The BCL2 gene is regulated by a special AT-rich sequence binding protein 1-mediated long range chromosomal interaction between the promoter and the distal element located within the 3'-UTR.

abstract：:Non-homologous end-joining (NHEJ) of DNA double-strand breaks (DSBs) is mediated by two protein complexes comprising Ku80/Ku70/DNA-PKcs/Artemis and XRCC4/LigaseIV/XLF. Loss of Ku or XRCC4/LigaseIV function compromises the rejoining of radiation-induced DSBs and leads to defective V(D)J recombination. In this study, we...

journal_title：Nucleic acids research

authors： Schulte-Uentrop L,El-Awady RA,Schliecker L,Willers H,Dahm-Daphi J

更新日期：2008-05-01 00:00:00

abstract：:MicroRNAs (miRNAs) are small non-coding RNAs of approximately 22 nucleotides, which negatively regulate the gene expression at the post-transcriptional level. This study describes an update of the miRTarBase (http://miRTarBase.mbc.nctu.edu.tw/) that provides information about experimentally validated miRNA-target inte...

journal_title：Nucleic acids research

authors： Chou CH,Chang NW,Shrestha S,Hsu SD,Lin YL,Lee WH,Yang CD,Hong HC,Wei TY,Tu SJ,Tsai TR,Ho SY,Jian TY,Wu HY,Chen PR,Lin NC,Huang HT,Yang TL,Pai CY,Tai CS,Chen WL,Huang CY,Liu CC,Weng SL,Liao KW,Hsu WL,Hu

更新日期：2016-01-04 00:00:00

abstract：:The availability of a draft human genome sequence and ability to monitor the transcription of thousands of genes with DNA microarrays has necessitated the need for new computational tools that can analyze cis-regulatory elements controlling genes that display similar expression patterns. We have developed a tool desig...

journal_title：Nucleic acids research

authors： Zhang H,Ramanathan Y,Soteropoulos P,Recce ML,Tolias PP

更新日期：2002-11-01 00:00:00

abstract：:Humans have two nearly identical copies of the survival motor neuron (SMN ) gene, SMN1 and SMN2. Homozygous loss of SMN1 causes spinal muscular atrophy (SMA). SMN2 is unable to prevent the disease due to skipping of exon 7. Using a systematic approach of in vivo selection, we have previously demonstrated that a weak 5...

journal_title：Nucleic acids research

authors： Singh NN,Singh RN,Androphy EJ

更新日期：2007-01-01 00:00:00

abstract：:Nucleotide excision DNA repair is mechanistically conserved across all kingdoms of life. In prokaryotes, this multi-enzyme process requires six proteins: UvrA-D, DNA polymerase I and DNA ligase. To examine how UvrC locates the UvrB-DNA pre-incision complex at a site of damage, we have labeled UvrB and UvrC with differ...

journal_title：Nucleic acids research

authors： Hughes CD,Wang H,Ghodke H,Simons M,Towheed A,Peng Y,Van Houten B,Kad NM

更新日期：2013-05-01 00:00:00

abstract：:The Genomes Online Database (GOLD) (https://gold.jgi.doe.gov) is a manually curated data management system that catalogs sequencing projects with associated metadata from around the world. In the current version of GOLD (v.6), all projects are organized based on a four level classification system in the form of a Stud...

journal_title：Nucleic acids research

authors： Mukherjee S,Stamatis D,Bertsch J,Ovchinnikova G,Verezemska O,Isbandi M,Thomas AD,Ali R,Sharma K,Kyrpides NC,Reddy TB

更新日期：2017-01-04 00:00:00

abstract：:The precursor to the Euglena light harvesting chlorophyll a/b binding protein of photosystem II (LHCPII) is a polyprotein containing multiple copies of LHCPII covalently joined by a decapeptide linker. cDNA and genomic clones encoding the 5' and 3' end of a 6.6 kb LHCPII mRNA were sequenced. A 3.1 kb genomic region en...

journal_title：Nucleic acids research

authors： Muchhal US,Schwartzbach SD

更新日期：1994-12-25 00:00:00

abstract：:RNA:5-methylcytosine (m5C) methyltransferases are currently the focus of intense research following a series of high-profile reports documenting their physiological links to several diseases. However, no methods exist which permit the specific analysis of RNA:m5C methyltransferases in cells. Herein, we described how a...

journal_title：Nucleic acids research

authors： Yang T,Low JJA,Woon ECY

更新日期：2020-01-10 00:00:00

abstract：:The specific function of RNA molecules frequently resides in their seemingly unstructured loop regions. We performed a systematic analysis of RNA loops extracted from experimentally determined three-dimensional structures of RNA molecules. A comprehensive loop-structure data set was created and organized into distinct...

