Abstract:
:Mitochondrial DNA (mtDNA) is entirely dependent on nuclear genes for its transcription and replication. One of these genes is TOP1MT, which encodes the mitochondrial DNA topoisomerase IB, involved in mtDNA relaxation. To elucidate TOP1MT regulation, we performed genome-wide profiling across the 60-cell line panel (the NCI-60) of the National Cancer Institute Developmental Therapeutics Program. We show that TOP1MT mRNA expression varies widely across these cell lines with the highest levels in leukemia (HL-60, K-562) and melanoma (SK-MEL-28), intermediate levels in breast (MDA-MB-231), ovarian (OVCAR) and colon (HCT-116, HCT-15, KM-12), and lowest levels in renal (ACHN, A498), prostate (PC-3, DU-145) and central nervous system cell lines (SF-539, SF-268, SF-295). Genome-wide analyses show that TOP1MT expression is significantly correlated with the other mitochondrial nuclear-encoded genes including the mitochondrial nucleoid genes, and demonstrate an overall co-regulation of the mitochondrial nuclear-encoded genes. We also find very high correlation between the expression of TOP1MT and the proto-oncogene MYC (c-myc). TOP1MT contains E-boxes (c-myc binding sites) and TOP1MT transcription follows MYC up- and down-regulation by MYC promoter activation and siRNA against MYC. Our finding implicates MYC as a novel regulator of TOP1MT and confirms its role as a master regulator of MNEGs and mitochondrial nucleoids.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Zoppoli G,Douarre C,Dalla Rosa I,Liu H,Reinhold W,Pommier Ydoi
10.1093/nar/gkr208subject
Has Abstractpub_date
2011-08-01 00:00:00pages
6620-32issue
15eissn
0305-1048issn
1362-4962pii
gkr208journal_volume
39pub_type
杂志文章abstract::The nucleotide excision repair pathway removes ultraviolet (UV) photoproducts from the human genome in the form of short oligonucleotides ∼ 30 nt in length. Because there are limitations to many of the currently available methods for investigating UV photoproduct repair in vivo, we developed a convenient non-radioisot...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1179
更新日期:2014-02-01 00:00:00
abstract::An oligodeoxyribonucleotide, d(GCTCACAAT-X-ATTGTGAGC), where X represents a hexaethylene glycol chain, was studied using circular dichroism spectroscopy. Its conformation and conformational stability were compared to those of compounds where X was replaced by four thymines and to the duplex of same sequence without lo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.21.6353
更新日期:1990-11-11 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::In order to facilitate the direct computation of the sizes of DNA fragments separated by gel electrophoresis, we have written and evaluated programmes for the Hewlett-Packard 41C programmable calculator. The sizes estimated for DNA fragments of known length using some of these programmes were found to be more accurate...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.1part2.845
更新日期:1984-01-11 00:00:00
abstract::R.E.D. Server is a unique, open web service, designed to derive non-polarizable RESP and ESP charges and to build force field libraries for new molecules/molecular fragments. It provides to computational biologists the means to derive rigorously molecular electrostatic potential-based charges embedded in force field l...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr288
更新日期:2011-07-01 00:00:00
abstract::MODPROPEP is a web server for knowledge-based modeling of protein-peptide complexes, specifically peptides in complex with major histocompatibility complex (MHC) proteins and kinases. The available crystal structures of protein-peptide complexes in PDB are used as templates for modeling peptides of desired sequence in...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm266
更新日期:2007-07-01 00:00:00
abstract::The distribution and amount of 5-methylcytosine (5-MeCyt) in DNA was measured for early embryos of mouse strain CF1 (2 to 4 cell stage to blastocyst) and mouse teratocarcinoma cells. In each case, the pattern of methylation was examined by use of the restriction enzymes Hha I and HPA II HPA II, which cut DNA at the si...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/7.8.2369
更新日期:1979-12-20 00:00:00
abstract::The PathoSystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics Resource Center funded by the National Institute of Allergy and Infectious Diseases (https://www.patricbrc.org). PATRIC supports bioinformatic analyses of all bacteria with a special emphasis on pathogens, offering a rich comparative...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz943
