Category Archives: Nucleic Acids Res

Mms1 binds to G-rich regions in Saccharomyces cerevisiae and influences replication and genome stability.






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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

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Algorithmic co-optimization of genetic constructs and growth conditions: application to 6-ACA, a potential nylon-6 precursor.






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






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






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.






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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What makes the lac-pathway switch: identifying the fluctuations that trigger phenotype switching in gene regulatory systems.






What makes the lac-pathway switch: identifying the fluctuations that trigger phenotype switching in gene regulatory systems.
Nucleic Acids Res. 2014 Sep 22;
Authors: Bhogale PM, Sorg RA, Veening JW, Berg J
Ab… Continue reading






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The multidrug ABC transporter BmrC/BmrD of Bacillus subtilis is regulated via a ribosome-mediated transcriptional attenuation mechanism.






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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






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Control of transcription elongation by GreA determines rate of gene expression in Streptococcus pneumoniae.






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






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Genomic organization and evolution of double minutes/homogeneously staining regions with MYC amplification in human cancer.






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.






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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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Detection of G-quadruplex DNA in mammalian cells.






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Detection of G-quadruplex DNA in mammalian cells.

Nucleic Acids Res. 2014 Jan;42(2):860-9

Authors: Henderson A, Wu Y, Huang YC, Chavez EA, Platt J,…

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SporeWeb: an interactive journey through the complete sporulation cycle of Bacillus subtilis.






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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.






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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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BAGEL3: Automated identification of genes encoding bacteriocins and (non-)bactericidal posttranslationally modified peptides.






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BAGEL3: Automated identification of genes encoding bacteriocins and (non-)bactericidal posttranslationally modified peptides.

Nucleic Acids Res. 2013 Jul;41(Web…

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antiSMASH 2.0–a versatile platform for genome mining of secondary metabolite producers.






antiSMASH 2.0–a versatile platform for genome mining of secondary metabolite producers.

Nucleic Acids Res. 2013 Jun 3;

Authors: Blin K, Medema MH, Kazempour D, Fischbach MA,…

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






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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.






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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.






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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






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microRNAs associated with the different human Argonaute proteins.






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.






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






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antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences.






antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences.

Nucleic Acids Res. 2011 Jul;39(Web…

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