scholarly journals DIVERSITY in binding, regulation, and evolution revealed from high-throughput ChIP

2017 ◽  
Author(s):  
Sneha Mitra ◽  
Anushua Biswas ◽  
Leelavati Narlikar
Keyword(s):  
High Throughput ◽  
Dna Sequences ◽  
Chromatin Immunoprecipitation ◽  
Direct Contact ◽  
Black Box ◽  
Cross Linking ◽  
Link Type ◽  
Chip Experiment ◽  
Long Range Interactions ◽  
Regulatory Functions

AbstractA high-throughput chromatin immunoprecipitation (ChIP) experiment is like a black-box: it reports all regions that are associated with the profiled protein based on the initial cross-linking step. These regions can be a highly diverse set of DNA sequences, with some making direct contact with the protein, some binding through intermediaries, and some being a result of long-range interactions involving the protein. We present diversity, a method that identifies the distinct components of such a mixture, leaving no data behind, while at the same time, using no prior motif knowledge. Using the example of the REST protein, we show that these different components give insights into the various complexes that may be forming along the chromatin and their regulatory functions.http://diversity.ncl.res.in/ (webserver)https://github.com/NarlikarLab/DIVERSITY (standalone for Mac OSX/Linux)

scholarly journals The role of CTCF in regulating nuclear organization

2008 ◽  
Vol 205 (4) ◽  
pp. 747-750 ◽  
Author(s):  
Adam Williams ◽  
Richard A. Flavell
Keyword(s):  
Long Range ◽  
Dna Sequences ◽  
Spatial Organization ◽  
Zinc Finger Protein ◽  
Nuclear Organization ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Binding Factor ◽  
Long Range Interactions ◽  
Regulatory Functions

The spatial organization of the genome is thought to play an important part in the coordination of gene regulation. New techniques have been used to identify specific long-range interactions between distal DNA sequences, revealing an ever-increasing complexity to nuclear organization. CCCTC-binding factor (CTCF) is a versatile zinc finger protein with diverse regulatory functions. New data now help define how CTCF mediates both long-range intrachromosomal and interchromosomal interactions, and highlight CTCF as an important factor in determining the three-dimensional structure of the genome.

scholarly journals AmpliconDesign – An interactive web server for the design of high-throughput targeted DNA methylation assays

2020 ◽  
Author(s):  
Maximilian Schönung ◽  
Jana Hess ◽  
Pascal Bawidamann ◽  
Sina Stäble ◽  
Joschka Hey ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Quality Control ◽  
High Throughput ◽  
Dna Sequences ◽  
Web Server ◽  
Dna Amplification ◽  
Pcr Primers ◽  
Primer Design ◽  
Link Type ◽  
Targeted Analysis

ABSTRACTTargeted analysis of DNA methylation patterns based on bisulfite-treated genomic DNA (BT-DNA) is considered as a gold-standard for epigenetic biomarker development. Existing software tools facilitate primer design, primer quality control or visualization of primer localization. However, high-throughput design of primers for BT-DNA amplification is hampered by limits in throughput and functionality of existing tools, requiring users to repeatedly perform specific tasks manually. Consequently, the design of PCR primers for BT-DNA remains a tedious and time-consuming process. To bridge this gap, we developed AmpliconDesign, a webserver providing a scalable and user-friendly platform for the design and analysis of targeted DNA methylation studies based on BT-DNA, e.g. deep amplicon bisulfite sequencing (ampBS-seq), EpiTYPER MassArray, or pyrosequencing. Core functionality of the web server includes high-throughput primer design and binding site validation based on in silico bisulfite-converted DNA sequences, prediction of fragmentation patterns for EpiTYPER MassArray, an interactive quality control as well as a streamlined analysis workflow for ampBS-seq.Availability and ImplementationThe AmpliconDesign webserver is freely available online at: https://amplicondesign.dkfz.de/. AmpliconDesign has been implemented using the R Shiny framework (Chang et al., 2018). The source code is publicly available under the GNU General Public License v3.0 (https://github.com/MaxSchoenung/AmpliconDesign).ContactDaniel B. Lipka ([email protected]) & Maximilian Schönung ([email protected])

scholarly journals kataegis: an R package for identification and visualization of the genomic localized hypermutation regions using high-throughput sequencing

