An mRNA-specific tRNAi carrier eIF2A plays a pivotal role in cell proliferation under stress conditions: stress-resistant translation of c-Src mRNA is mediated by eIF2A
c-Src, a non-receptor protein tyrosine kinase, activates NF-B and STAT3, which in turn triggers the transcription of anti-apoptosis- and cell cycle-related genes. c-Src protein regulates cell proliferation, cell motility and programmed cell death. And the elevated level of activated c-Src protein is related with solid tumor generation. Translation of c-Src mRNA is directed by an IRES element which mediates persistent translation under stress conditions when translation of most mRNAs is inhibited by a phosphorylation of the alpha subunit of eIF2 carrying the initiator tRNA (tRNAi) to 40S ribosomal subunit under normal condi...
Source: Nucleic Acids Research - January 8, 2017 Category: Research Authors: Kwon, O. S., An, S., Kim, E., Yu, J., Hong, K. Y., Lee, J. S., Jang, S. K. Tags: Molecular Biology Source Type: research
A single molecule study of a fluorescently labeled telomestatin derivative and G-quadruplex interactions
The potential use of G-quadruplex (GQ) stabilizing small molecules as anti-cancer drugs has created a flurry of activity on various aspects of these molecules. Telomestatin and oxazole telomestatin derivatives (OTD) are some of the most prominent of such molecules, yet the underlying dynamics of their interactions with GQ and the extent of heterogeneities in these interactions are not known. We performed single molecule measurements to study binding kinetics, rotational freedom, and dwell time distributions of a Cy5-labeled OTD (L1Cy5–7OTD) as it interacted with several different GQ structures. Our measurements show ...
Source: Nucleic Acids Research - January 8, 2017 Category: Research Authors: Maleki, P., Ma, Y., Iida, K., Nagasawa, K., Balci, H. Tags: Molecular Biology Source Type: research
Control of the negative IRES trans-acting factor KHSRP by ubiquitination
This study found that Lys109, Lys121 and Lys122 represent critical ubiquitination sites for far upstream element-binding protein 2 (KHSRP, also known as KH-type splicing regulatory protein or FBP2), a negative ITAF. Mutations at these sites subsequently reduced KHSRP ubiquitination and abolished its inhibitory effect on IRES-driven translation. We further found that interaction between the Kelch domain of Kelch-like protein 12 (KLHL12) and the C-terminal domain of KHSRP contributed to KHSRP ubiquitination, leading to downregulation of enterovirus IRES-mediated translation in infected cells and increased competition against...
Source: Nucleic Acids Research - January 8, 2017 Category: Research Authors: Kung, Y.-A., Hung, C.-T., Chien, K.-Y., Shih, S.-R. Tags: Molecular Biology Source Type: research
ATM induces MacroD2 nuclear export upon DNA damage
ADP-ribosylation is a dynamic post-translation modification that regulates the early phase of various DNA repair pathways by recruiting repair factors to chromatin. ADP-ribosylation levels are defined by the activities of specific transferases and hydrolases. However, except for the transferase PARP1/ARDT1 little is known about regulation of these enzymes. We found that MacroD2, a mono-ADP-ribosylhydrolase, is exported from the nucleus upon DNA damage, and that this nuclear export is induced by ATM activity. We show that the export is dependent on the phosphorylation of two SQ/TQ motifs, suggesting a novel direct interacti...
Source: Nucleic Acids Research - January 8, 2017 Category: Research Authors: Golia, B., Moeller, G. K., Jankevicius, G., Schmidt, A., Hegele, A., Preisser, J., Tran, M. L., Imhof, A., Timinszky, G. Tags: Genome Integrity, Repair and Replication Source Type: research
A double-strand break can trigger immunoglobulin gene conversion
All three B cell-specific activities of the immunoglobulin (Ig) gene re-modeling system—gene conversion, somatic hypermutation and class switch recombination—require activation-induced deaminase (AID). AID-induced DNA lesions must be further processed and dissected into different DNA recombination pathways. In order to characterize potential intermediates for Ig gene conversion, we inserted an I-SceI recognition site into the complementarity determining region 1 (CDR1) of the Ig light chain locus of the AID knockout DT40 cell line, and conditionally expressed I-SceI endonuclease. Here, we show that a double-str...
Source: Nucleic Acids Research - January 8, 2017 Category: Research Authors: Bastianello, G., Arakawa, H. Tags: Genome Integrity, Repair and Replication Source Type: research
Esc2 promotes Mus81 complex-activity via its SUMO-like and DNA binding domains
Replication across damaged DNA templates is accompanied by transient formation of sister chromatid junctions (SCJs). Cells lacking Esc2, an adaptor protein containing no known enzymatic domains, are defective in the metabolism of these SCJs. However, how Esc2 is involved in the metabolism of SCJs remains elusive. Here we show interaction between Esc2 and a structure-specific endonuclease Mus81-Mms4 (the Mus81 complex), their involvement in the metabolism of SCJs, and the effects Esc2 has on the enzymatic activity of the Mus81 complex. We found that Esc2 specifically interacts with the Mus81 complex via its SUMO-like domain...
