DOCSLIB.ORG

Epigenetics of Long-Range Chromatin Interactions

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Epigenetics of Long-Range Chromatin Interactions 0031-3998/07/6105-0011R PEDIATRIC RESEARCH Vol. 61, No. 5, Pt 2, 2007 Copyright © 2007 International Pediatric Research Foundation, Inc. Printed in U.S.A. Epigenetics of Long-Range Chromatin Interactions JIAN QUN LING, AND ANDREW R. HOFFMAN VA Palo Alto Health Care System and Stanford University, Stanford, California 94305 ABSTRACT: DNA segments that are separated from the promoter comprehensive epigenetic code regulating the transcription of region of a gene by many thousands of bases may nonetheless each gene (4). Genome-wide DNA hypomethylation and his- regulate the transcriptional activity of that gene. This finding has led tone hypoacetylation are now recognized as signature findings to the investigation of mechanisms underlying long-range chromatin in cancer, and efforts to describe the human cancer epigenome interactions. In intermitotic cells, chromosomes decondense, filling are underway in several labs throughout the world (5–7). the nucleus with distinct chromosome territories that interdigitate and intercalate with neighboring and even more distant chromosome territories. Both intrachromosomal and interchromosomal long-range NUCLEAR GEOGRAPHY AND CHROMOSOME associations have been demonstrated, and DNA binding proteins TERRITORIES have been implicated in the maintenance of these interactions. A single gene may have interactions with many distant DNA segments. The architecture and geography of the nucleus and its Genes that are monoallelically expressed, such as imprinted genes constituents represents a new dimension of regulatory control and odorant receptors, are frequently found to be regulated by these that is related to epigenetic marks and organization. During long-range interactions. These findings emphasize the importance of mitosis, chromosomes assume a very compact configuration, studying the geography and architecture of the nucleus as an impor- allowing them to segregate in anticipation of cell division. In tant factor in the regulation of gene transcription. (Pediatr Res 61: 11R–16R, 2007) intermitotic cells, however, much of the chromatin is decon- densed, and spreads out into a three-dimensional chromo- somal territory within a highly organized nuclear architecture. EPIGENETICS Controversy exists as to whether each chromosome has a fixed nuclear “address” throughout development, during oncogene- sis (8,9) and across cell types. In general, chromosomes with pigenetics refers to a system of inheritance that does not greater gene density occupy more central parts of the nucleus, E involve changes in the primary DNA sequence but that but loops and extensions may protrude from the central terri- can nevertheless be transmitted through cell and organismal tory. It is not known whether homologous chromosome terri- lineages and can result in changes in gene expression. Epige- tories are randomly situated, or if maternal and paternal netic alterations have been implicated in the initiation and chromosomes are somehow marked for specific nuclear lo- progression of malignancy, serving as primary disruptors of cales (10). cancer stem cells as well as Knudson “second hits” that The chromosome territories comprise heterochromatin, silence the expression of tumor suppressor genes (1). The chromatin loops, and other higher-order chromatin fibers, traditional study of epigenetic changes encompasses the ex- interspersed with DNA-free channels and interchromosomal amination of chromatin structure, of covalent histone modifi- domains, which may contain the transcription apparatus to cations, such as methylation, acetylation, phosphorylation, serve as transcription factories or active chromatin hubs. One ubiquitination, sumoylation, and ADP-ribosylation, as well as can envisage the nucleus as a well-ordered sponge composed of alterations in DNA methylation. For example, in a tran- of individual chromosome territories with interchromosomal scriptionally active gene, histone H3 is acetylated at K9 and interactions at the borders between adjacent chromosomes K14, dimethylated or trimethylated at K4, and phosphorylated (11). Moreover, recent studies have shown that these inter- at S10; histone H4 is acetylated at K5 and methylated at K3. chromosomal interactions may also take place well within the By contrast, histone H3 is dimethylated or trimethylated at K9 central portions of the chromosome territories, as the euchro- in inactive chromatin, and H4 sumoylation is found in inactive