Abstract:
:Aberrant CpG methylation changes occurring during tumour progression include the loss (hypomethylation) and gain (hypermethylation) of methyl groups. Techniques currently available for examining such changes either require selection of a region, then examination of methylation changes, or utilise methylation-sensitive restriction enzymes to identify an alteration. We describe here a novel method that identifies genomic regions as a consequence of altered methylation during tumourigenesis. A methyl-CpG binding domain column isolates methylated GC-rich sequences from both tumours and surrounding normal tissue. Subsequent subtractive hybridisation removes sequences common to both, leaving only methylated sequences unique to the tumour. Libraries of sequences generated using DNA derived from a breast tumour (histological grade; poorly differentiated) as 'tester' and from matched normal tissue as 'driver' were examined; 26% of clones had the sequence criteria of a CpG island (CGI). Analysis using the bisulfite technique revealed that a number of these sequences were methylated in tumour DNA relative to the normal control. We have therefore demonstrated the ability of this technique, the identification of CGI exhibiting altered methylation patterns (ICEAMP), to isolate tumour-specific methylated GC-rich sequences. This will allow a comprehensive identification of methylation changes during tumourigenesis and will lead to a better understanding of the processes involved.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Brock GJ,Huang TH,Chen CM,Johnson KJdoi
10.1093/nar/29.24.e123keywords:
subject
Has Abstractpub_date
2001-12-15 00:00:00pages
E123issue
24eissn
0305-1048issn
1362-4962journal_volume
29pub_type
杂志文章abstract::Staphylococcus aureus plasmid pT181 is thought to replicate via an asymmetric rolling-circle mechanism. By studying pulse labeled replicative intermediates, here we report that pT181 replication involves: (1) a post-replicative hypersupercoiled monomer and (2) a partially replicated intermediate which lacks superhelic...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.7.2897
更新日期:1988-04-11 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::We report here on a quantitative technique called COBRA to determine DNA methylation levels at specific gene loci in small amounts of genomic DNA. Restriction enzyme digestion is used to reveal methylation-dependent sequence differences in PCR products of sodium bisulfite-treated DNA as described previously. We show t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.12.2532
更新日期:1997-06-15 00:00:00
abstract::A high molecular weight reticulocyte protein factor, named Co-eIF-2, contains Co-eIF-2A, Co-eIF-2B, and Co-eIF-2C activities and stimulates Met-tRNAf binding to eIF-2 both in the presence and absence of Mg2+. Some characteristics of this stimulation in the absence of Mg2+ are: (1) Stimulation is most pronounced at low...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.20.6501
更新日期:1982-10-25 00:00:00
abstract::Although subtelomeric regions in humans are heterochromatic, the epigenetic nature of human telomeres remains controversial. This controversy might have been influenced by the confounding effect of subtelomeric regions and interstitial telomeric sequences (ITSs) on telomeric chromatin structure analyses. In addition, ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky006
更新日期:2018-03-16 00:00:00
abstract::We have used photo-crosslinking to investigate the structure and dynamics of four-way junction hairpin ribozyme constructs. Four phenylazide photo-crosslinkers were coupled to 2'-NH2-modified U+2 in the substrate and irradiated at different Mg2+ concentrations and temperatures. Consistent with the role of divalent met...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki237
更新日期:2005-02-18 00:00:00
abstract::The nucleoside analogs 1-(2'-deoxy-beta-D-ribofuranosyl)- 3-nitropyrrole (9), 1-(2'-deoxy-beta-D-ribofuranosyl)-4-nitropyrazole (10), 1-(2'-deoxy-beta-D-ribofuranosyl)-4-nitroimidazole (11) and 1-(2'-deoxy-beta-D-ribofuranosyl)-5-nitroindole (21) were incorporated into the oligonucleotide 5'-d(CGCXAATTYGCG)-3'in the f...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.10.1935
更新日期:1997-05-15 00:00:00
abstract::Thyroid hormone receptors (TRs) are members of the nuclear hormone receptor superfamily, which act as transcription factors upon binding to specific DNA sequences called thyroid hormone (T3) response elements (TREs). Such elements are found in the upstream regulatory region of promoters as well as in intragenic sequen...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.9.1774
