keyword
MENU ▼
Read by QxMD icon Read
search

DNA-binding proteins

keyword
https://www.readbyqxmd.com/read/28449087/methyl-cpg-binding-domain-protein-1-regulates-localization-and-activity-of-tet1-in-a-cxxc3-domain-dependent-manner
#1
Peng Zhang, Cathia Rausch, Florian D Hastert, Boyana Boneva, Alina Filatova, Sujit J Patil, Ulrike A Nuber, Yu Gao, Xinyu Zhao, M Cristina Cardoso
Cytosine modifications diversify and structure the genome thereby controlling proper development and differentiation. Here, we focus on the interplay of the 5-methylcytosine reader Mbd1 and modifier Tet1 by analyzing their dynamic subcellular localization and the formation of the Tet oxidation product 5-hydroxymethylcytosine in mammalian cells. Our results demonstrate that Mbd1 enhances Tet1-mediated 5-methylcytosine oxidation. We show that this is due to enhancing the localization of Tet1, but not of Tet2 and Tet3 at heterochromatic DNA...
April 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28448822/hssb1-phosphorylation-is-dynamically-regulated-by-dna-pk-and-ppp-family-protein-phosphatases
#2
Nicholas W Ashton, Nicolas Paquet, Sally L Shirran, Emma Bolderson, Ruvini Kariawasam, Christine Touma, Azadeh Fallahbaghery, Roland Gamsjaeger, Liza Cubeddu, Catherine Botting, Pamela M Pollock, Kenneth J O'Byrne, Derek J Richard
The maintenance of genomic stability is essential for cellular viability and the prevention of diseases such as cancer. Human single-stranded DNA-binding protein 1 (hSSB1) is a protein with roles in the stabilisation and restart of stalled DNA replication forks, as well as in the repair of oxidative DNA lesions and double-strand DNA breaks. In the latter process, phosphorylation of threonine 117 by the ATM kinase is required for hSSB1 stability and efficient DNA repair. The regulation of hSSB1 in other DNA repair pathways has however remained unclear...
April 6, 2017: DNA Repair
https://www.readbyqxmd.com/read/28448738/site-specific-recruitment-of-epigenetic-factors-with-a-modular-crispr-cas-system
#3
Tobias Anton, Sebastian Bultmann
Dissecting the complex network of epigenetic modifications requires tools that combine precise recognition of DNA sequences with the capability to modify epigenetic marks. The CRISPR/Cas system has been proven to be a valuable addition to existing methodologies that fulfill these tasks. So far, sequence-specific editing of epigenetic modifications such as DNA methylation and histone posttranslational modifications relied on direct fusions of enzymatically inactivated Cas9 (dCas9) with epigenetic effectors. Here, we report a novel, modular system that facilitates the recruitment of any GFP-tagged protein to desired genomic loci...
February 23, 2017: Nucleus
https://www.readbyqxmd.com/read/28448066/structural-basis-of-crispr-spycas9-inhibition-by-an-anti-crispr-protein
#4
De Dong, Minghui Guo, Sihan Wang, Yuwei Zhu, Shuo Wang, Zhi Xiong, Jianzheng Yang, Zengliang Xu, Zhiwei Huang
The CRISPR-Cas9 systems are bacterial encoded adaptive immune systems to defend against phages infection, through RNA-guided endonuclease activity of Cas9 to degrade double-stranded DNA bearing a protospacer adjacent motif (PAM) and complementary sequences to the guide RNA1,2,3,4,5. Recently, two anti-CRISPR proteins AcrIIA2 and AcrIIA4 from Listeria monocytogenes (Lmo) prophages have been identified, both of which potently inhibit Streptococcus pyogenes Cas9 (SpyCas9) and LmoCas9 activity in bacteria and human cells6...
April 27, 2017: Nature
https://www.readbyqxmd.com/read/28447752/islet-1-induces-the-differentiation-of-mesenchymal-stem-cells-into-cardiomyocyte-like-cells-through-the-regulation-of-gcn5-and-dnmt-1
#5
Qin Yi, Hao Xu, Ke Yang, Yue Wang, Bin Tan, Jie Tian, Jing Zhu
Previous studies from this group demonstrated that insulin gene enhancer binding protein ISL-1 (Islet-1) specifically induces the differentiation of mesenchymal stem cells (MSCs) into cardiomyocyte‑like cells through histone acetylation. However, the underlying mechanisms remain unclear. In the present study, the role of the histone acetylation and DNA methylation on the regulatory mechanism of the Islet‑1 was further investigated by methylation‑specific polymerase chain reaction (PCR), chromatin immunoprecipitation quantitative PCR and western blot analysis...
