovascular aging and possibly longevity. However, present methods to measure telomere length are fraught with shortcomings that limit their use. Here, we describe a novel method to measure the relative telomere DNA content by dot blot analysis. In each dot, the DNA co...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr235
更新日期：2011-07-01 00:00:00
abstract：:PsiB protein of plasmid R6-5 inhibits the induction of the SOS pathway. The F sex factor also carries a psiB gene homologous to that of R6-5. Yet, it fails to inhibit SOS induction. In order to solve this difference, we characterized the psiB genes of R6-5 and F. We found that (i) the sequences of the two psiB genes s...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.22.10669
更新日期：1988-11-25 00:00:00
abstract：:In general, synthetic RNA transcripts corresponding to the 3' ends of Saccharomyces cerevisiae genes appear to be accurately cleaved and polyadenylated in vitro under appropriate conditions in yeast cell extracts. Initially, however, the endpoints observed in vitro for the GAL7 gene failed to correlate adequately with...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.13.3683
更新日期：1991-07-11 00:00:00
abstract：:We present a new coarse grained method for the simulation of duplex DNA. The algorithm uses a generalized multi-harmonic model that can represent any multi-normal distribution of helical parameters, thus avoiding caveats of current mesoscopic models for DNA simulation and representing a breakthrough in the field. The ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa015
更新日期：2020-03-18 00:00:00
abstract：:Protein synthesis elongation factor 2 (EF-2) from all archaebacteria so far analysed, is susceptible to inactivation by diphtheria toxin, a property which it shares with EF-2 from the eukaryotic 8OS translation system. To resolve the structural basis of diphtheria toxin susceptibility, the structural gene for the EF-2...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.16.7817
更新日期：1988-08-25 00:00:00
abstract：:The centromere is a highly specialized chromosomal element that is essential for chromosome segregation during mitosis. Centromere integrity must therefore be properly preserved and is strictly dependent upon the establishment and maintenance of surrounding chromatin structure. Here we identify WDHD1, a WD40-domain an...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq1338
更新日期：2011-05-01 00:00:00
abstract：:Immature oocytes from Xenopus laevis contain a 42S ribonucleoprotein particle (RNP) containing 5S RNA, tRNA, a 43 kDa protein, and a 48 kDa protein. A particle containing 5S RNA and the 43 kDa protein (p43-5S) liberated from the 42S particle upon brief treatment with urea can be purified by anion exchange chromatograp...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.8.1797
更新日期：1991-04-25 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：:In silico prediction of transcription factor binding sites (TFBSs) is central to the task of gene regulatory network elucidation. Genomic DNA sequence information provides a basis for these predictions, due to the sequence specificity of TF-binding events. However, DNA sequence alone is an impoverished source of infor...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn866
更新日期：2009-01-01 00:00:00
abstract：:The Retinol-Binding Protein (RBP) is expressed primarily in the liver. The regulatory elements involved in its tissue-specific expression have been identified and mapped to the 5' flanking region of the RBP gene. In this paper heterokaryons and somatic cell-hybrids have been produced and analysed in order to demonstra...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.24.7235
更新日期：1990-12-25 00:00:00
abstract：:Current knowledge of parameters affecting RNA stability is very restricted in plants. Here we investigated factors which might contribute to the stability of a particular plant messenger RNA. To this end, insertion and deletion mutants were made in two different exons and an intron of the transcribed region of a well ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.10.2917
更新日期：1990-05-25 00:00:00
abstract：:Non-radioactive nucleic acid hybridization probes have been constructed in which the reporter group is long chain biotin chemically linked to a basic macromolecule (histone H1, cytochrome C or polyethyleneimine). The modified basic macromolecule which carries many biotin residues can, in turn, be covalently linked to ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.24.9965
更新日期：1986-12-22 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
