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    An Improved Method for Measuring Chromatin-binding Dynamics Using Time-dependent Formaldehyde Crosslinking
    [Abstract] Formaldehyde crosslinking is widely used in combination with chromatin immunoprecipitation (ChIP) to measure the locations along DNA and relative levels of transcription factor (TF)-DNA interactions in vivo. However, the measurements that are typically made do not provide unambiguous information about the dynamic properties of these ...
    Chromatin Affinity Purification (ChAP) from Arabidopsis thaliana Rosette Leaves Using in vivo Biotinylation System
    Authors:  Weronika Sura and Piotr A. Ziolkowski, date: 01/05/2018, view: 289, Q&A: 0
    [Abstract] Chromatin Affinity Purification (ChAP) is widely used to study chromatin architecture and protein complexes interacting with DNA. Here we present an efficient method for ChAP from Arabidopsis thaliana rosette leaves, in which in vivo biotinylation system is used. The chromatin is digested by Micrococcal Nuclease (MNase), hence ...
    Chromatin Immunoprecipitation Experiments from Whole Drosophila Embryos or Larval Imaginal Discs
    [Abstract] Chromatin Immunoprecipitation coupled either to qPCR (qChIP) or high-throughput sequencing (ChIP-Seq) has been extensively used in the last decades to identify the DNA binding sites of transcription factors or the localization of various histone marks along the genome. The ChIP experiment generally includes 7 steps: collection of biological ...
    Micro-chromatin Immunoprecipitation (μChIP) Protocol for Real-time PCR Analysis of a Limited Amount of Cells
    Authors:  Sébastien Gillotin and François Guillemot, date: 06/20/2016, view: 2245, Q&A: 0
    [Abstract] Chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) is an important strategy to study gene regulation. When availability of cells is limited, however, it can be useful to focus on specific genes to investigate in depth the role of transcription factors or histone marks. Unfortunately, performing ChIP experiments to study ...
    MNase Digestion for Nucleosome Mapping in Neurospora
    Authors:  Cigdem Sancar, Gencer Sancar and Michael Brunner, date: 06/05/2016, view: 2616, Q&A: 0
    [Abstract] Digestion of chromatin by micrococcal nuclease MNase followed by high throughput sequencing allows us to determine the location and occupancy of nucleosomes on the genome. Here in this protocol we have described optimized conditions of MNase digestion of filamentous fungus Neurospora crassa chromatin without a requirement of a nuclear ...
    Chromatin Immunoprecipitation (ChIP) Assay for Detecting Direct and Indirect Protein – DNA Interactions in Magnaporthe oryzae
    Authors:  Gang Li, Margarita Marroquin-Guzman and Richard A. Wilson, date: 11/05/2015, view: 4552, Q&A: 0
    [Abstract] Chromatin immunoprecipitation (ChIP) is a powerful technology for analyzing protein-DNA interactions in cells. Robust ChIP procedures have been established for investigating direct interactions between protein and DNA. However, detecting indirect protein-DNA interactions in vivo is challenging. Recently, we used ChIP to analyze an ...
    Random DNA Binding Selection Assay (RDSA)
    Authors:  Yafei Wang and Meizhong Luo, date: 04/20/2015, view: 3003, Q&A: 0
    [Abstract] Protein-DNA interaction is a very important cellular process, by which regulation of DNA biological function, usually gene expression, is exerted. The method of random DNA binding selection assay (RDSA) can be used to identify DNA elements bound by proteins with DNA-binding activities. This method is based on the enrichment of the target DNA ...
    Determination of Protein-DNA (ZMYND11-DNA) Interaction by a Label-Free Biolayer Interferometry Assay
    Authors:  Yuan-Yuan Li, Hong Wen, Xiao-Bing Shi and Hai-Tao Li, date: 02/20/2015, view: 5174, Q&A: 0
    [Abstract] This protocol describes a robust technique for the measurement of ZMYND11-DNA interaction by a label-free Biolayer Interferometry (BLI). ZMYND11 is a novel histone reader protein that specifically recognizes H3.3K36me3 via its tandem Bromodomain, zinc-finger and PWWP domain (BP). ZMYND11 links the histone-variant-mediated transcription elongation ...
    Purification and Sequencing of DNA Guides from Prokaryotic Argonaute
    Authors:  Daan C. Swarts, Edze R. Westra, Stan J. J. Brouns and John van der Oost, date: 11/20/2014, view: 4653, Q&A: 0
    [Abstract] Some proteins utilize nucleic acids to guide them to complementary nucleic acid targets. One example is prokaryotic Argonaute protein, which, binds small single stranded DNA molecules as guides (Swarts et al., 2014). This protocol describes a method to purify DNA guides from these proteins. It also describes a PCR-based method to enrich ...
    Chromatin Fractionation Assay in Fission Yeast
    Authors:  Tatsuki Kunoh and Toshiyuki Habu, date: 07/20/2014, view: 4351, Q&A: 0
    [Abstract] The protein recruitment onto chromatin is a critical process for DNA metabolism, including DNA replication, DNA repair and DNA recombination. Especially DNA modification enzymes and checkpoint proteins are loaded onto DNA damage sites in a context-dependent manner. In our recent study (Kunoh and Habu, 2014), the chromatin association of Pcf1, a ...