更新日期:1997-05-01 00:00:00
abstract::Expansions of (GAA)n repeats within the first intron of the frataxin gene reduce its expression, resulting in a hereditary neurodegenerative disorder, Friedreich's ataxia. While it is generally believed that expanded (GAA)n repeats block transcription elongation, fine mechanisms responsible for gene repression are not...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl1140
更新日期:2007-01-01 00:00:00
abstract::The thyroid hormone receptor alpha (THRA or c-erbA-1) gene belongs to a family of genes which encode nuclear receptors for various hydrophobic ligands such as steroids, vitamin D, retinoic acid and thyroid hormones. These receptors are composed of several domains important for hormone-binding, DNA-binding, dimerizatio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.5.1105
更新日期:1991-03-11 00:00:00
abstract::Bloom's syndrome helicase (BLM) is a member of the RecQ family of DNA helicases, which play key roles in the maintenance of genome integrity in all organism groups. We describe crystal structures of the BLM helicase domain in complex with DNA and with an antibody fragment, as well as SAXS and domain association studie...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv373
更新日期:2015-05-26 00:00:00
abstract::Cis-elements (-933 to -641) upstream of the human M creatine kinase gene cap site contain an enhancer that confers developmental and tissue-specific expression to the chloramphenicol acetyltransferase gene in C2C12 myogenic cells transfected in culture. Division of the enhancer at -770 into a 5' fragment that includes...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.9.2313
更新日期:1992-05-11 00:00:00
abstract::We have examined the absorption and circular dichroism spectra of intact Penicillium chrysogenum virus, empty capsid particles, and isolated double-stranded RNA. The absorbance at 260 nm of intact virus was less than 4% hypochromic relative to the absorbances of the free double-stranded RNA and free viral protein, ind...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.1.175
更新日期:1983-01-11 00:00:00
abstract::Plant specialized metabolites are chemically highly diverse, play key roles in host-microbe interactions, have important nutritional value in crops and are frequently applied as medicines. It has recently become clear that plant biosynthetic pathway-encoding genes are sometimes densely clustered in specific genomic lo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx305
更新日期:2017-07-03 00:00:00
abstract::Crotonaldehyde is a representative alpha,beta-unsaturated aldehyde endowed of mutagenic and carcinogenic properties related to its propensity to react with DNA. Cyclic crotonaldehyde-derived deoxyguanosine (CrA-PdG) adducts can undergo ring opening in duplex DNA to yield a highly reactive aldehydic moiety. Here, we de...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn334
更新日期:2008-07-01 00:00:00
abstract::Interactive Tree Of Life (http://itol.embl.de) is a web-based tool for the display, manipulation and annotation of phylogenetic trees. It is freely available and open to everyone. In addition to classical tree viewer functions, iTOL offers many novel ways of annotating trees with various additional data. Current versi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr201
更新日期:2011-07-01 00:00:00
abstract::Partial restriction digestion is used to map restriction sites and the location of genes within yeast artificial chromosomes (YACs). Locus-specific probes are hybridised to the partially digested YAC DNA and the fragments to which they hybridise are compared with the pattern of partial digestion products that include ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.22.4495
更新日期:1996-11-15 00:00:00
abstract::The helical twist of poly d(A-s4T) was determined from the periodicity of the cleavage patterns of the double stranded polydeoxynucleotide adsorbed on calcium phosphate and found to be 14 bp per turn. Both cleavage patterns and 31P NMR spectra indicate a mononucleotide structure rather than an alternating B DNA like p...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.5.2241
更新日期:1986-03-11 00:00:00
abstract::From a library of nucleic acid molecules, which are randomized in parts of their sequence, unique sequence variants can be selected for specific properties. The planning of such an in vitro selection experiment requires some consideration regarding how much DNA template or RNA transcript should be used initially. The ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.17.3437
