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Volle CB, Delaney S. AGG/CCT interruptions affect nucleosome formation and positioning of healthy-length CGG/CCG triplet repeats. BMC BIOCHEMISTRY 2013; 14:33. [PMID: 24261641 PMCID: PMC3870987 DOI: 10.1186/1471-2091-14-33] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 11/19/2013] [Indexed: 11/16/2022]
Abstract
Background Fragile X Syndrome (FXS), the most common inherited form of mental retardation, is caused by expansion of a CGG/CCG repeat tract in the 5′-untranslated region of the fragile X mental retardation (FMR1) gene, which changes the functional organization of the gene from euchromatin to heterochromatin. Interestingly, healthy-length repeat tracts possess AGG/CCT interruptions every 9–10 repeats, and clinical data shows that loss of these interruptions is linked to expansion of the repeat tract to disease-length. Thus, it is important to understand how these interruptions alter the behavior of the repeat tract in the packaged gene. Results To investigate how uninterrupted and interrupted CGG/CCG repeat tracts interact with the histone core, we designed experiments using the nucleosome core particle, the most basic unit of chromatin packaging. Using DNA containing 19 CGG/CCG repeats, flanked by either a nucleosome positioning sequence or the FMR1 gene sequence, we determined that the addition of a single AGG/CCT interruption modulates both the ability of the CGG/CCG repeat DNA to incorporate into a nucleosome and the rotational and translational position of the repeat DNA around the histone core when flanked by the nucleosome positioning sequence. The presence of these interruptions also alters the periodicity of the DNA in the nucleosome; interrupted repeat tracts have a greater periodicity than uninterrupted repeats. Conclusions This work defines the ability of AGG/CCT interruptions to modulate the behavior of the repeat tract in the packaged gene and contributes to our understanding of the role that AGG/CCT interruptions play in suppressing expansion and maintaining the correct functional organization of the FMR1 gene, highlighting a protective role played by the interruptions in genomic packaging.
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Affiliation(s)
| | - Sarah Delaney
- Department of Chemistry, Brown University, Providence, RI 02912, USA.
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Volle CB, Delaney S. CAG/CTG repeats alter the affinity for the histone core and the positioning of DNA in the nucleosome. Biochemistry 2012; 51:9814-25. [PMID: 23157165 DOI: 10.1021/bi301416v] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Trinucleotide repeats (TNRs) occur throughout the genome, and their expansion has been linked to several neurodegenerative disorders, including Huntington's disease. TNRs have been studied using both oligonucleotides and plasmids; however, less is know about how repetitive DNA responds to genomic packaging. Here, we investigate the behavior of CAG/CTG repeats incorporated into nucleosome core particles, the most basic unit of chromatin packaging. To assess the general interaction between CAG/CTG repeats and the histone core, we determined the efficiency with which various TNR-containing DNA substrates form nucleosomes, revealing that even short CAG/CTG tracts are robust incorporators. However, the presence of the Huntington gene flanking sequence (htt) decreases the rate of incorporation. Enzymatic and chemical probing revealed repositioning of the DNA in the nucleosome as the number of CAG/CTG repeats increased, regardless of the flanking sequence. Notably, the periodicity of the repeat tract remained unchanged as a function of length and is consistently 10.7 bp per helical turn. In contrast, the periodicity of the nonrepetitive flanking sequence varies and is smaller than the repeat tract at ~10.0-10.5 bp per turn. Furthermore, while the CAG/CTG repeats remain as a canonical duplex in the nucleosome, nucleosome formation causes kinking in a secondary repeat tract in the htt gene, comprised of CCG/CGG repeats. This work highlights the innate ability of CAG/CTG repeats to incorporate and to position in nucleosomes and how that behavior is modulated by the htt flanking sequence. In addition, it illuminates the differences in packaging of healthy and diseased length repeat tracts within the genome.
