Rev1 is a base excision repair enzyme with 5'-deoxyribose phosphate lyase activity
Rev1 is a member of the Y-family of DNA polymerases and is known for its deoxycytidyl transferase activity that incorporates dCMP into DNA and its ability to function as a scaffold factor for other Y-family polymerases in translesion bypass events. Rev1 also is involved in mutagenic processes during somatic hypermutation of immunoglobulin genes. In light of the mutation pattern consistent with dCMP insertion observed earlier in mouse fibroblast cells treated with a base excision repair-inducing agent, we questioned whether Rev1 could also be involved in base excision repair (BER). Here, we uncovered a weak 5'-deoxyribose p...
Source: Nucleic Acids Research - December 14, 2016 Category: Research Authors: Prasad, R., Poltoratsky, V., Hou, E. W., Wilson, S. H. Tags: Nucleic Acid Enzymes Source Type: research
Single-molecule analysis of {phi}C31 integrase-mediated site-specific recombination by tethered particle motion
Serine and tyrosine site-specific recombinases (SRs and YRs, respectively) provide templates for understanding the chemical mechanisms and conformational dynamics of strand cleavage/exchange between DNA partners. Current evidence suggests a rather intriguing mechanism for serine recombination, in which one half of the cleaved synaptic complex undergoes a 180° rotation relative to the other. The ‘small’ and ‘large’ SRs contain a compact amino-terminal catalytic domain, but differ conspicuously in their carboxyl-terminal domains. So far, only one serine recombinase has been analyzed using single s...
Source: Nucleic Acids Research - December 14, 2016 Category: Research Authors: Fan, H.-F., Hsieh, T.-s., Ma, C.-H., Jayaram, M. Tags: Nucleic Acid Enzymes Source Type: research
Altered biochemical specificity of G-quadruplexes with mutated tetrads
A fundamental motif in canonical nucleic acid structure is the base pair. Mutations that disrupt base pairs are typically destabilizing, but stability can often be restored by a second mutation that replaces the original base pair with an isosteric variant. Such concerted changes are a way to identify helical regions in secondary structures and to identify new functional motifs in sequenced genomes. In principle, such analysis can be extended to non-canonical nucleic acid structures, but this approach has not been utilized because the sequence requirements of such structures are not well understood. Here we investigate the...
Source: Nucleic Acids Research - December 14, 2016 Category: Research Authors: Svehlova, K., Lawrence, M. S., Bednarova, L., Curtis, E. A. Tags: Molecular Biology Source Type: research
Human eIF3b and eIF3a serve as the nucleation core for the assembly of eIF3 into two interconnected modules: the yeast-like core and the octamer
This study, outlining the mechanism of eIF3 assembly and illustrating how imbalanced expression of eIF3 subunits impacts the factor's overall expression profile, thus provides a comprehensive guide to the human eIF3 complex and to the relationship between eIF3 misregulation and cancer. (Source: Nucleic Acids Research)
Source: Nucleic Acids Research - December 14, 2016 Category: Research Authors: Wagner, S., Herrmannova, A., Sikrova, D., Valasek, L. S. Tags: Molecular Biology Source Type: research
FANCI-FANCD2 stabilizes the RAD51-DNA complex by binding RAD51 and protects the 5'-DNA end
The FANCI-FANCD2 (I-D) complex is considered to work with RAD51 to protect the damaged DNA in the stalled replication fork. However, the means by which this DNA protection is accomplished have remained elusive. In the present study, we found that the I-D complex directly binds to RAD51, and stabilizes the RAD51-DNA filament. Unexpectedly, the DNA binding activity of FANCI, but not FANCD2, is explicitly required for the I-D complex-mediated RAD51-DNA filament stabilization. The RAD51 filament stabilized by the I-D complex actually protects the DNA end from nucleolytic degradation by an FA-associated nuclease, FAN1. This DNA...
Source: Nucleic Acids Research - December 14, 2016 Category: Research Authors: Sato, K., Shimomuki, M., Katsuki, Y., Takahashi, D., Kobayashi, W., Ishiai, M., Miyoshi, H., Takata, M., Kurumizaka, H. Tags: Genome Integrity, Repair and Replication Source Type: research
Rad51 and Rad54 promote noncrossover recombination between centromere repeats on the same chromatid to prevent isochromosome formation
Centromeres consist of DNA repeats in many eukaryotes. Non-allelic homologous recombination (HR) between them can result in gross chromosomal rearrangements (GCRs). In fission yeast, Rad51 suppresses isochromosome formation that occurs between inverted repeats in the centromere. However, how the HR enzyme prevents homology-mediated GCRs remains unclear. Here, we provide evidence that Rad51 with the aid of the Swi/Snf-type motor protein Rad54 promotes non-crossover recombination between centromere repeats to prevent isochromosome formation. Mutations in Rad51 and Rad54 epistatically increased the rates of isochromosome form...
