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Z-DNA binding protein

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https://www.readbyqxmd.com/read/29721152/tumor-cell-death-after-electrotransfer-of-plasmid-dna-is-associated-with-cytosolic-dna-sensor-upregulation
#1
Katarina Znidar, Masa Bosnjak, Nina Semenova, Olga Pakhomova, Loree Heller, Maja Cemazar
Cytosolic DNA sensors are a subgroup of pattern recognition receptors (PRRs) and are activated by the abnormal presence of the DNA in the cytosol. Their activation leads to the upregulation of pro-inflammatory cytokines and chemokines and can also induce cell death. The presence of cytosolic DNA sensors and inflammatory cytokines in TS/A murine mammary adenocarcinoma and WEHI 164 fibrosarcoma cells was demonstrated using real time reverse transcription polymerase chain reaction (RT-PCR), western blotting and enzyme-linked immunosorbent assay (ELISA)...
April 10, 2018: Oncotarget
https://www.readbyqxmd.com/read/29679468/high-efficiency-affinity-precipitation-of-multiple-industrial-mabs-and-fc-fusion-proteins-from-cell-culture-harvests-using-z-elp-e2-nanocages
#2
Andrew R Swartz, Xuankuo Xu, Steven J Traylor, Zheng Jian Li, Wilfred Chen
Affinity precipitation using Z-ELP-E2 nanocages has been shown to be a promising alternative to Protein A chromatography for monoclonal antibody (mAb) purification. We have previously described a high-yielding, affinity precipitation process capable of rapidly capturing mAbs from cell culture through spontaneous, multi-valent crosslinking into large aggregates. To challenge the capabilities of this technology, nanocage affinity precipitation was investigated using four industrial mAbs (mAbs A-D) and one Fc fusion protein (Fc A) with diverse molecular properties...
April 21, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/29643509/structural-basis-for-atp-dependent-chromatin-remodelling-by-the-ino80-complex
#3
Sebastian Eustermann, Kevin Schall, Dirk Kostrewa, Kristina Lakomek, Mike Strauss, Manuela Moldt, Karl-Peter Hopfner
In the eukaryotic nucleus, DNA is packaged in the form of nucleosomes, each of which comprises about 147 base pairs of DNA wrapped around a histone protein octamer. The position and histone composition of nucleosomes is governed by ATP-dependent chromatin remodellers1-3 such as the 15-subunit INO80 complex 4 . INO80 regulates gene expression, DNA repair and replication by sliding nucleosomes, the exchange of histone H2A.Z with H2A, and the positioning of + 1 and -1 nucleosomes at promoter DNA5-8 . The structures and mechanisms of these remodelling reactions are currently unknown...
April 11, 2018: Nature
https://www.readbyqxmd.com/read/29604400/arabidopsis-swc4-binds-dna-and-recruits-the-swr1-complex-to-modulate-histone-h2a-z-deposition-at-key-regulatory-genes
#4
Ángeles Gómez-Zambrano, Pedro Crevillén, José M Franco-Zorrilla, Juan A López, Jordi Moreno-Romero, Pawel Roszak, Juan Santos-González, Silvia Jurado, Jesús Vázquez, Claudia Köhler, Roberto Solano, Manuel Piñeiro, José A Jarillo
Deposition of the H2A.Z histone variant by the SWR1 complex (SWR1-C) in regulatory regions of specific loci modulates transcription. Characterization of Arabidopsis thaliana mutations in homologs of the yeast SWR1-C has revealed a role for H2A.Z exchange in a variety of developmental processes; nevertheless, the exact composition of the plant SWR1-C and how it is recruited to target genes remains to be established. Here we show that SWC4, the Arabidopsis homolog of the yeast SANT domain protein Swc4/Eaf2, is a DNA-binding protein that interacts with SWR1-C subunits...
March 28, 2018: Molecular Plant
https://www.readbyqxmd.com/read/29584891/unveiling-the-pathway-to-z-dna-in-the-protein-induced-b-z-transition
#5
Sook Ho Kim, So-Hee Lim, Ae-Ree Lee, Do Hoon Kwon, Hyun Kyu Song, Joon-Hwa Lee, Minhaeng Cho, Albert Johner, Nam-Kyung Lee, Seok-Cheol Hong
Left-handed Z-DNA is an extraordinary conformation of DNA, which can form by special sequences under specific biological, chemical or physical conditions. Human ADAR1, prototypic Z-DNA binding protein (ZBP), binds to Z-DNA with high affinity. Utilizing single-molecule FRET assays for Z-DNA forming sequences embedded in a long inactive DNA, we measure thermodynamic populations of ADAR1-bound DNA conformations in both GC and TG repeat sequences. Based on a statistical physics model, we determined quantitatively the affinities of ADAR1 to both Z-form and B-form of these sequences...
