Abstract：
:Cell surface mannose 6-phosphate/insulin-like growth factor II receptors (M6P/IGF2R) bind and target exogenous insulin-like growth factor II (IGF2) to the prelysosomes where it is degraded. Loss of heterozygosity (LOH) for M6P/IGF2R is found in cancers, with mutational inactivation of the remaining allele. We exploited the normal allele-specific differential methylation of the M6P/IGF2R intron 2 CpG island to rapidly evaluate potential LOH in ovarian cancers, since every normal individual is informative. To this end, we developed a method for bisulfite modification of genomic DNA in 96-well format that allows for rapid methylation profiling. We identified ovarian cancers with M6P/IGF2R LOH, but unexpectedly also found frequent abnormal acquisition of methylation on the paternally inherited allele at intron 2. These results demonstrate the utility of our high-throughput method of bisulfite modification for analysis of large sample numbers. They further show that the methylation status of the intron 2 CpG island may be a useful indicator of LOH and biomarker of disease.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Huang Z,Wen Y,Shandilya R,Marks JR,Berchuck A,Murphy SKdoi
10.1093/nar/gkj468keywords:
subject
Has Abstractpub_date
2006-01-23 00:00:00pages
555-63issue
2eissn
0305-1048issn
1362-4962pii
34/2/555journal_volume
34pub_type
杂志文章abstract：:A 15-residue sequence motif has been found in many polymerases from various species and involving DNA and RNA dependence and product. The motif is characterized by a Tyr-Gly-Asp-(Thr)-Asp core flanked by hydrophobic spans five residues in length. An mRNA maturase segment is also suggested to display the motif pattern....
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.21.9909
更新日期：1988-11-11 00:00:00
abstract：:Mixed-lineage leukemia (MLL) maintains the expression of cellular memory genes during development, while leukemic MLL fusion proteins aberrantly maintain expression of hematopoietic stem cell program genes such as HOXA9 to cause leukemia. However, the molecular mechanism of gene activation is unclear. Here we show tha...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt1394
更新日期：2014-04-01 00:00:00
abstract：:The 'POU' (acronym of Pit-1, Oct-1, Unc-86) family of transcription factors share a common DNA-binding domain of approximately 160 residues, comprising so-called 'POUs' and 'POUh' sub-domains connected by a flexible linker. The importance of POU proteins as developmental regulators and tumor-promoting agents is due to...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm453
更新日期：2007-01-01 00:00:00
abstract：:Several authors have suggested or inferred that modest changes in microRNA expression can potentiate or impinge on their capacity to mediate gene repression, and that doing so could play a significant role in diseases. Such interpretations are based on several assumptions, namely: (i) changes in microRNA expression co...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv720
更新日期：2015-09-03 00:00:00
abstract：:Emerging evidence suggests that recombinant adeno-associated viral (rAAV) vectors can be used for specific gene targeting in human somatic cells. We have developed an rAAV vector construction procedure employing fusion PCR and a single cloning step that considerably simplifies the knockout process. We demonstrate its ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gnh009
更新日期：2004-01-02 00:00:00
abstract：:Toscana virus is an emerging bunyavirus in Mediterranean Europe where it accounts for 80% of pediatric meningitis cases during the summer. The negative-strand ribonucleic acid (RNA) genome of the virus is wrapped around the virally encoded nucleoprotein N to form the ribonucleoprotein complex (RNP). We determined crys...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku229
更新日期：2014-05-01 00:00:00
abstract：:As large-scale re-sequencing of genomes reveals many protein mutations, especially in human cancer tissues, prediction of their likely functional impact becomes important practical goal. Here, we introduce a new functional impact score (FIS) for amino acid residue changes using evolutionary conservation patterns. The ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr407
更新日期：2011-09-01 00:00:00
abstract：:The Bovine Genome Database (BGD) (http://bovinegenome.org) has been the key community bovine genomics database for more than a decade. To accommodate the increasing amount and complexity of bovine genomics data, BGD continues to advance its practices in data acquisition, curation, integration and efficient data retrie...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz944
更新日期：2020-01-08 00:00:00
abstract：:Since 2010, the Genomicus web server is available online at http://genomicus.biologie.ens.fr/genomicus. This graphical browser provides access to comparative genomic analyses in four different phyla (Vertebrate, Plants, Fungi, and non vertebrate Metazoans). Users can analyse genomic information from extant species, as...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx1003
更新日期：2018-01-04 00:00:00
abstract：:Multifunctional proteins challenge the conventional 'one protein-one function' paradigm. Here we note apparent multifunctional proteins with nucleic acid partners, tabulating eight examples. We then focus on eight additional cases of transcription factors that bind double-stranded DNA with sequence specificity, but th...
