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https://www.readbyqxmd.com/read/29786685/regulation-of-chromatin-states-and-gene-expression-during-hsn-neuronal-maturation-is-mediated-by-eor-1-plzf-mau-2-cohesin-loader-and-swi-snf-complex
#1
Yoichi Shinkai, Masahiro Kuramochi, Motomichi Doi
Newborn neurons mature by distinct and sequential steps through the timely induction of specific gene expression programs in concert with epigenetic changes. However, it has been difficult to investigate the relationship between gene expression and epigenetic changes at a single-cell resolution during neuronal maturation. In this study, we investigated the maturation of hermaphrodite-specific neurons (HSNs) in C. elegans, which provided the link between chromatin dynamics, gene expression, and the degree of neuronal maturation at a single-cell resolution...
May 21, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29786594/-brain-microbleeds-definition-pathophysiology-and-the-consequences
#2
Marek Mazurek, Ewa Papuć, Konrad Rejdak
Brain microbleeds are defined as small, circular hypointense changes in T2-sequensec of brain MRI, well demarcated from the surrounding tissue. They represent the phagocytized products of blood distribution extravasated from pathologically altered vessels. The echo-T2-dependent gradient (GRE) and magnetic susceptibility testing (SWI) sequences are usually used to visualize them. The pathogenesis of microbleeds very complex but angiopathy associated with arterial hypertension and cerebral amyloid angiopathy play a special role...
2018: Wiadomości Lekarskie: Organ Polskiego Towarzystwa Lekarskiego
https://www.readbyqxmd.com/read/29785963/swi-snf-and-rsc-cooperate-to-reposition-and-evict-promoter-nucleosomes-at-highly-expressed-genes-in-yeast
#3
Yashpal Rawal, Răzvan V Chereji, Hongfang Qiu, Sudha Ananthakrishnan, Chhabi K Govind, David J Clark, Alan G Hinnebusch
The nucleosome remodeling complex RSC functions throughout the yeast genome to set the positions of -1 and +1 nucleosomes and thereby determines the widths of nucleosome-depleted regions (NDRs). The related complex SWI/SNF participates in nucleosome remodeling/eviction and promoter activation at certain yeast genes, including those activated by transcription factor Gcn4, but did not appear to function broadly in establishing NDRs. By analyzing the large cohort of Gcn4-induced genes in mutants lacking the catalytic subunits of SWI/SNF or RSC, we uncovered cooperation between these remodelers in evicting nucleosomes from different locations in the promoter and repositioning the +1 nucleosome downstream to produce wider NDRs-highly depleted of nucleosomes-during transcriptional activation...
May 21, 2018: Genes & Development
https://www.readbyqxmd.com/read/29778836/interrogation-of-mammalian-protein-complex-structure-function-and-membership-using-genome-scale-fitness-screens
#4
Joshua Pan, Robin M Meyers, Brittany C Michel, Nazar Mashtalir, Ann E Sizemore, Jonathan N Wells, Seth H Cassel, Francisca Vazquez, Barbara A Weir, William C Hahn, Joseph A Marsh, Aviad Tsherniak, Cigall Kadoch
Protein complexes are assemblies of subunits that have co-evolved to execute one or many coordinated functions in the cellular environment. Functional annotation of mammalian protein complexes is critical to understanding biological processes, as well as disease mechanisms. Here, we used genetic co-essentiality derived from genome-scale RNAi- and CRISPR-Cas9-based fitness screens performed across hundreds of human cancer cell lines to assign measures of functional similarity. From these measures, we systematically built and characterized functional similarity networks that recapitulate known structural and functional features of well-studied protein complexes and resolve novel functional modules within complexes lacking structural resolution, such as the mammalian SWI/SNF complex...
May 14, 2018: Cell Systems
https://www.readbyqxmd.com/read/29776334/swi-snf-regulates-half-of-its-targets-without-the-need-of-atp-driven-nucleosome-remodeling-by-brahma
#5
Antonio Jordán-Pla, Simei Yu, Johan Waldholm, Thomas Källman, Ann-Kristin Östlund Farrants, Neus Visa
BACKGROUND: Brahma (BRM) is the only catalytic subunit of the SWI/SNF chromatin-remodeling complex of Drosophila melanogaster. The function of SWI/SNF in transcription has long been attributed to its ability to remodel nucleosomes, which requires the ATPase activity of BRM. However, recent studies have provided evidence for a non-catalytic function of BRM in the transcriptional regulation of a few specific genes. RESULTS: Here we have used RNA-seq and ChIP-seq to identify the BRM target genes in S2 cells, and we have used a catalytically inactive BRM mutant (K804R) that is unable to hydrolyze ATP to investigate the magnitude of the non-catalytic function of BRM in transcription regulation...