journal_title：Nucleic acids research

authors： Schudoma C,May P,Nikiforova V,Walther D

更新日期：2010-01-01 00:00:00

abstract：:The Genome Database for Rosaceae (GDR, http:/www.rosaceae.org), the long-standing central repository and data mining resource for Rosaceae research, has been enhanced with new genomic, genetic and breeding data, and improved functionality. Whole genome sequences of apple, peach and strawberry are available to browse o...

journal_title：Nucleic acids research

authors： Jung S,Ficklin SP,Lee T,Cheng CH,Blenda A,Zheng P,Yu J,Bombarely A,Cho I,Ru S,Evans K,Peace C,Abbott AG,Mueller LA,Olmstead MA,Main D

更新日期：2014-01-01 00:00:00

abstract：:Mitochondrial DNA is a sensitive target of chemical carcinogens (Backer and Weinstein (1980) Science 209, 297-299), suggesting that mutations of the mitochondrial genome occur in tumor cells. We examined this point by comparing mitochondrial DNA sequences in four rat tumors with those of normal rat liver. Some novel m...

journal_title：Nucleic acids research

authors： Taira M,Yoshida E,Kobayashi M,Yaginuma K,Koike K

更新日期：1983-03-25 00:00:00

abstract：:Hidden Markov models (HMMs) and their variants are widely used in Bioinformatics applications that analyze and compare biological sequences. Designing a novel application requires the insight of a human expert to define the model's architecture. The implementation of prediction algorithms and algorithms to train the m...

journal_title：Nucleic acids research

authors： Lam TY,Meyer IM

更新日期：2009-11-01 00:00:00

abstract：:For the first time mosaic nucleic acids composed of 50% RNA and 50% DNA can be obtained as transcripts with T7 RNA polymerase. Two NTPs could be replaced simultaneously in a transcription reaction. This means more than 40 deoxynucleotides were inserted in one transcript. Previously, a maximum of two deoxynucleotides c...

journal_title：Nucleic acids research

authors： Conrad F,Hanne A,Gaur RK,Krupp G

更新日期：1995-06-11 00:00:00

abstract：:The RosettaDesign server identifies low energy amino acid sequences for target protein structures (http://rosettadesign.med.unc.edu). The client provides the backbone coordinates of the target structure and specifies which residues to design. The server returns to the client the sequences, coordinates and energies of ...

journal_title：Nucleic acids research

authors： Liu Y,Kuhlman B

更新日期：2006-07-01 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

authors： Kundrotas PJ,Zhu Z,Vakser IA

更新日期：2010-01-01 00:00:00

abstract：:DNA mismatches are highly polymorphic and dynamic in nature, albeit poorly characterized structurally. We utilized the antitumour antibiotic CoII(Chro)2 (Chro = chromomycin A3) to stabilize the palindromic duplex d(TTGGCGAA) DNA with two G:G mismatches, allowing X-ray crystallography-based monitoring of mismatch polym...

journal_title：Nucleic acids research

authors： Satange R,Chuang CY,Neidle S,Hou MH

更新日期：2019-09-19 00:00:00

abstract：:The response to amino acid (AA) limitation of the entire aminoacyl-tRNA synthetase (ARS) gene family revealed that 16/20 of the genes encoding cytoplasmic-localized enzymes are transcriptionally induced by activating transcription factor 4 (Atf4) via C/ebp-Atf-Response-Element (CARE) enhancers. In contrast, only 4/19 ...

journal_title：Nucleic acids research

authors： Shan J,Zhang F,Sharkey J,Tang TA,Örd T,Kilberg MS

更新日期：2016-11-16 00:00:00

abstract：:The binding of transcription factors to specific regulatory sequence elements is a primary mechanism for controlling gene transcription. Eukaryotic genes are often regulated by several transcription factors whose binding sites are tightly clustered and form cis-regulatory modules. In this paper, we present a web serve...

journal_title：Nucleic acids research

authors： Sharan R,Ben-Hur A,Loots GG,Ovcharenko I

更新日期：2004-07-01 00:00:00

abstract：:Telomeric DNAs consist of tandem repeats of G-clusters such as TTAGGG and TG1-3, which are the human and yeast repeat sequences, respectively. In the yeast Saccharomyces cerevisiae, the telomeric repeats are non-nucleosomal, whereas in humans, they are organized in tightly packaged nucleosomes. However, previous in vi...

journal_title：Nucleic acids research

authors： Ichikawa Y,Morohashi N,Nishimura Y,Kurumizaka H,Shimizu M

更新日期：2014-02-01 00:00:00

abstract：:It is well established that gene regulation can be achieved through activator and repressor proteins that bind to DNA and switch particular genes on or off, and that complex metabolic networks determine the levels of transcription of a given gene at a given time. Using three complementary computational techniques to s...

journal_title：Nucleic acids research

authors： Sutthibutpong T,Matek C,Benham C,Slade GG,Noy A,Laughton C,K Doye JP,Louis AA,Harris SA

