251
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Cournac A, Koszul R, Mozziconacci J. The 3D folding of metazoan genomes correlates with the association of similar repetitive elements. Nucleic Acids Res 2016; 44:245-55. [PMID: 26609133 PMCID: PMC4705657 DOI: 10.1093/nar/gkv1292] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Revised: 10/13/2015] [Accepted: 11/04/2015] [Indexed: 12/11/2022] Open
Abstract
The potential roles of the numerous repetitive elements found in the genomes of multi-cellular organisms remain speculative. Several studies have suggested a role in stabilizing specific 3D genomic contacts. To test this hypothesis, we exploited inter-chromosomal contacts frequencies obtained from Hi-C experiments and show that the folding of the human, mouse and Drosophila genomes is associated with a significant co-localization of several specific repetitive elements, notably many elements of the SINE family. These repeats tend to be the oldest ones and are enriched in transcription factor binding sites. We propose that the co-localization of these repetitive elements may explain the global conservation of genome folding observed between homologous regions of the human and mouse genome. Taken together, these results support a contribution of specific repetitive elements in maintaining and/or reshaping genome architecture over evolutionary times.
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Affiliation(s)
- Axel Cournac
- LPTMC, Université Pierre et Marie Curie, Sorbonne université, 4 Place Jussieu 75005 Paris, France Institut Pasteur, Group Spatial Regulation of Genomes, Department of Genomes and Genetics, F-75015 Paris, France CNRS, UMR3525, F-75015 Paris, France
| | - Romain Koszul
- Institut Pasteur, Group Spatial Regulation of Genomes, Department of Genomes and Genetics, F-75015 Paris, France CNRS, UMR3525, F-75015 Paris, France
| | - Julien Mozziconacci
- LPTMC, Université Pierre et Marie Curie, Sorbonne université, 4 Place Jussieu 75005 Paris, France
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252
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Jabbari K, Nürnberg P. A genomic view on epilepsy and autism candidate genes. Genomics 2016; 108:31-6. [PMID: 26772991 DOI: 10.1016/j.ygeno.2016.01.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 12/15/2015] [Accepted: 01/01/2016] [Indexed: 01/25/2023]
Abstract
Epilepsy is a common complex disorder most frequently associated with psychiatric and neurological diseases. Massive parallel sequencing of individual or cohort genomes and exomes led the identification of several disease associated genes. We review here the candidate genes in epilepsy genetics with focus on exome and gene panel data. Together with the examination of brain expressed genes and post synaptic proteome the results show that: (1) Non-metabolic epilepsies and autism candidate genes tend to be AT-rich and (2) large transcript size and local AT-richness are characteristic features of genes involved in developmental brain disorders and synaptic functions. These results point to the preferential location of core epilepsy and autism candidate genes in late replicating, GC-poor chromosomal regions (isochores). These results indicate that the genomic alterations leading to some brain disorders are confined to responsive chromatin areas harboring brain critical genes.
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Affiliation(s)
- Kamel Jabbari
- Cologne Center for Genomics, University of Cologne, Cologne, Germany.
| | - Peter Nürnberg
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
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253
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Duband-Goulet I. Lamin ChIP from Chromatin Prepared by Micrococcal Nuclease Digestion. Methods Mol Biol 2016; 1411:325-339. [PMID: 27147052 DOI: 10.1007/978-1-4939-3530-7_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
It is now clearly demonstrated that nuclear lamins interact with the genomic DNA and largely contribute to its three-dimensional organization and transcriptional regulation. Emergence of genome-wide mapping techniques such as DamID technology or chromatin immunoprecipitation (ChIP) followed by array hybridization or high-throughput sequencing has allowed the mapping of large lamin-interacting genomic areas called lamina-associated domains. These cover up to 40 % of the genome and are preferentially located in transcriptionally silent heterochromatin at the nuclear periphery. We recently showed that the use of enzymatic rather than physical fragmentation of chromatin in ChIP experiments uncovers new chromatin compartments with features of euchromatin that interacts with A-type lamins. We describe here a detailed ChIP procedure to covalently cross-link protein-DNA, fragment the chromatin fibers by micrococcal nuclease digestion, and solubilize the lamin network with a short sonication pulse prior to immunoprecipitating the lamin-DNA complexes using specific antibodies. Enriched DNA fragments from the lamin-binding sites are then purified as suitable samples for qPCR analysis or high-throughput sequencing.
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Affiliation(s)
- Isabelle Duband-Goulet
- Pathophysiology of Striated Muscles Laboratory, Unit of Functional and Adaptive Biology, University Paris Diderot-UMR CNRS 8251, Paris, France.
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254
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Mapping Nuclear Lamin-Genome Interactions by Chromatin Immunoprecipitation of Nuclear Lamins. Methods Mol Biol 2016; 1411:315-24. [PMID: 27147051 DOI: 10.1007/978-1-4939-3530-7_20] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The nuclear lamina is a meshwork of A- and B-type lamins which interact with chromatin and regulate many nuclear functions. Recent studies have reported the discovery of chromatin domains interacting with nuclear lamins by chromatin immunoprecipitation (ChIP) of lamin A/C or B1 and identification of the associated DNA sequences by microarray or high-throughput sequencing. ChIP has been used over many years to get a snapshot of interactions between DNA and proteins in cells, including modified histones, transcription factors, chromatin remodelers, and recently, structural proteins such as nuclear lamins. We describe here the procedure we have established in our laboratory for ChIP of lamin A/C and lamin B1 from human cultured cells. The protocol is compatible with polymerase chain reaction and high-throughput sequencing analysis of the co-immunoprecipitated DNA.
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255
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Abstract
How the same DNA sequences can function in the three-dimensional architecture of interphase nucleus, fold in the very compact structure of metaphase chromosomes and go precisely back to the original interphase architecture in the following cell cycle remains an unresolved question to this day. The strategy used to address this issue was to analyze the correlations between chromosome architecture and the compositional patterns of DNA sequences spanning a size range from a few hundreds to a few thousands Kilobases. This is a critical range that encompasses isochores, interphase chromatin domains and boundaries, and chromosomal bands. The solution rests on the following key points: 1) the transition from the looped domains and sub-domains of interphase chromatin to the 30-nm fiber loops of early prophase chromosomes goes through the unfolding into an extended chromatin structure (probably a 10-nm "beads-on-a-string" structure); 2) the architectural proteins of interphase chromatin, such as CTCF and cohesin sub-units, are retained in mitosis and are part of the discontinuous protein scaffold of mitotic chromosomes; 3) the conservation of the link between architectural proteins and their binding sites on DNA through the cell cycle explains the "mitotic memory" of interphase architecture and the reversibility of the interphase to mitosis process. The results presented here also lead to a general conclusion which concerns the existence of correlations between the isochore organization of the genome and the architecture of chromosomes from interphase to metaphase.
