Programmed genome rearrangements in Oxytricha produce transcriptionally active extrachromosomal circular DNA.

abstract：:The conserved bacterial anticodon nuclease (ACNase) RloC and its phage-excluding homolog PrrC comprise respective ABC-adenosine triphosphatase (ATPase) and ACNase N- and C-domains but differ in three key attributes. First, prrC is always linked to an ACNase silencing, DNA restriction-modification (R-M) locus while rlo...

journal_title：Nucleic acids research

authors： Klaiman D,Steinfels-Kohn E,Krutkina E,Davidov E,Kaufmann G

更新日期：2012-09-01 00:00:00

abstract：:Peptidome similarity analysis enables researchers to gain insights into differential peptide profiles, providing a robust tool to discriminate strain-specific peptides, true intra-species differences among biological replicates or even microorganism-phenotype variations. However, no in silico peptide fingerprinting so...

journal_title：Nucleic acids research

authors： Blanco-Míguez A,Fdez-Riverola F,Lourenço A,Sánchez B

更新日期：2017-07-03 00:00:00

abstract：:The anaerobically-regulated nirB promoter was used to express heterologous genes in Escherichia coli. Under anaerobic conditions the promoter was able to express tetanus toxin fragment C at approximately 20% total cell protein (tcp) and the Bordetella pertussis antigen pertactin at greater than 30% tcp. These levels a...

journal_title：Nucleic acids research

authors： Oxer MD,Bentley CM,Doyle JG,Peakman TC,Charles IG,Makoff AJ

更新日期：1991-06-11 00:00:00

abstract：:Recognition of DNA by proteins depends on DNA sequence and structure. Often unanswered is whether the structure of naked DNA persists in a protein-DNA complex, or whether protein binding changes DNA shape. While X-ray structures of protein-DNA complexes are numerous, the structure of naked cognate DNA is seldom availa...

journal_title：Nucleic acids research

authors： Azad RN,Zafiropoulos D,Ober D,Jiang Y,Chiu TP,Sagendorf JM,Rohs R,Tullius TD

更新日期：2018-03-16 00:00:00

abstract：:Accurate maps and DNA sequences for human subtelomere regions, along with detailed knowledge of subtelomere variation and long-range telomere-terminal haplotypes in individuals, are critical for understanding telomere function and its roles in human biology. Here, we use a highly automated whole genome mapping technol...

journal_title：Nucleic acids research

authors： Young E,Pastor S,Rajagopalan R,McCaffrey J,Sibert J,Mak ACY,Kwok PY,Riethman H,Xiao M

更新日期：2017-05-19 00:00:00

abstract：:The PriA protein was identified in Escherichia coli as a factor involved in the replication of extrachromosomal elements such as bacteriophage phiX174 and plasmid pBR322. Recent data show that PriA plays an important role in chromosomal replication, by promoting reassembly of the replication machinery during reinitiat...

journal_title：Nucleic acids research

authors： Polard P,Marsin S,McGovern S,Velten M,Wigley DB,Ehrlich SD,Bruand C

更新日期：2002-04-01 00:00:00

abstract：:Over 50 introns have been reported in archaeal rRNA genes (rDNAs), a subset of which nests putative homing endonuclease (HEase) genes. Here, we report the identification and characterization of a novel archaeal LAGLIDADG-type HEase, I-ApeKI [corrected], encoded by the ApeK1.S908 intron within the 16S rDNA of Aeropyrum...

journal_title：Nucleic acids research

authors： Nomura N,Morinaga Y,Shirai N,Sako Y

更新日期：2005-07-26 00:00:00

abstract：:Selected groups of isolated 14C-labelled proteins from E. coli 30S ribosomal subunits were reconstituted with 32P-labelled 16S RNA, and the reconstituted complexes were partially digested with ribonuclease A. RNA fragments protected by the proteins were separated by gel electrophoresis and subjected to sequence analys...

journal_title：Nucleic acids research

authors： Wiener L,Schüler D,Brimacombe R

更新日期：1988-02-25 00:00:00

abstract：:DynOmics (dynomics.pitt.edu) is a portal developed to leverage rapidly growing structural proteomics data by efficiently and accurately evaluating the dynamics of structurally resolved systems, from individual molecules to large complexes and assemblies, in the context of their physiological environment. At the core o...

journal_title：Nucleic acids research

authors： Li H,Chang YY,Lee JY,Bahar I,Yang LW

更新日期：2017-07-03 00:00:00

abstract：:SMILE (small heterodimer partner interacting leucine zipper protein) has been identified as a coregulator in ER signaling. In this study, we have examined the effects of SMILE on other NRs (nuclear receptors). SMILE inhibits GR, CAR and HNF4 alpha-mediated transactivation. Knockdown of SMILE gene expression increases ...