更新日期：2016-11-02 00:00:00

abstract：:The DNA sequence of a 225.4 kilobase segment of the Escherichia coli K-12 genome is described here, from 76.0 to 81.5 minutes on the genetic map. This brings the total of contiguous sequence from the E.coli genome project to 725.1 kb (76.0 to 92.8 minutes). We found 191 putative coding genes (ORFs) of which 72 genes w...

journal_title：Nucleic acids research

authors： Sofia HJ,Burland V,Daniels DL,Plunkett G 3rd,Blattner FR

更新日期：1994-07-11 00:00:00

abstract：:The RNA bacteriophages of E. coli specifically encapsidate a single copy of the viral genome in a protein shell composed mainly of 180 molecules of coat protein. Coat protein is also a translational repressor and shuts off viral replicase synthesis by interaction with a RNA stem-loop containing the replicase initiatio...

journal_title：Nucleic acids research

authors： Pickett GG,Peabody DS

更新日期：1993-09-25 00:00:00

abstract：:Cytokines are cell-to-cell signaling proteins that play a central role in immune development, pathogen responses, and diseases. Cytokines are highly regulated at the transcriptional level by combinations of transcription factors (TFs) that recruit cofactors and the transcriptional machinery. Here, we mined through thr...

journal_title：Nucleic acids research

authors： Carrasco Pro S,Dafonte Imedio A,Santoso CS,Gan KA,Sewell JA,Martinez M,Sereda R,Mehta S,Fuxman Bass JI

更新日期：2018-10-12 00:00:00

abstract：:Adenine, thymine and cytosine PNA monomers have been prepared using 3-amino-1,2-propanediol as a starting material. The benzoyl group was used to protect the exocyclic amines of the heterocyclic bases of A and C PNA monomers and the backbone primary amine was protected with the monomethoxytrityl group. The thymine and...

journal_title：Nucleic acids research

authors： Finn PJ,Gibson NJ,Fallon R,Hamilton A,Brown T

更新日期：1996-09-01 00:00:00

abstract：:According to recent models, as yet poorly studied architectural proteins appear to be required for local regulation of enhancer-promoter interactions, as well as for global chromosome organization. Transcription factors ZIPIC, Pita and Zw5 belong to the class of chromatin insulator proteins and preferentially bind to ...

journal_title：Nucleic acids research

authors： Zolotarev N,Fedotova A,Kyrchanova O,Bonchuk A,Penin AA,Lando AS,Eliseeva IA,Kulakovskiy IV,Maksimenko O,Georgiev P

更新日期：2016-09-06 00:00:00

abstract：:We describe improve enzymatic methods for sequencing method for sequencing DNA. They are based on partial digestion of duplex DNA with exonuclease III to produce DNA molecules with 3' ends shortened to varying lengths, followed by repair synthesis to extend and label the 3' ends. After asymmetrical cleavage of the DNA...

journal_title：Nucleic acids research

authors： Guo LH,Wu R

更新日期：1982-03-25 00:00:00

abstract：:To explain biochemical and genetic data on spontaneous nucleotide replacements in nucleic acid biosynthesis all the 8 mispairs in normal tautomeric forms have been considered. Possible B-conformations of DNA fragments containing each of such mispairs incorporated between Watson-Crick pairs have been found using comput...

journal_title：Nucleic acids research

authors： Chuprina VP,Poltev VI

更新日期：1985-01-11 00:00:00

abstract：:SLM2 and Sam68 are splicing regulator paralogs that usually overlap in function, yet only SLM2 and not Sam68 controls the Neurexin2 AS4 exon important for brain function. Herein we find that SLM2 and Sam68 similarly bind to Neurexin2 pre-mRNA, both within the mouse cortex and in vitro. Protein domain-swap experiments ...

journal_title：Nucleic acids research

authors： Danilenko M,Dalgliesh C,Pagliarini V,Naro C,Ehrmann I,Feracci M,Kheirollahi-Chadegani M,Tyson-Capper A,Clowry GJ,Fort P,Dominguez C,Sette C,Elliott DJ

更新日期：2017-04-20 00:00:00

abstract：:FRS1 and FRS2, the structural genes encoding the large (alpha) and small (beta) subunits of yeast phenylalanyl-tRNA synthetase (PheRS) were placed under the control of the lacZ promoter by creating an artificial operon. The FRS2 gene was fused next to the promoter, followed by a 14 base pair intergenic sequence contai...

journal_title：Nucleic acids research

authors： Sanni A,Walter P,Ebel JP,Fasiolo F

更新日期：1990-04-25 00:00:00

abstract：:To investigate molecular controls of cardiomyocyte proliferation, we utilized cardiomyocytes induced to proliferate indefinitely by SV40 large T antigen (T-ag). In the T-ag-immortalized AT-1, AT-2 and HL-1 cardiomyocytes, normal cellular proteins associating with T-ag and p53 were identified, isolated and micro-sequen...

journal_title：Nucleic acids research

authors： Lanson NA Jr,Egeland DB,Royals BA,Claycomb WC

更新日期：2000-08-01 00:00:00