PubMed Central (PMC3 - NLM DTD)
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Archive of life sciences journal literature at the U.S. National Institutes of Health (NIH), developed and managed by NIH's National Center for Biotechnology Information (NCBI) in the National Library of Medicine (NLM).
Mostrando recursos 141 - 160 de 59,293
141.
The inhibition of the human cholesterol 7?-hydroxylase gene (CYP7A1) promoter by fibrates in cultured cells is mediated via the liver x receptor ? and peroxisome proliferator-activated receptor ? heterodimer - Gbaguidi, G. Franck; Agellon, Luis B.
In previous work, we showed that the binding of the liver x receptor ?:peroxisome proliferator-activated receptor ? (LXR?:PPAR?) heterodimer to the murine Cyp7a1 gene promoter antagonizes the stimulatory effect of their respective ligands. In this study, we determined if LXR?:PPAR? can also regulate human CYP7A1 gene promoter activity. Co-expression of LXR? and PPAR? in McArdle RH7777 hepatoma cells decreased the activity of the human CYP7A1 gene promoter in response to fibrates and 25-hydroxycholesterol. In vitro, the human CYP7A1 Site I bound LXR?:PPAR?, although with substantially less affinity compared with the murine Cyp7a1 Site I. The binding of LXR?:PPAR? to human...
142.
Interactions among CII protein, RNA polymerase and the ? PRE promoter: contacts between RNA polymerase and the 35 region of PRE are identical in the presence and absence of CII protein - Marr, Michael T.; Roberts, Jeffrey W.; Brown, Susan E.; Klee, Matthew; Gussin, Gary N.
The DNA recognition sequence for the transcriptional activator, CII protein, which is critical for lysogenization by bacteriophage ?, overlaps the 35 region of the PRE promoter. Data presented here show that activation by CII does not change the pattern of cleavage of the 35 region of PRE by iron (S)-1-(p-bromoacetamidobenzyl)-EDTA (Fe-BABE) conjugated to the ? subunit of RNA polymerase (RNAP). Thus, the overall interaction between ? and the 35 region of PRE is not significantly altered by CII. Therefore, the effects of the activator on RNAP binding to the promoter and formation of open complexes do not reflect a large-scale...
143.
Structurefunction correlations derived from faster variants of a RNA ligase deoxyribozyme - Prior, Tracey K.; Semlow, Daniel R.; Flynn-Charlebois, Amber; Rashid, Imran; Silverman, Scott K.
We previously reported the in vitro selection of several Mg2+-dependent deoxyribozymes (DNA enzymes) that synthesize a 2?5? RNA linkage from a 2?,3?-cyclic phosphate and a 5?-hydroxyl. Here we subjected the 9A2 deoxyribozyme to re-selection for improved ligation rate. We found two new DNA enzymes (7Z81 and 7Z48) that contain the catalytic core of 7Q10, a previously reported small deoxyribozyme that is unrelated in sequence to 9A2. A third new DNA enzyme (7Z101) is unrelated to either 7Q10 or 9A2. The new 7Z81 and 7Z48 DNA enzymes have ligation rates over an order of magnitude higher than that of 7Q10 itself...
144.
RBD-1, a nucleolar RNA-binding protein, is essential for Caenorhabditis elegans early development through 18S ribosomal RNA processing - Saijou, Eiko; Fujiwara, Toshinobu; Suzaki, Toshinobu; Inoue, Kunio; Sakamoto, Hiroshi
RBD-1 is the Caenorhabditis elegans homolog of Mrd1p, which was recently shown to be required for 18S ribosomal RNA (rRNA) processing in yeast. To gain insights into the relationship between ribosome biogenesis and the development of multicellular organisms, we examined the expression and function of RBD-1. Maternal RBD-1 in the fertilized egg disappears immediately after cleavage starts, whereas zygotic RBD-1 first appears in late embryos and is localized in the nucleolus in most cells, although zygotic transcription of pre-rRNA is known to be initiated as early as the one-cell stage. RNA interference of the rbd-1 gene severely inhibits the processing...
145.
Phosphatidyl inositol 3-kinase-like serine/threonine protein kinases (PIKKs) are required for DNA damage-induced phosphorylation of the 32 kDa subunit of replication protein A at threonine 21 - Block, Wesley D.; Yu, Yaping; Lees-Miller, Susan P.