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Affiliation(s)
- Giorgio Bernardi
- Science Department, Roma Tre University, Marconi, Rome, Italy
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy
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256
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Lund EG, Duband-Goulet I, Oldenburg A, Buendia B, Collas P. Distinct features of lamin A-interacting chromatin domains mapped by ChIP-sequencing from sonicated or micrococcal nuclease-digested chromatin. Nucleus 2015; 6:30-9. [PMID: 25602132 DOI: 10.4161/19491034.2014.990855] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The nuclear lamina has been shown to interact with the genome through lamina-associated domains (LADs). LADs have been identified by DamID, a proximity labeling assay, and more recently by chromatin immunoprecipitation-sequencing (ChIP-seq) of A- and B-type lamins. LADs form megabase-size domains at the nuclear periphery, they are gene-poor and mostly heterochromatic. Here, we show that the mode of chromatin fragmentation for ChIP, namely bath sonication or digestion with micrococcal nuclease (MNase), leads to the discovery of common but also distinct sets of lamin-interacting domains, or LiDs. Using ChIP-seq, we show the existence of lamin A/C (LMNA) LiDs with distinct gene contents, histone composition enrichment and relationships to lamin B1-interacting domains. The extent of genome coverage of lamin A/C (LMNA) LiDs in sonicated or MNase-digested chromatin is similar (∼730 megabases); however over half of these domains are uniquely detected in sonicated or MNase-digested chromatin. Sonication-specific LMNA LiDs are gene-poor and devoid of a broad panel of histone modifications, while MNase-specific LMNA LiDs are of higher gene density and are enriched in H3K9me3, H3K27me3 and in histone variant H2A.Z. LMNB1 LiDs are gene-poor and show no or little enrichment in these marks. Comparison of published LMNB1 DamID LADs with LMNB1 and LMNA LiDs identified here by ChIP-seq further shows that LMNA can associate with 'open' chromatin domains displaying euchromatin characteristics, and which are not associated with LMNB1. The differential genomic and epigenetic properties of lamin-interacting domains reflect the existence of distinct LiD populations identifiable in different chromatin contexts, including nuclease-accessible regions presumably localized in the nuclear interior.
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Affiliation(s)
- Eivind G Lund
- a Department of Molecular Medicine, Institute of Basic Medical Sciences ; University of Oslo, and Norwegian Center for Stem Cell Research , Oslo , Norway
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257
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Perinuclear Anchoring of H3K9-Methylated Chromatin Stabilizes Induced Cell Fate in C. elegans Embryos. Cell 2015; 163:1333-47. [PMID: 26607792 DOI: 10.1016/j.cell.2015.10.066] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 10/07/2015] [Accepted: 10/27/2015] [Indexed: 01/24/2023]
Abstract
Interphase chromatin is organized in distinct nuclear sub-compartments, reflecting its degree of compaction and transcriptional status. In Caenorhabditis elegans embryos, H3K9 methylation is necessary to silence and to anchor repeat-rich heterochromatin at the nuclear periphery. In a screen for perinuclear anchors of heterochromatin, we identified a previously uncharacterized C. elegans chromodomain protein, CEC-4. CEC-4 binds preferentially mono-, di-, or tri-methylated H3K9 and localizes at the nuclear envelope independently of H3K9 methylation and nuclear lamin. CEC-4 is necessary for endogenous heterochromatin anchoring, but not for transcriptional repression, in contrast to other known H3K9 methyl-binders in worms, which mediate gene repression but not perinuclear anchoring. When we ectopically induce a muscle differentiation program in embryos, cec-4 mutants fail to commit fully to muscle cell fate. This suggests that perinuclear sequestration of chromatin during development helps restrict cell differentiation programs by stabilizing commitment to a specific cell fate. PAPERCLIP.
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258
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Abstract
Recent studies show that nuclear lamins, the type V intermediate filament proteins, are required for proper building of at least some organs. As the major structural components of the nuclear lamina found underneath the inner nuclear membranes, lamins are ubiquitously expressed in all animal cells. How the broadly expressed lamins support the building of specific tissues is not understood. By studying Drosophila testis, we have uncovered a mechanism by which lamin-B functions in the cyst stem cell (CySC) and its differentiated cyst cell, the cell types known to form the niche/microenvironment for the germline stem cells (GSC) and the developing germ line, to ensure testis organogenesis (1). In this extra view, we discuss some remaining questions and the implications of our findings in the understanding of how the ubiquitous nuclear lamina regulates tissue building in a context-dependent manner.
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Affiliation(s)
- Haiyang Chen
- a Department of Embryology; Carnegie Institution for Science; Baltimore, MD USA
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259
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Kind J, Pagie L, de Vries SS, Nahidiazar L, Dey SS, Bienko M, Zhan Y, Lajoie B, de Graaf CA, Amendola M, Fudenberg G, Imakaev M, Mirny LA, Jalink K, Dekker J, van Oudenaarden A, van Steensel B. Genome-wide maps of nuclear lamina interactions in single human cells. Cell 2015; 163:134-47. [PMID: 26365489 PMCID: PMC4583798 DOI: 10.1016/j.cell.2015.08.040] [Citation(s) in RCA: 312] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 06/27/2015] [Accepted: 08/12/2015] [Indexed: 12/16/2022]
Abstract
Mammalian interphase chromosomes interact with the nuclear lamina (NL) through hundreds of large lamina-associated domains (LADs). We report a method to map NL contacts genome-wide in single human cells. Analysis of nearly 400 maps reveals a core architecture consisting of gene-poor LADs that contact the NL with high cell-to-cell consistency, interspersed by LADs with more variable NL interactions. The variable contacts tend to be cell-type specific and are more sensitive to changes in genome ploidy than the consistent contacts. Single-cell maps indicate that NL contacts involve multivalent interactions over hundreds of kilobases. Moreover, we observe extensive intra-chromosomal coordination of NL contacts, even over tens of megabases. Such coordinated loci exhibit preferential interactions as detected by Hi-C. Finally, the consistency of NL contacts is inversely linked to gene activity in single cells and correlates positively with the heterochromatic histone modification H3K9me3. These results highlight fundamental principles of single-cell chromatin organization. VIDEO ABSTRACT.
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Affiliation(s)
- Jop Kind
- Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, Cancer Genomics Netherlands, Uppsalalaan 8, 3584CT Utrecht, the Netherlands.
| | - Ludo Pagie
- Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Sandra S de Vries
- Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Leila Nahidiazar
- Division of Cell Biology I, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Siddharth S Dey
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, Cancer Genomics Netherlands, Uppsalalaan 8, 3584CT Utrecht, the Netherlands
| | - Magda Bienko
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 21 Stockholm, Sweden
| | - Ye Zhan
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605-0103, USA
| | - Bryan Lajoie
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605-0103, USA
| | - Carolyn A de Graaf
- Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Mario Amendola
- Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Geoffrey Fudenberg
- Graduate Program in Biophysics, Harvard University, Cambridge, MA 02138, USA
| | - Maxim Imakaev
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Leonid A Mirny
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Kees Jalink
- Division of Cell Biology I, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Job Dekker
- Howard Hughes Medical Institute, Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605-0103, USA
| | - Alexander van Oudenaarden
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, Cancer Genomics Netherlands, Uppsalalaan 8, 3584CT Utrecht, the Netherlands
| | - Bas van Steensel
- Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands.
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260
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Rønningen T, Shah A, Oldenburg AR, Vekterud K, Delbarre E, Moskaug JØ, Collas P. Prepatterning of differentiation-driven nuclear lamin A/C-associated chromatin domains by GlcNAcylated histone H2B. Genome Res 2015; 25:1825-35. [PMID: 26359231 PMCID: PMC4665004 DOI: 10.1101/gr.193748.115] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 09/10/2015] [Indexed: 12/15/2022]
Abstract
Dynamic interactions of nuclear lamins with chromatin through lamin-associated domains (LADs) contribute to spatial arrangement of the genome. Here, we provide evidence for prepatterning of differentiation-driven formation of lamin A/C LADs by domains of histone H2B modified on serine 112 by the nutrient sensor O-linked N-acetylglucosamine (H2BS112GlcNAc), which we term GADs. We demonstrate a two-step process of lamin A/C LAD formation during in vitro adipogenesis, involving spreading of lamin A/C–chromatin interactions in the transition from progenitor cell proliferation to cell-cycle arrest, and genome-scale redistribution of these interactions through a process of LAD exchange within hours of adipogenic induction. Lamin A/C LADs are found both in active and repressive chromatin contexts that can be influenced by cell differentiation status. De novo formation of adipogenic lamin A/C LADs occurs nonrandomly on GADs, which consist of megabase-size intergenic and repressive chromatin domains. Accordingly, whereas predifferentiation lamin A/C LADs are gene-rich, post-differentiation LADs harbor repressive features reminiscent of lamin B1 LADs. Release of lamin A/C from genes directly involved in glycolysis concurs with their transcriptional up-regulation after adipogenic induction, and with downstream elevations in H2BS112GlcNAc levels and O-GlcNAc cycling. Our results unveil an epigenetic prepatterning of adipogenic LADs by GADs, suggesting a coupling of developmentally regulated lamin A/C-genome interactions to a metabolically sensitive chromatin modification.