Source: Nucleic Acids Research - December 14, 2016 Category: Research Authors: Onaka, A. T., Toyofuku, N., Inoue, T., Okita, A. K., Sagawa, M., Su, J., Shitanda, T., Matsuyama, R., Zafar, F., Takahashi, T. S., Masukata, H., Nakagawa, T. Tags: Genome Integrity, Repair and Replication Source Type: research
Adaptive upregulation of DNA repair genes following benzo(a)pyrene diol epoxide protects against cell death at the expense of mutations
A coordinated and faithful DNA damage response is of central importance for maintaining genomic integrity and survival. Here, we show that exposure of human cells to benzo(a)pyrene 9,10-diol-7,8-epoxide (BPDE), the active metabolite of benzo(a)pyrene (B(a)P), which represents a most important carcinogen formed during food preparation at high temperature, smoking and by incomplete combustion processes, causes a prompt and sustained upregulation of the DNA repair genes DDB2, XPC, XPF, XPG and POLH. Induction of these repair factors on RNA and protein level enhanced the removal of BPDE adducts from DNA and protected cells aga...
Source: Nucleic Acids Research - December 14, 2016 Category: Research Authors: Christmann, M., Boisseau, C., Kitzinger, R., Berac, C., Allmann, S., Sommer, T., Aasland, D., Kaina, B., Tomicic, M. T. Tags: Genome Integrity, Repair and Replication Source Type: research
AKAP12 mediates PKA-induced phosphorylation of ATR to enhance nucleotide excision repair
Loss-of-function in melanocortin 1 receptor (MC1R), a GS protein-coupled receptor that regulates signal transduction through cAMP and protein kinase A (PKA) in melanocytes, is a major inherited melanoma risk factor. Herein, we report a novel cAMP-mediated response for sensing and responding to UV-induced DNA damage regulated by A-kinase-anchoring protein 12 (AKAP12). AKAP12 is identified as a necessary participant in PKA-mediated phosphorylation of ataxia telangiectasia mutated and Rad3-related (ATR) at S435, a post-translational event required for cAMP-enhanced nucleotide excision repair (NER). Moreover, UV exposure promo...
Source: Nucleic Acids Research - December 14, 2016 Category: Research Authors: Jarrett, S. G., Wolf Horrell, E. M., D'Orazio, J. A. Tags: Genome Integrity, Repair and Replication Source Type: research
Single-molecule FRET studies of the cooperative and non-cooperative binding kinetics of the bacteriophage T4 single-stranded DNA binding protein (gp32) to ssDNA lattices at replication fork junctions
Gene 32 protein (gp32) is the single-stranded (ss) DNA binding protein of the bacteriophage T4. It binds transiently and cooperatively to ssDNA sequences exposed during the DNA replication process and regulates the interactions of the other sub-assemblies of the replication complex during the replication cycle. We here use single-molecule FRET techniques to build on previous thermodynamic studies of gp32 binding to initiate studies of the dynamics of the isolated and cooperative binding of gp32 molecules within the replication complex. DNA primer/template (p/t) constructs are used as models to determine the effects of ssDN...
Source: Nucleic Acids Research - December 14, 2016 Category: Research Authors: Lee, W., Gillies, J. P., Jose, D., Israels, B. A., von Hippel, P. H., Marcus, A. H. Tags: Computational Methods, Nucleic Acid Enzymology Genome integrity, repair and replication Source Type: research
Nucleolytic processing of aberrant replication intermediates by an Exo1-Dna2-Sae2 axis counteracts fork collapse-driven chromosome instability
Problems during DNA replication underlie genomic instability and drive malignant transformation. The DNA damage checkpoint stabilizes stalled replication forks thus counteracting aberrant fork transitions, DNA breaks and chromosomal rearrangements. We analyzed fork processing in checkpoint deficient cells by coupling psoralen crosslinking with replication intermediate two-dimensional gel analysis. This revealed a novel role for Exo1 nuclease in resecting reversed replication fork structures and counteracting the accumulation of aberrant intermediates resembling fork cleavage products. Genetic analyses demonstrated a functi...
Source: Nucleic Acids Research - December 14, 2016 Category: Research Authors: Colosio, A., Frattini, C., Pellicano, G., Villa-Hernandez, S., Bermejo, R. Tags: Genome Integrity, Repair and Replication Source Type: research
PCAF-mediated acetylation of transcriptional factor HOXB9 suppresses lung adenocarcinoma progression by targeting oncogenic protein JMJD6
HOXB9 is a homeobox domain-containing transcription factor, playing an important role in embryonic development and cancer progression. However, the precise post-translational modifications (PTMs) of HOXB9 and the corresponding roles are unclear. Here, we report that acetyltransferase p300/CBP-associated factor (PCAF) interacts with and acetylates HOXB9 both in vivo and in vitro. Conversely, the acetylation of HOXB9 can be reversed by deacetylase SIRT1. Furthermore, we found that HOXB9 is acetylated at lysine 27 (AcK27). Functionally, in contrast to the wild type HOXB9, AcK27-HOXB9 decreased its capacity in promoting lung c...