March 23, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29549582/the-conserved-histone-variant-h2a-z-illuminates-meiotic-recombination-initiation
#6
REVIEW
Shintaro Yamada, Kazuto Kugou, Da-Qiao Ding, Yurika Fujita, Yasushi Hiraoka, Hiroshi Murakami, Kunihiro Ohta, Takatomi Yamada
Meiotic recombination ensures faithful chromosome segregation and confers genetic diversity to gametes, and thus, is a key DNA-templated reaction not only for sexual reproduction, but also evolution. This recombination is initiated by programmed DNA double strand breaks (DSBs), which are mainly formed at recombination hotspots. As meiotic DSB formation requires multiple proteins, it is regulated by chromatin structure. In particular, DSB occurs in a higher-order chromatin architecture termed "axis-loop", in which many loops protrude from proteinaceous axis...
March 16, 2018: Current Genetics
https://www.readbyqxmd.com/read/29532848/c8-guanine-modifications-effect-on-z-dna-formation-and-its-role-in-cancer
#7
REVIEW
V Vongsutilers, P M Gannett
Base modifications are known to affect the structure and function of DNA. C8-guanine adducts from various carcinogenic compounds have been shown to be potent Z-DNA inducers. Hence, it has been hypothesized that Z-DNA plays a role in cancer and other genetic diseases. In this comprehensive review, Z-DNA and the effect of prevalent C8-guanine adducts on the B-Z transition are addressed. The discoveries of Z-DNA binding proteins including ADAR1, E3L, DLM1, and PKZ have suggested the relevance of Z-DNA in living systems...
March 28, 2018: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/29531287/atomic-level-evidence-for-packing-and-positional-amyloid-polymorphism-by-segment-from-tdp-43-rrm2
#8
Elizabeth L Guenther, Peng Ge, Hamilton Trinh, Michael R Sawaya, Duilio Cascio, David R Boyer, Tamir Gonen, Z Hong Zhou, David S Eisenberg
Proteins in the fibrous amyloid state are a major hallmark of neurodegenerative disease. Understanding the multiple conformations, or polymorphs, of amyloid proteins at the molecular level is a challenge of amyloid research. Here, we detail the wide range of polymorphs formed by a segment of human TAR DNA-binding protein 43 (TDP-43) as a model for the polymorphic capabilities of pathological amyloid aggregation. Using X-ray diffraction, microelectron diffraction (MicroED) and single-particle cryo-EM, we show that the 247 DLIIKGISVHI257 segment from the second RNA-recognition motif (RRM2) forms an array of amyloid polymorphs...
April 2018: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/29518238/the-dnmt3a-r882h-mutant-displays-altered-flanking-sequence-preferences
#9
Max Emperle, Arumugam Rajavelu, Stefan Kunert, Paola B Arimondo, Richard Reinhardt, Renata Z Jurkowska, Albert Jeltsch
The DNMT3A R882H mutation is frequently observed in acute myeloid leukemia (AML). It is located in the subunit and DNA binding interface of DNMT3A and has been reported to cause a reduction in activity and dominant negative effects. We investigated the mechanistic consequences of the R882H mutation on DNMT3A showing a roughly 40% reduction in overall DNA methylation activity. Biochemical assays demonstrated that R882H does not change DNA binding affinity, protein stability or subnuclear distribution of DNMT3A...
April 6, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29509313/creutzfeldt-astrocytes-may-be-seen-in-idh-wildtype-glioblastoma-and-retain-expression-of-dna-repair-and-chromatin-binding-proteins
#10
Leomar Y Ballester, Zain Boghani, David S Baskin, Gavin W Britz, Randall Olsen, Gregory N Fuller, Suzanne Z Powell, Matthew D Cykowski
Astrocytes with multiple micronuclei ("Creutzfeldt cells") in a brain biopsy are classically associated with demyelinating disease. However, glioblastoma may also have prominent Creutzfeldt astrocytes, along with granular mitoses. Therefore, Creutzfeldt cells may raise the diagnostic dilemma of high-grade glioma vs tumefactive demyelination. While cases of glioblastoma (GBM) with Creutzfeldt astrocytes have been reported, their clinicopathologic spectrum and genetic features are not understood. Studies have proposed that micronuclei in Creutzfeldt cells are a consequence of DNA damage, or may be susceptible to DNA damage and chromothripsis, but their biology in the context of glioblastoma remains unclear...