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Affiliation(s)
- Torunn Rønningen
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0317 Oslo, Norway
| | - Akshay Shah
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0317 Oslo, Norway
| | - Anja R Oldenburg
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0317 Oslo, Norway; Norwegian Center for Stem Cell Research, Oslo University Hospital, 0317 Oslo, Norway
| | - Kristin Vekterud
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0317 Oslo, Norway
| | - Erwan Delbarre
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0317 Oslo, Norway
| | - Jan Øivind Moskaug
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0317 Oslo, Norway; Norwegian Center for Stem Cell Research, Oslo University Hospital, 0317 Oslo, Norway
| | - Philippe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0317 Oslo, Norway; Norwegian Center for Stem Cell Research, Oslo University Hospital, 0317 Oslo, Norway
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261
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Walker M, Billings T, Baker CL, Powers N, Tian H, Saxl RL, Choi K, Hibbs MA, Carter GW, Handel MA, Paigen K, Petkov PM. Affinity-seq detects genome-wide PRDM9 binding sites and reveals the impact of prior chromatin modifications on mammalian recombination hotspot usage. Epigenetics Chromatin 2015; 8:31. [PMID: 26351520 PMCID: PMC4562113 DOI: 10.1186/s13072-015-0024-6] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 08/26/2015] [Indexed: 12/31/2022] Open
Abstract
Background Genetic recombination plays an important role in evolution, facilitating the creation of new, favorable combinations of alleles and the removal of deleterious mutations by unlinking them from surrounding sequences. In most mammals, the placement of genetic crossovers is determined by the binding of PRDM9, a highly polymorphic protein with a long zinc finger array, to its cognate binding sites. It is one of over 800 genes encoding proteins with zinc finger domains in the human genome. Results We report a novel technique, Affinity-seq, that for the first time identifies both the genome-wide binding sites of DNA-binding proteins and quantitates their relative affinities. We have applied this in vitro technique to PRDM9, the zinc-finger protein that activates genetic recombination, obtaining new information on the regulation of hotspots, whose locations and activities determine the recombination landscape. We identified 31,770 binding sites in the mouse genome for the PRDM9Dom2 variant. Comparing these results with hotspot usage in vivo, we find that less than half of potential PRDM9 binding sites are utilized in vivo. We show that hotspot usage is increased in actively transcribed genes and decreased in genomic regions containing H3K9me2/3 histone marks or bound to the nuclear lamina. Conclusions These results show that a major factor determining whether a binding site will become an active hotspot and what its activity will be are constraints imposed by prior chromatin modifications on the ability of PRDM9 to bind to DNA in vivo. These constraints lead to the presence of long genomic regions depleted of recombination. Electronic supplementary material The online version of this article (doi:10.1186/s13072-015-0024-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Michael Walker
- Center for Genome Dynamics, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA
| | - Timothy Billings
- Center for Genome Dynamics, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA
| | - Christopher L Baker
- Center for Genome Dynamics, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA
| | - Natalie Powers
- Center for Genome Dynamics, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA
| | - Hui Tian
- Center for Genome Dynamics, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA
| | - Ruth L Saxl
- Center for Genome Dynamics, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA
| | - Kwangbom Choi
- Center for Genome Dynamics, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA
| | - Matthew A Hibbs
- Center for Genome Dynamics, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA
| | - Gregory W Carter
- Center for Genome Dynamics, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA
| | - Mary Ann Handel
- Center for Genome Dynamics, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA
| | - Kenneth Paigen
- Center for Genome Dynamics, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA
| | - Petko M Petkov
- Center for Genome Dynamics, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA
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262
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Fraser J, Williamson I, Bickmore WA, Dostie J. An Overview of Genome Organization and How We Got There: from FISH to Hi-C. Microbiol Mol Biol Rev 2015; 79:347-72. [PMID: 26223848 PMCID: PMC4517094 DOI: 10.1128/mmbr.00006-15] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
In humans, nearly two meters of genomic material must be folded to fit inside each micrometer-scale cell nucleus while remaining accessible for gene transcription, DNA replication, and DNA repair. This fact highlights the need for mechanisms governing genome organization during any activity and to maintain the physical organization of chromosomes at all times. Insight into the functions and three-dimensional structures of genomes comes mostly from the application of visual techniques such as fluorescence in situ hybridization (FISH) and molecular approaches including chromosome conformation capture (3C) technologies. Recent developments in both types of approaches now offer the possibility of exploring the folded state of an entire genome and maybe even the identification of how complex molecular machines govern its shape. In this review, we present key methodologies used to study genome organization and discuss what they reveal about chromosome conformation as it relates to transcription regulation across genomic scales in mammals.
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Affiliation(s)
- James Fraser
- Department of Biochemistry, and Goodman Cancer Research Center, McGill University, Montréal, Québec, Canada
| | - Iain Williamson
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Wendy A Bickmore
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Josée Dostie
- Department of Biochemistry, and Goodman Cancer Research Center, McGill University, Montréal, Québec, Canada
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263
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Shimi T, Kittisopikul M, Tran J, Goldman AE, Adam SA, Zheng Y, Jaqaman K, Goldman RD. Structural organization of nuclear lamins A, C, B1, and B2 revealed by superresolution microscopy. Mol Biol Cell 2015; 26:4075-86. [PMID: 26310440 PMCID: PMC4710238 DOI: 10.1091/mbc.e15-07-0461] [Citation(s) in RCA: 174] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 08/20/2015] [Indexed: 12/22/2022] Open
Abstract
Superresolution microscopy and computational image analysis demonstrate that the four nuclear lamin isoforms of mammalian cells are each organized into distinct meshwork structures sharing similar physical characteristics. Knockouts of single lamins alter the structure of the remaining lamins, suggesting interactions among the meshworks. The nuclear lamina is a key structural element of the metazoan nucleus. However, the structural organization of the major proteins composing the lamina is poorly defined. Using three-dimensional structured illumination microscopy and computational image analysis, we characterized the supramolecular structures of lamin A, C, B1, and B2 in mouse embryo fibroblast nuclei. Each isoform forms a distinct fiber meshwork, with comparable physical characteristics with respect to mesh edge length, mesh face area and shape, and edge connectivity to form faces. Some differences were found in face areas among isoforms due to variation in the edge lengths and number of edges per face, suggesting that each meshwork has somewhat unique assembly characteristics. In fibroblasts null for the expression of either lamins A/C or lamin B1, the remaining lamin meshworks are altered compared with the lamin meshworks in wild-type nuclei or nuclei lacking lamin B2. Nuclei lacking LA/C exhibit slightly enlarged meshwork faces and some shape changes, whereas LB1-deficient nuclei exhibit primarily a substantial increase in face area. These studies demonstrate that individual lamin isoforms assemble into complex networks within the nuclear lamina and that A- and B-type lamins have distinct roles in maintaining the organization of the nuclear lamina.