journal_title：Nucleic acids research
pub_type： 杂志文章,评审
doi：10.1093/nar/gkf512
更新日期：2002-10-01 00:00:00
abstract：:Using synthetic oligodeoxyribonucleotides to prime the transcription of interferon mRNA and cDNA, we recently determined the mRNA sequence coding for the 47 amino-terminal amino acids of mature human fibroblast interferon (1). From this sequence, we have now synthesised an oligodeoxyribonucleotide that is homologous w...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/8.13.2885
更新日期：1980-07-11 00:00:00
abstract：:Poly (ADP-ribose) polymerase 1 (PARP1) has emerged as an attractive target for cancer therapy due to its key role in DNA repair processes. Inhibition of PARP1 in BRCA-mutated cancers has been observed to be clinically beneficial. Recent genome-mapping experiments have identified a non-canonical G-quadruplex-forming se...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky1179
更新日期：2019-02-20 00:00:00
abstract：:We previously found that the splicing of exon 5 to exon 6 in the rat beta-TM gene required that exon 6 first be joined to the downstream common exon 8 (Helfman et al., Genes and Dev. 2, 1627-1638, 1988). Pre-mRNAs containing exon 5, intron 5 and exon 6 are not normally spliced in vitro. We have carried out a mutationa...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.12.2318
更新日期：1994-06-25 00:00:00
abstract：:Bile acid biosynthesis is subjected to feedback regulation whereby bile acids down-regulate their own synthesis. The major point of this regulation is at the level of cholesterol 7alpha-hydroxylase (7alpha-hydroxylase), which controls bile acid output from the classic pathway. This regulation is at the level of transc...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.18.3587
更新日期：2000-09-15 00:00:00
abstract：:CTCF plays a pivotal role in mediating chromatin interactions, but it does not do so alone. A number of factors have been reported to co-localize with CTCF and regulate CTCF loops, but no comprehensive analysis of binding partners has been performed. This prompted us to identify CTCF loop participants and regulators b...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa705
更新日期：2020-09-25 00:00:00
abstract：:Ribosome recycling factor (RRF), elongation factor G (EF-G) and GTP split 70S ribosomes into subunits. Here, we demonstrated that the splitting was transient and the exhaustion of GTP resulted in re-association of the split subunits into 70S ribosomes unless IF3 (initiation factor 3) was present. However, the splittin...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn647
更新日期：2008-12-01 00:00:00
abstract：:The coiled-coil coactivator (CoCoA) is a transcriptional coactivator for nuclear receptors and enhances nuclear receptor function by the interaction with the bHLH-PAS domain (AD3) of p160 coactivators. The C-terminal activation domain (AD) of CoCoA possesses strong transactivation activity and is required for the coac...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl361
更新日期：2006-05-22 00:00:00
abstract：:Camptothecin (CPT), a plant alkaloid with antitumor activity, is a specific inhibitor of eukaryotic DNA topoisomerase I. We have previously isolated and characterized a CPT-resistant topoisomerase I isolated from a CPT-resistant human leukemia cell line, CPT-K5. cDNA clones of topoisomerase I were isolated from the CP...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.1.69
更新日期：1991-01-11 00:00:00
abstract：:We describe conditions for producing uninterrupted expanded CTG repeats consisting of up to 2000 repeats using 29 DNA polymerase. Previously, generation of such repeats was hindered by CTG repeat instability in plasmid vectors maintained in Escherichia coli and poor in vitro ligation of CTG repeat concatemers due to s...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn025
更新日期：2008-03-01 00:00:00
abstract：:Puromycin, an analog of the 3' end of aminoacyl-tRNA, causes premature termination of translation by being linked non-specifically to growing polypeptide chains. Here we report the interesting phenomenon that puromycin acting as a non-inhibitor at very low concentration (e.g. 0.04 microM) can bond only to full-length ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.5.1176
