Global tRNA misacylation induced by anaerobiosis and antibiotic exposure broadly increases stress resistance in Escherichia coli
High translational fidelity is commonly considered a requirement for optimal cellular health and protein function. However, recent findings have shown that inducible mistranslation specifically with methionine engendered at the tRNA charging level occurs in mammalian cells, yeast and archaea, yet it was unknown whether bacteria were capable of mounting a similar response. Here, we demonstrate that Escherichia coli misacylates non-methionyl-tRNAs with methionine in response to anaerobiosis and antibiotic exposure via the methionyl–tRNA synthetase (MetRS). Two MetRS succinyl-lysine modifications independently confer hi...
Source: Nucleic Acids Research - December 1, 2016 Category: Research Authors: Schwartz, M. H., Waldbauer, J. R., Zhang, L., Pan, T. Tags: Molecular Biology Source Type: research
Differential cytokine sensitivities of STAT5-dependent enhancers rely on Stat5 autoregulation
This study provides, for the first time, molecular insight into the differential sensitivities of mammary-specific and universal cytokine-sensing enhancers. (Source: Nucleic Acids Research)
Source: Nucleic Acids Research - December 1, 2016 Category: Research Authors: Willi, M., Yoo, K. H., Wang, C., Trajanoski, Z., Hennighausen, L. Tags: Genomics Source Type: research
DNA damage response curtails detrimental replication stress and chromosomal instability induced by the dietary carcinogen PhIP
PhIP is an abundant heterocyclic aromatic amine (HCA) and important dietary carcinogen. Following metabolic activation, PhIP causes bulky DNA lesions at the C8-position of guanine. Although C8-PhIP-dG adducts are mutagenic, their interference with the DNA replication machinery and the elicited DNA damage response (DDR) have not yet been studied. Here, we analyzed PhIP-triggered replicative stress and elucidated the role of the apical DDR kinases ATR, ATM and DNA-PKcs in the cellular defense response. First, we demonstrate that PhIP induced C8-PhIP-dG adducts and DNA strand breaks. This stimulated ATR-CHK1 signaling, phosph...
Source: Nucleic Acids Research - December 1, 2016 Category: Research Authors: Mimmler, M., Peter, S., Kraus, A., Stroh, S., Nikolova, T., Seiwert, N., Hasselwander, S., Neitzel, C., Haub, J., Monien, B. H., Nicken, P., Steinberg, P., Shay, J. W., Kaina, B., Fahrer, J. Tags: Genome Integrity, Repair and Replication Source Type: research
Structural basis of damage recognition by thymine DNA glycosylase: Key roles for N-terminal residues
We report the first high-resolution structures of TDG in an enzyme-substrate complex, for G·U bound to TDG82-308 (1.54 Å) and TDG111-308 (1.71 Å), revealing new enzyme-substrate contacts, direct and water-mediated. We also report a structure of the TDG82-308 product complex (1.70 Å). TDG82-308 forms unique enzyme–DNA interactions, supporting its value for structure-function studies. The results advance understanding of how TDG recognizes and removes modified bases from DNA, particularly those resulting from deamination. (Source: Nucleic Acids Research)
Source: Nucleic Acids Research - December 1, 2016 Category: Research Authors: Coey, C. T., Malik, S. S., Pidugu, L. S., Varney, K. M., Pozharski, E., Drohat, A. C. Tags: Genome Integrity, Repair and Replication Source Type: research
Genome-wide identification and characterisation of human DNA replication origins by initiation site sequencing (ini-seq)
Next-generation sequencing has enabled the genome-wide identification of human DNA replication origins. However, different approaches to mapping replication origins, namely (i) sequencing isolated small nascent DNA strands (SNS-seq); (ii) sequencing replication bubbles (bubble-seq) and (iii) sequencing Okazaki fragments (OK-seq), show only limited concordance. To address this controversy, we describe here an independent high-resolution origin mapping technique that we call initiation site sequencing (ini-seq). In this approach, newly replicated DNA is directly labelled with digoxigenin-dUTP near the sites of its initiation...
Source: Nucleic Acids Research - December 1, 2016 Category: Research Authors: Langley, A. R., Gräf, S., Smith, J. C., Krude, T. Tags: Replication, Massively Parallel (Deep) Sequencing Genome integrity, repair and replication Source Type: research
Incision of damaged DNA in the presence of an impaired Smc5/6 complex imperils genome stability
The Smc5/6 complex is implicated in homologous recombination-mediated DNA repair during DNA damage or replication stress. Here, we analysed genome-wide replication dynamics in a hypomorphic budding yeast mutant, smc6-P4. The overall replication dynamics in the smc6 mutant is similar to that in the wild-type cells. However, we captured a difference in the replication profile of an early S phase sample in the mutant, prompting the hypothesis that the mutant incorporates ribonucleotides and/or accumulates single-stranded DNA gaps during replication. We tested if inhibiting the ribonucleotide excision repair pathway would exac...