更新日期:2020-01-08 00:00:00
abstract::Alternative splicing (AS) and alternative polyadenylation (APA) generate diverse transcripts in mammalian genomes during development and differentiation. Epigenetic marks such as trimethylation of histone H3 lysine 36 (H3K36me3) and DNA methylation play a role in generating transcriptome diversity. Intragenic CpG isla...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa556
更新日期:2020-09-04 00:00:00
abstract::A previously elaborated technique for fixing a chosen partially melted state of DNA with glyoxal was used in a study of the melting process of the replicative form (RF III) of phi X174 DNA. Electron-microscopic maps corresponding to five points of the melting curve of RF III were obtained and compared with the theoret...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.6.1867
更新日期:1982-03-25 00:00:00
abstract::Here, we describe two freely available web servers for molecular docking. The PatchDock method performs structure prediction of protein-protein and protein-small molecule complexes. The SymmDock method predicts the structure of a homomultimer with cyclic symmetry given the structure of the monomeric unit. The inputs t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki481
更新日期:2005-07-01 00:00:00
abstract::The principles of mRNA decoding are conserved among all extant life forms. We present an integrative view of all the interaction networks between mRNA, tRNA and rRNA: the intrinsic stability of codon-anticodon duplex, the conformation of the anticodon hairpin, the presence of modified nucleotides, the occurrence of no...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/gkw608
更新日期:2016-09-30 00:00:00
abstract::Synthesis of a small amount of 42S RNA in addition to the VSV specific mRNA species was observed in a coupled transcription-translation system containing ribonucleoprotein particles from L cell infected with vesicular stomatitis virus and nuclease-treated ribosomal extract obtained from uninfected HeLa cells. Analysis...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.20.6341
更新日期:1982-10-25 00:00:00
abstract::DNA polymerase mu is a member of the mammalian pol X family and reduces deletion during chromosome break repair by nonhomologous end joining (NHEJ). This biological role is linked to pol mu's ability to promote NHEJ of ends with noncomplementary 3' overhangs, but questions remain regarding how it performs this role. W...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn164
更新日期:2008-05-01 00:00:00
abstract::The engineering of new enzymes that efficiently and specifically modify DNA sequences is necessary for the development of enhanced gene therapies and genetic studies. To address this need, we developed a robust strategy for evolving site-specific recombinases with novel substrate specificities. In this system, recombi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq125
更新日期:2010-07-01 00:00:00
abstract::A linear method for the search of eukaryotic nuclear tRNA genes in DNA databases is described. Based on a modified version of the general weight matrix procedure, our algorithm relies on the recognition of two intragenic control regions known as A and B boxes, a transcription termination signal, and on the evaluation ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.7.1247
更新日期:1994-04-11 00:00:00
abstract::In the last decade polycistronic vectors have become essential tools for both basic science and gene therapy applications. In order to co-express heterologous polypeptides, different systems have been developed from Internal Ribosome Entry Site (IRES) based vectors to the use of the 2A peptide. Unfortunately, these me...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp716
更新日期:2009-11-01 00:00:00
abstract::The rates of acid-catalyzed hydrolysis of a hypermodified nucleoside, wyosine and its 5'-monophosphate were determined at various pH, temperature and buffer concentrations. The results show that despite distinct differences in structure and the glycosyl bond stability, the hydrolysis of wyosine proceeds via cleavage o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.7.2443
更新日期:1985-04-11 00:00:00
abstract::Live-cell measurement of protein binding to chromatin allows probing cellular biochemistry in physiological conditions, which are difficult to mimic in vitro. However, different studies have yielded widely discrepant predictions, and so it remains uncertain how to make the measurements accurately. To establish a bench...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks701