matin loops migrate by Brownian motion and make numerous chromatin (2,3). In general, DNA methylation of promoter interactions at the surface and inside of nearby territories (12). regions leads to silencing of that gene. There are important The nuclear matrix and its attachments also give form to this syncretic interactions between this putative histone code and conglomeration of chromosome territories (13). It is highly DNA methylation, and it is now possible to describe a more Abbreviations: ACH, active chromosome hub; ACT, associated chromo- Received November 1, 2006; accepted December 7, 2006. some trap; CT, chromosome territory; DMR, differentially methylated region; Correspondence: Andrew R. Hoffman, M.D., Medical Service (111), VA Palo Alto Health Care System, 3801 Miranda Ave., Palo Alto, CA 94304; e-mail: [email protected] ICR, imprinting control region; LCR, locus control region; 3C, chromosome Supported by National Institutes of Health grants DK36054, the March of Dimes, and conformation capture; 4C, chromosome conformation capture-on-a-chip, or the Research Service of the Department of Veterans Affairs. circular chromosome conformation capture; 5C, chromosome conformation DOI: 10.1203/pdr.0b013e31804575db capture carbon copy 11R 12R LING AND HOFFMAN likely that many of these interactions between distant DNA STAT6 and GATA3 (32), as well as SATB1, an anchoring segments are mediated or strengthened by DNA-binding pro- protein that organizes nuclear architecture and recruits chro- teins, including the insulating protein CTCF (14), SATB1 matin remodeling factors (15). (15), MeCP2 (16), and the DNA architectural protein HMG Using 3C methodology, Wolf Reik and his colleagues I/Y (17). In addition to providing protein-protein bridges elegantly demonstrated that on mouse paternal chromosome 7, between DNA loops, these DNA-binding proteins might also the Igf2 differentially methylated region-2 (DMR2) loops out tether DNA segments to the nucleolus and perhaps other to interact with the distant methylated Igf2/H19 imprinting nuclear structures (18). control region (ICR), thereby pushing the Igf2 promoter into Recently, it has become clear that nuclear architecture and close contact with the H19-enhancer, which lies 100 kb chromatin geography are important factors in the regulation of downstream. This interaction results in Igf2 transcription from gene expression (19), and that these components may play a this allele. In contrast, on the maternal chromosome, DMR1 vital epigenetic role both in normal physiology as well as in interacts with the unmethylated ICR via CTCF binding, the initiation and progression of malignancies (8,20). Loops of thereby partitioning the Igf2 promoter into a silent loop, DNA bulge out from euchromatic portions of chromosomes, inhibiting Igf2 and promoting H19 transcription (33). Chro- and the genes on these loops may localize to active chromatin mosome looping has now been shown to be an important hubs where gene transcription takes place (21). Chromosome mechanism whereby distant DNA elements can interact in looping allows distant segments of DNA from the same other gene systems as well (34,35). Intrachromosomal looping chromosome or from different chromosomes to interact and, has now been described for the Dlx5/Dlx6 imprinted dyad potentially, to modify the expression of genes that are very (16), for immune genes (32), for the immunoglobin heavy- distant from another. The propinquity of these loops may chain locus (36–38), and for human chromosome 4q35 locus also facilitate recombination and chromatin rearrangements D4Z4 polymorphic repeat involved in fascioscapulohumeral (22–24). muscular dystrophy (FSHD) (39). Thus, these intrachromo- somal chromatin loops constitute an important element in the DNA LOOPING AND LONG-RANGE architecture of the nucleus and in regulatory control of a INTRACHROMOSOMAL INTERACTIONS number of genes (40). The existence of long-range interactions between regions of a chromosome separated by more than 100,000 bases led to INTERCHROMOSOMAL INTERACTIONS the discovery of intrachromosomal loops that juxtapose down- stream enhancers close to promoter regions to increase gene Physiologically important, nonrandom interactions between transcription (25–27). Two techniques have been essential for chromosomes have now been observed in a number of normal characterizing these long-range interactions. In the chromo- and malignant cells. Genomic imprinting is a form of non- some conformation capture (3C) technique (28,29), formalde- Mendelian inheritance in which only one of the parental hyde is used to cross-link nearby DNA sequences. The DNA alleles is expressed, while the other parental allele is epige- is digested with a restriction enzyme and then allowed to netically silenced. A number of genes on human chromosome undergo intramolecular ligation. The cross-links are then re- 15q11-q13 are imprinted; loss of the paternal genome in this versed and the resulting DNA sequence, which is a chimera of region results in Prader-Willi syndrome, whereas loss of the two distant sequences, is determined. RNA-TRAP