May 18, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29775508/lfr-is-functionally-associated-with-as2-to-mediate-leaf-development-in-arabidopsis
#6
Xiaowei Lin, Dandan Gu, Hongtao Zhao, Yue Peng, Guofang Zhang, Mengge Li, Zhijuan Wang, Xiutang Wang, Sujuan Cui
Leaves are essential organs for plants. We previously identified a functional gene possibly encoding a component of the SWI/SNF complex named LFR (Leaf and Flower Related) in Arabidopsis thaliana. Loss-of-function mutants of LFR displayed obvious defects in leaf morphogenesis, indicating its vital role in leaf development. Here an allelic null mutant of ASYMMETRIC LEAVES2 (AS2), as2-6, was isolated as an enhancer of lfr-1 in petiole length, vasculature pattern and leaf margin development. The lfr as2 double mutants showed enhanced ectopic expression of BP than each of the single mutant, which is consistent with their synergistic genetic enhancement in multiple BP-dependent development processes...
May 18, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29773426/stem-cell-transcription-factor-sox2-in-synovial-sarcoma-and-other-soft-tissue-tumors
#7
Heba Zayed, Iver Petersen
BACKGROUND: SOX2 has gained considerable interest as a pluripotency inducing gene. Co-transfection of SOX2 together with NANOG, KLF4 and c-MYC into adult fibroblasts was able to generate pluripotent stem cells. SOX2 has been reported to be expressed in synovial sarcoma, a tumor being characterized by the SS18-SSX gene fusion forming part of the SWI/SNF chromatin remodeling complex that affects histone methylation. The role of SOX2 in this tumor type as well as other soft tissue tumor entities however is still poorly characterized...
May 4, 2018: Pathology, Research and Practice
https://www.readbyqxmd.com/read/29771637/quantitative-imaging-of-chromatin-decompaction-in-living-cells
#8
Elisa Dultz, Roberta Mancini, Guido Polles, Pascal Vallotton, Frank Alber, Karsten Weis
Chromatin organization is highly dynamic and regulates transcription. Upon transcriptional activation, chromatin is remodeled and referred to as "open", but quantitative and dynamic data of this decompaction process are lacking. Here, we have developed a quantitative high-resolution microscopy assay in living yeast cells to visualize and quantify chromatin dynamics using the GAL7-10-1 locus as a model system. Upon transcriptional activation of these three clustered genes, we detect an increase of the mean distance across this locus by >100 nm...
May 17, 2018: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/29769717/swi2-snf2-atpase-chr2-remodels-pri-mirnas-via-serrate-to-impede-mirna-production
#9
Zhiye Wang, Zeyang Ma, Claudia Castillo-González, Di Sun, Yanjun Li, Bin Yu, Baoyu Zhao, Pingwei Li, Xiuren Zhang
Chromatin remodelling factors (CHRs) typically function to alter chromatin structure. CHRs also reside in ribonucleoprotein complexes, but little is known about their RNA-related functions. Here we show that CHR2 (also known as BRM), the ATPase subunit of the large switch/sucrose non-fermentable (SWI/SNF) complex, is a partner of the Microprocessor component Serrate (SE). CHR2 promotes the transcription of primary microRNA precursors (pri-miRNAs) while repressing miRNA accumulation in vivo. Direct interaction with SE is required for post-transcriptional inhibition of miRNA accumulation by CHR2 but not for its transcriptional activity...
May 16, 2018: Nature
https://www.readbyqxmd.com/read/29761958/-magnitude-image-guided-phase-unwrapping-algorithm-of-susceptibility-weighted-images
#10
Xinling Li, Yunzhi Huang, Luyi Han, Qi Liu, Ling He, Jin Zhang, Junpeng Zhang, Jiang Zhang
To better use the phase information to compensate the influence of blood flow, the phase unwrapping problem in susceptibility weighted imaging (SWI) is studied in this paper. In order to improve the accuracy of unwrapping, this paper proposes a magnitude image-guided phase unwrapping algorithm of SWI. The basic idea is as follows: (1) reduce the influence of noise by improving the rotational invariant non-local principal component analysis method (PRI-NL-PCA); (2) extract the corresponding solid region in the phase image to avoid the influence of the background noise on the phase unwrapping method; (3) use the phase compensation method to constrain the phase image reconstructed by the K-space...
