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https://www.readbyqxmd.com/read/28724529/coactivators-and-general-transcription-factors-have-two-distinct-dynamic-populations-dependent-on%C3%A2-transcription
#1
Nikolaos Vosnakis, Marc Koch, Elisabeth Scheer, Pascal Kessler, Yves Mély, Pascal Didier, László Tora
SAGA and ATAC are two distinct chromatin modifying co-activator complexes with distinct enzymatic activities involved in RNA polymerase II (Pol II) transcription regulation. To investigate the mobility of co-activator complexes and general transcription factors in live-cell nuclei, we performed imaging experiments based on photobleaching. SAGA and ATAC, but also two general transcription factors (TFIID and TFIIB), were highly dynamic, exhibiting mainly transient associations with chromatin, contrary to Pol II, which formed more stable chromatin interactions...
July 19, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28723572/robust-identification-of-developmentally-active-endothelial-enhancers-in-zebrafish-using-fans-assisted-atac-seq
#2
Aurelie Quillien, Mary Abdalla, Jun Yu, Jianhong Ou, Lihua Julie Zhu, Nathan D Lawson
Identification of tissue-specific and developmentally active enhancers provides insights into mechanisms that control gene expression during embryogenesis. However, robust detection of these regulatory elements remains challenging, especially in vertebrate genomes. Here, we apply fluorescent-activated nuclei sorting (FANS) followed by Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) to identify developmentally active endothelial enhancers in the zebrafish genome. ATAC-seq of nuclei from Tg(fli1a:egfp)(y1) transgenic embryos revealed expected patterns of nucleosomal positioning at transcriptional start sites throughout the genome and association with active histone modifications...
July 18, 2017: Cell Reports
https://www.readbyqxmd.com/read/28704389/differential-chromatin-profiles-partially-determine-transcription-factor-binding
#3
Rujian Chen, David K Gifford
We characterize how genomic variants that alter chromatin accessibility influence regulatory factor binding with a new method called DeltaBind that predicts condition specific factor binding more accurately than other methods based on DNase-seq data. Using DeltaBind and DNase-seq experiments we predicted the differential binding of 18 factors in K562 and GM12878 cells with an average precision of 28% at 10% recall, with the prediction of individual factors ranging from 5% to 65% precision. We further found that genome variants that alter chromatin accessibility are not necessarily predictive of altering proximal factor binding...
2017: PloS One
https://www.readbyqxmd.com/read/28680085/prediction-of-chromatin-accessibility-in-gene-regulatory-regions-from-transcriptomics-data
#4
Sascha Jung, Vladimir Espinosa Angarica, Miguel A Andrade-Navarro, Noel J Buckley, Antonio Del Sol
The epigenetics landscape of cells plays a key role in the establishment of cell-type specific gene expression programs characteristic of different cellular phenotypes. Different experimental procedures have been developed to obtain insights into the accessible chromatin landscape including DNase-seq, FAIRE-seq and ATAC-seq. However, current downstream computational tools fail to reliably determine regulatory region accessibility from the analysis of these experimental data. In particular, currently available peak calling algorithms are very sensitive to their parameter settings and show highly heterogeneous results, which hampers a trustworthy identification of accessible chromatin regions...
July 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28671995/dr-seq2-a-quality-control-and-analysis-pipeline-for-parallel-single-cell-transcriptome-and-epigenome-data
#5
Chengchen Zhao, Sheng'en Hu, Xiao Huo, Yong Zhang
An increasing number of single cell transcriptome and epigenome technologies, including single cell ATAC-seq (scATAC-seq), have been recently developed as powerful tools to analyze the features of many individual cells simultaneously. However, the methods and software were designed for one certain data type and only for single cell transcriptome data. A systematic approach for epigenome data and multiple types of transcriptome data is needed to control data quality and to perform cell-to-cell heterogeneity analysis on these ultra-high-dimensional transcriptome and epigenome datasets...
2017: PloS One
https://www.readbyqxmd.com/read/28655330/nice-seq-high-resolution-open-chromatin-profiling
#6
V K Chaithanya Ponnaluri, Guoqiang Zhang, Pierre-Olivier Estève, George Spracklin, Stephanie Sian, Shuang-Yong Xu, Touati Benoukraf, Sriharsa Pradhan
Open chromatin profiling integrates information across diverse regulatory elements to reveal the transcriptionally active genome. Tn5 transposase and DNase I sequencing-based methods prefer native or high cell numbers. Here, we describe NicE-seq (nicking enzyme assisted sequencing) for high-resolution open chromatin profiling on both native and formaldehyde-fixed cells. NicE-seq captures and reveals open chromatin sites (OCSs) and transcription factor occupancy at single nucleotide resolution, coincident with DNase hypersensitive and ATAC-seq sites at a low sequencing burden...