Load more

Recommended publications
  • Chromosome Territories
    Downloaded from http://cshperspectives.cshlp.org/ on October 4, 2021 - Published by Cold Spring Harbor Laboratory Press Chromosome Territories Thomas Cremer1,2 and Marion Cremer1 1Biozentrum, Department of Biology II (Chair of Anthropology and Human Genetics), Ludwig-Maximilians- University, Grosshadernerstrasse 2, 82152 Martinsried, Germany 2Munich Center for Integrated Protein Sciences (CIPSM), 81377 Munich, Germany Correspondence: [email protected] Chromosome territories (CTs) constitute a major feature of nuclear architecture. In a brief statement, the possible contribution of nuclear architecture studies to the field of epigenom- ics is considered, followed bya historical account of the CT concept and the final compelling experimental evidence of a territorial organization of chromosomes in all eukaryotes studied to date. Present knowledge of nonrandom CT arrangements, of the internal CT archi- tecture, and of structural interactions with other CTs is provided as well as the dynamics of CT arrangements during cell cycle and postmitotic terminal differentiation. The article concludes with a discussion of open questions and new experimental strategies to answer them. mpressive progress has been achieved during for an integrated understanding of the structural Ithe last decade with regard to the functional and functional aspects of epigenetics with nu- implications of DNA methylation, histone mo- clear architecture during the differentiation of difications, and chromatin remodeling events toti- or pluripotent cells to functionally distinct for gene regulation (Fuks 2005; Kouzarides cell types. 2007; Maier et al. 2008; Jiang and Pugh 2009). The territorial organization of chromo- It has, however, also become obvious that somes in interphase (chromosome territories, decoding the chromatin language does not suf- CTs) constitutes a basic feature of nuclear archi- fice to fully understand the ways in which the tecture.
    [Show full text]
  • Three-Dimensional Genome Architecture: Players and Mechanisms
    REVIEWS Three-dimensional genome architecture: players and mechanisms Ana Pombo1 and Niall Dillon2 Abstract | The different cell types of an organism share the same DNA, but during cell differentiation their genomes undergo diverse structural and organizational changes that affect gene expression and other cellular functions. These can range from large-scale folding of whole chromosomes or of smaller genomic regions, to the re-organization of local interactions between enhancers and promoters, mediated by the binding of transcription factors and chromatin looping. The higher-order organization of chromatin is also influenced by the specificity of the contacts that it makes with nuclear structures such as the lamina. Sophisticated methods for mapping chromatin contacts are generating genome-wide data that provide deep insights into the formation of chromatin interactions, and into their roles in the organization and function of the eukaryotic cell nucleus. Chromatin The 2-metre length of DNA in a mammalian cell is more than 30 years ago, it has become clear that this type immunoprecipitation organized into chromosomes, which are packaged and of genetic element can regulate gene trans­cription over A method in which chromatin folded through various mechanisms and occupy discrete large distances. Looping out of the DNA that separates bound by a protein is positions in the nucleus. The multiple levels of DNA promoters and distally located enhancers was proposed immunoprecipitated with an antibody against that protein, folding generate extensive contacts between different as a mechanism by which factors that are bound to to allow the extraction and genomic regions. These contacts are influenced by the enhancers can directly contact their target promoters analysis of the bound DNA proximity of DNA sequences to one another, by the fold- and influence the composition of transcription initiation by quantitative PCR or ing architecture of local and long-range chromatin con- complexes (FIG.