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Affiliation(s)
- Catherine B Volle
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
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Celona B, Weiner A, Di Felice F, Mancuso FM, Cesarini E, Rossi RL, Gregory L, Baban D, Rossetti G, Grianti P, Pagani M, Bonaldi T, Ragoussis J, Friedman N, Camilloni G, Bianchi ME, Agresti A. Substantial histone reduction modulates genomewide nucleosomal occupancy and global transcriptional output. PLoS Biol 2011; 9:e1001086. [PMID: 21738444 PMCID: PMC3125158 DOI: 10.1371/journal.pbio.1001086] [Citation(s) in RCA: 157] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2010] [Accepted: 05/05/2011] [Indexed: 11/18/2022] Open
Abstract
The basic unit of genome packaging is the nucleosome, and nucleosomes have long been proposed to restrict DNA accessibility both to damage and to transcription. Nucleosome number in cells was considered fixed, but recently aging yeast and mammalian cells were shown to contain fewer nucleosomes. We show here that mammalian cells lacking High Mobility Group Box 1 protein (HMGB1) contain a reduced amount of core, linker, and variant histones, and a correspondingly reduced number of nucleosomes, possibly because HMGB1 facilitates nucleosome assembly. Yeast nhp6 mutants lacking Nhp6a and -b proteins, which are related to HMGB1, also have a reduced amount of histones and fewer nucleosomes. Nucleosome limitation in both mammalian and yeast cells increases the sensitivity of DNA to damage, increases transcription globally, and affects the relative expression of about 10% of genes. In yeast nhp6 cells the loss of more than one nucleosome in four does not affect the location of nucleosomes and their spacing, but nucleosomal occupancy. The decrease in nucleosomal occupancy is non-uniform and can be modelled assuming that different nucleosomal sites compete for available histones. Sites with a high propensity to occupation are almost always packaged into nucleosomes both in wild type and nucleosome-depleted cells; nucleosomes on sites with low propensity to occupation are disproportionately lost in nucleosome-depleted cells. We suggest that variation in nucleosome number, by affecting nucleosomal occupancy both genomewide and gene-specifically, constitutes a novel layer of epigenetic regulation.
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Affiliation(s)
| | - Assaf Weiner
- School of Computer Science and Engineering, Hebrew University, Jerusalem, Israel
- Alexander Silberman Institute of Life Sciences, Hebrew University, Jerusalem, Israel
| | - Francesca Di Felice
- Dipartimento di Biologia e Biotecnologie, Università di Roma La Sapienza, Rome, Italy
| | | | - Elisa Cesarini
- Dipartimento di Biologia e Biotecnologie, Università di Roma La Sapienza, Rome, Italy
| | - Riccardo L. Rossi
- Integrative Biology Program, Istituto Nazionale di Genetica Molecolare, Milan, Italy
| | - Lorna Gregory
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Dilair Baban
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Grazisa Rossetti
- Integrative Biology Program, Istituto Nazionale di Genetica Molecolare, Milan, Italy
| | - Paolo Grianti
- Dipartimento di Scienze Biomolecolari e Biotecnologie, Università degli Studi di Milano, Milan, Italy
| | - Massimiliano Pagani
- Integrative Biology Program, Istituto Nazionale di Genetica Molecolare, Milan, Italy
| | | | - Jiannis Ragoussis
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Nir Friedman
- School of Computer Science and Engineering, Hebrew University, Jerusalem, Israel
- Alexander Silberman Institute of Life Sciences, Hebrew University, Jerusalem, Israel
| | - Giorgio Camilloni
- Dipartimento di Biologia e Biotecnologie, Università di Roma La Sapienza, Rome, Italy
- Istituto di Biologia e Patologia Molecolari, CNR, Rome, Italy
| | - Marco E. Bianchi
- San Raffaele University, Milan, Italy
- Division of Genetics and Cell Biology, San Raffaele Research Institute, Milan, Italy
- * E-mail: (MEB); (AA)
| | - Alessandra Agresti
- Division of Genetics and Cell Biology, San Raffaele Research Institute, Milan, Italy
- * E-mail: (MEB); (AA)
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Fujita N, Wade PA. Use of bifunctional cross-linking reagents in mapping genomic distribution of chromatin remodeling complexes. Methods 2005; 33:81-5. [PMID: 15039090 DOI: 10.1016/j.ymeth.2003.10.022] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/30/2003] [Indexed: 11/26/2022] Open
Abstract
Chromatin remodeling complexes consist of multiple subunits, some of which are in intimate contact with DNA while others are not. The ability to effectively cross-link proteins to DNA with formaldehyde is impacted by the average distance between the two species. Productive cross-linking of proteins not in direct contact with DNA is greatly facilitated by the inclusion of an initial cross-linking reaction using bifunctional imidoester cross-linking reagents.
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Affiliation(s)
- Naoyuki Fujita
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Whitehead Building, Room 142, 615 Michael Street, Atlanta, GA 30322, USA
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