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Добірка наукової літератури з теми "ARID (AT-rich interacting domain)"

Автор: Grafiati

Опубліковано: 6 вересня 2023

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Статті в журналах з теми "ARID (AT-rich interacting domain)"

Li, Siyi, Zhulin Wu, Qiuyue Li, Qiting Liang, Hengli Zhou, Yafei Shi, Rong Zhang, and Huafeng Pan. "The Prognostic Value of AT-Rich Interaction Domain (ARID) Family Members in Patients with Hepatocellular Carcinoma." Evidence-Based Complementary and Alternative Medicine 2022 (August 18, 2022): 1–16. http://dx.doi.org/10.1155/2022/1150390.

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Objective. Hepatocellular carcinoma (HCC) is one of the most lethal malignancies with a poor prognosis. The AT-rich interaction domain (ARID) family plays an essential regulatory role in the pathogenesis and progression of cancers. This study aims to evaluate the prognostic value and clinical significance of human ARID family genes in HCC. Methods. ONCOMINE and The Cancer Genome Atlas (TCGA) databases were employed to retrieve ARIDs expression profile and clinicopathological information of HCC. Kaplan–Meier plotter and MethSurv were applied to the survival analysis of patients with HCC. CBioPortal was used to analyze genetic mutations of ARIDs. Gene Expression Profiling Interactive Analysis (GEPIA) and Metascape were used to perform hub gene identification and functional enrichment. Results. Expression levels of 11 ARIDs were upregulated in HCC, and 2 ARIDs were downregulated. Also, 4 ARIDs and 5 ARIDs were correlated with pathologic stages and histologic grades, respectively. Furthermore, higher expression of ARID1A, ARID1B, ARID2, ARID3A, ARID3B, ARID5B, KDM5A, KDM5B, KDM5C, and JARID2 was remarkably correlated with worse overall survival of patients with HCC, and the high ARID3C/KDM5D expression was related to longer overall survival. Multivariate Cox analysis indicated that ARID3A, KDM5C, and KDM5D were independent risk factors for HCC prognosis. Moreover, ARIDs mutations and 127 CpGs methylation in all ARIDs were observed to be significantly associated with the prognosis of HCC patients. Besides, our data showed that ARIDs could regulate tumor-related pathways and distinct immune cells in the HCC microenvironment. Conclusions. ARIDs present the potential prognostic value for HCC. Our findings suggest that ARID3A, KDM5C, and KDM5D may be the prognostic biomarkers for patients with HCC.

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Dallas, Peter B., Stephen Pacchione, Deborah Wilsker, Valerie Bowrin, Ryuji Kobayashi, and Elizabeth Moran. "The Human SWI-SNF Complex Protein p270 Is an ARID Family Member with Non-Sequence-Specific DNA Binding Activity." Molecular and Cellular Biology 20, no. 9 (May 1, 2000): 3137–46. http://dx.doi.org/10.1128/mcb.20.9.3137-3146.2000.

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ABSTRACT p270 is an integral member of human SWI-SNF complexes, first identified through its shared antigenic specificity with p300 and CREB binding protein. The deduced amino acid sequence of p270 reported here indicates that it is a member of an evolutionarily conserved family of proteins distinguished by the presence of a DNA binding motif termed ARID (AT-rich interactive domain). The ARID consensus and other structural features are common to both p270 and yeast SWI1, suggesting that p270 is a human counterpart of SWI1. The approximately 100-residue ARID sequence is present in a series of proteins strongly implicated in the regulation of cell growth, development, and tissue-specific gene expression. Although about a dozen ARID proteins can be identified from database searches, to date, only Bright (a regulator of B-cell-specific gene expression), dead ringer (a Drosophila melanogastergene product required for normal development), and MRF-2 (which represses expression from the cytomegalovirus enhancer) have been analyzed directly in regard to their DNA binding properties. Each binds preferentially to AT-rich sites. In contrast, p270 shows no sequence preference in its DNA binding activity, thereby demonstrating that AT-rich binding is not an intrinsic property of ARID domains and that ARID family proteins may be involved in a wider range of DNA interactions.