更新日期:1996-09-01 00:00:00
abstract::Conventional chemotherapy remains the primary treatment option for triple-negative breast cancer (TNBC). However, the current chemotherapeutic drugs have limited effects on TNBC, and often lead to serious side effects as well as drug resistance. Thus, more effective therapeutic options are sorely needed. As c-MYC onco...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz835
更新日期:2019-11-18 00:00:00
abstract::The 5' portions and flanking sequences of genes encoding types 1, 12, 24, and 6 M proteins were compared. Although the DNA sequences encoding the amino-termini of the mature M proteins had no obvious similarity, upstream sequences, and those encoding the signal peptides (leader sequences) of the four M protein genes h...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.10.4667
更新日期:1988-05-25 00:00:00
abstract::Escherichia coli mRNA translation is facilitated by sequences upstream and downstream of the initiation codon, called Shine-Dalgarno (SD) and downstream box (DB) sequences, respectively. In E.coli enhancing the complementarity between the DB sequences and the 16S rRNA penultimate stem resulted in increased protein acc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.4.970
更新日期:2001-02-15 00:00:00
abstract::Several derivatives of N2,N2-7-trimethylguanosine (m3(2,2,7G)-cap, which was found at the 5' ends of small nuclear RNAs, were synthesized by use of S-phenyl N2,N2,7-trimethylguanosine 5'-phosphorothioate (PhSpm3(2,2,7)G) as a key intermediate. This compound was activated by iodine in the presence of phosphoric acid an...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.22.8979
更新日期:1989-11-25 00:00:00
abstract::The replication control circuit of the FII plasmids R1, R100 and R6-5 involves a small untranslated RNA molecule of about 93 nucleotides. This RNA, designated CopA RNA in plasmid R1, acts in vivo as a post-transcriptional inhibitor of the expression of the RepA protein whose synthesis is required for each round of pla...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.6.2523
更新日期:1986-03-25 00:00:00
abstract::A mutation in a gene dicA of Escherichia coli leads to temperature-sensitive cell division, by allowing expression of a nearby division inhibition gene dicB (1). We have now established the sequence of the DicA region and identified DicA as a 15.5 KD protein. A second gene dicC transcribed divergently from dicA and co...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.17.6821
更新日期:1986-09-11 00:00:00
abstract::Chromatin fragments released from intact Friend erythroleukemia cell nuclei during limited incubation with micrococcal nuclease, DNase II or DNase I were analyzed to determine the distribution of DNA methyltransferase in chromatin. The enzyme was released in a free form when internucleosomal DNA was digested with micr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.20.5359
更新日期:1981-10-24 00:00:00
abstract::LOCtarget is a web server and database that predicts and annotates sub-cellular localization for structural genomics targets; LOCnet is one of the methods used in LOCtarget that can predict sub-cellular localization for all eukaryotic and prokaryotic proteins. Targets are taken from the central registration database f...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh441
更新日期:2004-07-01 00:00:00
abstract::Tumor formation is partially driven by DNA copy number changes, which are typically measured using array comparative genomic hybridization, SNP arrays and DNA sequencing platforms. Many techniques are available for detecting recurring aberrations across multiple tumor samples, including CMAR, STAC, GISTIC and KC-SMART...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt155
更新日期:2013-05-01 00:00:00
abstract::Cellular senescence, an integral component of aging and cancer, arises in response to diverse triggers, including telomere attrition, macromolecular damage and signaling from activated oncogenes. At present, senescent cells are identified by the combined presence of multiple traits, such as senescence-associated prote...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz555
更新日期:2019-08-22 00:00:00
abstract::A single base change in 16S rRNA (C726 to G) has previously been shown to have a dramatic effect on protein synthesis in E. coli (1). This paper more specifically details the effects of the mutation on mRNA binding and translation-termination. The in vitro technique of toeprinting (2) was used to demonstrate that 30S ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.18.5381
更新日期:1990-09-25 00:00:00