June 28, 2017: Genome Biology
https://www.readbyqxmd.com/read/28644665/giant-paramagnetism-induced-valley-polarization-of-electrons-in-charge-tunable-monolayer-mose_-2
#7
Patrick Back, Meinrad Sidler, Ovidiu Cotlet, Ajit Srivastava, Naotomo Takemura, Martin Kroner, Atac Imamoğlu
For applications exploiting the valley pseudospin degree of freedom in transition metal dichalcogenide monolayers, efficient preparation of electrons or holes in a single valley is essential. Here, we show that a magnetic field of 7 T leads to a near-complete valley polarization of electrons in a MoSe_{2} monolayer with a density 1.6×10^{12}  cm^{-2}; in the absence of exchange interactions favoring single-valley occupancy, a similar degree of valley polarization would have required a pseudospin g factor of 38...
June 9, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28625481/chromatin-accessibility-landscape-of-cutaneous-t-cell-lymphoma-and-dynamic-response-to-hdac-inhibitors
#8
Kun Qu, Lisa C Zaba, Ansuman T Satpathy, Paul G Giresi, Rui Li, Yonghao Jin, Randall Armstrong, Chen Jin, Nathalie Schmitt, Ziba Rahbar, Hideki Ueno, William J Greenleaf, Youn H Kim, Howard Y Chang
Here, we define the landscape and dynamics of active regulatory DNA in cutaneous T cell lymphoma (CTCL) by ATAC-seq. Analysis of 111 human CTCL and control samples revealed extensive chromatin signatures that distinguished leukemic, host, and normal CD4(+) T cells. We identify three dominant patterns of transcription factor (TF) activation that drive leukemia regulomes, as well as TF deactivations that alter host T cells in CTCL patients. Clinical response to histone deacetylase inhibitors (HDACi) is strongly associated with a concurrent gain in chromatin accessibility...
July 10, 2017: Cancer Cell
https://www.readbyqxmd.com/read/28572580/uropa-a-tool-for-universal-robust-peak-annotation
#9
Maria Kondili, Annika Fust, Jens Preussner, Carsten Kuenne, Thomas Braun, Mario Looso
The annotation of genomic ranges of interest represents a recurring task for bioinformatics analyses. These ranges can originate from various sources, including peaks called for transcription factor binding sites (TFBS) or histone modification ChIP-seq experiments, chromatin structure and accessibility experiments (such as ATAC-seq), but also from other types of predictions that result in genomic ranges. While peak annotation primarily driven by ChiP-seq was extensively explored, many approaches remain simplistic ("most closely located TSS"), rely on fixed pre-built references, or require complex scripting tasks on behalf of the user...
June 1, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28555639/clonally-stable-v%C3%AE%C2%BA-allelic-choice-instructs-ig%C3%AE%C2%BA-repertoire
#10
Rena Levin-Klein, Shira Fraenkel, Michal Lichtenstein, Louise S Matheson, Osnat Bartok, Yuval Nevo, Sebastian Kadener, Anne E Corcoran, Howard Cedar, Yehudit Bergman
Although much has been done to understand how rearrangement of the Igκ locus is regulated during B-cell development, little is known about the way the variable (V) segments themselves are selected. Here we show, using B6/Cast hybrid pre-B-cell clones, that a limited number of V segments on each allele is stochastically activated as characterized by the appearance of non-coding RNA and histone modifications. The activation states are clonally distinct, stable across cell division and developmentally important in directing the Ig repertoire upon differentiation...
May 30, 2017: Nature Communications
https://www.readbyqxmd.com/read/28550296/reducing-mitochondrial-reads-in-atac-seq-using-crispr-cas9
#11
Lindsey Montefiori, Liana Hernandez, Zijie Zhang, Yoav Gilad, Carole Ober, Gregory Crawford, Marcelo Nobrega, Noboru Jo Sakabe
ATAC-seq is a high-throughput sequencing technique that identifies open chromatin. Depending on the cell type, ATAC-seq samples may contain ~20-80% of mitochondrial sequencing reads. As the regions of open chromatin of interest are usually located in the nuclear genome, mitochondrial reads are typically discarded from the analysis. We tested two approaches to decrease wasted sequencing in ATAC-seq libraries generated from lymphoblastoid cell lines: targeted cleavage of mitochondrial DNA fragments using CRISPR technology and removal of detergent from the cell lysis buffer...