更新日期：2000-03-01 00:00:00
abstract：:Despite two decades of study, the full scope of RNAi in mammalian cells has remained obscure. Here we combine: (i) Knockout of argonaute (AGO) variants; (ii) RNA sequencing analysis of gene expression changes and (iii) Enhanced Crosslinking Immunoprecipitation Sequencing (eCLIP-seq) using anti-AGO2 antibody to identif...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa478
更新日期：2020-07-27 00:00:00
abstract：:Previous studies have shown that (i) several RNAs induced by heat shock of Drosophila melanogaster cells are homologous to tandemly repeated alpha beta units found in cloned segments of D. melanogaster DNA, and (ii) the alpha beta sequences are present both at a major heat shock locus, 87Cl, and the chromocenter of po...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.20.5297
更新日期：1981-10-24 00:00:00
abstract：:Dimerization of HIV-1 genomic RNA is an essential step of the viral cycle, initiated at a conserved stem-loop structure which forms a 'kissing complex' involving loop-loop interactions (dimerization initiation site, DIS). A 19mer RNA oligonucleotide (DIS-19) has been synthesized which forms a stable symmetrical dimer ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.15.3567
更新日期：1998-08-01 00:00:00
abstract：:The function of non-coding RNA genes largely depends on their secondary structure and the interaction with other molecules. Thus, an accurate prediction of secondary structure and RNA-RNA interaction is essential for the understanding of biological roles and pathways associated with a specific RNA gene. We present web...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr248
更新日期：2011-07-01 00:00:00
abstract：:The role of Ribonuclease H1 (RNase H1) during primer removal and ligation at the mitochondrial origin of light-strand DNA synthesis (OriL) is a key, yet poorly understood, step in mitochondrial DNA maintenance. Here, we reconstitute the replication cycle of L-strand synthesis in vitro using recombinant mitochondrial p...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky708
更新日期：2018-10-12 00:00:00
abstract：:Unfolding of the nucleosomes in transcriptionally active chromatin uncovers the sulfhydryl groups of histone H3 and permits the selective recovery of the unfolded nucleosomes by mercury-affinity chromatography. This new technique has been used to compare the nucleosomal proteins and their postsynthetic modifications i...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.11.4375
更新日期：1987-06-11 00:00:00
abstract：:E2F transcription factors (E2F1-8) are known to coordinately regulate the expression of a plethora of target genes, including those coding for microRNAs (miRNAs), to control cell cycle progression. Recent work has described the atypical E2F factor E2F7 as a transcriptional repressor of cell cycle-related protein-codin...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw146
更新日期：2016-07-08 00:00:00
abstract：:We have used gel retardation analysis to show that human DNA topoisomerase IIbeta can bind a 40 bp linear duplex containing a single DNA topoisomerase IIbeta cleavage site. Furthermore, we demonstrate for the first time that human DNA topoisomerase IIbeta binds to four-way junction DNA. This supports previous suggesti...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.4.984
更新日期：1999-02-15 00:00:00
abstract：:We have sequenced the genome of Shigella flexneri serotype 2a, the most prevalent species and serotype that causes bacillary dysentery or shigellosis in man. The whole genome is composed of a 4 607 203 bp chromosome and a 221 618 bp virulence plasmid, designated pCP301. While the plasmid shows minor divergence from th...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkf566
更新日期：2002-10-15 00:00:00
abstract：:DNA predominantly contains Watson-Crick (WC) base pairs, but a non-negligible fraction of base pairs are in the Hoogsteen (HG) hydrogen bonding motif at any time. In HG, the purine is rotated ∼180° relative to the WC motif. The transitions between WC and HG may play a role in recognition and replication, but are diffi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz837
更新日期：2019-12-02 00:00:00