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HURLSTONE, Adam F. L., Ivan A. OLAVE, Nick BARKER, Mascha van NOORT, and Hans CLEVERS. "Cloning and characterization of hELD/OSA1, a novel BRG1 interacting protein." Biochemical Journal 364, no. 1 (May 8, 2002): 255–64. http://dx.doi.org/10.1042/bj3640255.

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A highly conserved multisubunit enzymic complex, SWI/SNF, participates in the regulation of eukaryote gene expression through its ability to remodel chromatin. While a single component of SWI/SNF, Swi2 or a related protein, can perform this function in vitro, the other components appear to modulate the activity and specificity of the complex in vivo. Here we describe the cloning of hELD/OSA1, a 189KDa human homologue of Drosophila Eld/Osa protein, a constituent of Drosophila SWI/SNF. By comparing conserved peptide sequences in Eld/Osa homologues we define three domains common to all family members. A putative DNA binding domain, or ARID (AT-rich DNA-interacting domain), may function in targetting SWI/SNF to chromatin. Two other domains unique to Eld/Osa proteins, EHD1 and EHD2, map to the C-teminus. We show that EHD2 mediates binding to Brahma-related gene 1 (BRG1), a human homologue of yeast Swi2. EHD1 and EHD2 also appear capable of interacting with each other. Using an antibody raised against EHD2 of hELD/OSA1, we detected Eld/Osa1 in endogenous SWI/SNF complexes derived from mouse brain.

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Iwahara, J. "Solution structure of the DNA binding domain from Dead ringer, a sequence-specific AT-rich interaction domain (ARID)." EMBO Journal 18, no. 21 (November 1, 1999): 6084–94. http://dx.doi.org/10.1093/emboj/18.21.6084.

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Kusunoki, Hideki, Tsukasa Hasegawa, Chieko Komatsu, Takashi Takeuchi, and Toshiyuki Kohno. "1H, 13C and 15N Resonance Assignments of the AT-Rich Interaction Domain (ARID) of Jumonji." Journal of Biomolecular NMR 33, no. 1 (September 2005): 74. http://dx.doi.org/10.1007/s10858-005-1282-6.

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Hirose-Yotsuya, Lisa, Fumio Okamoto, Takahiro Yamakawa, Robert H. Whitson, Yoko Fujita-Yamaguchi та Keiichi Itakura. "Knockdown of AT-rich interaction domain (ARID) 5B gene expression induced AMPKα2 activation in cardiac myocytes". BioScience Trends 9, № 6 (2015): 377–85. http://dx.doi.org/10.5582/bst.2015.01159.

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Liu, Gaohua, Yuanpeng J. Huang, Rong Xiao, Dongyan Wang, Thomas B. Acton, and Gaetano T. Montelione. "Solution NMR structure of the ARID domain of human AT-rich interactive domain-containing protein 3A: A human cancer protein interaction network target." Proteins: Structure, Function, and Bioinformatics 78, no. 9 (March 18, 2010): 2170–75. http://dx.doi.org/10.1002/prot.22718.

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Roy, Adrita, Arkajyoti Dutta, Dipan Roy, Payel Ganguly, Ritesh Ghosh, Rajiv K. Kar, Anirban Bhunia, Jayanta Mukhobadhyay, and Shubho Chaudhuri. "Deciphering the role of the AT-rich interaction domain and the HMG-box domain of ARID-HMG proteins of Arabidopsis thaliana." Plant Molecular Biology 92, no. 3 (August 9, 2016): 371–88. http://dx.doi.org/10.1007/s11103-016-0519-y.

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Loesch, Robin, Linda Chenane, and Sabine Colnot. "ARID2 Chromatin Remodeler in Hepatocellular Carcinoma." Cells 9, no. 10 (September 23, 2020): 2152. http://dx.doi.org/10.3390/cells9102152.