Source: Nucleic Acids Research - December 14, 2016 Category: Research Authors: Wan, J., Xu, W., Zhan, J., Ma, J., Li, X., Xie, Y., Wang, J., Zhu, W.-g., Luo, J., Zhang, H. Tags: Gene regulation, Chromatin and Epigenetics Source Type: research
The lncRNA HOTAIR impacts on mesenchymal stem cells via triple helix formation
In this study, we analyzed the role of the lncRNA HOTAIR in mesenchymal stem cells (MSCs) with particular focus on senescence-associated changes in gene expression and DNA-methylation (DNAm). HOTAIR binding sites were enriched at genomic regions that become hypermethylated with increasing cell culture passage. Overexpression and knockdown of HOTAIR inhibited or stimulated adipogenic differentiation of MSCs, respectively. Modification of HOTAIR expression evoked only very moderate effects on gene expression, particularly of polycomb group target genes. Furthermore, overexpression and knockdown of HOTAIR resulted in DNAm cha...
Source: Nucleic Acids Research - December 14, 2016 Category: Research Authors: Kalwa, M., Hänzelmann, S., Otto, S., Kuo, C.-C., Franzen, J., Joussen, S., Fernandez-Rebollo, E., Rath, B., Koch, C., Hofmann, A., Lee, S.-H., Teschendorff, A. E., Denecke, B., Lin, Q., Widschwendter, M., Weinhold, E., Costa, I. G., Wagner, W. Tags: Gene regulation, Chromatin and Epigenetics Source Type: research
Transcription-coupled changes to chromatin underpin gene silencing by transcriptional interference
Long non-coding RNA (lncRNA) transcription into a downstream promoter frequently results in transcriptional interference. However, the mechanism of this repression is not fully understood. We recently showed that drug tolerance in fission yeast Schizosaccharomyces pombe is controlled by lncRNA transcription upstream of the tgp1+ permease gene. Here we demonstrate that transcriptional interference of tgp1+ involves several transcription-coupled chromatin changes mediated by conserved elongation factors Set2, Clr6CII, Spt6 and FACT. These factors are known to travel with RNAPII and establish repressive chromatin in order to ...
Source: Nucleic Acids Research - December 14, 2016 Category: Research Authors: Ard, R., Allshire, R. C. Tags: Gene regulation, Chromatin and Epigenetics Source Type: research
A feedback loop comprising PRMT7 and miR-24-2 interplays with Oct4, Nanog, Klf4 and c-Myc to regulate stemness
Self-renewal and pluripotency are two fundamental characteristics of embryonic stem cells (ESCs) and are controlled by diverse regulatory factors, including pluripotent factors, epigenetic regulators and microRNAs (miRNAs). Although histone methyltransferases are key epigenetic regulators, whether and how a histone methyltransferase forms a network with miRNAs and the core pluripotent factor system to regulate ESC stemness is little known. Here, we show that the protein arginine methyltransferase 7 (PRMT7) is a pluripotent factor essential for the stemness of mouse ESCs. PRMT7 repressed the miR-24-2 gene encoding miR-24-3p...
Source: Nucleic Acids Research - December 14, 2016 Category: Research Authors: Lee, S.-H., Chen, T.-Y., Dhar, S. S., Gu, B., Chen, K., Kim, Y. Z., Li, W., Lee, M. G. Tags: Gene regulation, Chromatin and Epigenetics Source Type: research
CTCF modulates Estrogen Receptor function through specific chromatin and nuclear matrix interactions
Enhancer regions and transcription start sites of estrogen-target regulated genes are connected by means of Estrogen Receptor long-range chromatin interactions. Yet, the complete molecular mechanisms controlling the transcriptional output of engaged enhancers and subsequent activation of coding genes remain elusive. Here, we report that CTCF binding to enhancer RNAs is enriched when breast cancer cells are stimulated with estrogen. CTCF binding to enhancer regions results in modulation of estrogen-induced gene transcription by preventing Estrogen Receptor chromatin binding and by hindering the formation of additional enhan...
Source: Nucleic Acids Research - December 14, 2016 Category: Research Authors: Fiorito, E., Sharma, Y., Gilfillan, S., Wang, S., Singh, S. K., Satheesh, S. V., Katika, M. R., Urbanucci, A., Thiede, B., Mills, I. G., Hurtado, A. Tags: Gene regulation, Chromatin and Epigenetics Source Type: research