    [Show full text]
  • Chromosome Territories, Nuclear Architecture and Gene Regulation in Mammalian Cells
    REVIEWS CHROMOSOME TERRITORIES, NUCLEAR ARCHITECTURE AND GENE REGULATION IN MAMMALIAN CELLS T. Cremer* ‡ and C. Cremer‡§ The expression of genes is regulated at many levels. Perhaps the area in which least is known is how nuclear organization influences gene expression. Studies of higher-order chromatin arrangements and their dynamic interactions with other nuclear components have been boosted by recent technical advances. The emerging view is that chromosomes are compartmentalized into discrete territories. The location of a gene within a chromosome territory seems to influence its access to the machinery responsible for specific nuclear functions, such as transcription and splicing. This view is consistent with a topological model for gene regulation. EPIGENETICS Despite all the celebrations associated with the tion of gene expression and other nuclear functions — Any heritable influence (in the sequencing of the human genome, and the genomes of namely the architecture of the nucleus as a whole3–14.In progeny of cells or of individuals) other model organisms, our abilities to interpret particular, we describe evidence for a compartmental- on gene activity, unaccompanied genome sequences are quite limited. For example, we ized nuclear architecture in the mammalian cell nucle- by a change in DNA sequence. cannot understand the orchestrated activity — and the us based on chromosome territories (CTs) and an silencing — of many thousands of genes in any given interchromatin compartment (IC) that contains *Institute of Anthropology cell just on the basis of DNA sequences, such as pro- macromolecular complexes that are required for repli- and Human Genetics, 12 Ludwig Maximilians moter and enhancer elements. How are the profound cation, transcription, splicing and repair (summa- University, Richard Wagner differences in gene activities established and main- rized in FIG.
    [Show full text]
  • Chromosome Territories, Nuclear Architecture and Gene Regulation in Mammalian Cells
    REVIEWS CHROMOSOME TERRITORIES, NUCLEAR ARCHITECTURE AND GENE REGULATION IN MAMMALIAN CELLS T. Cremer* ‡ and C. Cremer‡§ The expression of genes is regulated at many levels. Perhaps the area in which least is known is how nuclear organization influences gene expression. Studies of higher-order chromatin arrangements and their dynamic interactions with other nuclear components have been boosted by recent technical advances. The emerging view is that chromosomes are compartmentalized into discrete territories. The location of a gene within a chromosome territory seems to influence its access to the machinery responsible for specific nuclear functions, such as transcription and splicing. This view is consistent with a topological model for gene regulation. EPIGENETICS Despite all the celebrations associated with the tion of gene expression and other nuclear functions — Any heritable influence (in the sequencing of the human genome, and the genomes of namely the architecture of the nucleus as a whole3–14.In progeny of cells or of individuals) other model organisms, our abilities to interpret particular, we describe evidence for a compartmental- on gene activity, unaccompanied genome sequences are quite limited. For example, we ized nuclear architecture in the mammalian cell nucle- by a change in DNA sequence. cannot understand the orchestrated activity — and the us based on chromosome territories (CTs) and an silencing — of many thousands of genes in any given interchromatin compartment (IC) that contains *Institute of Anthropology cell just on the basis of DNA sequences, such as pro- macromolecular complexes that are required for repli- and Human Genetics, 12 Ludwig Maximilians moter and enhancer elements. How are the profound cation, transcription, splicing and repair (summa- University, Richard Wagner differences in gene activities established and main- rized in FIG.
    [Show full text]
  • Highly Structured Homolog Pairing Reflects Functional Organization Of
    ARTICLE https://doi.org/10.1038/s41467-019-12208-3 OPEN Highly structured homolog pairing reflects functional organization of the Drosophila genome Jumana AlHaj Abed 1,9, Jelena Erceg1,9, Anton Goloborodko 2,9, Son C. Nguyen 1,6, Ruth B. McCole1, Wren Saylor 1, Geoffrey Fudenberg 2,7, Bryan R. Lajoie3,8, Job Dekker 3, Leonid A. Mirny 2,4 & C.-ting Wu1,5 Trans-homolog interactions have been studied extensively in Drosophila, where homologs are 1234567890():,; paired in somatic cells and transvection is prevalent. Nevertheless, the detailed structure of pairing and its functional impact have not been thoroughly investigated. Accordingly, we generated a diploid cell line from divergent parents and applied haplotype-resolved Hi-C, showing that homologs pair with varying precision genome-wide, in addition to establishing trans-homolog domains and compartments. We also elucidate the structure of pairing with unprecedented detail, observing significant variation across the genome and revealing at least two forms of pairing: tight pairing, spanning contiguous small domains, and loose pairing, consisting of single larger domains. Strikingly, active genomic regions (A-type compartments, active chromatin, expressed genes) correlated with tight pairing, suggesting that pairing has a functional implication genome-wide. Finally, using RNAi and haplotype-resolved Hi-C, we show that disruption of pairing-promoting factors results in global changes in pairing, including the disruption of some interaction peaks. 1 Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. 2 Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA. 3 Howard Hughes Medical Institute and Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605-0103, USA.