Source: Nucleic Acids Research - December 1, 2016 Category: Research Authors: Peng, J., Feng, W. Tags: Genome Integrity, Repair and Replication Source Type: research
Novel TDP2-ubiquitin interactions and their importance for the repair of topoisomerase II-mediated DNA damage
Tyrosyl DNA phosphodiesterase 2 (TDP2) is a multifunctional protein implicated in DNA repair, signal transduction and transcriptional regulation. In its DNA repair role, TDP2 safeguards genome integrity by hydrolyzing 5'-tyrosyl DNA adducts formed by abortive topoisomerase II (Top2) cleavage complexes to allow error-free repair of DNA double-strand breaks, thereby conferring cellular resistance against Top2 poisons. TDP2 consists of a C-terminal catalytic domain responsible for its phosphodiesterase activity, and a functionally uncharacterized N-terminal region. Here, we demonstrate that this N-terminal region contains a u...
Source: Nucleic Acids Research - December 1, 2016 Category: Research Authors: Rao, T., Gao, R., Takada, S., Al Abo, M., Chen, X., Walters, K. J., Pommier, Y., Aihara, H. Tags: Genome Integrity, Repair and Replication Source Type: research
Insights into the regulation of small RNA expression: SarA represses the expression of two sRNAs in Staphylococcus aureus
The opportunistic pathogen Staphylococcus aureus expresses transcription factors (TFs) and regulatory small RNAs (sRNAs) which are essential for bacterial adaptation and infectivity. Until recently, the study of S. aureus sRNA gene expression regulation was under investigated, but it is now an expanding field. Here we address the regulation of Srn_3610_SprC sRNA, an attenuator of S. aureus virulence. We demonstrate that SarA TF represses srn_3610_sprC transcription. DNase I footprinting and deletion analyses show that the SarA binding site on srn_3610_sprC belongs to an essential 22 bp DNA region. Comparative analysis also...
Source: Nucleic Acids Research - December 1, 2016 Category: Research Authors: Mauro, T., Rouillon, A., Felden, B. Tags: Gene regulation, Chromatin and Epigenetics Source Type: research
Distinctive Klf4 mutants determine preference for DNA methylation status
We examined the role of Glu446 by mutagenesis. Substituting Glu446 with aspartate (E446D) resulted in preference for unmodified cytosine, due to decreased affinity for 5mC. In contrast, substituting Glu446 with proline (E446P) increased affinity for 5mC by two orders of magnitude. Structural analysis revealed hydrophobic interaction between the proline's aliphatic cyclic structure and the 5-methyl group of the pyrimidine (5mC or T). As in wild-type Klf4 (E446), the proline at position 446 does not interact directly with either the 5mC N4 nitrogen or the thymine O4 oxygen. In contrast, the unmethylated cytosine's exocyclic ...
Source: Nucleic Acids Research - December 1, 2016 Category: Research Authors: Hashimoto, H., Wang, D., Steves, A. N., Jin, P., Blumenthal, R. M., Zhang, X., Cheng, X. Tags: Gene regulation, Chromatin and Epigenetics Source Type: research
Denys-Drash syndrome associated WT1 glutamine 369 mutants have altered sequence-preferences and altered responses to epigenetic modifications
We examined three DDS associated mutations in ZF2 of human WT1 where the normal glutamine at position 369 is replaced by arginine (Q369R), lysine (Q369K) or histidine (Q369H). These mutations alter the sequence-specificity of ZF2, we find, changing its affinity for certain bases and certain epigenetic forms of cytosine. X-ray crystallography of the DNA binding domains of normal WT1, Q369R and Q369H in complex with preferred sequences revealed the molecular interactions responsible for these affinity changes. DDS is inherited in an autosomal dominant fashion, implying a gain of function by mutant WT1 proteins. This gain, we...
Source: Nucleic Acids Research - December 1, 2016 Category: Research Authors: Hashimoto, H., Zhang, X., Zheng, Y., Wilson, G. G., Cheng, X. Tags: Protein-nucleic acid interaction, Targeted inhibition of gene function Gene regulation, Chromatin and Epigenetics Source Type: research
Genome-wide co-localization of active EGFR and downstream ERK pathway kinases mirrors mitogen-inducible RNA polymerase 2 genomic occupancy
Genome-wide mechanisms that coordinate expression of subsets of functionally related genes are largely unknown. Recent studies show that receptor tyrosine kinases and components of signal transduction cascades including the extracellular signal-regulated protein kinase (ERK), once thought to act predominantly in the vicinity of plasma membrane and in the cytoplasm, can be recruited to chromatin encompassing transcribed genes. Genome-wide distribution of these transducers and their relationship to transcribing RNA polymerase II (Pol2) could provide new insights about co-regulation of functionally related gene subsets. Chrom...