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Affiliation(s)
- Takeshi Shimi
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Mark Kittisopikul
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390
| | - Joseph Tran
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218
| | - Anne E Goldman
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Stephen A Adam
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Yixian Zheng
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218
| | - Khuloud Jaqaman
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390
| | - Robert D Goldman
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
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264
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Kubo N, Toh H, Shirane K, Shirakawa T, Kobayashi H, Sato T, Sone H, Sato Y, Tomizawa SI, Tsurusaki Y, Shibata H, Saitsu H, Suzuki Y, Matsumoto N, Suyama M, Kono T, Ohbo K, Sasaki H. DNA methylation and gene expression dynamics during spermatogonial stem cell differentiation in the early postnatal mouse testis. BMC Genomics 2015; 16:624. [PMID: 26290333 PMCID: PMC4546090 DOI: 10.1186/s12864-015-1833-5] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 08/07/2015] [Indexed: 12/18/2022] Open
Abstract
Background In the male germline, neonatal prospermatogonia give rise to spermatogonia, which include stem cell population (undifferentiated spermatogonia) that supports continuous spermatogenesis in adults. Although the levels of DNA methyltransferases change dynamically in the neonatal and early postnatal male germ cells, detailed genome-wide DNA methylation profiles of these cells during the stem cell formation and differentiation have not been reported. Results To understand the regulation of spermatogonial stem cell formation and differentiation, we examined the DNA methylation and gene expression dynamics of male mouse germ cells at the critical stages: neonatal prospermatogonia, and early postntal (day 7) undifferentiated and differentiating spermatogonia. We found large partially methylated domains similar to those found in cancer cells and placenta in all these germ cells, and high levels of non-CG methylation and 5-hydroxymethylcytosines in neonatal prospermatogonia. Although the global CG methylation levels were stable in early postnatal male germ cells, and despite the reported scarcity of differential methylation in the adult spermatogonial stem cells, we identified many regions showing stage-specific differential methylation in and around genes important for stem cell function and spermatogenesis. These regions contained binding sites for specific transcription factors including the SOX family members. Conclusions Our findings show a distinctive and dynamic regulation of DNA methylation during spermatogonial stem cell formation and differentiation in the neonatal and early postnatal testes. Furthermore, we revealed a unique accumulation and distribution of non-CG methylation and 5hmC marks in neonatal prospermatogonia. These findings contrast with the reported scarcity of differential methylation in adult spermatogonial stem cell differentiation and represent a unique phase of male germ cell development. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1833-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Naoki Kubo
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan.,Research Institute for Disease of the Chest, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Hidehiro Toh
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Kenjiro Shirane
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Takayuki Shirakawa
- Department of Histology and Cell Biology, Yokohama City University School of Medicine, Yokohama, 236-0004, Japan
| | - Hisato Kobayashi
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, 156-8502, Japan
| | - Tetsuya Sato
- Division of Bioinformatics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Hidetoshi Sone
- Department of Histology and Cell Biology, Yokohama City University School of Medicine, Yokohama, 236-0004, Japan
| | - Yasuyuki Sato
- Department of Histology and Cell Biology, Yokohama City University School of Medicine, Yokohama, 236-0004, Japan
| | - Shin-ichi Tomizawa
- Department of Histology and Cell Biology, Yokohama City University School of Medicine, Yokohama, 236-0004, Japan
| | - Yoshinori Tsurusaki
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, 236-0004, Japan
| | - Hiroki Shibata
- Division of Genomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Hirotomo Saitsu
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, 236-0004, Japan
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha 5-1-5, Kashiwa, Chiba, 277-8568, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, 236-0004, Japan
| | - Mikita Suyama
- Division of Bioinformatics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Tomohiro Kono
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, 156-8502, Japan.,Department of BioScience, Tokyo University of Agriculture, Tokyo, 156-8502, Japan
| | - Kazuyuki Ohbo
- Department of Histology and Cell Biology, Yokohama City University School of Medicine, Yokohama, 236-0004, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan.
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265
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Camozzi D, Capanni C, Cenni V, Mattioli E, Columbaro M, Squarzoni S, Lattanzi G. Diverse lamin-dependent mechanisms interact to control chromatin dynamics. Focus on laminopathies. Nucleus 2015; 5:427-40. [PMID: 25482195 PMCID: PMC4164485 DOI: 10.4161/nucl.36289] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Interconnected functional strategies govern chromatin dynamics in eukaryotic cells. In this context, A and B type lamins, the nuclear intermediate filaments, act on diverse platforms involved in tissue homeostasis. On the nuclear side, lamins elicit large scale or fine chromatin conformational changes, affect DNA damage response factors and transcription factor shuttling. On the cytoplasmic side, bridging-molecules, the LINC complex, associate with lamins to coordinate chromatin dynamics with cytoskeleton and extra-cellular signals.
Consistent with such a fine tuning, lamin mutations and/or defects in their expression or post-translational processing, as well as mutations in lamin partner genes, cause a heterogeneous group of diseases known as laminopathies. They include muscular dystrophies, cardiomyopathy, lipodystrophies, neuropathies, and progeroid syndromes. The study of chromatin dynamics under pathological conditions, which is summarized in this review, is shedding light on the complex and fascinating role of the nuclear lamina in chromatin regulation.
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Affiliation(s)
- Daria Camozzi
- a CNR Institute for Molecular Genetics; Unit of Bologna and SC Laboratory of Musculoskeletal Cell Biology; Rizzoli Orthopedic Institute; Bologna, Italy
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266
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Xu Y, Zhang H, Nguyen VTM, Angelopoulos N, Nunes J, Reid A, Buluwela L, Magnani L, Stebbing J, Giamas G. LMTK3 Represses Tumor Suppressor-like Genes through Chromatin Remodeling in Breast Cancer. Cell Rep 2015; 12:837-49. [PMID: 26212333 DOI: 10.1016/j.celrep.2015.06.073] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 06/11/2015] [Accepted: 06/25/2015] [Indexed: 01/23/2023] Open
Abstract
LMTK3 is an oncogenic receptor tyrosine kinase (RTK) implicated in various types of cancer, including breast, lung, gastric, and colorectal cancer. It is localized in different cellular compartments, but its nuclear function has not been investigated so far. We mapped LMTK3 binding across the genome using ChIP-seq and found that LMTK3 binding events are correlated with repressive chromatin markers. We further identified KRAB-associated protein 1 (KAP1) as a binding partner of LMTK3. The LMTK3/KAP1 interaction is stabilized by PP1α, which suppresses KAP1 phosphorylation specifically at LMTK3-associated chromatin regions, inducing chromatin condensation and resulting in transcriptional repression of LMTK3-bound tumor suppressor-like genes. Furthermore, LMTK3 functions at distal regions in tethering the chromatin to the nuclear periphery, resulting in H3K9me3 modification and gene silencing. In summary, we propose a model where a scaffolding function of nuclear LMTK3 promotes cancer progression through chromatin remodeling.
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Affiliation(s)
- Yichen Xu
- Division of Cancer, Imperial College London, Department of Surgery and Cancer, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Hua Zhang
- Division of Cancer, Imperial College London, Department of Surgery and Cancer, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Van Thuy Mai Nguyen
- Division of Cancer, Imperial College London, Department of Surgery and Cancer, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Nicos Angelopoulos
- Division of Cancer, Imperial College London, Department of Surgery and Cancer, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Joao Nunes
- Division of Cancer, Imperial College London, Department of Surgery and Cancer, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Alistair Reid
- Division of Cancer, Imperial College London, Department of Surgery and Cancer, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Laki Buluwela
- Division of Cancer, Imperial College London, Department of Surgery and Cancer, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Luca Magnani
- Division of Cancer, Imperial College London, Department of Surgery and Cancer, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK.
| | - Justin Stebbing
- Division of Cancer, Imperial College London, Department of Surgery and Cancer, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Georgios Giamas
- Division of Cancer, Imperial College London, Department of Surgery and Cancer, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK.