March 16, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28447716/par1%C3%A2-mediated-c%C3%A2-jun-activation-promotes-heat-stress%C3%A2-induced-early-stage-apoptosis-of-human-umbilical-vein-endothelial-cells
#6
Shuang Zhang, Yanan Liu, Zhenglian Wang, Jingxian Liu, Zhengtao Gu, Qiulin Xu, Lei Su
Our previous study indicated that when human umbilical vein endothelial cells (HUVECs), which are involved in endothelial barrier function, are heat stressed, levels of protease‑activated receptor 1 (PAR1) are increased significantly. In the present study, it was demonstrated that PAR1 serves a vital role in heat stress‑induced HUVEC apoptosis. When the PAR1 inhibitor, SCH79797 (SCH), or a small interfering RNA (siRNA) targeting PAR1 were used to inhibit PAR1 signaling, a marked decrease in cell apoptosis, caspase‑3 activity and the expression of the pro‑apoptotic protein B‑cell lymphoma 2 (Bcl‑2) associated X (Bax), as well as increased expression of the anti‑apoptotic Bcl‑2 family member, myeloid cell leukemia 1 (Mcl‑1), were observed...
March 9, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28447620/dna-replication-licensing-factor-cdc6-and-plk4-kinase-antagonistically-regulate-centrosome-duplication-via-sas-6
#7
Xiaowei Xu, Shijiao Huang, Boyan Zhang, Fan Huang, Wangfei Chi, Jingyan Fu, Gang Wang, Si Li, Qing Jiang, Chuanmao Zhang
Centrosome number is tightly controlled during the cell cycle to ensure proper spindle assembly and cell division. However, the underlying mechanism that controls centrosome number remains largely unclear. We show herein that the DNA replication licensing factor Cdc6 is recruited to the proximal side of the centrioles via cyclin A to negatively regulate centrosome duplication by binding and inhibiting the cartwheel protein Sas-6 from forming a stable complex with another centriole duplication core protein, STIL...
April 27, 2017: Nature Communications
https://www.readbyqxmd.com/read/28446765/three-dimensional-modeling-of-single-stranded-dna-hairpins-for-aptamer-based-biosensors
#8
Iman Jeddi, Leonor Saiz
Aptamers consist of short oligonucleotides that bind specific targets. They provide advantages over antibodies, including robustness, low cost, and reusability. Their chemical structure allows the insertion of reporter molecules and surface-binding agents in specific locations, which have been recently exploited for the development of aptamer-based biosensors and direct detection strategies. Mainstream use of these devices, however, still requires significant improvements in optimization for consistency and reproducibility...
April 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28446751/crl4b-dcaf11-e3-ligase-targets-p21-for-degradation-to-control-cell-cycle-progression-in-human-osteosarcoma-cells
#9
Zhi Chen, Kun Wang, Canglong Hou, Kaibiao Jiang, Bin Chen, Jianwei Chen, Lifeng Lao, Lie Qian, Guibin Zhong, Zude Liu, Caiguo Zhang, Hongxing Shen
Cell cycle progression in mammals is strictly controlled by a number of cyclin-dependent kinases (CDKs) and CDK inhibitors (CKIs), the expression of which is often dysregulated in cancer cells. Our previous work revealed that Cullin 4B (CUL4B), a critical component of the Cullin4B-RING E3 ligase complex (CRL4B), is overexpressed in human osteosarcoma cells through an unknown mechanism. Here, we demonstrated that CUL4B forms an E3 ligase with RBX1 (RING-box 1), DDB1 (DNA damage binding protein 1), and DCAF11 (DDB1 and CUL4 associated factor 11) in human osteosarcoma cells...
April 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28446240/molecular-mechanisms-by-which-herv-k-gag-interferes-with-hiv-1-gag-assembly-and-particle-infectivity
#10
Kazuaki Monde, Hiromi Terasawa, Yusuke Nakano, Ferri Soheilian, Kunio Nagashima, Yosuke Maeda, Akira Ono
BACKGROUND: Human endogenous retroviruses (HERVs), the remnants of ancient retroviral infections, constitute approximately 8% of human genomic DNA. Since HERV-K Gag expression is induced by HIV-1 Tat in T cells, induced HERV-K proteins could affect HIV-1 replication. Indeed, previously we showed that HERV-K Gag and HIV-1 Gag coassemble and that this appears to correlate with the effect of HERV-K Gag expression on HIV-1 particle release and its infectivity. We further showed that coassembly requires both MA and NC domains, which presumably serve as scaffolding for Gag via their abilities to bind membrane and RNA, respectively...
