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  1. Article ; Online: Disruption of polyhomeotic polymerization decreases nucleosome occupancy and alters genome accessibility.

    Amin, Adfar / Kadam, Sangram / Mieczkowski, Jakub / Ahmed, Ikhlak / Bhat, Younus A / Shah, Fouziya / Tolstorukov, Michael Y / Kingston, Robert E / Padinhateeri, Ranjith / Wani, Ajazul H

    Life science alliance

    2023  Volume 6, Issue 5

    Abstract: Chromatin attains its three-dimensional (3D) conformation by establishing contacts between different noncontiguous regions. Sterile Alpha Motif (SAM)-mediated polymerization of the polyhomeotic (PH) protein regulates subnuclear clustering of Polycomb ... ...

    Abstract Chromatin attains its three-dimensional (3D) conformation by establishing contacts between different noncontiguous regions. Sterile Alpha Motif (SAM)-mediated polymerization of the polyhomeotic (PH) protein regulates subnuclear clustering of Polycomb Repressive Complex 1 (PRC1) and chromatin topology. The mutations that perturb the ability of the PH to polymerize, disrupt long-range chromatin contacts, alter Hox gene expression, and lead to developmental defects. To understand the underlying mechanism, we combined the experiments and theory to investigate the effect of this SAM domain mutation on nucleosome occupancy and accessibility on a genome wide scale. Our data show that disruption of PH polymerization because of SAM domain mutation decreases nucleosome occupancy and alters accessibility. Polymer simulations investigating the interplay between distant chromatin contacts and nucleosome occupancy, both of which are regulated by PH polymerization, suggest that nucleosome density increases when contacts between different regions of chromatin are established. Taken together, it appears that SAM domain-mediated PH polymerization biomechanically regulates the organization of chromatin at multiple scales from nucleosomes to chromosomes and we suggest that higher order organization can have a top-down causation effect on nucleosome occupancy.
    MeSH term(s) Nucleosomes/genetics ; Polymerization ; Chromatin/genetics ; Mutation/genetics ; Cell Nucleus ; Drosophila Proteins
    Chemical Substances Nucleosomes ; Chromatin ; Drosophila Proteins
    Language English
    Publishing date 2023-02-27
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2575-1077
    ISSN (online) 2575-1077
    DOI 10.26508/lsa.202201768
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Subnuclear distribution of proteins: Links with genome architecture.

    Shah, Fouziya R / Bhat, Younus A / Wani, Ajazul H

    Nucleus (Austin, Tex.)

    2017  Volume 9, Issue 1, Page(s) 42–55

    Abstract: Metazoan genomes have a hierarchal 3-dimensional (3D) organization scaling from nucleosomes, loops, topologically associating domains (TADs), compartments, to chromosome territories. The 3D organization of genome has been linked with development, ... ...

    Abstract Metazoan genomes have a hierarchal 3-dimensional (3D) organization scaling from nucleosomes, loops, topologically associating domains (TADs), compartments, to chromosome territories. The 3D organization of genome has been linked with development, differentiation and disease. However, the principles governing the 3D chromatin architecture are just beginning to get unraveled. The nucleus has very high concentration of proteins and these proteins are either diffusely distributed throughout the nucleus, or aggregated in the form of foci/bodies/clusters/speckles or in combination of both. Several evidences suggest that the distribution of proteins within the nuclear space is linked to the organization and function of genome. Here, we describe advances made in understanding the relationship between subnuclear distribution of proteins and genome architecture.
    MeSH term(s) Animals ; Cell Nucleus/genetics ; Cell Nucleus/metabolism ; Humans ; Nuclear Proteins/metabolism ; Nucleosomes/metabolism
    Chemical Substances Nuclear Proteins ; Nucleosomes
    Language English
    Publishing date 2017-09-14
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2619626-8
    ISSN 1949-1042 ; 1949-1042
    ISSN (online) 1949-1042
    ISSN 1949-1042
    DOI 10.1080/19491034.2017.1361578
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Subnuclear distribution of proteins: Links with genome architecture

    Shah, Fouziya R / Bhat, Younus A / Wani, Ajazul H

    Nucleus. 2018 Dec. 31, v. 9, no. 1

    2018  

    Abstract: Metazoan genomes have a hierarchal 3-dimensional (3D) organization scaling from nucleosomes, loops, topologically associating domains (TADs), compartments, to chromosome territories. The 3D organization of genome has been linked with development, ... ...