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Xue Lin ◽  
Yingying Hua ◽  
Shuanglin Gu ◽  
Li Lv ◽  
Xingyu Li ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Somatic Mutations ◽  
R Package ◽  
Frequency Of Occurrence ◽  
Link Type ◽  
Genomic Landscape ◽  
One Step ◽  
Flanking Regions

Abstract Background Genomic localized hypermutation regions were found in cancers, which were reported to be related to the prognosis of cancers. This genomic localized hypermutation is quite different from the usual somatic mutations in the frequency of occurrence and genomic density. It is like a mutations “violent storm”, which is just what the Greek word “kataegis” means. Results There are needs for a light-weighted and simple-to-use toolkit to identify and visualize the localized hypermutation regions in genome. Thus we developed the R package “kataegis” to meet these needs. The package used only three steps to identify the genomic hypermutation regions, i.e., i) read in the variation files in standard formats; ii) calculate the inter-mutational distances; iii) identify the hypermutation regions with appropriate parameters, and finally one step to visualize the nucleotide contents and spectra of both the foci and flanking regions, and the genomic landscape of these regions. Conclusions The kataegis package is available on Bionconductor/Github (https://github.com/flosalbizziae/kataegis), which provides a light-weighted and simple-to-use toolkit for quickly identifying and visualizing the genomic hypermuation regions.

scholarly journals Fully automated high-throughput chromatin immunoprecipitation for ChIP-seq: Identifying ChIP-quality p300 monoclonal antibodies

2014 ◽  
Vol 4 (1) ◽  
Author(s):  
William C. Gasper ◽  
Georgi K. Marinov ◽  
Florencia Pauli-Behn ◽  
Max T. Scott ◽  
Kimberly Newberry ◽  
...  
Keyword(s):  
Monoclonal Antibodies ◽  
High Throughput ◽  
Chromatin Immunoprecipitation ◽  
Chip Quality

scholarly journals High throughput automated chromatin immunoprecipitation as a platform for drug screening and antibody validation

Lab on a Chip ◽  
2012 ◽  
Vol 12 (12) ◽  
pp. 2190 ◽  
Author(s):  
Angela R. Wu ◽  
Tiara L.A. Kawahara ◽  
Nicole A. Rapicavoli ◽  
Jan van Riggelen ◽  
Emelyn H. Shroff ◽  
...  
Keyword(s):  
High Throughput ◽  
Drug Screening ◽  
Chromatin Immunoprecipitation ◽  
Antibody Validation

scholarly journals Elucidation of the BMI1 interactome identifies novel regulatory roles in glioblastoma

NAR Cancer ◽  
2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Verónica Freire-Benéitez ◽  
Nicola Pomella ◽  
Thomas O Millner ◽  
Anaëlle A Dumas ◽  
Maria Victoria Niklison-Chirou ◽  
...  
Keyword(s):  
Chromatin Immunoprecipitation ◽  
Protein Composition ◽  
Mrna Splicing ◽  
Cholesterol Transport ◽  
Normal Brain ◽  
Regulatory Functions ◽  
Polycomb Repressive Complex 1 ◽  
Normal Brain Development

Abstract Glioblastoma (GBM) is the most common and aggressive intrinsic brain tumour in adults. Epigenetic mechanisms controlling normal brain development are often dysregulated in GBM. Among these, BMI1, a structural component of the Polycomb Repressive Complex 1 (PRC1), which promotes the H2AK119ub catalytic activity of Ring1B, is upregulated in GBM and its tumorigenic role has been shown in vitro and in vivo. Here, we have used protein and chromatin immunoprecipitation followed by mass spectrometry (MS) analysis to elucidate the protein composition of PRC1 in GBM and transcriptional silencing of defining interactors in primary patient-derived GIC lines to assess their functional impact on GBM biology. We identify novel regulatory functions in mRNA splicing and cholesterol transport which could represent novel targetable mechanisms in GBM.

scholarly journals Computational Method for Simulating Thermoset Polymer Curing and Prediction of Thermophysical Properties