    [Show full text]
  • Network Analysis Identifies Chromosome Intermingling Regions
    Network analysis identifies chromosome intermingling regions as regulatory hotspots for transcription Anastasiya Belyaevaa,b, Saradha Venkatachalapathyc, Mallika Nagarajanc, G. V. Shivashankarc,d, and Caroline Uhlera,b,1 aLaboratory for Information and Decision Systems, Massachusetts Institute of Technology, Cambridge, MA 02139; bInstitute for Data, Systems, and Society, Massachusetts Institute of Technology, Cambridge, MA 02139; cMechanobiology Institute, National University of Singapore, Singapore 117411; and dInstitute of Molecular Oncology, Italian Foundation for Cancer Research, Milan 20139, Italy Edited by David A. Weitz, Harvard University, Cambridge, MA, and approved November 13, 2017 (received for review May 15, 2017) The 3D structure of the genome plays a key role in regulatory con- transcriptional machinery, and regulatory factors to coordinate trol of the cell. Experimental methods such as high-throughput expression, also known as transcription factories, has been pro- chromosome conformation capture (Hi-C) have been developed posed as a model for gene regulation (14–16). Collectively, to probe the 3D structure of the genome. However, it remains these studies suggest that interchromosomal regions could har- a challenge to deduce from these data chromosome regions bor coregulated gene clusters. However, missing in this picture is that are colocalized and coregulated. Here, we present an inte- a systematic analysis linking 1D epigenetic marks and 3D inter- grative approach that leverages 1D functional genomic features mingling regions and their roles in transcription control. (e.g., epigenetic marks) with 3D interactions from Hi-C data to Various methods have been developed to infer the spatial con- identify functional interchromosomal interactions. We construct nectivity of the whole genome from Hi-C data.
    [Show full text]
  • Chromosome Conformation Paints Reveal the Role of Lamina Association in Genome Organization and Regulation
    bioRxiv preprint doi: https://doi.org/10.1101/122226; this version posted March 30, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Chromosome Conformation Paints Reveal the Role of Lamina Association in Genome Organization and Regulation Teresa R Luperchio1 , Michael EG Sauria2 , Xianrong Wong1, Marie-Cécile Gaillard1, Peter Tsang3, Katja Pekrun3, ,∗ ,∗ Robert A Ach 3, N Alice Yamada3, James Taylor2 , Karen L Reddy1 4 ,† , ,† 1 Center for Epigenetics and Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore MD 212015 2 Departments of Biology and Computer Science, Johns Hopkins University, Baltimore MD 21218 3 Agilent Technologies, Santa Clara CA 95051 4 Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine These authors contributed equally to this work ∗ Correspondence should be addressed to JT ([email protected]) and KLR ([email protected]) † Summary Non-random, dynamic three-dimensional organization of the nucleus is important for regulation of gene ex- pression. Numerous studies using chromosome conformation capture strategies have uncovered ensemble organizational principles of individual chromosomes, including organization into active (A) and inactive (B) com- partments. In addition, large inactive regions of the genome appear to be associated with the nuclear lamina, the so-called Lamina Associated Domains (LADs). However, the interrelationship between overall chromosome conformation and association of domains with the nuclear lamina remains unclear. In particular, the 3D organiza- tion of LADs within the context of the entire chromosome has not been investigated.