    Abstract Metazoan genomes have a hierarchal 3-dimensional (3D) organization scaling from nucleosomes, loops, topologically associating domains (TADs), compartments, to chromosome territories. The 3D organization of genome has been linked with development, differentiation and disease. However, the principles governing the 3D chromatin architecture are just beginning to get unraveled. The nucleus has very high concentration of proteins and these proteins are either diffusely distributed throughout the nucleus, or aggregated in the form of foci/bodies/clusters/speckles or in combination of both. Several evidences suggest that the distribution of proteins within the nuclear space is linked to the organization and function of genome. Here, we describe advances made in understanding the relationship between subnuclear distribution of proteins and genome architecture.
    Keywords Animalia ; genome ; nucleosomes
    Language English
    Dates of publication 2018-1231
    Size p. 42-55.
    Publishing place Taylor & Francis
    Document type Article
    Note NAL-AP-2-clean
    ZDB-ID 2619626-8
    ISSN 1949-1042 ; 1949-1034
    ISSN (online) 1949-1042
    ISSN 1949-1034
    DOI 10.1080/19491034.2017.1361578
    Database NAL-Catalogue (AGRICOLA)

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  4. Book ; Online: Chromosome-wide simulations uncover folding pathway and 3D organization of interphase chromosomes

    Michieletto, Davide / Marenduzzo, Davide / Wani, Ajazul H.

    2016  

    Abstract: Three-dimensional interphase organization of metazoan genomes has been linked to cellular identity. However, the principles governing 3D interphase genome architecture and its faithful transmission through disruptive events of cell-cycle, like mitosis, ... ...

    Abstract Three-dimensional interphase organization of metazoan genomes has been linked to cellular identity. However, the principles governing 3D interphase genome architecture and its faithful transmission through disruptive events of cell-cycle, like mitosis, are not fully understood. By using Brownian dynamics simulations of Drosophila chromosome 3R up to time-scales of minutes, we show that chromatin binding profile of Polycomb-repressive-complex-1 robustly predicts a sub-set of topologically associated domains (TADs), and inclusion of other factors recapitulates the profile of all TADs, as observed experimentally. Our simulations show that chromosome 3R attains interphase organization from mitotic state by a two-step process in which formation of local TADs is followed by long-range interactions. Our model also explains statistical features and tracks the assembly kinetics of polycomb subnuclear clusters. In conclusion, our approach can be used to predict structural and kinetic features of 3D chromosome folding and its associated proteins in biological relevant genomic and time scales.

    Comment: 20 pages; text + SI; submitted version; supplementary movies can be found at http://www2.ph.ed.ac.uk/~dmichiel/
    Keywords Quantitative Biology - Subcellular Processes ; Condensed Matter - Soft Condensed Matter ; Physics - Biological Physics
    Subject code 612
    Publishing date 2016-04-11
    Publishing country us
    Document type Book ; Online
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  5. Article ; Online: A polycomb group protein is retained at specific sites on chromatin in mitosis.

    Follmer, Nicole E / Wani, Ajazul H / Francis, Nicole J

    PLoS genetics

    2012  Volume 8, Issue 12, Page(s) e1003135

    Abstract: Epigenetic regulation of gene expression, including by Polycomb Group (PcG) proteins, may depend on heritable chromatin states, but how these states can be propagated through mitosis is unclear. Using immunofluorescence and biochemical fractionation, we ... ...