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267
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Maskell DP, Renault L, Serrao E, Lesbats P, Matadeen R, Hare S, Lindemann D, Engelman AN, Costa A, Cherepanov P. Structural basis for retroviral integration into nucleosomes. Nature 2015; 523:366-9. [PMID: 26061770 PMCID: PMC4530500 DOI: 10.1038/nature14495] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Accepted: 04/15/2015] [Indexed: 01/01/2023]
Abstract
Retroviral integration is catalysed by a tetramer of integrase (IN) assembled on viral DNA ends in a stable complex, known as the intasome. How the intasome interfaces with chromosomal DNA, which exists in the form of nucleosomal arrays, is currently unknown. Here we show that the prototype foamy virus (PFV) intasome is proficient at stable capture of nucleosomes as targets for integration. Single-particle cryo-electron microscopy reveals a multivalent intasome-nucleosome interface involving both gyres of nucleosomal DNA and one H2A-H2B heterodimer. While the histone octamer remains intact, the DNA is lifted from the surface of the H2A-H2B heterodimer to allow integration at strongly preferred superhelix location ±3.5 positions. Amino acid substitutions disrupting these contacts impinge on the ability of the intasome to engage nucleosomes in vitro and redistribute viral integration sites on the genomic scale. Our findings elucidate the molecular basis for nucleosome capture by the viral DNA recombination machinery and the underlying nucleosome plasticity that allows integration.
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Affiliation(s)
- Daniel P. Maskell
- Chromatin Structure and Mobile DNA, Clare Hall Laboratories, The Francis Crick Institute, Blanche Lane, South Mimms, EN6 3LD, UK
| | - Ludovic Renault
- Architecture and Dynamics of Macromolecular Machines, Clare Hall Laboratories, The Francis Crick Institute, Blanche Lane, South Mimms, EN6 3LD, UK
- National Institute for Biological Standards and Control, Microscopy and Imaging, Blanche Lane, South Mimms, EN6 3QG, UK
| | - Erik Serrao
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Paul Lesbats
- Chromatin Structure and Mobile DNA, Clare Hall Laboratories, The Francis Crick Institute, Blanche Lane, South Mimms, EN6 3LD, UK
| | - Rishi Matadeen
- NeCEN, Gorlaeus Laboratory, Einsteinweg 55, Leiden, 2333, The Netherlands
| | - Stephen Hare
- Division of Medicine, Imperial College London, St Mary's Campus, Norfolk Place, London, W2 1PG, UK
| | - Dirk Lindemann
- Institute of Virology, Technische Universität Dresden, Fetscherstr.74, Dresden, 01307, Germany
| | - Alan N. Engelman
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Alessandro Costa
- Architecture and Dynamics of Macromolecular Machines, Clare Hall Laboratories, The Francis Crick Institute, Blanche Lane, South Mimms, EN6 3LD, UK
| | - Peter Cherepanov
- Chromatin Structure and Mobile DNA, Clare Hall Laboratories, The Francis Crick Institute, Blanche Lane, South Mimms, EN6 3LD, UK
- Division of Medicine, Imperial College London, St Mary's Campus, Norfolk Place, London, W2 1PG, UK
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268
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Zheng X, Kim Y, Zheng Y. Identification of lamin B-regulated chromatin regions based on chromatin landscapes. Mol Biol Cell 2015; 26:2685-97. [PMID: 25995381 PMCID: PMC4501365 DOI: 10.1091/mbc.e15-04-0210] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 05/11/2015] [Accepted: 05/11/2015] [Indexed: 11/11/2022] Open
Abstract
Lamins, the major structural components of the nuclear lamina (NL) found beneath the nuclear envelope, are known to interact with most of the nuclear peripheral chromatin in metazoan cells. Although NL-chromatin associations correlate with a repressive chromatin state, the role of lamins in tethering chromatin to NL and how such tether influences gene expression have remained challenging to decipher. Studies suggest that NL proteins regulate chromatin in a context-dependent manner. Therefore understanding the context of chromatin states based on genomic features, including chromatin-NL interactions, is important to the study of lamins and other NL proteins. By modeling genome organization based on combinatorial patterns of chromatin association with lamin B1, core histone modification, and core and linker histone occupancy, we report six distinct large chromatin landscapes, referred to as histone lamin landscapes (HiLands)-red (R), -orange (O), -yellow (Y), -green (G), -blue (B), and -purple (P), in mouse embryonic stem cells (mESCs). This HiLands model demarcates the previously mapped lamin-associated chromatin domains (LADs) into two HiLands, HiLands-B and HiLands-P, which are similar to facultative and constitutive heterochromatins, respectively. Deletion of B-type lamins in mESCs caused a reduced interaction between regions of HiLands-B and NL as measured by emerin-chromatin interaction. Our findings reveal the importance of analyzing specific chromatin types when studying the function of NL proteins in chromatin tether and regulation.
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Affiliation(s)
- Xiaobin Zheng
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218
| | - Youngjo Kim
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218
| | - Yixian Zheng
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218
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269
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Chromatin at the nuclear periphery and the regulation of genome functions. Histochem Cell Biol 2015; 144:111-22. [PMID: 26170147 DOI: 10.1007/s00418-015-1346-y] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/28/2015] [Indexed: 01/01/2023]
Abstract
Chromatin is not randomly organized in the nucleus, and its spatial organization participates in the regulation of genome functions. However, this spatial organization is also not entirely fixed and modifications of chromatin architecture are implicated in physiological processes such as differentiation or senescence. One of the most striking features of chromatin architecture is the concentration of heterochromatin at the nuclear periphery. A closer examination of the association of chromatin at the nuclear periphery reveals that heterochromatin accumulates at the nuclear lamina, whereas nuclear pores are usually devoid of heterochromatin. After summarizing the current techniques used to study the attachment of chromatin at the nuclear lamina or the nuclear pores, we review the mechanisms underlying these attachments, their plasticity and their consequences on the regulation of gene expression, DNA repair and replication.
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270
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MacDonald WA, Sachani SS, White CR, Mann MRW. A role for chromatin topology in imprinted domain regulation. Biochem Cell Biol 2015. [PMID: 26222733 DOI: 10.1139/bcb-2015-0032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Recently, many advancements in genome-wide chromatin topology and nuclear architecture have unveiled the complex and hidden world of the nucleus, where chromatin is organized into discrete neighbourhoods with coordinated gene expression. This includes the active and inactive X chromosomes. Using X chromosome inactivation as a working model, we utilized publicly available datasets together with a literature review to gain insight into topologically associated domains, lamin-associated domains, nucleolar-associating domains, scaffold/matrix attachment regions, and nucleoporin-associated chromatin and their role in regulating monoallelic expression. Furthermore, we comprehensively review for the first time the role of chromatin topology and nuclear architecture in the regulation of genomic imprinting. We propose that chromatin topology and nuclear architecture are important regulatory mechanisms for directing gene expression within imprinted domains. Furthermore, we predict that dynamic changes in chromatin topology and nuclear architecture play roles in tissue-specific imprint domain regulation during early development and differentiation.