2020 ◽  
Author(s):  
Jeffrey Sanders ◽  
Carla E. Estridge ◽  
Matthew B Jackson ◽  
Thomas JL Mustard ◽  
Samuel J. Tucker ◽  
...  
Keyword(s):  
High Throughput ◽  
Thermophysical Properties ◽  
High Throughput Screening ◽  
Simulation Analysis ◽  
Low Cost ◽  
Polymer Network ◽  
Thermomechanical Properties ◽  
Computational Method ◽  
Cross Linking ◽  
Automated Simulation

Thermoset polymers are an area of intense research due to their low cost, ease of processing, environmental resistance, and unique physical properties. The favorable properties of this class of polymers have many applications in aerospace, automotive, marine, and sports equipment industries. Molecular simulations of thermosets are frequently used to model formation of the polymer network, and to predict the thermomechanical properties. These simulations usually require custom algorithms that are not easily accessible to non-experts and not suited for high throughput screening. To address these issues, we have developed a robust cross-linking algorithm that can incorporate different types of chemistries and leverage GPU-enabled molecular dynamics simulations. Automated simulation analysis tools for cross-linking simulations are also presented. Using four well known epoxy/amine formulations as a foundational case study and benzoxazine as an example of how additional chemistries can be modeled, we demonstrate the power of the algorithm to accurately predict curing and thermophysical properties. These tools are able to streamline the thermoset simulation process, opening up avenues to in-silico high throughput screening for advanced material development.

scholarly journals DNAContentViewer a BioJS component to visualise GC/AT Content

F1000Research ◽  
2014 ◽  
Vol 3 ◽  
pp. 54 ◽  
Author(s):  
Anil S. Thanki ◽  
Shabhonam Caim ◽  
Manuel Corpas ◽  
Robert P. Davey
Keyword(s):  
Dna Sequences ◽  
Genome Analysis ◽  
Biological Function ◽  
Structure And Function ◽  
Link Type ◽  
And Function ◽  
Potential Interactions

Summary: Compositional GC/AT content of DNA sequences is a useful feature in genome analysis. GC/AT content provides useful information about evolution, structure and function of genomes, giving clues about their biological function and organisation. We have developed DNAContentViewer, a BioJS component for visualisation of compositional GC/AT content in raw sequences. DNAContentViewer has been integrated in the BioJS project as part of the BioJS registry of components. DNAContentViewer requires a simple configuration and installation. Its design allows potential interactions with other components via predefined events. Availability: http://github.com/biojs/biojs; doi: 10.5281/zenodo.7722.

scholarly journals XlinkCyNET: a Cytoscape application for visualization of protein interaction networks based on cross-linking mass-spectrometry identifications

2020 ◽  
Author(s):  
Diogo Borges Lima ◽  
Ying Zhu ◽  
Fan Liu
Keyword(s):  
Mass Spectrometry ◽  
Protein Interaction ◽  
Large Scale ◽  
Interaction Network ◽  
Protein Interaction Networks ◽  
Interaction Networks ◽  
Cross Linking ◽  
Protein Interaction Data ◽  
Interaction Data ◽  
Link Type

ABSTRACTSoftware tools that allow visualization and analysis of protein interaction networks are essential for studies in systems biology. One of the most popular network visualization tools in biology is Cytoscape, which offers a large selection of plugins for interpretation of protein interaction data. Chemical cross-linking coupled to mass spectrometry (XL-MS) is an increasingly important source for such interaction data, but there are currently no Cytoscape tools to analyze XL-MS results. In light of the suitability of Cytoscape platform but also to expand its toolbox, here we introduce XlinkCyNET, an open-source Cytoscape Java plugin for exploring large-scale XL-MS-based protein interaction networks. XlinkCyNET offers rapid and easy visualization of intra and intermolecular cross-links and the locations of protein domains in a rectangular bar style, allowing subdomain-level interrogation of the interaction network. XlinkCyNET is freely available from the Cytoscape app store: http://apps.cytoscape.org/apps/xlinkcynet and at https://www.theliulab.com/software/xlinkcynet.

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