Source: Nucleic Acids Research - December 1, 2016 Category: Research Authors: Mikula, M., Skrzypczak, M., Goryca, K., Paczkowska, K., Ledwon, J. K., Statkiewicz, M., Kulecka, M., Grzelak, M., Dabrowska, M., Kuklinska, U., Karczmarski, J., Rumienczyk, I., Jastrzebski, K., Miaczynska, M., Ginalski, K., Bomsztyk, K., Ostrowski, J. Tags: Gene regulation, Chromatin and Epigenetics Source Type: research
Interdependence of PRC1 and PRC2 for recruitment to Polycomb Response Elements
Polycomb Group (PcG) proteins are epigenetic repressors essential for control of development and cell differentiation. They form multiple complexes of which PRC1 and PRC2 are evolutionary conserved and obligatory for repression. The targeting of PRC1 and PRC2 is poorly understood and was proposed to be hierarchical and involve tri-methylation of histone H3 (H3K27me3) and/or monoubiquitylation of histone H2A (H2AK118ub). Here, we present a strict test of this hypothesis using the Drosophila model. We discover that neither H3K27me3 nor H2AK118ub is required for targeting PRC complexes to Polycomb Response Elements (PREs). We...
Source: Nucleic Acids Research - December 1, 2016 Category: Research Authors: Kahn, T. G., Dorafshan, E., Schultheis, D., Zare, A., Stenberg, P., Reim, I., Pirrotta, V., Schwartz, Y. B. Tags: Gene regulation, Chromatin and Epigenetics Source Type: research
Silencing of cryptic prophages in Corynebacterium glutamicum
In this study, we describe the nucleoid-associated protein CgpS, which represents an essential protein functioning as a xenogeneic silencer in the Gram-positive Corynebacterium glutamicum. CgpS is encoded by the cryptic prophage CGP3 of the C. glutamicum strain ATCC 13032 and was first identified by DNA affinity chromatography using an early phage promoter of CGP3. Genome-wide profiling of CgpS binding using chromatin affinity purification and sequencing (ChAP-Seq) revealed its association with AT-rich DNA elements, including the entire CGP3 prophage region (187 kbp), as well as several other elements acquired by horizonta...
Source: Nucleic Acids Research - December 1, 2016 Category: Research Authors: Pfeifer, E., Hünnefeld, M., Popa, O., Polen, T., Kohlheyer, D., Baumgart, M., Frunzke, J. Tags: Gene regulation, Chromatin and Epigenetics Source Type: research
Evaluating the impact of single nucleotide variants on transcription factor binding
Diseases and phenotypes caused by disrupted transcription factor (TF) binding are being identified, but progress is hampered by our limited capacity to predict such functional alterations. Improving predictions may be dependent on expanding the set of bona fide TF binding alterations. Allele-specific binding (ASB) events, where TFs preferentially bind to one of the two alleles at heterozygous sites, reveal the impact of sequence variations in altered TF binding. Here, we present the largest ASB compilation to our knowledge, 10 765 ASB events retrieved from 45 ENCODE ChIP-Seq data sets. Our analysis showed that ASB events w...
Source: Nucleic Acids Research - December 1, 2016 Category: Research Authors: Shi, W., Fornes, O., Mathelier, A., Wasserman, W. W. Tags: Gene regulation, Chromatin and Epigenetics Source Type: research
Dissecting relative contributions of cis- and trans-determinants to nucleosome distribution by comparing Tetrahymena macronuclear and micronuclear chromatin
The ciliate protozoan Tetrahymena thermophila contains two types of structurally and functionally differentiated nuclei: the transcriptionally active somatic macronucleus (MAC) and the transcriptionally silent germ-line micronucleus (MIC). Here, we demonstrate that MAC features well-positioned nucleosomes downstream of transcription start sites and flanking splice sites. Transcription-associated trans-determinants promote nucleosome positioning in MAC. By contrast, nucleosomes in MIC are dramatically delocalized. Nucleosome occupancy in MAC and MIC are nonetheless highly correlated with each other, as well as with in vitro...
Source: Nucleic Acids Research - December 1, 2016 Category: Research Authors: Xiong, J., Gao, S., Dui, W., Yang, W., Chen, X., Taverna, S. D., Pearlman, R. E., Ashlock, W., Miao, W., Liu, Y. Tags: Gene regulation, Chromatin and Epigenetics Source Type: research