    Abstract Epigenetic regulation of gene expression, including by Polycomb Group (PcG) proteins, may depend on heritable chromatin states, but how these states can be propagated through mitosis is unclear. Using immunofluorescence and biochemical fractionation, we find PcG proteins associated with mitotic chromosomes in Drosophila S2 cells. Genome-wide sequencing of chromatin immunoprecipitations (ChIP-SEQ) from mitotic cells indicates that Posterior Sex Combs (PSC) is not present at well-characterized PcG targets including Hox genes in mitosis, but does remain at a subset of interphase sites. Many of these persistent sites overlap with chromatin domain borders described by Sexton et al. (2012), which are genomic regions characterized by low levels of long range contacts. Persistent PSC binding sites flank both Hox gene clusters. We hypothesize that disruption of long-range chromatin contacts in mitosis contributes to PcG protein release from most sites, while persistent binding at sites with minimal long-range contacts may nucleate re-establishment of PcG binding and chromosome organization after mitosis.
    MeSH term(s) Animals ; Binding Sites ; Cell Line ; Chromatin/genetics ; Chromosomes/genetics ; Drosophila melanogaster/genetics ; Epigenesis, Genetic ; Gene Expression Regulation, Developmental ; Genes, Homeobox/genetics ; Genome, Insect ; Mitosis/genetics ; Polycomb-Group Proteins/genetics ; Polycomb-Group Proteins/metabolism ; Protein Binding
    Chemical Substances Chromatin ; Polycomb-Group Proteins
    Language English
    Publishing date 2012-12-20
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2186725-2
    ISSN 1553-7404 ; 1553-7390
    ISSN (online) 1553-7404
    ISSN 1553-7390
    DOI 10.1371/journal.pgen.1003135
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Chromatin topology is coupled to Polycomb group protein subnuclear organization

    Ajazul H. Wani / Alistair N. Boettiger / Patrick Schorderet / Ayla Ergun / Christine Münger / Ruslan I. Sadreyev / Xiaowei Zhuang / Robert E. Kingston / Nicole J. Francis

    Nature Communications, Vol 7, Iss 1, Pp 1-

    2016  Volume 13

    Abstract: Polycomb Group (PcG) proteins regulate gene expression and genome architecture. Using super-resolution microscopy and molecular simulations, Waniet al. describe the organization of PcG proteins into hundreds of nano-scale protein clusters and suggest ... ...

    Abstract Polycomb Group (PcG) proteins regulate gene expression and genome architecture. Using super-resolution microscopy and molecular simulations, Waniet al. describe the organization of PcG proteins into hundreds of nano-scale protein clusters and suggest these clusters shape genome architecture.
    Keywords Science ; Q
    Language English
    Publishing date 2016-01-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
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  7. Article ; Online: Chromatin topology is coupled to Polycomb group protein subnuclear organization.

    Wani, Ajazul H / Boettiger, Alistair N / Schorderet, Patrick / Ergun, Ayla / Münger, Christine / Sadreyev, Ruslan I / Zhuang, Xiaowei / Kingston, Robert E / Francis, Nicole J

    Nature communications

    2016  Volume 7, Page(s) 10291

    Abstract: The genomes of metazoa are organized at multiple scales. Many proteins that regulate genome architecture, including Polycomb group (PcG) proteins, form subnuclear structures. Deciphering mechanistic links between protein organization and chromatin ... ...

