keyword
MENU ▼
Read by QxMD icon Read
search

SNF

keyword
https://www.readbyqxmd.com/read/29778836/interrogation-of-mammalian-protein-complex-structure-function-and-membership-using-genome-scale-fitness-screens
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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/29766017/outcomes-according-to-discharge-location-for-persons-who-inject-drugs-receiving-outpatient-parenteral-antimicrobial-therapy
#7
Helen T D'Couto, Gregory K Robbins, Kevin L Ard, Sarah E Wakeman, Justin Alves, Sandra B Nelson
Background: Opioid use disorder poses a significant public health risk. Persons who inject drugs (PWID) suffer from high mortality and morbidity secondary to serious infectious diseases, often requiring prolonged courses of outpatient parenteral antibiotics. The goal of this study was to determine the outcomes of PWID discharged to home or to a skilled nursing or rehabilitation facility (SNF/rehab) with parenteral antibiotic treatment under an outpatient parenteral antimicrobial therapy (OPAT) program...
May 2018: Open Forum Infectious Diseases
https://www.readbyqxmd.com/read/29760405/arid1a-mutation-sensitizes-most-ovarian-clear-cell-carcinomas-to-bet-inhibitors
#8
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/29751772/expression-profiling-of-cell-intrinsic-regulators-in-the-process-of-differentiation-of-human-ipscs-into-retinal-lineages
#9
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/29751608/tetrel-bonding-as-a-vehicle-for-strong-and-selective-anion-binding
#10
Steve Scheiner
Tetrel atoms T (T = Si, Ge, Sn, and Pb) can engage in very strong noncovalent interactions with nucleophiles, which are commonly referred to as tetrel bonds. The ability of such bonds to bind various anions is assessed with a goal of designing an optimal receptor. The Sn atom seems to form the strongest bonds within the tetrel family. It is most effective in the context of a -SnF₃ group and a further enhancement is observed when a positive charge is placed on the receptor. Connection of the -SnF₃ group to either an imidazolium or triazolium provides a strong halide receptor, which can be improved if its point of attachment is changed from the C to an N atom of either ring...
May 11, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29748386/frequent-irf1-binding-at-remote-elements-without-histone-modification
#11
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/29748087/trends-in-hospital-snf-relationships-in-the-care-of-medicare-beneficiaries
#12
Joshua M Liao, R Tamara Konetzka, Rachel M Werner
Improving the value of post-acute care at skilled nursing facilities (SNFs) has become a Medicare policy priority. Anecdotally, hospitals have responded by formally acquiring or pursuing tighter informal connections with SNFs. We evaluated the trend in connections between US acute care hospitals and Medicare-certified SNFs between 2000 and 2013 using vertical integration and two novel network-based measures (number of SNF partners, and discharge concentration). Among 4441 hospitals and 17,215 SNFs, hospitals with weaker connections with SNFs were more often non-profit, major teaching hospitals with a larger number of discharges and beds...
May 7, 2018: Healthcare
https://www.readbyqxmd.com/read/29746689/impact-of-hospital-context-on-transitioning-patients-from-hospital-to-skilled-nursing-facility-a-grounded-theory-study
#13
Barbara J King, Andrea L Gilmore-Bykovskyi, Tonya J Roberts, Korey A Kennelty, Jacquelyn F Mirr, Michael B Gehring, Melissa N Dattalo, Amy J H Kind
Background: Twenty-five percentage of patients who are transferred from hospital settings to skilled nursing facilities (SNFs) are rehospitalized within 30 days. One significant factor in poorly executed transitions is the discharge process used by hospital providers. Objective: The objective of this study was to examine how health care providers in hospitals transition care from hospital to SNF, what actions they took based on their understanding of transitioning care, and what conditions influence provider behavior...
May 8, 2018: Gerontologist
https://www.readbyqxmd.com/read/29742888/atypical-teratoid-rhabdoid-tumour-from-tumours-to-therapies
#14
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
#15
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/29740476/milk-composition-for-admixed-dairy-cattle-in-tanzania
#16
Evans K Cheruiyot, Rawlynce C Bett, Joshua O Amimo, Fidalis D N Mujibi
It is well established that milk composition is affected by the breed and genotype of a cow. The present study investigated the relationship between the proportion of exotic genes and milk composition in Tanzanian crossbred dairy cows. Milk samples were collected from 209 animals kept under smallholder production systems in Rungwe and Lushoto districts of Tanzania. The milk samples were analyzed for the content of components including fat, protein, casein, lactose, solids-not-fat (SNF), and the total solids (TS) through infrared spectroscopy using Milko-Scan FT1 analyzer (Foss Electric, Denmark)...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29739311/transcriptome-analysis-reveals-new-micrornas-mediated-pathway-involved-in-anther-development-in-male-sterile-wheat
#17
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/29730444/arid1a-loss-in-cancer-towards-a-mechanistic-understanding
#18
REVIEW
Radhika Mathur
Genes encoding subunits of SWI/SNF chromatin remodeling complexes are collectively mutated in 20% of all human cancers. ARID1A is the SWI/SNF subunit gene that is most frequently mutated, at variable frequencies across molecular and histological subtypes of cancer. Mouse modeling has revealed that the role of ARID1A in tumor suppression is highly dependent upon context. Recent mechanistic studies have identified a crucial role for ARID1A in targeting SWI/SNF complexes to tissue-specific enhancers and in maintaining their chromatin accessibility...
May 3, 2018: Pharmacology & Therapeutics
https://www.readbyqxmd.com/read/29728458/the-epigenetic-regulator-sirt7-guards-against-mammalian-cellular-senescence-induced-by-ribosomal-dna-instability
#19
Silvana Paredes, Maria Angulo-Ibanez, Luisa Tasselli, Scott M Carlson, Wei Zheng, Tie-Mei Li, Katrin F Chua
In the yeast Saccharomyces cerevisiae, genomic instability in rDNA repeat sequences is an underlying cause of cell aging and is suppressed by the chromatin-silencing factor Sir2. In humans, rDNA instability is observed in cancers and premature aging syndromes, but its underlying mechanisms and functional consequences remain unclear. Here, we uncovered a pivotal role of sirtuin 7 (SIRT7), a mammalian Sir2 homolog, in guarding against rDNA instability and show that this function of SIRT7 protects against senescence in primary human cells...
May 4, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29725455/alternative-lengthening-of-telomeres-phenotype-and-loss-of-atrx-expression-in-sarcomas
#20
REVIEW
Xiaolei Ren, Chao Tu, Zhenchu Tang, Ruofei Ma, Zhihong Li
Sarcoma is a rare and heterogeneous type of cancer with an early mean onset age and a poor prognosis. However, its genetic basis remains unclear. A series of recent genomic studies in sarcomas have identified the occurrence of mutations in the α-thalassemia/mental retardation syndrome X-linked (ATRX) gene. The ATRX protein belongs to the SWI/SNF family of chromatin remodeling proteins, which are frequently associated with α-thalassemia syndrome. Cancer cells depend on telomerase or the alternative lengthening of telomeres (ALT) pathway to overcome replicative programmed mortality...
May 2018: Oncology Letters
keyword
keyword
20787
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"