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Nucleic Acids Research

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https://www.readbyqxmd.com/read/28633417/polypyrimidine-tract-binding-protein-ptb-and-ptb-associated-splicing-factor-in-cvb3-infection-an-itaf-for-an-itaf
#1
Pratik Dave, Biju George, Divya Khandige Sharma, Saumitra Das
The 5΄ UTR of Coxsackievirus B3 (CVB3) contains internal ribosome entry site (IRES), which allows cap-independent translation of the viral RNA and a 5΄-terminal cloverleaf structure that regulates viral replication, translation and stability. Here, we demonstrate that host protein PSF (PTB associated splicing factor) interacts with the cloverleaf RNA as well as the IRES element. PSF was found to be an important IRES trans acting factor (ITAF) for efficient translation of CVB3 RNA. Interestingly, cytoplasmic abundance of PSF protein increased during CVB3 infection and this is regulated by phosphorylation status at two different amino acid positions...
June 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28633355/how-proteins-bind-to-dna-target-discrimination-and-dynamic-sequence-search-by-the-telomeric-protein-trf1
#2
Milosz Wieczór, Jacek Czub
Target search as performed by DNA-binding proteins is a complex process, in which multiple factors contribute to both thermodynamic discrimination of the target sequence from overwhelmingly abundant off-target sites and kinetic acceleration of dynamic sequence interrogation. TRF1, the protein that binds to telomeric tandem repeats, faces an intriguing variant of the search problem where target sites are clustered within short fragments of chromosomal DNA. In this study, we use extensive (>0.5 ms in total) MD simulations to study the dynamical aspects of sequence-specific binding of TRF1 at both telomeric and non-cognate DNA...
June 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28609788/resolving-sugar-puckers-in-rna-excited-states-exposes-slow-modes-of-repuckering-dynamics
#3
Mary C Clay, Laura R Ganser, Dawn K Merriman, Hashim M Al-Hashimi
Recent studies have shown that RNAs exist in dynamic equilibrium with short-lived low-abundance 'excited states' that form by reshuffling base pairs in and around non-canonical motifs. These conformational states are proposed to be rich in non-canonical motifs and to play roles in the folding and regulatory functions of non-coding RNAs but their structure proves difficult to characterize given their transient nature. Here, we describe an approach for determining sugar pucker conformation in RNA excited states through nuclear magnetic resonance measurements of C1΄ and C4΄ rotating frame spin relaxation (R1ρ) in uniformly 13C/15N labeled RNA samples...
June 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28609787/molecular-structures-guide-the-engineering-of-chromatin
#4
Stefan J Tekel, Karmella A Haynes
Chromatin is a system of proteins, RNA, and DNA that interact with each other to organize and regulate genetic information within eukaryotic nuclei. Chromatin proteins carry out essential functions: packing DNA during cell division, partitioning DNA into sub-regions within the nucleus, and controlling levels of gene expression. There is a growing interest in manipulating chromatin dynamics for applications in medicine and agriculture. Progress in this area requires the identification of design rules for the chromatin system...
June 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28609784/genome-wide-profiling-of-s-mar-based-replicon-contact-sites
#5
Claudia Hagedorn, Andreas Gogol-Döring, Sabrina Schreiber, Jörg T Epplen, Hans J Lipps
Autonomously replicating vectors represent a simple and versatile model system for genetic modifications, but their localization in the nucleus and effect on endogenous gene expression is largely unknown. Using circular chromosome conformation capture we mapped genomic contact sites of S/MAR-based replicons in HeLa cells. The influence of cis-active sequences on genomic localization was assessed using replicons containing either an insulator sequence or an intron. While the original and the insulator-containing replicons displayed distinct contact sites, the intron-containing replicon showed a rather broad genomic contact pattern...
June 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28609783/balancing-gene-expression-without-library-construction-via-a-reusable-srna-pool
#6
Amar Ghodasara, Christopher A Voigt
Balancing protein expression is critical when optimizing genetic systems. Typically, this requires library construction to vary the genetic parts controlling each gene, which can be expensive and time-consuming. Here, we develop sRNAs corresponding to 15nt 'target' sequences that can be inserted upstream of a gene. The targeted gene can be repressed from 1.6- to 87-fold by controlling sRNA expression using promoters of different strength. A pool is built where six sRNAs are placed under the control of 16 promoters that span a ∼103-fold range of strengths, yielding ∼107 combinations...
June 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28609782/influence-of-dna-sequence-on-the-structure-of-minicircles-under-torsional-stress
#7
Qian Wang, Rossitza N Irobalieva, Wah Chiu, Michael F Schmid, Jonathan M Fogg, Lynn Zechiedrich, B Montgomery Pettitt
The sequence dependence of the conformational distribution of DNA under various levels of torsional stress is an important unsolved problem. Combining theory and coarse-grained simulations shows that the DNA sequence and a structural correlation due to topology constraints of a circle are the main factors that dictate the 3D structure of a 336 bp DNA minicircle under torsional stress. We found that DNA minicircle topoisomers can have multiple bend locations under high torsional stress and that the positions of these sharp bends are determined by the sequence, and by a positive mechanical correlation along the sequence...