更新日期:2012-08-01 00:00:00
abstract::The mammalian target of rapamycin (mTOR) is a critical regulator of cell growth, integrating multiple signalling cues and pathways. Key among the downstream activities of mTOR is the control of the protein synthesis machinery. This is achieved, in part, via the co-ordinated regulation of mRNAs that contain a terminal ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa1189
更新日期:2021-01-11 00:00:00
abstract::U4 RNA from chicken, rat and man was examined for nucleotide sequence and secondary structure. Three molecular species, U4A, U4B and U4C were detected in the three animal species. U4A is 146 nucleotide long and U4B RNA only lacks the 3' terminal G. four nucleotides are missing at the 3'-end of U4C RNA which, in additi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.12.2699
更新日期:1981-06-25 00:00:00
abstract::The analysis of chromatin fine structure and transcription factor occupancy of differentially expressed genes by in vivo footprinting and ligation-mediated-PCR (LMPCR) is a powerful tool to understand the impact of chromatin on gene expression. However, as with all PCR-based techniques, the accuracy of the experiments...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm1159
更新日期:2008-02-01 00:00:00
abstract::Human ADAR3 is a catalytically inactive member of the Adenosine Deaminase Acting on RNA (ADAR) protein family, whose active members catalyze A-to-I RNA editing in metazoans. Until now, the reasons for the catalytic incapability of ADAR3 has not been defined and its biological function rarely explored. Yet, its exclusi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz815
更新日期:2019-11-18 00:00:00
abstract::We have constructed and tested several new vectors for P element-mediated gene transfer. These vectors contain restriction sites for cloning a wide variety of DNA fragments within a small, non-autonomous P element and can be used to efficiently transduce microinjected DNA sequences into the germ line chromosomes of D....
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.18.6341
更新日期:1983-09-24 00:00:00
abstract::CeR-2 RNA is one of the newly identified Caenorhabditis elegans noncoding RNAs (ncRNAs). The characterization of CeR-2 by RNomic studies has failed to classify it into any known ncRNA family. In this study, we examined the spatiotemporal expression patterns of CeR-2 to gain insight into its function. CeR-2 is expresse...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq335
更新日期:2010-09-01 00:00:00
abstract::Members of the basic helix-loop-helix (bHLH) family of transcription factors regulate a wide array of developmental processes in many cell types, including cell fate specification, differentiation and morphogenesis. Our studies describe the cloning of a gene from the nematode Caenorhabditis elegans that is closely rel...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.21.4423
更新日期:2001-11-01 00:00:00
abstract::A single locus in the mouse, rat and chicken encodes both alkali myosin light chains, MLC1F and MLC3F. This gene has two distinct promoters and gives rise to two different primary transcripts, which are processed by alternative and different modes of splicing to form MLC1F and MLC3F mRNAs. The MLC1F/MLC3F gene is very...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.13.4623
更新日期:1985-07-11 00:00:00
abstract::Melanotransferrin (MTf) is a tumor associated antigen found in abundance on the surface of melanoma cells. It is a transferrin-like protein found in low amount in most adult tissues and whose gene is reminiscent of house-keeping genes. With the goal of understanding the regulatory mechanisms which might explain the en...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.11.2853
更新日期:1992-06-11 00:00:00
abstract::A problem in EST clustering is the presence of repeat sequences. To avoid false matches, repeats have to be masked. This can be a time-consuming process, and it depends on available repeat libraries. We present a fast and effective method that aims to eliminate the problems repeats cause in the process of clustering. ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki511
更新日期:2005-04-14 00:00:00
abstract::Two different genomic genes for the COUP-transcription factor, COUP-TF I and COUP-TF II, have been isolated from a human cosmid genomic library using a [32P]-labeled cDNA probe. Data obtained from Southern blot analysis of these cosmid clones indicated that two closely related genes exist in the human genome and have ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.23.6857
更新日期:1990-12-11 00:00:00