journal_title：Nucleic acids research

authors： Xie YB,Nedumaran B,Choi HS

更新日期：2009-07-01 00:00:00

abstract：:Protein p56 (56 amino acids) from the Bacillus subtilis phage 29 inactivates the host uracil-DNA glycosylase (UDG), an enzyme involved in the base excision repair pathway. At present, p56 is the only known example of a UDG inhibitor encoded by a non-uracil containing viral DNA. Using analytical ultracentrifugation met...

journal_title：Nucleic acids research

authors： Serrano-Heras G,Ruiz-Masó JA,del Solar G,Espinosa M,Bravo A,Salas M

更新日期：2007-01-01 00:00:00

abstract：:We have examined the replication patterns of ribosomal DNA plasmids in vivo and in vitro using Xenopus eggs. Plasmids carrying different parts of the Xenopus ribosomal DNA sequence were allowed to replicate either in vitro in an egg extract or in vivo after microinjection into unfertilized eggs. The replication interm...

journal_title：Nucleic acids research

authors： Hyrien O,Méchali M

更新日期：1992-04-11 00:00:00

abstract：:Cdc48/p97 is an evolutionary conserved ubiquitin-dependent chaperone involved in a broad array of cellular functions due to its ability to associate with multiple cofactors. Aside from its role in removing RNA polymerase II from chromatin after DNA damage, little is known about how this AAA-ATPase is involved in the t...

journal_title：Nucleic acids research

authors： Bonizec M,Hérissant L,Pokrzywa W,Geng F,Wenzel S,Howard GC,Rodriguez P,Krause S,Tansey WP,Hoppe T,Dargemont C

更新日期：2014-01-01 00:00:00

abstract：:Complete genomes of three closely related Gram-positive bacteria Streptococcus pyogenes, Streptococcus pneumoniae and Lactococcus lactis are analyzed for abundances of short DNA sequence motifs (frequent words). The character and extent of frequent words are strikingly different among these genomes. The frequent words...

journal_title：Nucleic acids research

authors： Mrázek J,Gaynon LH,Karlin S

更新日期：2002-10-01 00:00:00

abstract：:The 338.5 kb of the Escherichia coli genome described here together with previously described segments bring the total of contiguous finished sequence of this genome to > 1 Mb. Of 319 open reading frames (ORFs) found in this 338.5 kb segment, 147 (46%) are potential new genes. The positions of several genes which had ...

journal_title：Nucleic acids research

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

更新日期：1995-06-25 00:00:00

abstract：:Translation initiation of eukaryotic mRNAs generally occurs by cap-dependent ribosome scanning. However, certain mRNAs contain internal ribosome entry sites (IRES) allowing cap-independent translation. Several of these IRES-competent transcripts and their corresponding proteins are involved in tumourigenesis. This stu...

journal_title：Nucleic acids research

authors： Petz M,Kozina D,Huber H,Siwiec T,Seipelt J,Sommergruber W,Mikulits W

更新日期：2007-01-01 00:00:00

abstract：:In Xenopus oocytes in vitro transcribed mouse U7 RNA is assembled into small nuclear ribonucleoproteins (snRNPs) that are functional in histone RNA 3' processing. If the special Sm binding site of U7 (AAUUUGUCUAG, U7 Sm WT) is converted into the canonical Sm sequence derived from the major snRNAs (AAUUUUUGGAG, U7 Sm O...

journal_title：Nucleic acids research

authors： Stefanovic B,Hackl W,Lührmann R,Schümperli D

更新日期：1995-08-25 00:00:00

abstract：:Chinese hamster genomic DNA sequences from the region downstream of the dihydrofolate reductase (DHFR) gene reported to contain a chromosomal origin of bidirectional DNA replication (OBR-1) were tested for their ability to support autonomous DNA replication in human cells. A 13.3 kilobase fragment containing OBR-1 and...

journal_title：Nucleic acids research

authors： Caddle MS,Calos MP

更新日期：1992-11-25 00:00:00

abstract：:A challenge for large-scale siRNA loss-of-function studies is the biological pleiotropy resulting from multiple modes of action of siRNA reagents. A major confounding feature of these reagents is the microRNA-like translational quelling resulting from short regions of oligonucleotide complementarity to many different ...

journal_title：Nucleic acids research

authors： Zhong R,Kim J,Kim HS,Kim M,Lum L,Levine B,Xiao G,White MA,Xie Y

更新日期：2014-07-01 00:00:00

abstract：:The dicistrovirus intergenic internal ribosome entry site (IGR IRES) directly recruits the ribosome and initiates translation using a non-AUG codon. A subset of IGR IRESs initiates translation in either of two overlapping open reading frames (ORFs), resulting in expression of the 0 frame viral structural polyprotein a...