    [Show full text]
  • Organization of Transcription
    Organization of Transcription Lyubomira Chakalova1,2 and Peter Fraser1 1Laboratory of Chromatin and Gene Expression, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, United Kingdom 2Research Centre for Genetic Engineering and Biotechnology, Macedonian Academy of Sciences and Arts, Skopje 1000, Republic of Macedonia Correspondence: [email protected] Investigations into the organization of transcription have their origins in cell biology. Early studies characterized nascent transcription in relation to discernable nuclear structures and components. Advances in light microscopy, immunofluorescence, and in situ hybridi- zation helped to begin the difficult task of naming the countless individual players and com- ponents of transcription and placing them in context. With the completion of mammalian genome sequences, the seemingly boundless task of understanding transcription of the genome became finite and began a new period of rapid advance. Here we focus on the organization of transcription in mammals drawing upon information from lower organisms where necessary. The emerging picture is one of a highly organized nucleus with specific conformations of the genome adapted for tissue-specific programs of transcription and gene expression. uch of what is known about eukaryotic distant, sequence elements required for regu- Mtranscription is dominated by decades of lated transcription of some genes has added to advances in in vitro biochemistry with whole- the intricacy of the transcriptional process that cell extracts, or subfractionated and recom- occurs in vivo. Though there is still much to binant proteins on purified DNA templates. learn, the difficult task of integrating this infor- These reductionist approaches have lead to mation and placing it in the context of the nu- seminal findings describing the basic DNA se- cleus is gathering momentum.
    [Show full text]
  • Transcription-Driven Genome Organization: a Model for Chromosome Structure and the Regulation of Gene Expression Tested Through Simulations
    Transcription-driven genome organization: a model for chromosome structure and the regulation of gene expression tested through simulations Peter R. Cook 1, and Davide Marenduzzo 2∗ 1Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, and 2SUPA, School of Physics, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK Current models for the folding of the human genome see a hierarchy stretching down from chro- mosome territories, through A/B compartments and TADs (topologically-associating domains), to contact domains stabilized by cohesin and CTCF. However, molecular mechanisms underlying this folding, and the way folding affects transcriptional activity, remain obscure. Here we review physical principles driving proteins bound to long polymers into clusters surrounded by loops, and present a parsimonious yet comprehensive model for the way the organization determines function. We ar- gue that clusters of active RNA polymerases and their transcription factors are major architectural features; then, contact domains, TADs, and compartments just reflect one or more loops and clus- ters. We suggest tethering a gene close to a cluster containing appropriate factors { a transcription factory { increases the firing frequency, and offer solutions to many current puzzles concerning the actions of enhancers, super-enhancers, boundaries, and eQTLs (expression quantitative trait loci). As a result, the activity of any gene is directly influenced by the activity of other transcription units around it in 3D space, and this is supported by Brownian-dynamics simulations of transcription factors binding to cognate sites on long polymers. INTRODUCTION ter crescentus [14]). Therefore, it seems likely that loops stabilized by CTCF are a recent arrival in evolutionary Current reviews of DNA folding in interphase human history.
    [Show full text]
  • Chromosome Territory Position and Active Relocation in Normal and Hutchinson-Gilford Progeria Fibroblasts
    Chromosome Territory Position and Active Relocation in Normal and Hutchinson-Gilford Progeria Fibroblasts A thesis submitted for the degree of Doctor of Philosophy by Ishita Shailesh Mehta School of Health Sciences and Social Care Brunel University September 2009 Abstract: Radial chromosome positioning in interphase nuclei is non-random and can alter according to developmental, differentiation, proliferation or disease status. The aim of this thesis is to understand how chromosome re-positioning is elicited and to identify the nuclear structures that assist this re-localisation event. By positioning all human chromosomes in primary fibroblasts that have left the proliferative cell cycle, the study within this thesis has demonstrated that in cells made quiescent by reversible growth arrest, chromosome positioning is altered considerably. Upon removal of serum from the culture medium, chromosome re- positioning took less than 15 minutes, required energy and was inhibited by drugs affecting the polymerization of myosin and actin. The nuclear distribution of nuclear myosin 1β was dramatically different in quiescent cells as compared to proliferating cells. If the expression of nuclear myosin 1β was suppressed using interference RNA procedures the movement of chromosomes after 15 minutes in low serum was inhibited. When high serum was restored to the serum starved cultures chromosome repositioning was only evident after 24-36 hours that coincided with a return to a proliferating distribution of nuclear myosin 1β. Hutchinson-Gilford Progeria Syndrome (HGPS) is a premature ageing syndrome due to a mutation in LMNA gene that codes for lamin A protein – a critical component of the nuclear lamina and the nuclear matrix.