April 26, 2017: Retrovirology
https://www.readbyqxmd.com/read/28445747/physical-and-functional-characterization-of-a-viral-genome-maturation-complex
#11
Teng-Chieh Yang, David Ortiz, Qin Yang, Rolando W De Angelis, Saurarshi J Sanyal, Carlos E Catalano
Genome packaging is strongly conserved in the complex double-stranded DNA viruses, including the herpesviruses and many bacteriophages. In these cases, viral DNA is packaged into a procapsid shell by a terminase enzyme. The packaging substrate is typically a concatemer composed of multiple genomes linked in a head-to-tail fashion, and terminase enzymes perform two essential functions: 1) excision of a unit length genome from the concatemer (genome maturation) and 2) translocation of the duplex into a procapsid (genome packaging)...
April 25, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28445713/deregulation-of-%C3%AE-synuclein-in-parkinson-s-disease-insight-from-epigenetic-structure-and-transcriptional-regulation-of-snca
#12
REVIEW
Subhrangshu Guhathakurta, Eugene Bok, Baggio A Evangelista, Yoon-Seong Kim
Understanding regulation of α-synuclein has long been a central focus for Parkinson's disease (PD) researchers. Accumulation of this protein in the Lewy body or neurites, mutations in the coding region of the gene and strong association of α-synuclein encoding gene multiplication (duplication/triplication) with familial form of PD have indicated the importance of this molecule in pathogenesis of the disease. Several years of research identified many potential faulty pathways associated with accumulation of α-synuclein inside dopaminergic neurons and its transmission to neighboring ones...
April 23, 2017: Progress in Neurobiology
https://www.readbyqxmd.com/read/28445466/human-pluripotent-stem-cells-recurrently-acquire-and-expand-dominant-negative-p53-mutations
#13
Florian T Merkle, Sulagna Ghosh, Nolan Kamitaki, Jana Mitchell, Yishai Avior, Curtis Mello, Seva Kashin, Shila Mekhoubad, Dusko Ilic, Maura Charlton, Genevieve Saphier, Robert E Handsaker, Giulio Genovese, Shiran Bar, Nissim Benvenisty, Steven A McCarroll, Kevin Eggan
Human pluripotent stem cells (hPS cells) can self-renew indefinitely, making them an attractive source for regenerative therapies. This expansion potential has been linked with the acquisition of large copy number variants that provide mutated cells with a growth advantage in culture. The nature, extent and functional effects of other acquired genome sequence mutations in cultured hPS cells are not known. Here we sequence the protein-coding genes (exomes) of 140 independent human embryonic stem cell (hES cell) lines, including 26 lines prepared for potential clinical use...
April 26, 2017: Nature
https://www.readbyqxmd.com/read/28444956/structural-insights-into-the-recognition-of-n%C3%A2-aryl-and-c8-aryl-dna-lesions-by-the-repair-protein-xpa-rad14
#14
Charlotte Ebert, Nina Simon, Sabine Schneider, Thomas Carell
Aromatic amines are strongly carcinogenic compounds. They are activated in the liver to give reactive nitrenium ions that are known to react with the nucleobases within the DNA duplex. The reaction occurs predominantly at the C8-position of the dG base, which gives C8-acetyl-aryl-, or C8-aryl-dG adducts in an electrophilic aromatic substitution reaction. Alternatively, reaction with the exocyclic 2-NH₂ group is observed. While the C8-adducts retain the base pairing properties, base pairing is strongly compromised in the case of the N²-adducts...
April 26, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28444616/genome-wide-identification-of-grain-filling-genes-regulated-by-the-ossmf1-transcription-factor-in-rice
#15
Joung Sug Kim, Songhwa Chae, Kyong Mi Jun, Yoon-Mok Pahk, Tae-Ho Lee, Pil Joong Chung, Yeon-Ki Kim, Baek Hie Nahm
BACKGROUND: Spatial- and temporal-specific expression patterns are primarily regulated at the transcriptional level by gene promoters. Therefore, it is important to identify the binding motifs of transcription factors to better understand the networks associated with embryogenesis. RESULTS: Here, we used a protein-binding microarray (PBM) to identify the binding motifs of OsSMF1, which is a basic leucine zipper transcription factor involved in the regulation of rice seed maturation...