March 6, 2018: Brain Pathology
https://www.readbyqxmd.com/read/29460483/molecular-cloning-and-expression-analysis-of-tyr-and-tyrp1-genes-in-normal-and-albino-yellow-catfish-tachysurus-fulvidraco
#11
X T Zhang, K J Wei, Y Y Chen, Z C Shi, L K Liu, J Li, G R Zhang, W Ji
The full-length complementary DNA of two genes related to vertebrate albinism, the tyrosinase gene tyr and tyrosinase-related protein 1 gene tyrp1, were cloned and analysed from normal and albino yellow catfish Tachysurus fulvidraco. The open reading frames (ORF) of tyr and tyrp1 encode putative peptides of 533 and 526 amino acids (amino-acid), both of which possess two conserved copper binding sites. The homologous identities of deduced amino-acid sequences showed that both Tyr and Tyrp1 of T. fulvidraco share considerable similarity with that of channel catfish Ictalurus punctatus...
April 2018: Journal of Fish Biology
https://www.readbyqxmd.com/read/29443623/calprotectin-and-the-initiation-and-progression-of-head-and-neck-cancer
#12
P P Argyris, Z M Slama, K F Ross, A Khammanivong, M C Herzberg
Calprotectin (S100A8/A9), a heterodimeric complex of calcium-binding proteins S100A8 and S100A9, is encoded by genes mapping to the chromosomal locus 1q21.3 of the epidermal differentiation complex. Whereas extracellular calprotectin shows proinflammatory and antimicrobial properties by signaling through RAGE and TLR4, intracytoplasmic S100A8/A9 appears to be important for cellular development, maintenance, and survival. S100A8/A9 is constitutively expressed in myeloid cells and the stratified mucosal epithelia lining the oropharyngeal and genitourinary mucosae...
February 1, 2018: Journal of Dental Research
https://www.readbyqxmd.com/read/29432187/global-changes-of-h3k27me3-domains-and-polycomb-group-protein-distribution-in-the-absence-of-recruiters-spps-or-pho
#13
J Lesley Brown, Ming-An Sun, Judith A Kassis
Polycomb group (PcG) proteins maintain the silenced state of key developmental genes in animals, but how these proteins are recruited to specific regions of the genome is still poorly understood. In Drosophila , PcG proteins are recruited to Polycomb response elements (PREs) that include combinations of sites for sequence specific DNA binding "PcG recruiters," including Pho, Cg, and Spps. To understand their roles in PcG recruitment, we compared Pho-, Cg-, and Spps-binding sites against H3K27me3 and key PcG proteins by ChIP-seq in wild-type and mutant third instar larvae...
February 20, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29400712/noncanonical-hedgehog-pathway-activation-through-srf-mkl1-promotes-drug-resistance-in-basal-cell-carcinomas
#14
Ramon J Whitson, Alex Lee, Nicole M Urman, Amar Mirza, Catherine Y Yao, Alexander S Brown, Jiang R Li, Gautam Shankar, Micah A Fry, Scott X Atwood, Eunice Y Lee, S Tyler Hollmig, Sumaira Z Aasi, Kavita Y Sarin, Matthew P Scott, Ervin H Epstein, Jean Y Tang, Anthony E Oro
Hedgehog pathway-dependent cancers can escape Smoothened (SMO) inhibition through mutations in genes encoding canonical hedgehog pathway components; however, around 50% of drug-resistant basal cell carcinomas (BCCs) lack additional variants of these genes. Here we use multidimensional genomics analysis of human and mouse drug-resistant BCCs to identify a noncanonical hedgehog activation pathway driven by the transcription factor serum response factor (SRF). Active SRF along with its coactivator megakaryoblastic leukemia 1 (MKL1) binds DNA near hedgehog target genes and forms a previously unknown protein complex with the hedgehog transcription factor glioma-associated oncogene family zinc finger-1 (GLI1), causing amplification of GLI1 transcriptional activity...
March 2018: Nature Medicine
https://www.readbyqxmd.com/read/29389011/reprogramming-cell-fate-with-artificial-transcription-factors
#15
REVIEW
Evan A Heiderscheit, Asuka Eguchi, Mackenzie C Spurgat, Aseem Z Ansari
Transcription factors (TFs) reprogram cell states by exerting control over gene regulatory networks and the epigenetic landscape of a cell. Artificial transcription factors (ATFs) are designer regulatory proteins comprised of modular units that can be customized to overcome challenges faced by natural TFs in establishing and maintaining desired cell states. Decades of research on DNA-binding proteins and synthetic molecules has provided a molecular toolkit for ATF design and the construction of genome-scale libraries of ATFs capable of phenotypic manipulation and reprogramming of cell states...