Source: Nucleic Acids Research - January 8, 2017 Category: Research Authors: Sebesta, M., Urulangodi, M., Stefanovie, B., Szakal, B., Pacesa, M., Lisby, M., Branzei, D., Krejci, L. Tags: Genome Integrity, Repair and Replication Source Type: research
RHAU helicase stabilizes G4 in its nucleotide-free state and destabilizes G4 upon ATP hydrolysis
The DEAH-box ATP-dependent RHAU helicases specifically unfold RNA and DNA G-quadruplexes (G4s). However, it remains unclear how the RHAU's G4 unfolding activity is coupled to different stages of the ATPase cycle. Here, using a single-molecule manipulation approach, we show that binding of Drosophila RHAU stabilizes an intramolecularly folded parallel DNA G4 against mechanical unfolding in its nucleotide-free and in its AMP-PNP or ADP bound states, while it destabilizes the G4 when coupled to ATP hydrolysis. Importantly, our results show that the ADP·AlF$_4^-$-bound RHAU does not stabilize the G4. We also found that ...
Source: Nucleic Acids Research - January 8, 2017 Category: Research Authors: You, H., Lattmann, S., Rhodes, D., Yan, J. Tags: Genome Integrity, Repair and Replication Source Type: research
Activation of cGAS-dependent antiviral responses by DNA intercalating agents
Acridine dyes, including proflavine and acriflavine, were commonly used as antiseptics before the advent of penicillins in the mid-1940s. While their mode of action on pathogens was originally attributed to their DNA intercalating activity, work in the early 1970s suggested involvement of the host immune responses, characterized by induction of interferon (IFN)-like activities through an unknown mechanism. We demonstrate here that sub-toxic concentrations of a mixture of acriflavine and proflavine instigate a cyclic-GMP-AMP (cGAMP) synthase (cGAS)-dependent type-I IFN antiviral response. This pertains to the capacity of th...
Source: Nucleic Acids Research - January 8, 2017 Category: Research Authors: Pepin, G., Nejad, C., Thomas, B. J., Ferrand, J., McArthur, K., Bardin, P. G., Williams, B. R. G., Gantier, M. P. Tags: Genome Integrity, Repair and Replication Source Type: research
SAC3B, a central component of the mRNA export complex TREX-2, is required for prevention of epigenetic gene silencing in Arabidopsis
Epigenetic regulation is important for organismal development and response to the environment. Alteration in epigenetic status has been known mostly from the perspective of enzymatic actions of DNA methylation and/or histone modifications. In a genetic screen for cellular factors involved in preventing epigenetic silencing, we isolated an Arabidopsis mutant defective in SAC3B, a component of the conserved TREX-2 complex that couples mRNA transcription with nuleo-cytoplasmic export. Arabidopsis SAC3B dysfunction causes gene silencing at transgenic and endogenous loci, accompanied by elevation in the repressive histone mark ...
Source: Nucleic Acids Research - January 8, 2017 Category: Research Authors: Yang, Y., La, H., Tang, K., Miki, D., Yang, L., Wang, B., Duan, C.-G., Nie, W., Wang, X., Wang, S., Pan, Y., Tran, E. J., An, L., Zhang, H., Zhu, J.-K. Tags: Gene regulation, Chromatin and Epigenetics Source Type: research
H3K9me3 demethylase Kdm4d facilitates the formation of pre-initiative complex and regulates DNA replication
DNA replication is tightly regulated to occur once and only once per cell cycle. How chromatin, the physiological substrate of DNA replication machinery, regulates DNA replication remains largely unknown. Here we show that histone H3 lysine 9 demethylase Kdm4d regulates DNA replication in eukaryotic cells. Depletion of Kdm4d results in defects in DNA replication, which can be rescued by the expression of H3K9M, a histone H3 mutant transgene that reverses the effect of Kdm4d on H3K9 methylation. Kdm4d interacts with replication proteins, and its recruitment to DNA replication origins depends on the two pre-replicative compl...
Source: Nucleic Acids Research - January 8, 2017 Category: Research Authors: Wu, R., Wang, Z., Zhang, H., Gan, H., Zhang, Z. Tags: Gene regulation, Chromatin and Epigenetics Source Type: research
ADAR1 restricts LINE-1 retrotransposition
Adenosine deaminases acting on RNA (ADARs) are involved in RNA editing that converts adenosines to inosines in double-stranded RNAs. ADAR1 was demonstrated to be functional on different viruses exerting either antiviral or proviral effects. Concerning HIV-1, several studies showed that ADAR1 favors viral replication. The aim of this study was to investigate the composition of the ADAR1 ribonucleoprotein complex during HIV-1 expression. By using a dual-tag affinity purification procedure in cells expressing HIV-1 followed by mass spectrometry analysis, we identified 14 non-ribosomal ADAR1-interacting proteins, most of which...