October 1, 2017: Sheng Wu Yi Xue Gong Cheng Xue za Zhi, Journal of Biomedical Engineering, Shengwu Yixue Gongchengxue Zazhi
https://www.readbyqxmd.com/read/29761118/susceptibility-weighted-and-diffusion-kurtosis-imaging-to-evaluate-encephalomalacia-with-epilepsy-after-traumatic-brain-injury
#11
Wenbin Li, Xuan Wang, Xiaoer Wei, Mingliang Wang
Objective: Encephalomalacia after traumatic brain injury (TBI) is one of the factors leading to epilepsy. In this study, magnetic resonance imaging (MRI) was used to explore the brain image features of epilepsy after traumatic encephalomalacia, and to provide objective evidence for predicting the possible occurrence of epilepsy after traumatic encephalomalacia. Methods: Two-hundred-fifty-two patients with traumatic encephalomalacia were prospectively enrolled in the study...
May 2018: Annals of Clinical and Translational Neurology
https://www.readbyqxmd.com/read/29761003/the-asymmetry-of-neural-symptoms-in-wilson-s-disease-patients-detecting-by-diffusion-tensor-imaging-resting-state-functional-mri-and-susceptibility-weighted-imaging
#12
Xiang-Xue Zhou, Xun-Hua Li, Ding-Bang Chen, Chao Wu, Li Feng, Jian-Ping Chu, Zhi-Yun Yang, Xin-Bei Li, Haolin Qin, Gui-Dian Li, Hai-Wei Huang, Ying-Ying Liang, Xiu-Ling Liang
Objective: To investigate the cause of the motor asymmetry in Wilson's disease (WD) patients using functional MRI. Methods: Fifty patients with WD and 20 age-matched healthy controls were enrolled. Neurological symptoms were scored using the modified Young Scale. All study subjects underwent diffusion tensor imaging (DTI), susceptibility-weighted imaging (SWI), and resting-state functional MRI (rs-fMRI) of the brain. Six regions of interest (ROI) were chosen. Fiber volumes between ROIs on DTI, corrected phase (CP) values on SWI, amplitude of low-frequency fluctuation (ALFF), and regional homogeneity (REHO) values on rs-fMRI were determined...
May 2018: Brain and Behavior
https://www.readbyqxmd.com/read/29760405/arid1a-mutation-sensitizes-most-ovarian-clear-cell-carcinomas-to-bet-inhibitors
#13
Katrien Berns, Joseph J Caumanns, E Marielle Hijmans, Annemiek M C Gennissen, Tesa M Severson, Bastiaan Evers, G Bea A Wisman, Gert Jan Meersma, Cor Lieftink, Roderick L Beijersbergen, Hiroaki Itamochi, Ate G J van der Zee, Steven de Jong, René Bernards
Current treatment for advanced stage ovarian clear cell cancer is severely hampered by a lack of effective systemic therapy options, leading to a poor outlook for these patients. Sequencing studies revealed that ARID1A is mutated in over 50% of ovarian clear cell carcinomas. To search for a rational approach to target ovarian clear cell cancers with ARID1A mutations, we performed kinome-centered lethality screens in a large panel of ovarian clear cell carcinoma cell lines. Using the largest OCCC cell line panel established to date, we show here that BRD2 inhibition is predominantly lethal in ARID1A mutated ovarian clear cell cancer cells...
May 15, 2018: Oncogene
https://www.readbyqxmd.com/read/29754089/combating-hypoxia-anoxia-at-sediment-water-interfaces-a-preliminary-study-of-oxygen-nanobubble-modified-clay-materials
#14
Honggang Zhang, Tao Lyu, Lei Bi, Grant Tempero, David P Hamilton, Gang Pan
Combating hypoxia/anoxia is an increasingly common need for restoring natural waters suffering from eutrophication. Oxygen nanobubble modified natural particles were investigated for mitigating hypoxia/anoxia at the sediment-water interface (SWI) in a simulated column experiment. By adding oxygen nanobubble modified zeolites (ONMZ) and local soils (ONMS), the oxygen nanobubble concentrations (105 -107  particles/mL) were several orders of magnitude higher in the water than the original water solution (104  particles/mL) within 24 h...
May 10, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/29751772/expression-profiling-of-cell-intrinsic-regulators-in-the-process-of-differentiation-of-human-ipscs-into-retinal-lineages
#15
Jen-Hua Chuang, Aliaksandr A Yarmishyn, De-Kuang Hwang, Chih-Chien Hsu, Mong-Lien Wang, Yi-Ping Yang, Ke-Hung Chien, Shih-Hwa Chiou, Chi-Hsien Peng, Shih-Jen Chen
BACKGROUND: Differentiation of human induced pluripotent stem cells (hiPSCs) into retinal lineages offers great potential for medical application. Therefore, it is of crucial importance to know the key intrinsic regulators of differentiation and the specific biomarker signatures of cell lineages. METHODS: In this study, we used microarrays to analyze transcriptomes of terminally differentiated retinal ganglion cell (RGC) and retinal pigment epithelium (RPE) lineages, as well as intermediate retinal progenitor cells of optic vesicles (OVs) derived from hiPSCs...