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Affiliation(s)
- William A MacDonald
- a Departments of Obstetrics & Gynecology, and Biochemistry, University of Western Ontario, Schulich School of Medicine and Dentistry, London, Ontario, Canada.,b Children's Health Research Institute, 4th Floor, Victoria Research Laboratories, A4-130a, 800 Commissioners Rd E, London, ON N6C 2V5, Canada
| | - Saqib S Sachani
- a Departments of Obstetrics & Gynecology, and Biochemistry, University of Western Ontario, Schulich School of Medicine and Dentistry, London, Ontario, Canada.,b Children's Health Research Institute, 4th Floor, Victoria Research Laboratories, A4-130a, 800 Commissioners Rd E, London, ON N6C 2V5, Canada
| | - Carlee R White
- a Departments of Obstetrics & Gynecology, and Biochemistry, University of Western Ontario, Schulich School of Medicine and Dentistry, London, Ontario, Canada.,b Children's Health Research Institute, 4th Floor, Victoria Research Laboratories, A4-130a, 800 Commissioners Rd E, London, ON N6C 2V5, Canada
| | - Mellissa R W Mann
- a Departments of Obstetrics & Gynecology, and Biochemistry, University of Western Ontario, Schulich School of Medicine and Dentistry, London, Ontario, Canada.,b Children's Health Research Institute, 4th Floor, Victoria Research Laboratories, A4-130a, 800 Commissioners Rd E, London, ON N6C 2V5, Canada
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271
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Moore BL, Aitken S, Semple CA. Integrative modeling reveals the principles of multi-scale chromatin boundary formation in human nuclear organization. Genome Biol 2015; 16:110. [PMID: 26013771 PMCID: PMC4443654 DOI: 10.1186/s13059-015-0661-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 04/24/2015] [Indexed: 12/31/2022] Open
Abstract
Background Interphase chromosomes adopt a hierarchical structure, and recent data have characterized their chromatin organization at very different scales, from sub-genic regions associated with DNA-binding proteins at the order of tens or hundreds of bases, through larger regions with active or repressed chromatin states, up to multi-megabase-scale domains associated with nuclear positioning, replication timing and other qualities. However, we have lacked detailed, quantitative models to understand the interactions between these different strata. Results Here we collate large collections of matched locus-level chromatin features and Hi-C interaction data, representing higher-order organization, across three human cell types. We use quantitative modeling approaches to assess whether locus-level features are sufficient to explain higher-order structure, and identify the most influential underlying features. We identify structurally variable domains between cell types and examine the underlying features to discover a general association with cell-type-specific enhancer activity. We also identify the most prominent features marking the boundaries of two types of higher-order domains at different scales: topologically associating domains and nuclear compartments. We find parallel enrichments of particular chromatin features for both types, including features associated with active promoters and the architectural proteins CTCF and YY1. Conclusions We show that integrative modeling of large chromatin dataset collections using random forests can generate useful insights into chromosome structure. The models produced recapitulate known biological features of the cell types involved, allow exploration of the antecedents of higher-order structures and generate testable hypotheses for further experimental studies. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0661-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Benjamin L Moore
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK.
| | - Stuart Aitken
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK.
| | - Colin A Semple
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK.
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272
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Pang B, de Jong J, Qiao X, Wessels LFA, Neefjes J. Chemical profiling of the genome with anti-cancer drugs defines target specificities. Nat Chem Biol 2015; 11:472-80. [PMID: 25961671 DOI: 10.1038/nchembio.1811] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 04/08/2015] [Indexed: 01/05/2023]
Abstract
Many anticancer drugs induce DNA breaks to eliminate tumor cells. The anthracycline topoisomerase II inhibitors additionally cause histone eviction. Here, we performed genome-wide high-resolution mapping of chemotherapeutic effects of various topoisomerase I and II (TopoI and II) inhibitors and integrated this mapping with established maps of genomic or epigenomic features to show their activities in different genomic regions. The TopoI inhibitor topotecan and the TopoII inhibitor etoposide are similar in inducing DNA damage at transcriptionally active genomic regions. The anthracycline daunorubicin induces DNA breaks and evicts histones from active chromatin, thus quenching local DNA damage responses. Another anthracycline, aclarubicin, has a different genomic specificity and evicts histones from H3K27me3-marked heterochromatin, with consequences for diffuse large B-cell lymphoma cells with elevated levels of H3K27me3. Modifying anthracycline structures may yield compounds with selectivity for different genomic regions and activity for different tumor types.
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Affiliation(s)
- Baoxu Pang
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Johann de Jong
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Xiaohang Qiao
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Lodewyk F A Wessels
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Jacques Neefjes
- 1] Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, the Netherlands. [2] Institute for Chemical Immunology, the Netherlands
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273
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Popken J, Graf A, Krebs S, Blum H, Schmid VJ, Strauss A, Guengoer T, Zakhartchenko V, Wolf E, Cremer T. Remodeling of the Nuclear Envelope and Lamina during Bovine Preimplantation Development and Its Functional Implications. PLoS One 2015; 10:e0124619. [PMID: 25932910 PMCID: PMC4416817 DOI: 10.1371/journal.pone.0124619] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 03/17/2015] [Indexed: 11/19/2022] Open
Abstract
The present study demonstrates a major remodeling of the nuclear envelope and its underlying lamina during bovine preimplantation development. Up to the onset of major embryonic genome activation (MGA) at the 8-cell stage nuclei showed a non-uniform distribution of nuclear pore complexes (NPCs). NPCs were exclusively present at sites where DNA contacted the nuclear lamina. Extended regions of the lamina, which were not contacted by DNA, lacked NPCs. In post-MGA nuclei the whole lamina was contacted rather uniformly by DNA. Accordingly, NPCs became uniformly distributed throughout the entire nuclear envelope. These findings shed new light on the conditions which control the integration of NPCs into the nuclear envelope. The switch from maternal to embryonic production of mRNAs was accompanied by multiple invaginations covered with NPCs, which may serve the increased demands of mRNA export and protein import. Other invaginations, as well as interior nuclear segments and vesicles without contact to the nuclear envelope, were exclusively positive for lamin B. Since the abundance of these invaginations and vesicles increased in concert with a massive nuclear volume reduction, we suggest that they reflect a mechanism for fitting the nuclear envelope and its lamina to a shrinking nuclear size during bovine preimplantation development. In addition, a deposit of extranuclear clusters of NUP153 (a marker for NPCs) without associated lamin B was frequently observed from the zygote stage up to MGA. Corresponding RNA-Seq data revealed deposits of spliced, maternally provided NUP153 mRNA and little unspliced, newly synthesized RNA prior to MGA, which increased strongly at the initiation of embryonic expression of NUP153 at MGA.
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Affiliation(s)
- Jens Popken
- Division of Anthropology and Human Genetics, Biocenter, LMU Munich, Planegg-Martinsried, Germany
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center, LMU Munich, Munich, Germany
- * E-mail: (JP); (EW); (TC)
| | - Alexander Graf
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Munich, Germany
| | | | - Axel Strauss
- Division of Genetics, Biocenter, LMU Munich, Planegg-Martinsried, Germany
| | - Tuna Guengoer
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center, LMU Munich, Munich, Germany
| | - Valeri Zakhartchenko
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center, LMU Munich, Munich, Germany
| | - Eckhard Wolf
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center, LMU Munich, Munich, Germany
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Munich, Germany
- * E-mail: (JP); (EW); (TC)
| | - Thomas Cremer
- Division of Anthropology and Human Genetics, Biocenter, LMU Munich, Planegg-Martinsried, Germany
- * E-mail: (JP); (EW); (TC)
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274
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Boulos RE, Drillon G, Argoul F, Arneodo A, Audit B. Structural organization of human replication timing domains. FEBS Lett 2015; 589:2944-57. [PMID: 25912651 DOI: 10.1016/j.febslet.2015.04.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 04/09/2015] [Accepted: 04/10/2015] [Indexed: 12/16/2022]
Abstract
Recent analysis of genome-wide epigenetic modification data, mean replication timing (MRT) profiles and chromosome conformation data in mammals have provided increasing evidence that flexibility in replication origin usage is regulated locally by the epigenetic landscape and over larger genomic distances by the 3D chromatin architecture. Here, we review the recent results establishing some link between replication domains and chromatin structural domains in pluripotent and various differentiated cell types in human. We reconcile the originally proposed dichotomic picture of early and late constant timing regions that replicate by multiple rather synchronous origins in separated nuclear compartments of open and closed chromatins, with the U-shaped MRT domains bordered by "master" replication origins specified by a localized (∼200-300 kb) zone of open and transcriptionally active chromatin from which a replication wave likely initiates and propagates toward the domain center via a cascade of origin firing. We discuss the relationships between these MRT domains, topologically associated domains and lamina-associated domains. This review sheds a new light on the epigenetically regulated global chromatin reorganization that underlies the loss of pluripotency and the determination of differentiation properties.