journal_title：Nucleic acids research

authors： Ren Q,Au HH,Wang QS,Lee S,Jan E

更新日期：2014-08-01 00:00:00

abstract：:Sequences from -3500 to +1365 of the chicken histone H5 gene have been analyzed for the presence of cis-acting elements in H5 expressing (transformed CFU-E) and non-expressing cells (fibroblasts). The region from -3500 to -115 had little effect on transcription. Proximal upstream sequences contain a negative element (...

journal_title：Nucleic acids research

authors： Rousseau S,Renaud J,Ruiz-Carrillo A

更新日期：1989-09-25 00:00:00

abstract：:The early DNa products of reverse transcription have been analyzed from reconstructed reactions containing avian myeloblastosis virus 35S RNA . tRNAtrp complex and highly purified reverse transcriptase. We describe conditions for the synthesis of genome-length complementary DNA and two discrete species of plus strand ...

journal_title：Nucleic acids research

authors： Olsen JC,Watson KF

更新日期：1982-02-11 00:00:00

abstract：:Microbial biosynthetic gene clusters are a valuable source of bioactive molecules. However, because they typically represent a small fraction of genomic material in most metagenomic samples, it remains challenging to deeply sequence them. We present an approach to isolate and sequence gene clusters in metagenomic samp...

journal_title：Nucleic acids research

authors： Xu P,Modavi C,Demaree B,Twigg F,Liang B,Sun C,Zhang W,Abate AR

更新日期：2020-05-07 00:00:00

abstract：:Gene expression patterns have been demonstrated to be highly variable between similar cell types, for example lab strains and wild strains of Saccharomyces cerevisiae cultured under identical growth conditions exhibit a wide range of expression differences. We have used a genome-wide approach to characterize transcrip...

journal_title：Nucleic acids research

authors： Llinás M,Bozdech Z,Wong ED,Adai AT,DeRisi JL

更新日期：2006-02-21 00:00:00

abstract：:Uracil-Specific Exision Reagent (USER) fusion is a recently developed technique that allows for assembly of multiple DNA fragments in a few simple steps. However, designing primers for USER fusion is both tedious and time consuming. Here, we present the Primer Help for USER (PHUSER) software, a novel tool for designin...

journal_title：Nucleic acids research

authors： Olsen LR,Hansen NB,Bonde MT,Genee HJ,Holm DK,Carlsen S,Hansen BG,Patil KR,Mortensen UH,Wernersson R

更新日期：2011-07-01 00:00:00

abstract：:Key components of the translational apparatus, i.e. ribosomes, elongation factor EF-Tu and most aminoacyl-tRNA synthetases, are stereoselective and prevent incorporation of d-amino acids (d-aa) into polypeptides. The rare appearance of d-aa in natural polypeptides arises from post-translational modifications or non-ri...

journal_title：Nucleic acids research

authors： Achenbach J,Jahnz M,Bethge L,Paal K,Jung M,Schuster M,Albrecht R,Jarosch F,Nierhaus KH,Klussmann S

更新日期：2015-07-13 00:00:00

abstract：:Underlying higher order chromatin organization are Structural Maintenance of Chromosomes (SMC) complexes, large protein rings that entrap DNA. The molecular mechanism by which SMC complexes organize chromatin is as yet incompletely understood. Two prominent models posit that SMC complexes actively extrude DNA loops (l...

journal_title：Nucleic acids research

authors： Gerguri T,Fu X,Kakui Y,Khatri BS,Barrington C,Bates PA,Uhlmann F

更新日期：2021-01-12 00:00:00

abstract：:We report the latest release (version 3.0) of the CATH protein domain database (http://www.cathdb.info). There has been a 20% increase in the number of structural domains classified in CATH, up to 86 151 domains. Release 3.0 comprises 1110 fold groups and 2147 homologous superfamilies. To cope with the increases in di...

journal_title：Nucleic acids research

authors： Greene LH,Lewis TE,Addou S,Cuff A,Dallman T,Dibley M,Redfern O,Pearl F,Nambudiry R,Reid A,Sillitoe I,Yeats C,Thornton JM,Orengo CA

更新日期：2007-01-01 00:00:00

abstract：:Double-strand breaks (DSBs) are dangerous chromosomal lesions that must be efficiently repaired in order to avoid loss of genetic information or cell death. In all organisms studied to date, two different mechanisms are used to repair DSBs: homologous recombination (HR) and non-homologous end joining (NHEJ). Previous ...

journal_title：Nucleic acids research

authors： Haviv-Chesner A,Kobayashi Y,Gabriel A,Kupiec M

更新日期：2007-01-01 00:00:00

abstract：:Tunable induction of gene expression is an essential tool in biology and biotechnology. In spite of that, current induction systems often exhibit unpredictable behavior and performance shortcomings, including high sensitivity to transactivator dosage and plasmid take-up variation, and excessive consumption of cellular...

journal_title：Nucleic acids research

authors： Lillacci G,Benenson Y,Khammash M

更新日期：2018-10-12 00:00:00