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Chromatin remodelers are found highly mutated in cancer including hepatocellular carcinoma. These mutations frequently occur in ARID (AT-rich Interactive Domain) genes, encoding subunits of the ATP-dependent SWI/SNF remodelers. The increasingly prevalent complexity that surrounds the functions and specificities of the highly modular BAF (BG1/BRM-associated factors) and PBAF (polybromo-associated BAF) complexes, including ARID1A/B or ARID2, is baffling. The involvement of the SWI/SNF complexes in diverse tissues and processes, and especially in the regulation of gene expression, multiplies the specific outcomes of specific gene alterations. A better understanding of the molecular consequences of specific mutations impairing chromatin remodelers is needed. In this review, we summarize what we know about the tumor-modulating properties of ARID2 in hepatocellular carcinoma.

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Roy, Adrita, Arkajyoti Dutta, Dipan Roy, Payel Ganguly, Ritesh Ghosh, Rajiv K. Kar, Anirban Bhunia, Jayanta Mukhopadhyay, and Shubho Chaudhuri. "Erratum to: Deciphering the role of the AT-rich interaction domain and the HMG-box domain of ARID-HMG proteins of Arabidopsis thaliana." Plant Molecular Biology 92, no. 3 (September 5, 2016): 389–90. http://dx.doi.org/10.1007/s11103-016-0534-z.

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Дисертації з теми "ARID (AT-rich interacting domain)"

Giri, Malyasree. "Structural and DNA binding properties of ARID domains present in hSWI/SNF chromatin remodeling complex subunits." Thesis, 2020. https://etd.iisc.ac.in/handle/2005/5168.

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The SWI/SNF complexes are multisubunit-containing protein complexes that are involved in chromatin-remodeling processes in the eukaryotic cells. In higher eukaryotes, SWI/SNF complexes contain one or more mutually exclusive AT-rich interaction domain (ARID)-containing proteins as one of the subunit. The SWI/SNF complexes can be further classified into sub complexes. Association of ARID-containing proteins BAF250a (also known as ARID1a) and BAF250b (also known as ARID1b) with the SWI/SNF complex results in BAF-A and BAF-B complexes respectively, whereas the association of ARID-containing BAF200 (also known as ARID2) results in PBAF complex. BAF250a, BAF250b and BAF200 subunits have an AT-rich interaction domain named as ARID. It has been proposed that BAF250a/b and BAF200 subunits likely recruit SWI/SNF complex through ARID domain to heterochromatin that allows transcriptional activation of normally silenced chromatin, thereby regulating the specific gene expression. The ARID is a conserved, all helical DNA binding domain found in several eukaryotic proteins. ARIDs in proteins such as human modulator recognition factor 2 (Mrf2), Drosophila Dead Ringer (Dri), and murine protein Bright were shown to recognize specific AT-rich DNA sequences. The evidences so far suggest that ARIDs of human SWI/SNF complexes interact with DNA without any sequence preference, therefore questioning the recruitment of SWI/SNF complexes by BAF250a to the target genes via its interaction with specific DNA sequences. The structure and functional annotation of BAF250a/b (> 2200 residues long proteins) remains poorly understood. The folded regions and domain boundaries of these lengthy proteins have not been clearly defined. Likewise, their DNA-binding specificities have not been studied systematically. With this background, we proposed to study the structure and DNA binding specificities of ARID domains in BAF250a, BAF250b, and BAF200 in this thesis. First, we have defined the domain architecture of BAF250a/ reveals the ARID and ARM-repeat domains with implication in function and assembly of the BAF remodeling complex. Next, systematically we have defined the domain boundary and DNA binding specificities of BAF250a ARID. Using NMR spectroscopy and ITC methods, our results showed that BAF250a ARID binds to AT rich DNA in a ‘specific’ manner with thermodynamic signatures for a specific DNA binding. NMR CSP driven model of BAF250a ARID – DNA complexes were generated and validated using mutagenesis approach. We have also completed the NMR chemical shift assignment of ARID domains of BAF250b and BAF200. We have generated a CS-Rosetta model structure of BAF200 ARID and currently we are in the process of refining the structure. DNA binding properties of BAF250b ARID have been studied using NMR and ITC methods. NMR CSP driven HADDOCK models of BAF250b ARID/DNA complexes suggest plausible mode of specific complex formation via DNA major groove recognition by helix H5 and minor groove interactions by loop L1. A temperature independent DNA binding thermodynamics was observed for BAF250b ARID unlike BAF250a ARID though these two proteins share > than 80% identity in their sequences. The reason of such differences may be due to the small and subtle deviations in loop L1 region. In case of BAF200 ARID, we have some preliminary results on its DNA binding properties obtained from NMR and SPR studies using AT-12 and GC-12 DNA.