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Affiliation(s)
- Rasha E Boulos
- Université de Lyon, F-69000 Lyon, France; Laboratoire de Physique, CNRS UMR5672, Ecole Normale Supérieure de Lyon, F-69007 Lyon, France
| | - Guénola Drillon
- Université de Lyon, F-69000 Lyon, France; Laboratoire de Physique, CNRS UMR5672, Ecole Normale Supérieure de Lyon, F-69007 Lyon, France
| | - Françoise Argoul
- Université de Lyon, F-69000 Lyon, France; Laboratoire de Physique, CNRS UMR5672, Ecole Normale Supérieure de Lyon, F-69007 Lyon, France
| | - Alain Arneodo
- Université de Lyon, F-69000 Lyon, France; Laboratoire de Physique, CNRS UMR5672, Ecole Normale Supérieure de Lyon, F-69007 Lyon, France
| | - Benjamin Audit
- Université de Lyon, F-69000 Lyon, France; Laboratoire de Physique, CNRS UMR5672, Ecole Normale Supérieure de Lyon, F-69007 Lyon, France.
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275
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Vieux-Rochas M, Fabre PJ, Leleu M, Duboule D, Noordermeer D. Clustering of mammalian Hox genes with other H3K27me3 targets within an active nuclear domain. Proc Natl Acad Sci U S A 2015; 112:4672-7. [PMID: 25825760 PMCID: PMC4403207 DOI: 10.1073/pnas.1504783112] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Embryogenesis requires the precise activation and repression of many transcriptional regulators. The Polycomb group proteins and the associated H3K27me3 histone mark are essential to maintain the inactive state of many of these genes. Mammalian Hox genes are targets of Polycomb proteins and form local 3D clusters centered on the H3K27me3 mark. More distal contacts have also been described, yet their selectivity, dynamics, and relation to other layers of chromatin organization remained elusive. We report that repressed Hox genes form mutual intra- and interchromosomal interactions with other genes located in strong domains labeled by H3K27me3. These interactions occur in a central and active nuclear environment that consists of the HiC compartment A, away from peripheral lamina-associated domains. Interactions are independent of nearby H3K27me3-marked loci and determined by chromosomal distance and cell-type-specific scaling factors, thus inducing a moderate reorganization during embryogenesis. These results provide a simplified view of nuclear organization whereby Polycomb proteins may have evolved to repress genes located in gene-dense regions whose position is restricted to central, active, nuclear environments.
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Affiliation(s)
- Maxence Vieux-Rochas
- School of Life Sciences, Swiss Federal Institute of Technology - Lausanne (EPFL), 1015 Lausanne, Switzerland; and
| | - Pierre J Fabre
- School of Life Sciences, Swiss Federal Institute of Technology - Lausanne (EPFL), 1015 Lausanne, Switzerland; and
| | - Marion Leleu
- School of Life Sciences, Swiss Federal Institute of Technology - Lausanne (EPFL), 1015 Lausanne, Switzerland; and
| | - Denis Duboule
- School of Life Sciences, Swiss Federal Institute of Technology - Lausanne (EPFL), 1015 Lausanne, Switzerland; and Department of Genetics and Evolution, University of Geneva, 1205 Geneva, Switzerland
| | - Daan Noordermeer
- School of Life Sciences, Swiss Federal Institute of Technology - Lausanne (EPFL), 1015 Lausanne, Switzerland; and
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276
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3D genome architecture from populations to single cells. Curr Opin Genet Dev 2015; 31:36-41. [DOI: 10.1016/j.gde.2015.04.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 04/02/2015] [Indexed: 02/03/2023]
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277
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Amendola M, van Steensel B. Nuclear lamins are not required for lamina-associated domain organization in mouse embryonic stem cells. EMBO Rep 2015; 16:610-7. [PMID: 25784758 DOI: 10.15252/embr.201439789] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 02/16/2015] [Indexed: 11/09/2022] Open
Abstract
In mammals, the nuclear lamina interacts with hundreds of large genomic regions, termed lamina-associated domains (LADs) that are generally in a transcriptionally repressed state. Lamins form the major structural component of the lamina and have been reported to bind DNA and chromatin. Here, we systematically evaluate whether lamins are necessary for the LAD organization in murine embryonic stem cells. Surprisingly, removal of essentially all lamins does not have any detectable effect on the genome-wide interaction pattern of chromatin with emerin, a marker of the inner nuclear membrane. This suggests that other components of the lamina mediate these interactions.
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Affiliation(s)
- Mario Amendola
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Bas van Steensel
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands
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278
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Chen H, Zheng X, Zheng Y. Age-associated loss of lamin-B leads to systemic inflammation and gut hyperplasia. Cell 2015; 159:829-43. [PMID: 25417159 DOI: 10.1016/j.cell.2014.10.028] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 07/29/2014] [Accepted: 09/10/2014] [Indexed: 01/19/2023]
Abstract
Aging of immune organs, termed as immunosenescence, is suspected to promote systemic inflammation and age-associated disease. The cause of immunosenescence and how it promotes disease, however, has remained unclear. We report that the Drosophila fat body, a major immune organ, undergoes immunosenescence and mounts strong systemic inflammation that leads to deregulation of immune deficiency (IMD) signaling in the midgut of old animals. Inflamed old fat bodies secrete circulating peptidoglycan recognition proteins that repress IMD activity in the midgut, thereby promoting gut hyperplasia. Further, fat body immunosenecence is caused by age-associated lamin-B reduction specifically in fat body cells, which then contributes to heterochromatin loss and derepression of genes involved in immune responses. As lamin-associated heterochromatin domains are enriched for genes involved in immune response in both Drosophila and mammalian cells, our findings may provide insights into the cause and consequence of immunosenescence during mammalian aging. PAPERFLICK:
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Affiliation(s)
- Haiyang Chen
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218, USA
| | - Xiaobin Zheng
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218, USA
| | - Yixian Zheng
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218, USA.
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279
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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.
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280
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Harr JC, Luperchio TR, Wong X, Cohen E, Wheelan SJ, Reddy KL. Directed targeting of chromatin to the nuclear lamina is mediated by chromatin state and A-type lamins. ACTA ACUST UNITED AC 2015; 208:33-52. [PMID: 25559185 PMCID: PMC4284222 DOI: 10.1083/jcb.201405110] [Citation(s) in RCA: 216] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nuclear organization has been implicated in regulating gene activity. Recently, large developmentally regulated regions of the genome dynamically associated with the nuclear lamina have been identified. However, little is known about how these lamina-associated domains (LADs) are directed to the nuclear lamina. We use our tagged chromosomal insertion site system to identify small sequences from borders of fibroblast-specific variable LADs that are sufficient to target these ectopic sites to the nuclear periphery. We identify YY1 (Ying-Yang1) binding sites as enriched in relocating sequences. Knockdown of YY1 or lamin A/C, but not lamin A, led to a loss of lamina association. In addition, targeted recruitment of YY1 proteins facilitated ectopic LAD formation dependent on histone H3 lysine 27 trimethylation and histone H3 lysine di- and trimethylation. Our results also reveal that endogenous loci appear to be dependent on lamin A/C, YY1, H3K27me3, and H3K9me2/3 for maintenance of lamina-proximal positioning.