May 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28538187/bivariate-genomic-footprinting-detects-changes-in-transcription-factor-activity
#12
Songjoon Baek, Ido Goldstein, Gordon L Hager
In response to activating signals, transcription factors (TFs) bind DNA and regulate gene expression. TF binding can be measured by protection of the bound sequence from DNase digestion (i.e., footprint). Here, we report that 80% of TF binding motifs do not show a measurable footprint, partly because of a variable cleavage pattern within the motif sequence. To more faithfully portray the effect of TFs on chromatin, we developed an algorithm that captures two TF-dependent effects on chromatin accessibility: footprinting and motif-flanking accessibility...
May 23, 2017: Cell Reports
https://www.readbyqxmd.com/read/28505247/single-cell-regulome-data-analysis-by-scrat
#13
Zhicheng Ji, Weiqiang Zhou, Hongkai Ji
Summary: Emerging single-cell technologies (e.g., single-cell ATAC-seq, DNase-seq or ChIP-seq) have made it possible to assay regulome of individual cells. Single-cell regulome data are highly sparse and discrete. Analyzing such data is challenging. User-friendly software tools are still lacking. We present SCRAT, a Single-Cell Regulome Analysis Toolbox with a graphical user interface, for studying cell heterogeneity using single-cell regulome data. SCRAT can be used to conveniently summarize regulatory activities according to different features (e...
May 12, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28498703/realization-of-a-cascaded-quantum-system-heralded-absorption-of-a-single-photon-qubit-by-a-single-electron-charged-quantum-dot
#14
Aymeric Delteil, Zhe Sun, Stefan Fält, Atac Imamoğlu
Photonic losses pose a major limitation for the implementation of a quantum state transfer between nodes of a quantum network. A measurement that heralds a successful transfer without revealing any information about the qubit may alleviate this limitation. Here, we demonstrate the heralded absorption of a single photonic qubit, generated by a single neutral quantum dot, by a single-electron charged quantum dot that is located 5 m away. The transfer of quantum information to the spin degree of freedom takes place upon the emission of a photon; for a properly chosen or prepared quantum dot, the detection of this photon yields no information about the qubit...
April 28, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28494403/her2-status-predicts-for-upfront-ai-benefit-a%C3%A2-trans-aiog-meta-analysis-of-12-129-patients-from%C3%A2-atac-big-1-98-and-team-with-centrally-determined-her2
#15
John M S Bartlett, Ikhlaaq Ahmed, Meredith M Regan, Ivana Sestak, Elizabeth A Mallon, Patrizia Dell'Orto, Beat Thürlimann, Caroline Seynaeve, Hein Putter, Cornelis J H Van de Velde, Cassandra L Brookes, John F Forbes, Giuseppe Viale, Jack Cuzick, Mitchell Dowsett, Daniel W Rea
BACKGROUND: A meta-analysis of the effects of HER2 status, specifically within the first 2-3 years of adjuvant endocrine therapy, has the potential to inform patient selection for upfront aromatase inhibitor (AI) therapy or switching strategy tamoxifen followed by AI. The pre-existing standardisation of methodology for HER2 (immunohistochemistry/fluorescence in situ hybridization) facilitates analysis of existing data for this key marker. METHODS: Following a prospectively designed statistical analysis plan, patient data from 3 phase III trials Arimidex, Tamoxifen, Alone or in Combination Trial (ATAC), Breast International Group (BIG) 1-98 and Tamoxifen Exemestane Adjuvant Multicentre Trial (TEAM)] comparing an AI to tamoxifen during the first 2-3 years of adjuvant endocrine treatment were collected and a treatment-by-marker analysis of distant recurrence-free interval-censored at 2-3 years treatment - for HER2 status × AI versus tamoxifen treatment was performed to address the clinical question relating to efficacy of 'upfront' versus 'switch' strategies for AIs...