May 11, 2018: Stem Cell Research & Therapy
https://www.readbyqxmd.com/read/29748386/frequent-irf1-binding-at-remote-elements-without-histone-modification
#16
Mohamed Abou El Hassan, Katherine Huang, Zhaodong Xu, Tao Yu, Rod Bremner
Transcriptional activators bind DNA and recruit cofactors to modify chromatin.  The extent to which these two events are separable is unclear.  Here, using a custom ChIP tiling array to map chromatin modifications, we show that Interferon-γ-induced DNA-binding of signal transducer and activator of transcription 1 (STAT1), typically associated with the transcription factor IFN regulatory factor 1 (IRF1), causes histone acetylation (H3ac, H4ac). In contrast, among IRF1 sites lacking concomitant STAT1 recruitment, only 25% underwent inducible histone acetylation, 31% exhibited constitutive histone acetylation, and 44% had no histone acetylation...
May 10, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29742888/atypical-teratoid-rhabdoid-tumour-from-tumours-to-therapies
#17
REVIEW
Elizabeth Anne Richardson, Ben Ho, Annie Huang
Atypical teratoid rhabdoid tumours (ATRTs) are the most common malignant central nervous system tumours in children ≤1 year of age and represent approximately 1-2% of all pediatric brain tumours. ATRT is a primarily monogenic disease characterized by the bi-allelic loss of the SMARCB1 gene, which encodes the hSNF5 subunit of the SWI/SNF chromatin remodeling complex. Though conventional dose chemotherapy is not effective in most ATRT patients, high dose chemotherapy with autologous stem cell transplant, radiotherapy and/or intrathecal chemotherapy all show significant potential to improve patient survival...
May 2018: Journal of Korean Neurosurgical Society
https://www.readbyqxmd.com/read/29742437/atp-binding-to-rad5-initiates-replication-fork-reversal-by-inducing-the-unwinding-of-the-leading-arm-and-the-formation-of-the-holliday-junction
#18
Soochul Shin, Kwangbeom Hyun, Jaehoon Kim, Sungchul Hohng
Replication fork reversal is one of the major pathways for reactivating stalled DNA replication. Many enzymes with replication fork reversal activity have DNA-unwinding activity as well, but none of the fork reversal enzymes in the SWI/SNF family shows a separate DNA-unwinding activity, raising the question of how they initiate the remodeling process. Here, we found ATP binding to Rad5 induces the unwinding of the leading arm of the replication fork and proximally positions the leading and lagging arms. This facilitates the spontaneous remodeling of the replication fork into a four-way junction...
May 8, 2018: Cell Reports
https://www.readbyqxmd.com/read/29739311/transcriptome-analysis-reveals-new-micrornas-mediated-pathway-involved-in-anther-development-in-male-sterile-wheat
#19
Longqing Sun, Genlou Sun, Chenxia Shi, Dongfa Sun
BACKGROUND: 337S is a novel bi-pole-photo-thermo-sensitive genic male sterile line in wheat, and sensitive to both long day length/high temperature and short day length/low temperature condition. Although the regulatory function of MicroRNAs (miRNAs) in reproductive development has been increasingly studied, their roles in pre-meiotic and meiotic cells formation of plants have not been clearly explored. Here, we explored the roles of miRNAs in regulating male sterility of 337S at short day length/low temperature condition...
May 8, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29737070/-diagnostic-performance-of-susceptibility-weighted-imaging-in-the-grading-of-hepatocellular-carcinoma
#20
Ting Duan, Jie Chen, Chun-Chao Xia, Bin Song
OBJECTIVE: To test the capability of intratumoral susceptibility signal intensity (ITSS) in the differentiation of hepatocellular carcinoma (HCC) grades. METHODS: Retrospective reviews of 53 patients with pathologically proven HCCs were performed. All patients underwent both conventional MRI and SWI examinations. The morphological score of ITSS and the number of ITSS per square centimeter were calculated,then compared among low-grade and high-grade HCCs. Spearman correlation coefficients were determined between the morphological scores of ITSS,the number of ITSS per square centimeter and HCC grades...
March 2018: Sichuan da Xue Xue Bao. Yi Xue Ban, Journal of Sichuan University. Medical Science Edition
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