Molecular Biology

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    Protocols in Current Issue
    OxiDIP-Seq for Genome-wide Mapping of Damaged DNA Containing 8-Oxo-2'-Deoxyguanosine
    Authors:  Francesca Gorini, Giovanni Scala, Susanna Ambrosio, Barbara Majello and Stefano Amente, date: 11/05/2022, view: 573, Q&A: 0
    [Abstract]

    8-oxo-7,8-dihydro-2′-deoxyguanosine (8-oxodG) is considered to be a premutagenic DNA lesion generated by 2'-deoxyguanosine (dG) oxidation due to reactive oxygen species (ROS). In recent years, the 8-oxodG distribution in human, mouse, and yeast genomes has been underlined using various next-generation sequencing (NGS)–based strategies.

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    ATAC-Seq of a Single Myofiber from Mus musculus
    Authors:  Korin Sahinyan, Darren M. Blackburn and Vahab D. Soleimani, date: 06/20/2022, view: 2063, Q&A: 0
    [Abstract]

    Chromatin accessibility is a key determinant of gene expression that can be altered under different physiological and disease conditions. Skeletal muscle is made up of myofibers that are highly plastic and adaptive. Therefore, assessing the genome-wide chromatin state of myofibers under various conditions is very important to gain insight into the

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    A Highly Sensitive Method to Efficiently Profile the Histone Modifications of FFPE Samples
    Authors:  Linxuan Zhao, Vamsi Krishna Polavarapu, Ram Prakash Yadav, Pengwei Xing and Xingqi Chen, date: 05/20/2022, view: 1482, Q&A: 0
    [Abstract]

    The majority of biopsies in both basic research and translational cancer studies are preserved in the format of archived formalin-fixed paraffin-embedded (FFPE) samples. Profiling histone modifications in archived FFPE tissues is critically important to understand gene regulation in human disease. The required input for current genome-wide

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    ATAC Sequencing Protocol For Cryopreserved Mammalian Cells
    Authors:  Juan Manuel Caravaca, Monika Mehta, Sujatha Gowda and Bao Tran, date: 01/20/2022, view: 2355, Q&A: 0
    [Abstract]

    ATAC-seq (assay for transposase-accessible chromatin with high-throughput sequencing) is a powerful method to evaluate chromatin accessibility and nucleosome positioning at a genome-wide scale. This assay uses a hyperactive Tn5 transposase, to simultaneously cut open chromatin and insert adapter sequences. After sequencing, the reads generated

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    Isolation of Plant Nuclei Compatible with Microfluidic Single-nucleus ATAC-sequencing
    Authors:  Sandra B. Thibivilliers, Dirk K. Anderson and Marc Y. Libault, date: 12/05/2021, view: 2389, Q&A: 0
    [Abstract]

    Gene expression depends on the binding of transcription factors with DNA regulatory sequences. The level of accessibility for these sequences varies between cells and cell types. Until recently, using the Tn5 assay for transposase-accessible chromatin for sequencing (ATAC-seq) technology allowed assessing the profiles of chromatin from an entire

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    A High-throughput Pipeline to Determine DNA and Nucleosome Conformations by AFM Imaging
    Authors:  Sebastian F. Konrad, Willem Vanderlinden and Jan Lipfert, date: 10/05/2021, view: 1766, Q&A: 0
    [Abstract]

    Atomic force microscopy (AFM) is a powerful tool to image macromolecular complexes with nanometer resolution and exquisite single-molecule sensitivity. While AFM imaging is well-established to investigate DNA and nucleoprotein complexes, AFM studies are often limited by small datasets and manual image analysis that is slow and prone to user bias.

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    Simplified Epigenome Profiling Using Antibody-tethered Tagmentation
    Authors:  Steven Henikoff, Jorja G. Henikoff and Kami Ahmad, date: 06/05/2021, view: 4068, Q&A: 0
    [Abstract]

    We previously introduced Cleavage Under Targets & Tagmentation (CUT&Tag), an epigenomic profiling method in which antibody tethering of the Tn5 transposase to a chromatin epitope of interest maps specific chromatin features in small samples and single cells. With CUT&Tag, intact cells or nuclei are permeabilized, followed by successive

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    DNase I Chromatin Accessibility Analysis
    Authors:  Brook S. Nepon-Sixt and Mark G. Alexandrow, date: 12/05/2019, view: 4064, Q&A: 0
    [Abstract] Chromatin consists of compacted DNA in complex with proteins and contributes to the organization of DNA and its stability. Furthermore, chromatin plays key roles in regulating cellular processes such as DNA replication, transcription, DNA repair, and mitosis. Chromatin assumes more compact (inaccessible) or decondensed (accessible) conformations ...
    Determination of Chromatin Accessibility in Drosophila Midgut Enterocytes by in situ 5mC Labeling
    Authors:  Eliya Bitman-Lotan, Hector Rincon-Arano, Gal Raz and Amir Orian, date: 11/20/2019, view: 3029, Q&A: 0
    [Abstract] Regulation of gene expression involves dynamic changes in chromatin organization, where in many cases open chromatin structure correlates with gene activation. Several methods enable monitoring changes in chromatin accessibility, including ATAC-seq, FAIRE-seq, MNase-seq and DNAse-seq methods, which involve Next-generation-sequencing (NGS). ...
    ATAC-seq on Sorted Adult Mouse Neurons
    Authors:  Erin A. Clark, Yasuyuki Shima and Sacha Nelson, date: 10/05/2019, view: 5787, Q&A: 0
    [Abstract] Transcription regulation is a key aspect of cellular identity established during development and maintained into adulthood. Molecular and biochemical assays that probe the genome are critical tools in exploring mechanisms of transcription regulation and cell type identity. The mammalian brain is composed of a huge diversity of cell types with ...



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