May 8, 2017: European Journal of Cancer
https://www.readbyqxmd.com/read/28473594/evaluation-of-sinus-edge-corrected-zte-based-attenuation-correction-in-brain-pet-mri
#16
Jaewon Yang, Florian Wiesinger, Sandeep Kaushik, Dattesh Shanbhag, Thomas A Hope, Peder E Z Larson, Youngho Seo
Purpose: In brain positron emission tomography/magnetic resonance imaging (PET/MRI), the major challenge of zero-echo-time (ZTE)-based attenuation correction (ZTAC) is the misclassification of air/tissue/bone mixtures or their boundaries. Our study aimed to evaluate a sinus/edge corrected (SEC) ZTAC (ZTACSEC), relative to an "uncorrected (UC)" ZTAC (ZTACUC) and a computed tomography (CT) atlas-based attenuation correction (ATAC). Materials and Methods: Whole-body fluorodeoxyglucose PET/MRI scans were performed for twelve patients, following PET/CT scans...
May 4, 2017: Journal of Nuclear Medicine: Official Publication, Society of Nuclear Medicine
https://www.readbyqxmd.com/read/28472346/a-c-myb-mutant-causes-deregulated-differentiation-due-to-impaired-histone-binding-and-abrogated-pioneer-factor-function
#17
Bettina M Fuglerud, Roza B Lemma, Pimthanya Wanichawan, Arvind Y M Sundaram, Ragnhild Eskeland, Odd S Gabrielsen
The transcription factor c-Myb is involved in early differentiation and proliferation of haematopoietic cells, where it operates as a regulator of self-renewal and multi-lineage differentiation. Deregulated c-Myb plays critical roles in leukaemias and other human cancers. Due to its role as a master regulator, we hypothesized it might function as a pioneer transcription factor. Our approach to test this was to analyse a mutant of c-Myb, D152V, previously reported to cause haematopoietic defects in mice by an unknown mechanism...
May 2, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28459457/conserved-roles-of-mouse-dux-and-human-dux4-in-activating-cleavage-stage-genes-and-mervl-hervl-retrotransposons
#18
Peter G Hendrickson, Jessie A Doráis, Edward J Grow, Jennifer L Whiddon, Jong-Won Lim, Candice L Wike, Bradley D Weaver, Christian Pflueger, Benjamin R Emery, Aaron L Wilcox, David A Nix, C Matthew Peterson, Stephen J Tapscott, Douglas T Carrell, Bradley R Cairns
To better understand transcriptional regulation during human oogenesis and preimplantation development, we defined stage-specific transcription, which highlighted the cleavage stage as being highly distinctive. Here, we present multiple lines of evidence that a eutherian-specific multicopy retrogene, DUX4, encodes a transcription factor that activates hundreds of endogenous genes (for example, ZSCAN4, KDM4E and PRAMEF-family genes) and retroviral elements (MERVL/HERVL family) that define the cleavage-specific transcriptional programs in humans and mice...
June 2017: Nature Genetics
https://www.readbyqxmd.com/read/28439570/epigenomics-of-human-cd8-t-cell-differentiation-and-aging
#19
David M Moskowitz, David W Zhang, Bin Hu, Sabine Le Saux, Rolando E Yanes, Zhongde Ye, Jason D Buenrostro, Cornelia M Weyand, William J Greenleaf, Jörg J Goronzy
The efficacy of the adaptive immune response declines dramatically with age, but the cell-intrinsic mechanisms driving immune aging in humans remain poorly understood. Immune aging is characterized by a loss of self-renewing naïve cells and the accumulation of differentiated but dysfunctional cells within the CD8 T cell compartment. Using ATAC-seq, we inferred the transcription factor binding activities correlated with naive and central and effector memory CD8 T cell states in young adults. Integrating our results with RNA-seq, we identified transcription networks associated with CD8 T cell differentiation, with prominent roles implicated for BATF, ETS1, Eomes, and Sp1...
February 2017: Science Immunology
https://www.readbyqxmd.com/read/28381412/the-ddr-at-telomeres-lacking-intact-shelterin-does-not-require-substantial-chromatin-decompaction
#20
Leonid A Timashev, Hazen Babcock, Xiaowei Zhuang, Titia de Lange
Telomeres are protected by shelterin, a six-subunit protein complex that represses the DNA damage response (DDR) at chromosome ends. Extensive data suggest that TRF2 in shelterin remodels telomeres into the t-loop structure, thereby hiding telomere ends from double-stranded break repair and ATM signaling, whereas POT1 represses ATR signaling by excluding RPA. An alternative protection mechanism was suggested recently by which shelterin subunits TRF1, TRF2, and TIN2 mediate telomeric chromatin compaction, which was proposed to minimize access of DDR factors...
March 15, 2017: Genes & Development
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