    Abstract The genomes of metazoa are organized at multiple scales. Many proteins that regulate genome architecture, including Polycomb group (PcG) proteins, form subnuclear structures. Deciphering mechanistic links between protein organization and chromatin architecture requires precise description and mechanistic perturbations of both. Using super-resolution microscopy, here we show that PcG proteins are organized into hundreds of nanoscale protein clusters. We manipulated PcG clusters by disrupting the polymerization activity of the sterile alpha motif (SAM) of the PcG protein Polyhomeotic (Ph) or by increasing Ph levels. Ph with mutant SAM disrupts clustering of endogenous PcG complexes and chromatin interactions while elevating Ph level increases cluster number and chromatin interactions. These effects can be captured by molecular simulations based on a previously described chromatin polymer model. Both perturbations also alter gene expression. Organization of PcG proteins into small, abundant clusters on chromatin through Ph SAM polymerization activity may shape genome architecture through chromatin interactions.
    MeSH term(s) Amino Acid Motifs ; Animals ; Cell Line ; Chromatin/metabolism ; Chromatin Immunoprecipitation ; DNA-Binding Proteins/metabolism ; Drosophila ; Drosophila Proteins/metabolism ; Fluorescent Antibody Technique ; Intranuclear Space/metabolism ; Microscopy ; Molecular Dynamics Simulation ; Optical Imaging ; Polycomb Repressive Complex 1/metabolism ; Polycomb-Group Proteins/metabolism ; Polymers ; Protein Structure, Quaternary ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; Sequence Analysis, RNA
    Chemical Substances Chromatin ; DNA-Binding Proteins ; Drosophila Proteins ; Polycomb-Group Proteins ; Polymers ; ph-d protein, Drosophila ; Polycomb Repressive Complex 1 (EC 2.3.2.27)
    Language English
    Publishing date 2016-01-13
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/ncomms10291
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  8. Article ; Online: The PNA-DNA hybrid I-motif: implications for sugar-sugar contacts in i-motif tetramerization.

    Modi, Souvik / Wani, Ajazul Hamid / Krishnan, Yamuna

    Nucleic acids research

    2006  Volume 34, Issue 16, Page(s) 4354–4363

    Abstract: ... and CD experiments revealed that the structure was held together by C-H+-C base pairs. High resolution ... NMR spectroscopy confirmed that PNA and DNA form a unique complex comprising five C-H+-C base pairs ...

    Abstract We have created a hybrid i-motif composed of two DNA and two peptide nucleic acid (PNA) strands from an equimolar mixture of a C-rich DNA and analogous PNA sequence. Nano-electrospray ionization mass spectrometry confirmed the formation of a tetrameric species, composed of PNA-DNA heteroduplexes. Thermal denaturation and CD experiments revealed that the structure was held together by C-H+-C base pairs. High resolution NMR spectroscopy confirmed that PNA and DNA form a unique complex comprising five C-H+-C base pairs per heteroduplex. The imino protons are protected from D2O exchange suggesting intercalation of the heteroduplexes as seen in DNA4 i-motifs. FRET established the relative DNA and PNA strand polarities in the hybrid. The DNA strands were arranged antiparallel with respect to one another. The same topology was observed for PNA strands. Fluorescence quenching revealed that both PNA-DNA parallel heteroduplexes are intercalated, such that both DNA strands occupy one of the narrow grooves. H1'-H1' NOEs show that both heteroduplexes are fully intercalated and that both DNA strands are disposed towards a narrow groove, invoking sugar-sugar interactions as seen in DNA4 i-motifs. The hybrid i-motif shows enhanced thermal stability, intermediate pH dependence and forms at relatively low concentrations making it an ideal nanoscale structural element for pH-based molecular switches. It also serves as a good model system to assess the contribution of sugar-sugar contacts in i-motif tetramerization.
    MeSH term(s) Base Pairing ; Carbohydrates/chemistry ; Circular Dichroism ; Cytosine/chemistry ; DNA/chemistry ; Deuterium Exchange Measurement ; Electrophoresis, Polyacrylamide Gel ; Fluorescence Resonance Energy Transfer ; G-Quadruplexes ; Nuclear Magnetic Resonance, Biomolecular ; Peptide Nucleic Acids/chemistry ; Spectrometry, Mass, Electrospray Ionization ; Temperature
    Chemical Substances Carbohydrates ; Peptide Nucleic Acids ; Cytosine (8J337D1HZY) ; DNA (9007-49-2)
    Language English
    Publishing date 2006-08-26
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkl443
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