Source: Nucleic Acids Research - January 8, 2017 Category: Research Authors: Orecchini, E., Doria, M., Antonioni, A., Galardi, S., Ciafre, S. A., Frassinelli, L., Mancone, C., Montaldo, C., Tripodi, M., Michienzi, A. Tags: Gene regulation, Chromatin and Epigenetics Source Type: research
The dual role of LSD1 and HDAC3 in STAT5-dependent transcription is determined by protein interactions, binding affinities, motifs and genomic positions
STAT5 interacts with other factors to control transcription, and the mechanism of regulation is of interest as constitutive active STAT5 has been reported in malignancies. Here, LSD1 and HDAC3 were identified as novel STAT5a interacting partners in pro-B cells. Characterization of STAT5a, LSD1 and HDAC3 target genes by ChIP-seq and RNA-seq revealed gene subsets regulated by independent or combined action of the factors and LSD1/HDAC3 to play dual role in their activation or repression. Genes bound by STAT5a alone or in combination with weakly associated LSD1 or HDAC3 were enriched for the canonical STAT5a GAS motif, and su...
Source: Nucleic Acids Research - January 8, 2017 Category: Research Authors: Nanou, A., Toumpeki, C., Lavigne, M. D., Lazou, V., Demmers, J., Paparountas, T., Thanos, D., Katsantoni, E. Tags: Gene regulation, Chromatin and Epigenetics Source Type: research
BRD4 localization to lineage-specific enhancers is associated with a distinct transcription factor repertoire
In this study we examined the role of BRD4 in promoting lineage-specific gene expression and show that BRD4 is essential for osteoblast differentiation. Genome-wide analyses demonstrate that BRD4 is recruited to the transcriptional start site of differentiation-induced genes. Unexpectedly, while promoter-proximal BRD4 occupancy correlated with gene expression, genes which displayed moderate expression and promoter-proximal BRD4 occupancy were most highly regulated and sensitive to BRD4 inhibition. Therefore, we examined distal BRD4 occupancy and uncovered a specific co-localization of BRD4 with the transcription factors C/...
Source: Nucleic Acids Research - January 8, 2017 Category: Research Authors: Najafova, Z., Tirado-Magallanes, R., Subramaniam, M., Hossan, T., Schmidt, G., Nagarajan, S., Baumgart, S. J., Mishra, V. K., Bedi, U., Hesse, E., Knapp, S., Hawse, J. R., Johnsen, S. A. Tags: Gene regulation, Chromatin and Epigenetics Source Type: research
Identification of a novel distal regulatory element of the human Neuroglobin gene by the chromosome conformation capture approach
In this study, we hypothesized that distal regulatory elements (DREs) are involved in optimal expression of the NGB gene. By chromosome conformation capture we identified two novel DREs located –70 kb upstream and +100 kb downstream from the NGB gene. ENCODE database showed the presence of DNaseI hypersensitive and transcription factors binding sites in these regions. Further analyses using luciferase reporters and chromatin immunoprecipitation suggested that the –70 kb region upstream of the NGB gene contained a neuronal-specific enhancer and GATA transcription factor binding sites. Knockdown of GATA-2 caused ...
Source: Nucleic Acids Research - January 8, 2017 Category: Research Authors: Tam, K. T., Chan, P. K., Zhang, W., Law, P. P., Tian, Z., Fung Chan, G. C., Philipsen, S., Festenstein, R., Tan-Un, K. C. Tags: Gene regulation, Chromatin and Epigenetics Source Type: research
A Pap1-Oxs1 signaling pathway for disulfide stress in Schizosaccharomyces pombe
We describe a Pap1–Oxs1 pathway for diamide-induced disulfide stress in Schizosaccharomyces pombe, where the nucleocytoplasmic HMG protein Oxs1 acts cooperatively with Pap1 to regulate transcription. Oxs1 and Pap1 form a complex when cells are exposed to diamide or Cd that causes disulfide stress. When examined for promoters up-regulated by diamide, effective Pap1 binding to these targets requires Oxs1, and vice versa. With some genes, each protein alone enhances transcription, but the presence of both exerts an additive positive effect. In other genes, although transcription is induced by diamide, Oxs1 or Pap1 plays...
Source: Nucleic Acids Research - January 8, 2017 Category: Research Authors: He, Y., Chen, Y., Song, W., Zhu, L., Dong, Z., Ow, D. W. Tags: Gene regulation, Chromatin and Epigenetics Source Type: research