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Тези доповідей конференцій з теми "ARID (AT-rich interacting domain)"

Furuta, Mayuko, Ha H. Nguyen, Akihiro Fujimoto, Yuichi Shiraishi, Satoru Miyano, Tatsuhiko Tsunoda, and Hidewaki Nakagawa. "Abstract 5200: Genome-wide integrative analysis for the determination of the consequence of AT-rich interacting domain 2 (ARID2) depletion in hepatocellular carcinoma." In Proceedings: AACR 104th Annual Meeting 2013; Apr 6-10, 2013; Washington, DC. American Association for Cancer Research, 2013. http://dx.doi.org/10.1158/1538-7445.am2013-5200.

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Moussafir, J., C. Olry, M. Nibart, A. Albergel, P. Armand, C. Duchenne, F. Mahé, L. Thobois, S. Loaëc, and O. Oldrini. "AIRCITY: A Very High Resolution Atmospheric Dispersion Modeling System for Paris." In ASME 2014 4th Joint US-European Fluids Engineering Division Summer Meeting collocated with the ASME 2014 12th International Conference on Nanochannels, Microchannels, and Minichannels. American Society of Mechanical Engineers, 2014. http://dx.doi.org/10.1115/fedsm2014-21820.

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The AIRCITY project, partly funded by the European Union, is now successfully achieved. It aimed at developing a 4D innovative numerical simulation tool dedicated to the dispersion of traffic-induced air pollution at local scale on the whole urban area of PARIS. AIRCITY modeling system is based on PMSS (Parallel-Micro-SWIFT-SPRAY) software, which has been developed by ARIA Technologies in close collaboration with CEA and MOKILI. PMSS is a simplified CFD solution which is an alternative to micro-scale simulations usually carried out with full-CFD. Yet, AIRCITY challenge was to model the flow and pollutant dispersion with a 3 m resolution over the whole city of Paris covering a 14 km × 11,5 km domain. Thus, the choice was to run a mass-consistent diagnostic flow model (SWIFT) associated with a Lagrangian Particle Dispersion Model (SPRAY) on a massively parallel architecture. With a 3 m resolution on this huge domain, parallelization was applied to the computation of both the flow (by domain splitting) and the Lagrangian dispersion (management of particles is split over several processors). This MPI parallelization is more complex but gives a large flexibility to optimize the number of CPU, the available RAM and the CPU time. So, it makes possible to process arbitrarily large domains (only limited by the memory of the available nodes). As CEA operates the largest computing center in Europe, with parallel machines ranging from a few hundred to several thousand cores, the modeling system was tested on huge parallel clusters. More usual and affordable computers with a few tens of cores were also utilized during the project by ARIA Technologies and by AIRPARIF, the Regional Air Quality Management Board of Paris region, whose role was also to build the end-users requirements. These computations were performed on a simulation domain restricted to the hypercenter of Paris with dimensions around 2 km × 2 km (at the same resolution of 3 m). The focus was on the improvements needed to adapt simulation codes initially designed for emergency response to urban air quality applications: • Coupling with the MM5 / CHIMERE operational photochemical model at AIRPARIF (as the forecast background), • Turbulence generated by traffic / coupling with traffic model, • Inclusion of chemical reactions / Interaction with background substances (especially NO / NO2). Finally, in-depth validation of the modeling system was undertaken using both the routine air quality measurements in Paris (at four stations influenced by the road traffic) and a field experiment specially arranged for the project, with LIDARs provided by LEOSPHERE Inc. Comparison of PMSS and measurements gave excellent results concerning NO / NO2 and PM10 hourly concentrations for a monthly period of time while the LIDAR campaign results were also promising. In the paper, more details are given regarding the modeling system principles and developments and its validation. Perspectives of the project will also be discussed as AIRCITY system. The TRL must now be elevated from a demonstration to a robust and systematically validated modeling tool that could be used to predict routinely the air quality in Paris and in other large cities around the world.

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