December 2017: Rice
https://www.readbyqxmd.com/read/28444573/the-effect-of-different-types-of-nanoparticles-on-fus-and-tdp-43-solubility-and-subcellular-localization
#16
Jasna Lojk, Sonja Prpar Mihevc, Vladimir Boštjan Bregar, Mojca Pavlin, Boris Rogelj
Increased environmental pollution has been suggested as one of the possible causes for increased incidence of neurodegenerative and developmental disorders. Through the environmental pollution, everyday consumer products and nanomedical applications, we are also exposed to various nanoparticles (NPs). Specific types of NPs have been shown to be able to cause neural damage in vivo through processes such as disruption of the blood-brain barrier, induction of neuroinflammation, increase in oxidative stress and protein aggregation...
April 25, 2017: Neurotoxicity Research
https://www.readbyqxmd.com/read/28444448/the-5-untranslated-region-of-potato-sbglr-gene-contributes-to-pollen-specific-expression
#17
Yujie Chang, Min Yan, Jingjuan Yu, Dengyun Zhu, Qian Zhao
The 5'UTR of SBgLR enhances gene expression by regulating both its transcription and translation. SBgLR (Solanum tuberosum genomic lysine rich) is a pollen-specific gene in Solanum tuberosum that encodes a microtubule-associated protein. The region from -85 to +180 (transcription start site at +1) was determined to be critical for specific expression in pollen grains. Transient and stable expression assays showed that the 5'UTR (from +1 to +184) enhanced gene expression in all detected tissues of transgenic tobacco...
April 25, 2017: Planta
https://www.readbyqxmd.com/read/28444308/investigating-dna-supercoiling-in-eukaryotic-genomes
#18
Samuel Corless, Nick Gilbert
Supercoiling is a fundamental property of DNA, generated by polymerases and other DNA-binding proteins as a consequence of separating/bending the DNA double helix. DNA supercoiling plays a key role in gene expression and genome organization, but has proved difficult to study in eukaryotes because of the large, complex and chromatinized genomes. Key approaches to study DNA supercoiling in eukaryotes are (1) centrifugation-based or electrophoresis-based techniques in which supercoiled plasmids extracted from eukaryotic cells form a compacted writhed structure that migrates at a rate proportional to the level of DNA supercoiling; (2) in vivo approaches based on the preferential intercalation of psoralen molecules into under-wound DNA...
April 24, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/28442904/anti-fgfr1-aptamer-tagged-superparamagnetic-conjugates-for-anticancer-hyperthermia-therapy
#19
Przemysław M Jurek, Konrad Zabłocki, Urszula Waśko, Maciej P Mazurek, Jacek Otlewski, Filip Jeleń
Compounds that recognize and strongly bind to molecular targets are one of the cornerstones of modern pharmaceutics. Work has been ongoing for the past 25 years on the therapeutic use of aptamers, nucleic acid molecules, whose three-dimensional structure is the result of interactions between complementary base pairs. The aptamers selection methods allow the oligonucleotides which bind the molecular target in its native environment to be quickly isolated from a large library of random oligonucleotides. The possibilities presented for aptamers in the field of targeted therapy require the application of effective carriers to counter the renal clearance effect and/or functional cargo to exert therapeutic action if the aptamer is only used as a targeting moiety...
2017: International Journal of Nanomedicine
https://www.readbyqxmd.com/read/28442756/crystal-structure-based-discovery-of-a-novel-synthesized-parp1-inhibitor-ol-1-with-apoptosis-inducing-mechanisms-in-triple-negative-breast-cancer
#20
Leilei Fu, Shuya Wang, Xuan Wang, Peiqi Wang, Yaxin Zheng, Dahong Yao, Mingrui Guo, Lan Zhang, Liang Ouyang
Poly (ADP-ribose) polymerase-1 (PARP1) is a highly conserved enzyme focused on the self-repair of cellular DNA damage. Until now, numbers of PARP inhibitors have been reported and used for breast cancer therapy in recent years, especially in TNBC. However, developing a new type PARP inhibitor with distinctive skeleton is alternatively promising strategy for TNBC therapy. In this study, based on co-crystallization studies and pharmacophore-docking-based virtual screening, we discovered a series of dihydrodibenzo[b,e]-oxepin compounds as PARP1 inhibitors...
December 5, 2016: Scientific Reports
keyword
keyword
25186
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"