Category Archives: Nucleic Acids Res

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High-resolution analysis of the pneumococcal transcriptome under a wide range of infection-relevant conditions.
Nucleic Acids Res. 2018 Aug 27;:
Authors: Aprianto R, Slager J, Holsappel S, Veening JW
… Continue reading →

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Mms1 binds to G-rich regions in Saccharomyces cerevisiae and influences replication and genome stability.
Nucleic Acids Res. 2017 May 23;:
Authors: Wanzek K, Schwindt E, Capra JA, Paeschke K
A… Continue reading →

Algorithmic co-optimization of genetic constructs and growth conditions: application to 6-ACA, a potential nylon-6 precursor.
Nucleic Acids Res. 2015 Oct 30;
Authors: Zhou H, Vonk B, Roubos JA, Bovenberg RA, Voigt CA… Continue reading →

Genome-wide profiling of nucleosome sensitivity and chromatin accessibility in Drosophila melanogaster.

Nucleic Acids Res. 2015 Oct 1;

Authors: Chereji RV, Kan TW, Grudniewska MK, Romashchenko AV, Berezikov E, Zhimulev IF, Guryev V, Morozov AV, Moshkin YM

Abstract
Nucleosomal DNA is thought to be generally inaccessible to DNA-binding factors, such as micrococcal nuclease (MNase). Here, we digest Drosophila chromatin with high and low concentrations of MNase to reveal two distinct nucleosome types: MNase-sensitive and MNase-resistant. MNase-resistant nucleosomes assemble on sequences depleted of A/T and enriched in G/C-containing dinucleotides, whereas MNase-sensitive nucleosomes form on A/T-rich sequences found at transcription start and termination sites, enhancers and DNase I hypersensitive sites. Estimates of nucleosome formation energies indicate that MNase-sensitive nucleosomes tend to be less stable than MNase-resistant ones. Strikingly, a decrease in cell growth temperature of about 10°C makes MNase-sensitive nucleosomes less accessible, suggesting that observed variations in MNase sensitivity are related to either thermal fluctuations of chromatin fibers or the activity of enzymatic machinery. In the vicinity of active genes and DNase I hypersensitive sites nucleosomes are organized into periodic arrays, likely due to ‘phasing’ off potential barriers formed by DNA-bound factors or by nucleosomes anchored to their positions through external interactions. The latter idea is substantiated by our biophysical model of nucleosome positioning and energetics, which predicts that nucleosomes immediately downstream of transcription start sites are anchored and recapitulates nucleosome phasing at active genes significantly better than sequence-dependent models.

PMID: 26429969 [PubMed – as supplied by publisher]

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Guanine quadruplex structures localize to heterochromatin.
Nucleic Acids Res. 2015 Sep 17;
Authors: Hoffmann RF, Moshkin YM, Mouton S, Grzeschik NA, Kalicharan RD, Kuipers J, Wolters AH, Nishida K, Romashchenko AV, P… Continue reading →

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The multidrug ABC transporter BmrC/BmrD of Bacillus subtilis is regulated via a ribosome-mediated transcriptional attenuation mechanism.
Nucleic Acids Res. 2014 Sep 12;
Authors: Reilman E, Mars RA, va… Continue reading →

Control of transcription elongation by GreA determines rate of gene expression in Streptococcus pneumoniae.
Nucleic Acids Res. 2014 Sep 4;
Authors: Yuzenkova Y, Gamba P, Herber M, Attaiech L, Shafeeq S, Kuipers OP, K… Continue reading →

Genomic organization and evolution of double minutes/homogeneously staining regions with MYC amplification in human cancer.
Nucleic Acids Res. 2014 Jul 17;
Authors: L’Abbate A, Macchia G, D’Addabbo P, Lonoce A, Tolom… Continue reading →

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Induced DNA demethylation by targeting Ten-Eleven Translocation 2 to the human ICAM-1 promoter.
Nucleic Acids Res. 2014 Feb;42(3):1563-74
Authors: Chen H, Kazemier HG, de Groote ML, Ruiters MH, Xu G… Continue reading →

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SporeWeb: an interactive journey through the complete sporulation cycle of Bacillus subtilis.
Nucleic Acids Res. 2014 Jan;42(Database issue):D685-91
Authors: Eijlander RT, de Jong A, Krawczyk AO, Holsappel S, … Continue reading →

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WormQTLHD–a web database for linking human disease to natural variation data in C. elegans.
Nucleic Acids Res. 2014 Jan;42(Database issue):D794-801
Authors: van der Velde KJ, de Haan M, Zych K, Arends D, Snoe… Continue reading →

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Epigenetic Editing: targeted rewriting of epigenetic marks to modulate expression of selected target genes.

Nucleic Acids Res. 2012 Nov;40(21):10596-613
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WormQTL–public archive and analysis web portal for natural variation data in Caenorhabditis spp.
Nucleic Acids Res. 2012 Nov 24;
Authors: Snoek LB, Van der Velde KJ, Arends D, Li Y, Beyer A, Elvin M, Fisher J,… Continue reading →

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Targeted silencing of the oncogenic transcription factor SOX2 in breast cancer.
Nucleic Acids Res. 2012 Aug;40(14):6725-40
Authors: Stolzenburg S, Rots MG, Beltran AS, Rivenbark AG, Yuan X, Qian H, Strahl BD,… Continue reading →

microRNAs associated with the different human Argonaute proteins.

Nucleic Acids Res. 2012 Jul 25;

Authors: Dueck A, Ziegler C, Eichner A, Berezikov E, Meister G

Abstract

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Regulation of AT1R expression through HuR by insulin.
Nucleic Acids Res. 2012 Feb 23;
Authors: Paukku K, Backlund M, De Boer RA, Kalkkinen N, Kontula KK, Lehtonen JY
Abstract
Angiotensin II type 1 receptor (AT1… Continue reading →