    [Show full text]
  • Wheat Chromatin Architecture Is Organized in Genome Territories and Transcription Factories Lorenzo Concia1, Alaguraj Veluchamy2, Juan S
    Concia et al. Genome Biology (2020) 21:104 https://doi.org/10.1186/s13059-020-01998-1 RESEARCH Open Access Wheat chromatin architecture is organized in genome territories and transcription factories Lorenzo Concia1, Alaguraj Veluchamy2, Juan S. Ramirez-Prado1, Azahara Martin-Ramirez3, Ying Huang1, Magali Perez1, Severine Domenichini1, Natalia Y. Rodriguez Granados1, Soonkap Kim2, Thomas Blein1, Susan Duncan4, Clement Pichot1, Deborah Manza-Mianza1, Caroline Juery5, Etienne Paux5, Graham Moore3, Heribert Hirt1,2, Catherine Bergounioux1, Martin Crespi1, Magdy M. Mahfouz2, Abdelhafid Bendahmane1, Chang Liu6, Anthony Hall4, Cécile Raynaud1, David Latrasse1 and Moussa Benhamed1,7* Abstract Background: Polyploidy is ubiquitous in eukaryotic plant and fungal lineages, and it leads to the co-existence of several copies of similar or related genomes in one nucleus. In plants, polyploidy is considered a major factor in successful domestication. However, polyploidy challenges chromosome folding architecture in the nucleus to establish functional structures. Results: We examine the hexaploid wheat nuclear architecture by integrating RNA-seq, ChIP-seq, ATAC-seq, Hi-C, and Hi-ChIP data. Our results highlight the presence of three levels of large-scale spatial organization: the arrangement into genome territories, the diametrical separation between facultative and constitutive heterochromatin, and the organization of RNA polymerase II around transcription factories. We demonstrate the micro-compartmentalization of transcriptionally active genes determined by physical interactions between genes with specific euchromatic histone modifications. Both intra- and interchromosomal RNA polymerase-associated contacts involve multiple genes displaying similar expression levels. Conclusions: Our results provide new insights into the physical chromosome organization of a polyploid genome, as well as on the relationship between epigenetic marks and chromosome conformation to determine a 3D spatial organization of gene expression, a key factor governing gene transcription in polyploids.
    [Show full text]
  • How Chromatin Topology Links Genome Structure to Function in Mechanisms Underlying Learning and Memory
    In the loop: how chromatin topology links genome structure to function in mechanisms underlying learning and memory The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Watson, L. Ashley et al. "In the loop: how chromatin topology links genome structure to function in mechanisms underlying learning and memory." Current Opinion in Neurobiology 43 (April 2017): 48-55 © 2016 Elsevier Ltd As Published http://dx.doi.org/10.1016/j.conb.2016.12.002 Publisher Elsevier BV Version Author's final manuscript Citable link https://hdl.handle.net/1721.1/122458 Terms of Use Creative Commons Attribution-NonCommercial-NoDerivs License Detailed Terms http://creativecommons.org/licenses/by-nc-nd/4.0/ HHS Public Access Author manuscript Author ManuscriptAuthor Manuscript Author Curr Opin Manuscript Author Neurobiol. Author Manuscript Author manuscript; available in PMC 2018 April 01. Published in final edited form as: Curr Opin Neurobiol. 2017 April ; 43: 48–55. doi:10.1016/j.conb.2016.12.002. In the loop: how chromatin topology links genome structure to function in mechanisms underlying learning and memory L. Ashley Watsona and Li-Huei Tsaia,b,c aPicower Institute for Learning and Memory, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Building 46, Room 4235A, Cambridge, MA, USA 02139 bDepartment of Brain and Cognitive Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Building 46, Room 4235A, Cambridge, MA, USA 02139 Abstract Different aspects of learning, memory, and cognition are regulated by epigenetic mechanisms such as covalent DNA modifications and histone post-translational modifications. More recently, the modulation of chromatin architecture and nuclear organization is emerging as a key factor in dynamic transcriptional regulation of the post-mitotic neuron.
    [Show full text]