March 2018: FEBS Letters
https://www.readbyqxmd.com/read/29360983/modification-of-histone-by-glyoxal-recognition-of-glycated-histone-containing-advanced-glycation-adducts-by-serum-antibodies-of-type-1-diabetes-patients
#16
Nadeem Ahmad Ansari, Dharmendra Kumar Chaudhary, Debabrata Dash
Dicarbonyl compounds react more rapidly, than glucose, with arginine and lysine in proteins to form advanced glycation end products (AGEs) and further produce free radicals which cause DNA damage. AGEs are reliable diagnostic biomarkers for most of the age-related diseases. In the present study histone was modified with glyoxal and it was characterized by various spectral techniques. Binding characteristics of the modified histone towards serum antibodies from type 1 diabetes patients was evaluated by solid phase enzyme immunoassay and the results were compared with normal human subjects...
April 1, 2018: Glycobiology
https://www.readbyqxmd.com/read/29354301/celecoxib-induces-cell-death-on-non-small-cell-lung-cancer-cells-through-endoplasmic-reticulum-stress
#17
Bomi Kim, Jayoung Kim, Yeong Seok Kim
Cyclooxygenase-2 (COX-2) is an enzyme induced by various proinflammatory and mitogenic stimuli. Celecoxib is a selective inhibitor of COX-2 that have been shown to affect cell growth and apoptosis. Lung cancer cells expressing COX-2 is able to be a target of celecoxib, this study focuses on investigating that celecoxib induces apoptosis via endoplasmic reticulum (ER) stress on lung cancer cells. We investigated whether celecoxib induced apoptosis on non-small cell lung cancer cell line, A549 and H460. The 50 µM of celecoxib increased apoptotic cells and 100 µM of celecoxib significantly induced apoptosis...
December 2017: Anatomy & Cell Biology
https://www.readbyqxmd.com/read/29343810/mitochondrial-dna-damage-and-subsequent-activation-of-z-dna-binding-protein-1-links-oxidative-stress-to-inflammation-in-epithelial-cells
#18
Bartosz Szczesny, Michela Marcatti, Akbar Ahmad, Mauro Montalbano, Attila Brunyánszki, Sofia-Iris Bibli, Andreas Papapetropoulos, Csaba Szabo
This report identifies mitochondrial DNA (mtDNA) as a target and active mediator that links low-level oxidative stress to inflammatory response in pulmonary epithelial cells. Extrusion of mtDNA into the bronchoalveolar lavage fluid occurs as an early event in mice subjected to cigarette smoke injury, concomitantly with the depletion of mtDNA in the lung tissue. In cultured lung epithelial cells, prolonged, low-level oxidative stress damages the mtDNA, without any detectable damage to the nuclear DNA. In turn, cellular depletion of the mtDNA occurs, together with a transient remodeling of cellular bioenergetics and morphology - all without any detectable impairment in overall cell viability...
January 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29339104/region-specific-innate-antiviral-responses-of-the-human-epididymis
#19
James A Browne, Shih-Hsing Leir, Scott E Eggener, Ann Harris
Viral infections of the epididymis are associated with epididymitis, which damages the epithelium and impairs fertility. We showed previously that innate immune response genes were differentially expressed in the corpus and cauda region of the human epididymis in comparison to the caput. Here we investigate the antiviral defense response mechanisms of human epididymis epithelial (HEE) cells. Toll-like receptor (TLR) 3 and retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs) are enriched in HEE cells from the corpus and cauda region...
January 13, 2018: Molecular and Cellular Endocrinology
https://www.readbyqxmd.com/read/29321274/irf1-is-a-transcriptional-regulator-of-zbp1-promoting-nlrp3-inflammasome-activation-and-cell-death-during-influenza-virus-infection
#20
Teneema Kuriakose, Min Zheng, Geoffrey Neale, Thirumala-Devi Kanneganti
Innate immune sensing of influenza A virus (IAV) induces activation of various immune effector mechanisms, including the nucleotide and oligomerization domain, leucine-rich repeat-containing protein family, pyrin domain containing 3 (NLRP3) inflammasome and programmed cell death pathways. Although type I IFNs are identified as key mediators of inflammatory and cell death responses during IAV infection, the involvement of various IFN-regulated effectors in facilitating these responses are less studied. In this study, we demonstrate the role of IFN regulatory factor (IRF)1 in promoting NLRP3 inflammasome activation and cell death during IAV infection...
February 15, 2018: Journal of Immunology: Official Journal of the American Association of Immunologists
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