June 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28609781/a-data-driven-structural-model-of-hssb1-nabp2-obfc2b-self-oligomerization
#8
Christine Touma, Mark N Adams, Nicholas W Ashton, Michael Mizzi, Serene El-Kamand, Derek J Richard, Liza Cubeddu, Roland Gamsjaeger
The maintenance of genome stability depends on the ability of the cell to repair DNA efficiently. Single-stranded DNA binding proteins (SSBs) play an important role in DNA processing events such as replication, recombination and repair. While the role of human single-stranded DNA binding protein 1 (hSSB1/NABP2/OBFC2B) in the repair of double-stranded breaks has been well established, we have recently shown that it is also essential for the base excision repair (BER) pathway following oxidative DNA damage. However, unlike in DSB repair, the formation of stable hSSB1 oligomers under oxidizing conditions is an important prerequisite for its proper function in BER...
June 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28605523/retrotransposons-are-specified-as-dna-replication-origins-in-the-gene-poor-regions-of-arabidopsis-heterochromatin
#9
Zaida Vergara, Joana Sequeira-Mendes, Jordi Morata, Ramón Peiró, Elizabeth Hénaff, Celina Costas, Josep M Casacuberta, Crisanto Gutierrez
Genomic stability depends on faithful genome replication. This is achieved by the concerted activity of thousands of DNA replication origins (ORIs) scattered throughout the genome. The DNA and chromatin features determining ORI specification are not presently known. We have generated a high-resolution genome-wide map of 3230 ORIs in cultured Arabidopsis thaliana cells. Here, we focused on defining the features associated with ORIs in heterochromatin. In pericentromeric gene-poor domains ORIs associate almost exclusively with the retrotransposon class of transposable elements (TEs), in particular of the Gypsy family...
June 10, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28605514/flipping-states-a-few-key-residues-decide-the-winning-conformation-of-the-only-universally-conserved-transcription-factor
#10
Da Shi, Dmitri Svetlov, Ruben Abagyan, Irina Artsimovitch
Transcription factors from the NusG family bind to the elongating RNA polymerase to enable synthesis of long RNAs in all domains of life. In bacteria, NusG frequently co-exists with specialized paralogs that regulate expression of a small set of targets, many of which encode virulence factors. Escherichia coli RfaH is the exemplar of this regulatory mechanism. In contrast to NusG, which freely binds to RNA polymerase, RfaH exists in a structurally distinct autoinhibitory state in which the RNA polymerase-binding site is buried at the interface between two RfaH domains...
June 10, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28605556/family-specific-scaling-laws-in-bacterial-genomes
#11
Eleonora De Lazzari, Jacopo Grilli, Sergei Maslov, Marco Cosentino Lagomarsino
Among several quantitative invariants found in evolutionary genomics, one of the most striking is the scaling of the overall abundance of proteins, or protein domains, sharing a specific functional annotation across genomes of given size. The size of these functional categories change, on average, as power-laws in the total number of protein-coding genes. Here, we show that such regularities are not restricted to the overall behavior of high-level functional categories, but also exist systematically at the level of single evolutionary families of protein domains...
June 9, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28605464/strand-specific-cpg-hemimethylation-a-novel-epigenetic-modification-functional-for-genomic-imprinting
#12
Iris Patiño-Parrado, Álvaro Gómez-Jiménez, Noelia López-Sánchez, José M Frade
Imprinted genes are regulated by allele-specific differentially DNA-methylated regions (DMRs). Epigenetic methylation of the CpGs constituting these DMRs is established in the germline, resulting in a 5-methylcytosine-specific pattern that is tightly maintained in somatic tissues. Here, we show a novel epigenetic mark, characterized by strand-specific hemimethylation of contiguous CpG sites affecting the germline DMR of the murine Peg3, but not Snrpn, imprinted domain. This modification is enriched in tetraploid cortical neurons, a cell type where evidence for a small proportion of formylmethylated CpG sites within the Peg3-controlling DMR is also provided...
June 9, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28605461/determining-the-folding-and-binding-free-energy-of-dna-based-nanodevices-and-nanoswitches-using-urea-titration-curves
#13
Andrea Idili, Francesco Ricci, Alexis Vallée-Bélisle
DNA nanotechnology takes advantage of the predictability of DNA interactions to build complex DNA-based functional nanoscale structures. However, when DNA functional and responsive units that are based on non-canonical DNA interactions are employed it becomes quite challenging to predict, understand and control their thermodynamics. In response to this limitation, here we demonstrate the use of isothermal urea titration experiments to estimate the free energy involved in a set of DNA-based systems ranging from unimolecular DNA-based nanoswitches to more complex DNA folds (e...