Replication protein A (RPA) is a single-stranded DNA (ssDNA) binding protein involved in various processes, including nucleotide excision repair and DNA replication. The 32 kDa subunit of RPA (RPA32) is phosphorylated in response to various DNA-damaging agents, and two protein kinases, ataxia-telangiectasia mutated (ATM) and the DNA-dependent protein kinase (DNA-PK) have been implicated in DNA damage-induced phosphorylation of RPA32. However, the relative roles of ATM and DNA-PK in the site-specific DNA damage-induced phosphorylation of RPA32 have not been reported. Here we generated a phosphospecific antibody that recognizes Thr21-phosphorylated RPA32. We show that both DNA-PK and ATM phosphorylate RPA32 on Thr21...
146.
Atypical archaeal tRNA pyrrolysine transcript behaves towards EF-Tu as a typical elongator tRNA - Théobald-Dietrich, Anne; Frugier, Magali; Giegé, Richard; Rudinger-Thirion, Joëlle
The newly discovered tRNAPyl is involved in specific incorporation of pyrrolysine in the active site of methylamine methyltransferases in the archaeon Methanosarcina barkeri. In solution probing experiments, a transcript derived from tRNAPyl displays a secondary fold slightly different from the canonical cloverleaf and interestingly similar to that of bovine mitochondrial tRNASer(uga). Aminoacylation of tRNAPyl transcript by a typical class II synthetase, LysRS from yeast, was possible when its amber anticodon CUA was mutated into a lysine UUU anticodon. Hydrolysis protection assays show that lysylated tRNAPyl can be recognized by bacterial elongation factor. This indicates that no antideterminant sequence is present...
147.
Psoralen interstrand cross-link repair is specifically altered by an adjacent triple-stranded structure - Guillonneau, F.; Guieysse, A. L.; Nocentini, S.; Giovannangeli, C.; Praseuth, D.
Targeting DNA-damaging agents to specific DNA sites by using sequence-specific DNA ligands has been successful in directing genomic modifications. The understanding of repair processing of such targeted damage and the influence of the adjacent complex is largely unknown. In this way, directed interstrand cross-links (ICLs) have already been generated by psoralen targeting. The mechanisms responsible for ICL removal are far from being understood in mammalian cells, with the proposed involvement of both mutagenic and recombinogenic pathways. Here, a unique ICL was introduced at a selected site by photoactivation of a psoralen moiety with the use of psoralen conjugates of triplex-forming...
148.
A mutation in polynucleotide phosphorylase from Escherichia coli impairing RNA binding and degradosome stability - Regonesi, Maria Elena; Briani, Federica; Ghetta, Andrea; Zangrossi, Sandro; Ghisotti, Daniela; Tortora, Paolo; Dehò, Gianni
Polynucleotide phosphorylase (PNPase), a 3? to 5? exonuclease encoded by pnp, plays a key role in Escherichia coli RNA decay. The enzyme, made of three identical 711 amino acid subunits, may also be assembled in the RNA degradosome, a heteromultimeric complex involved in RNA degradation. PNPase autogenously regulates its expression by promoting the decay of pnp mRNA, supposedly by binding at the 5?-untranslated leader region of an RNase III-processed form of this transcript. The KH and S1 RNA-binding domains at the C-terminus of the protein (amino acids 552711) are thought to be involved in pnp mRNA recognition. Here we show...
149.
A thymine tetrad in d(TGGGGT) quadruplexes stabilized with Tl+/Na+ ions - Cáceres, Carmen; Wright, Glenford; Gouyette, Catherine; Parkinson, Gary; Subirana, Juan A.
We report two new structures of the quadruplex d(TGGGGT)4 obtained by single crystal X-ray diffraction. In one of them a thymine tetrad is found. Thus the yeast telomere sequences d(TG13) might be able to form continuous quadruplex structures, involving both guanine and thymine tetrads. Our study also shows substantial differences in the arrangement of thymines when compared with previous studies. We find five different types of organization: (i) groove binding with hydrogen bonds to guanines from a neighbour quadruplex; (ii) partially ordered groove binding, without any hydrogen bond; (iii) stacked thymine triads, formed at the 3?ends of the quadruplexes; (iv)...
150.
A novel strategy to engineer DNA polymerases for enhanced processivity and improved performance in vitro - Wang, Yan; Prosen, Dennis E.; Mei, Li; Sullivan, John C.; Finney, Michael; Vander Horn, Peter B.
