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  1. Analyses of Promoter , Enhancer, and Nucleosome Organization in Mammalian Cells by MNase-Seq

    MNase-Seq is a genome-wide procedure that allows map** of DNA associated to nucleosomes following micrococcal nuclease digestion. It is a rapid and...
    Cyril Esnault, Talha Magat, ... Jean-Christophe Andrau in Enhancers and Promoters
    Protocol 2021

  2. Determining the Binding Constant of LANA Protein Fragment with Nucleosome

    Abstract

    On the surface of the nucleosome, there are many regions for interaction with chromatin proteins, but an acidic patch, a negatively charged...

    R. V. Novikov, E. A. Bondarenko, ... A. K. Shaytan in Moscow University Biological Sciences Bulletin
    Article 01 October 2020

  3. Genome-wide profiling of nucleosome position and chromatin accessibility in single cells using scMNase-seq

    Nucleosome organization is important for chromatin compaction and accessibility. Profiling nucleosome positioning genome-wide in single cells...

    Weiwu Gao, Binbin Lai, ... Keji Zhao in Nature Protocols
    Article 13 December 2019

  4. Position Effect Variegation: Role of the Local Chromatin Context in Gene Expression Regulation

    Abstract

    Position effect variegation (PEV) is a phenomenon wherein the expression level of a gene strongly depends on its genomic position. PEV can be...

    L. V. Boldyreva, E. N. Andreyeva, A. V. Pindyurin in Molecular Biology
    Article 03 June 2022

  5. The structure of a virus-encoded nucleosome

    Certain large DNA viruses, including those in the Marseilleviridae family, encode histones. Here we show that fused histone pairs Hβ-Hα and Hδ-Hγ...

    Marco Igor Valencia-Sánchez, Stephen Abini-Agbomson, ... Karim-Jean Armache in Nature Structural & Molecular Biology
    Article 29 April 2021

  6. Structure of the ISW1a complex bound to the dinucleosome

    Nucleosomes are basic repeating units of chromatin and form regularly spaced arrays in cells. Chromatin remodelers alter the positions of nucleosomes...

    Lifei Li, Kang**g Chen, ... Zhucheng Chen in Nature Structural & Molecular Biology
    Article 04 January 2024

  7. Picking a nucleosome lock: Sequence- and structure-specific recognition of the nucleosome

    The nucleosome presents a formidable barrier to DNA-templated transcription by the RNA polymerase II machinery. Overcoming this transcriptional...

    Matthew M Makowski, Guillaume Gaullier, Karolin Luger in Journal of Biosciences
    Article 20 January 2020

  8. Structural and mechanistic basis for nucleosomal H2AK119 deubiquitination by single-subunit deubiquitinase USP16

    Epigenetic regulators have a crucial effect on gene expression based on their manipulation of histone modifications. Histone H2AK119...

    Huasong Ai, Zaozhen He, ... Lei Liu in Nature Structural & Molecular Biology
    Article 25 June 2024

  9. Structural insights into histone exchange by human SRCAP complex

    Histone variant H2A.Z is found at promoters and regulates transcription. The ATP-dependent chromatin remodeler SRCAP complex (SRCAP-C) promotes the...

    Jiali Yu, Fengrui Sui, ... Yanhui Xu in Cell Discovery
    Article Open access 08 February 2024

  10. A novel fungal gene regulation system based on inducible VPR-dCas9 and nucleosome map-guided sgRNA positioning

    Abstract

    Programmable transcriptional regulation is a powerful tool to study gene functions. Current methods to selectively regulate target genes are...

    Andreas Schüller, Lisa Wolansky, ... Joseph Strauss in Applied Microbiology and Biotechnology
    Article Open access 02 October 2020

  11. CORENup: a combination of convolutional and recurrent deep neural networks for nucleosome positioning identification

    Background

    Nucleosomes wrap the DNA into the nucleus of the Eukaryote cell and regulate its transcription phase. Several studies indicate that...

    Domenico Amato, Giosue’ Lo Bosco, Riccardo Rizzo in BMC Bioinformatics
    Article Open access 16 September 2020

  12. Energy-driven genome regulation by ATP-dependent chromatin remodellers

    The packaging of DNA into chromatin in eukaryotes regulates gene transcription, DNA replication and DNA repair. ATP-dependent chromatin remodelling...

    Sebastian Eustermann, Avinash B. Patel, ... Philipp Korber in Nature Reviews Molecular Cell Biology
    Article 11 December 2023

  13. Histone Dynamics During Transcription: Exchange of H2A/H2B Dimers and H3/H4 Tetramers During Pol II Elongation

    Chromatin within eukaryotic cell nuclei accommodates many complex activities that require at least partial disassembly and reassembly of...
    Christophe Thiriet, Jeffrey J. Hayes in Chromatin Dynamics in Cellular Function
    Chapter

  14. The Roles of Chromatin Remodelling Factors in Replication

    Dynamic changes of chromatin structure control DNA-dependent events, including DNA replication. Along with DNA, chromatin organization must be...
    Ana Neves-Costa, Patrick Varga-Weisz in Chromatin Dynamics in Cellular Function
    Chapter

  15. Manipulating chromatin architecture in C. elegans

    Background

    Nucleosome-mediated chromatin compaction has a direct effect on the accessibility of trans-acting activators and repressors to DNA targets...

    John L. Carter, Colton E. Kempton, ... Steven M. Johnson in Epigenetics & Chromatin
    Article Open access 29 November 2022

  17. Studying Structure and Functions of Nucleosomes with Atomic Force Microscopy

    Abstract

    Chromatin is an epigenetic platform for implementation of DNA-dependent processes. Nucleosome, as a basic level of chromatin compaction,...

    Alexander A. Ukraintsev, Mikhail M. Kutuzov, Olga I. Lavrik in Biochemistry (Moscow)
    Article 01 April 2024

  18. Self-assembling viral histones are evolutionary intermediates between archaeal and eukaryotic nucleosomes

    Nucleosomes are DNA–protein complexes composed of histone proteins that form the basis of eukaryotic chromatin. The nucleosome was a key innovation...

    Nicholas A. T. Irwin, Thomas A. Richards in Nature Microbiology
    Article Open access 28 May 2024

  19. Dynamic epistasis analysis reveals how chromatin remodeling regulates transcriptional bursting

    Transcriptional bursting has been linked to the stochastic positioning of nucleosomes. However, how bursting is regulated by the remodeling of...

    Ineke Brouwer, Emma Kerklingh, ... Tineke L. Lenstra in Nature Structural & Molecular Biology
    Article Open access 01 May 2023

  20. Molecular mechanism of histone variant H2A.B on stability and assembly of nucleosome and chromatin structures

    Background

    H2A.B, the most divergent histone variant of H2A, can significantly modulate nucleosome and chromatin structures. However, the related...

    Junhui Peng, Chuang Yuan, ... Zhiyong Zhang in Epigenetics & Chromatin
    Article Open access 14 July 2020
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