June 9, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28605458/prioritizing-tests-of-epistasis-through-hierarchical-representation-of-genomic-redundancies
#14
Tyler Cowman, Mehmet Koyutürk
Epistasis is defined as a statistical interaction between two or more genomic loci in terms of their association with a phenotype of interest. Epistatic loci that are identified using data from Genome-Wide Association Studies (GWAS) provide insights into the interplay among multiple genetic factors, with applications including assessment of susceptibility to complex diseases, decision making in precision medicine, and gaining insights into disease mechanisms. Since the number of genomic loci assayed by GWAS is extremely large (usually in the order of millions), identification of epistatic loci is a statistically difficult and computationally intensive problem...
June 9, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28595329/a-mechanism-for-a-single-nucleotide-intron-shift
#15
Erzsébet Fekete, Michel Flipphi, Norbert Ág, Napsugár Kavalecz, Gustavo Cerqueira, Claudio Scazzocchio, Levente Karaffa
Spliceosomal introns can occupy nearby rather than identical positions in orthologous genes (intron sliding or shifting). Stwintrons are complex intervening sequences, where an 'internal' intron interrupts one of the sequences essential for splicing, generating after its excision, a newly formed canonical intron defined as 'external'. In one experimentally demonstrated configuration, two alternatively excised internal introns, overlapping by one G, disrupt respectively the donor and the acceptor sequence of an external intron, leading to mRNAs encoding identical proteins...
June 8, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28591869/alternative-splicing-of-cnot7-diversifies-ccr4-not-functions
#16
Clément Chapat, Kamel Chettab, Pierre Simonet, Peng Wang, Pierre De La Grange, Muriel Le Romancer, Laura Corbo
The CCR4-associated factor CAF1, also called CNOT7, is a catalytic subunit of the CCR4-NOT complex, which has been implicated in all aspects of the mRNA life cycle, from mRNA synthesis in the nucleus to degradation in the cytoplasm. In human cells, alternative splicing of the CNOT7 gene yields a second CNOT7 transcript leading to the formation of a shorter protein, CNOT7 variant 2 (CNOT7v2). Biochemical characterization indicates that CNOT7v2 interacts with CCR4-NOT subunits, although it does not bind to BTG proteins...
June 7, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28591846/visualization-of-conformational-variability-in-the-domains-of-long-single-stranded-rna-molecules
#17
Jamie L Gilmore, Aiko Yoshida, James A Hejna, Kunio Takeyasu
We demonstrate an application of atomic force microscopy (AFM) for the structural analysis of long single-stranded RNA (>1 kb), focusing on 28S ribosomal RNA (rRNA). Generally, optimization of the conditions required to obtain three-dimensional (3D) structures of long RNA molecules is a challenging or nearly impossible process. In this study, we overcome these limitations by developing a method using AFM imaging combined with automated, MATLAB-based image analysis algorithms for extracting information about the domain organization of single RNA molecules...
June 7, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28591844/new-insights-into-a-classic-aptamer-binding-sites-cooperativity-and-more-sensitive-adenosine-detection
#18
Zijie Zhang, Olatunji Oni, Juewen Liu
The DNA aptamer for adenosine (also for AMP and ATP) is a highly conserved sequence that has recurred in a few selections. It it a widely used model aptamer for biosensor development, and its nuclear magnetic resonance structure shows that each aptamer binds two AMP molecules. In this work, each binding site was individually removed by rational sequence design, while the remaining site still retained a similar binding affinity and specificity as confirmed by isothermal titration calorimetry. The thermodynamic parameters of binding are presented, and its biochemical implications are discussed...
June 7, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28591841/rsat-matrix-clustering-dynamic-exploration-and-redundancy-reduction-of-transcription-factor-binding-motif-collections
#19
Jaime Abraham Castro-Mondragon, Sébastien Jaeger, Denis Thieffry, Morgane Thomas-Chollier, Jacques van Helden
Transcription factor (TF) databases contain multitudes of binding motifs (TFBMs) from various sources, from which non-redundant collections are derived by manual curation. The advent of high-throughput methods stimulated the production of novel collections with increasing numbers of motifs. Meta-databases, built by merging these collections, contain redundant versions, because available tools are not suited to automatically identify and explore biologically relevant clusters among thousands of motifs. Motif discovery from genome-scale data sets (e...
June 7, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28591827/tethering-not-required-the-glucocorticoid-receptor-binds-directly-to-activator-protein-1-recognition-motifs-to-repress-inflammatory-genes
#20
Emily R Weikum, Ian Mitchelle S de Vera, Jerome C Nwachukwu, William H Hudson, Kendall W Nettles, Douglas J Kojetin, Eric A Ortlund
The glucocorticoid receptor (GR) is a ligand-regulated transcription factor that controls the expression of extensive gene networks, driving both up- and down-regulation. GR utilizes multiple DNA-binding-dependent and -independent mechanisms to achieve context-specific transcriptional outcomes. The DNA-binding-independent mechanism involves tethering of GR to the pro-inflammatory transcription factor activator protein-1 (AP-1) through protein-protein interactions. This mechanism has served as the predominant model of GR-mediated transrepression of inflammatory genes...
June 7, 2017: Nucleic Acids Research
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