Mechanisms that allow replicative DNA polymerases to attain high processivity are often specific to a given polymerase and cannot be generalized to others. Here we report a protein engineering-based approach to significantly improve the processivity of DNA polymerases by covalently linking the polymerase domain to a sequence non-specific dsDNA binding protein. Using Sso7d from Sulfolobus solfataricus as the DNA binding protein, we demonstrate that the processivity of both family A and family B polymerases can be significantly enhanced. By introducing point mutations in Sso7d, we show that the dsDNA binding property of Sso7d is essential for the enhancement. We present...
151.
Delineation of the mechanisms of aberrant splicing caused by two unusual intronic mutations in the RSK2 gene involved in CoffinLowry syndrome - Zeniou, Maria; Gattoni, Renata; Hanauer, André; Stévenin, James
CoffinLowry syndrome (CLS) is caused by mutations in the RSK2 gene encoding a protein kinase of the Ras signalling pathway. We have studied two point mutations which cause aberrant splicing but do not concern the invariant GT or AG nucleotides of splice sites. The first, an A?G transition at position +3 of the 5? splice site of exon 6, results in vivo and in vitro in exon skipping and premature translation termination. The natural 5? splice site, although intrinsically weak, is not transactivated under normal conditions. Consequently, replacement of an A/U by a G/U base pairing with U1 snRNA reduces...
152.
Analysis and recognition of 5? UTR intron splice sites in human pre-mRNA - Eden, E.; Brunak, S.
Prediction of splice sites in non-coding regions of genes is one of the most challenging aspects of gene structure recognition. We perform a rigorous analysis of such splice sites embedded in human 5? untranslated regions (UTRs), and investigate correlations between this class of splice sites and other features found in the adjacent exons and introns. By restricting the training of neural network algorithms to pure UTRs (not extending partially into protein coding regions), we for the first time investigate the predictive power of the splicing signal proper, in contrast to conventional splice site prediction, which typically relies on the change...
153.
Length-dependent structure formation in Friedreich ataxia (GAA)n·(TTC)n repeats at neutral pH - Potaman, V. N.; Oussatcheva, E. A.; Lyubchenko, Y. L.; Shlyakhtenko, L. S.; Bidichandani, S. I.; Ashizawa, T.; Sinden, R. R.
More than 15 human genetic diseases have been associated with the expansion of trinucleotide DNA repeats, which may involve the formation of non-duplex DNA structures. The slipped-strand nucleation of duplex DNA within GC-rich trinucleotide repeats may result in the changes of repeat length; however, such a mechanism seems less likely for the AT-rich (GAA)n·(TTC)n repeats. Using two-dimensional agarose gels, chemical probing and atomic force microscopy, we characterized the formation of non-B-DNA structures in the Friedreich ataxia-associated (GAA)n·(TTC)n repeats from the FRDA gene that were cloned with flanking genomic sequences into plasmids. For the normal genomic repeat length (n = 9)...
154.
ETR-3 and CELF4 protein domains required for RNA binding and splicing activity in vivo - Singh, Gopal; Charlet-B., Nicolas; Han, Jin; Cooper, Thomas A.
Members of the CUG-BP and ETR-3 like factor (CELF) protein family bind within conserved intronic elements (called MSEs) flanking the cardiac troponin T (cTNT) alternative exon 5 and promote exon inclusion in vivo and in vitro. Here we use a comparative deletion analysis of two family members (ETR-3 and CELF4) to identify separate domains required for RNA binding and splicing activity in vivo. CELF proteins contain two adjacent RNA binding domains (RRM1 and RRM2) near the N-terminus and one RRM (RRM3) near the C-terminus, which are separated by a 160230 residue divergent domain of unknown function. Either RRM1 or RRM2...
155.
Enhanced gene silencing of HIV-1 specific siRNA using microRNA designed hairpins - Boden, Daniel; Pusch, Oliver; Silbermann, Rebecca; Lee, Fred; Tucker, Lynne; Ramratnam, Bharat
Post-transcriptional inhibition of HIV-1 replication can be achieved by RNA interference (RNAi). The cellular expression of short interfering RNA (siRNA) or short hairpin RNA (shRNA) homologous to regions of the HIV-1 genome decreases viral replication by the selective degradation of targeted RNA. Here, we demonstrate that another class of noncoding regulatory RNA, termed microRNA (miRNA), can be used to deliver antiviral RNAi. By incorporating sequences encoding siRNA targeting the HIV-1 transactivator protein tat into a human miR-30 pre-microRNA (pre-miRNA) backbone, we were able to express tat siRNA in cells. The tat siRNA delivered as pre-miRNA precursor was 80% more effective...
156.
Translesion synthesis of acetylaminofluorene-dG adducts by DNA polymerase ? is stimulated by yeast Rev1 protein - Guo, Dongyu; Xie, Zhongwen; Shen, Huiyun; Zhao, Bo; Wang, Zhigang
Translesion synthesis is an important mechanism in response to unrepaired DNA lesions during replication. The DNA polymerase ? (Pol?) mutagenesis pathway is a major error-prone translesion synthesis mechanism requiring Pol? and Rev1. In addition to its dCMP transferase, a non-catalytic function of Rev1 is suspected in cellular response to certain types of DNA lesions. However, it is not well understood about the non-catalytic function of Rev1 in translesion synthesis. We have analyzed the role of Rev1 in translesion synthesis of an acetylaminofluorene (AAF)-dG DNA adduct. Purified yeast Rev1 was essentially unresponsive to a template AAF-dG DNA adduct, in contrast to...
157.
Gene repeat expansion and contraction by spontaneous intrachromosomal homologous recombination in mammalian cells - Read, Leah R.; Raynard, Steven J.; Ruk??, Ania; Baker, Mark D.
Homologous recombination (HR) is important in repairing errors of replication and other forms of DNA damage. In mammalian cells, potential templates include the homologous chromosome, and after DNA replication, the sister chromatid. Previous work has shown that the mammalian recombination machinery is organized to suppress interchromosomal recombination while preserving intrachromosomal HR. In the present study, we investigated spontaneous intrachromosomal HR in mouse hybridoma cell lines in which variously numbered tandem repeats of the µ heavy chain constant (Cµ) region reside at the haploid, chromosomal immunoglobulin µ heavy chain locus. This organization provides the opportunity to investigate recombination between homologous gene...
158.
Mer1p is a modular splicing factor whose function depends on the conserved U2 snRNP protein Snu17p - Spingola, Marc; Armisen, Javier; Ares, Manuel
Mer1p activates the splicing of at least three pre-mRNAs (AMA1, MER2, MER3) during meiosis in the yeast Saccharomyces cerevisiae. We demonstrate that enhancer recognition by Mer1p is separable from Mer1p splicing activation. The C-terminal KH-type RNA-binding domain of Mer1p recognizes introns that contain the Mer1p splicing enhancer, while the N-terminal domain interacts with the spliceosome and activates splicing. Prior studies have implicated the U1 snRNP and recognition of the 5? splice site as key elements in Mer1p-activated splicing. We provide new evidence that Mer1p may also function at later steps of spliceosome assembly. First, Mer1p can activate splicing of introns...
159.
Overexpression of phage-type RNA polymerase RpoTp in tobacco demonstrates its role in chloroplast transcription by recognizing a distinct promoter type - Liere, Karsten; Kaden, Daniela; Maliga, Pal; Börner, Thomas
Plant cells possess three DNA-containing compartments, the nucleus, the mitochondria and the plastids. Accordingly, plastid gene regulation is fairly complex. Albeit plastids retained their own genome and prokaryotic-type gene expression system by a plastid-encoded RNA polymerase (PEP), they need a second nuclear-encoded plastid transcription activity, NEP. Candidate genes for putative NEP catalytic subunits have been cloned in Arabidopsis thaliana (AtRpoTp) and Nicotiana sylvestris (NsRpoTp). To provide evidence for RpoTp as a gene encoding a NEP catalytic subunit, we introduced the AtRpoTp and NsRpoTp cDNAs into the tobacco nucleus under the control of the strong constitutive CaMV 35S promoter. Analysis of...
160.
Identification of NH N hydrogen bonds by magic angle spinning solid state NMR in a double-stranded RNA associated with myotonic dystrophy - Leppert, Jörg; Urbinati, Carl R.; Häfner, Sabine; Ohlenschläger, Oliver; Swanson, Maurice S.; Görlach, Matthias; Ramachandran, Ramadurai
RNA plays a central role in biological processes and exhibits a variety of secondary and tertiary structural features that are often stabilized via hydrogen bonds. The distance between the donor and acceptor nitrogen nuclei involved in NH N hydrogen bonds in nucleic acid base pairs is typically in the range of 2.62.9 ?. Here, we show for the first time that such spatial proximity between 15N nitrogen nuclei can be conveniently monitored via magic angle spinning solid state NMR on a uniformly 15N-labelled RNA. The presence of NH N hydrogen bonds is reflected as cross-peaks between the donor and acceptor nitrogen nuclei...
141.