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Affiliation(s)
- Jennifer C Harr
- Department of Biological Chemistry, Center for Epigenetics, and Department of Oncology Biostatistics and Bioinformatics, Johns Hopkins University, Baltimore, MD 21205 Department of Biological Chemistry, Center for Epigenetics, and Department of Oncology Biostatistics and Bioinformatics, Johns Hopkins University, Baltimore, MD 21205
| | - Teresa Romeo Luperchio
- Department of Biological Chemistry, Center for Epigenetics, and Department of Oncology Biostatistics and Bioinformatics, Johns Hopkins University, Baltimore, MD 21205 Department of Biological Chemistry, Center for Epigenetics, and Department of Oncology Biostatistics and Bioinformatics, Johns Hopkins University, Baltimore, MD 21205
| | - Xianrong Wong
- Department of Biological Chemistry, Center for Epigenetics, and Department of Oncology Biostatistics and Bioinformatics, Johns Hopkins University, Baltimore, MD 21205 Department of Biological Chemistry, Center for Epigenetics, and Department of Oncology Biostatistics and Bioinformatics, Johns Hopkins University, Baltimore, MD 21205
| | - Erez Cohen
- Department of Biological Chemistry, Center for Epigenetics, and Department of Oncology Biostatistics and Bioinformatics, Johns Hopkins University, Baltimore, MD 21205 Department of Biological Chemistry, Center for Epigenetics, and Department of Oncology Biostatistics and Bioinformatics, Johns Hopkins University, Baltimore, MD 21205
| | - Sarah J Wheelan
- Department of Biological Chemistry, Center for Epigenetics, and Department of Oncology Biostatistics and Bioinformatics, Johns Hopkins University, Baltimore, MD 21205
| | - Karen L Reddy
- Department of Biological Chemistry, Center for Epigenetics, and Department of Oncology Biostatistics and Bioinformatics, Johns Hopkins University, Baltimore, MD 21205 Department of Biological Chemistry, Center for Epigenetics, and Department of Oncology Biostatistics and Bioinformatics, Johns Hopkins University, Baltimore, MD 21205
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281
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Babaei S, Akhtar W, de Jong J, Reinders M, de Ridder J. 3D hotspots of recurrent retroviral insertions reveal long-range interactions with cancer genes. Nat Commun 2015; 6:6381. [PMID: 25721899 PMCID: PMC4351571 DOI: 10.1038/ncomms7381] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Accepted: 01/26/2015] [Indexed: 11/09/2022] Open
Abstract
Genomically distal mutations can contribute to the deregulation of cancer genes by engaging in chromatin interactions. To study this, we overlay viral cancer-causing insertions obtained in a murine retroviral insertional mutagenesis screen with genome-wide chromatin conformation capture data. Here we find that insertions tend to cluster in 3D hotspots within the nucleus. The identified hotspots are significantly enriched for known cancer genes, and bear the expected characteristics of bona fide regulatory interactions, such as enrichment for transcription factor-binding sites. In addition, we observe a striking pattern of mutual exclusive integration. This is an indication that insertions in these loci target the same gene, either in their linear genomic vicinity or in their 3D spatial vicinity. Our findings shed new light on the repertoire of targets obtained from insertional mutagenesis screening and underline the importance of considering the genome as a 3D structure when studying effects of genomic perturbations.
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Affiliation(s)
- Sepideh Babaei
- Delft Bioinformatics Lab, Faculty of Electrical Engineering Mathematics and Computer Science, Delft University of Technology, Mekelweg 4, 2628 CD Delft, The Netherlands
| | - Waseem Akhtar
- Division of Molecular Genetics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Johann de Jong
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Marcel Reinders
- Delft Bioinformatics Lab, Faculty of Electrical Engineering Mathematics and Computer Science, Delft University of Technology, Mekelweg 4, 2628 CD Delft, The Netherlands
| | - Jeroen de Ridder
- Delft Bioinformatics Lab, Faculty of Electrical Engineering Mathematics and Computer Science, Delft University of Technology, Mekelweg 4, 2628 CD Delft, The Netherlands
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282
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Gruenbaum Y, Foisner R. Lamins: nuclear intermediate filament proteins with fundamental functions in nuclear mechanics and genome regulation. Annu Rev Biochem 2015; 84:131-64. [PMID: 25747401 DOI: 10.1146/annurev-biochem-060614-034115] [Citation(s) in RCA: 368] [Impact Index Per Article: 40.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Lamins are intermediate filament proteins that form a scaffold, termed nuclear lamina, at the nuclear periphery. A small fraction of lamins also localize throughout the nucleoplasm. Lamins bind to a growing number of nuclear protein complexes and are implicated in both nuclear and cytoskeletal organization, mechanical stability, chromatin organization, gene regulation, genome stability, differentiation, and tissue-specific functions. The lamin-based complexes and their specific functions also provide insights into possible disease mechanisms for human laminopathies, ranging from muscular dystrophy to accelerated aging, as observed in Hutchinson-Gilford progeria and atypical Werner syndromes.
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Affiliation(s)
- Yosef Gruenbaum
- Department of Genetics, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel;
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283
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Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, Sarkar A, Quon G, Sandstrom RS, Eaton ML, Wu YC, Pfenning AR, Wang X, Claussnitzer M, Liu Y, Coarfa C, Harris RA, Shoresh N, Epstein CB, Gjoneska E, Leung D, Xie W, Hawkins RD, Lister R, Hong C, Gascard P, Mungall AJ, Moore R, Chuah E, Tam A, Canfield TK, Hansen RS, Kaul R, Sabo PJ, Bansal MS, Carles A, Dixon JR, Farh KH, Feizi S, Karlic R, Kim AR, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer TR, Neph SJ, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari RC, Siebenthall KT, Sinnott-Armstrong NA, Stevens M, Thurman RE, Wu J, Zhang B, Zhou X, Beaudet AE, Boyer LA, De Jager PL, Farnham PJ, Fisher SJ, Haussler D, Jones SJM, Li W, Marra MA, McManus MT, Sunyaev S, Thomson JA, Tlsty TD, Tsai LH, Wang W, Waterland RA, Zhang MQ, Chadwick LH, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M. Integrative analysis of 111 reference human epigenomes. Nature 2015; 518:317-30. [PMID: 25693563 PMCID: PMC4530010 DOI: 10.1038/nature14248] [Citation(s) in RCA: 4184] [Impact Index Per Article: 464.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 01/21/2015] [Indexed: 02/06/2023]
Abstract
The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but epigenomic studies lack a similar reference. To address this need, the NIH Roadmap Epigenomics Consortium generated the largest collection so far of human epigenomes for primary cells and tissues. Here we describe the integrative analysis of 111 reference human epigenomes generated as part of the programme, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression. We establish global maps of regulatory elements, define regulatory modules of coordinated activity, and their likely activators and repressors. We show that disease- and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease. Our results demonstrate the central role of epigenomic information for understanding gene regulation, cellular differentiation and human disease.
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Affiliation(s)
- Anshul Kundaje
- 1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA. [3] Department of Genetics, Department of Computer Science, 300 Pasteur Dr., Lane Building, L301, Stanford, California 94305-5120, USA
| | - Wouter Meuleman
- 1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Jason Ernst
- 1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA. [3] Department of Biological Chemistry, University of California, Los Angeles, 615 Charles E Young Dr South, Los Angeles, California 90095, USA
| | - Misha Bilenky
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, British Columbia V5Z 1L3, Canada
| | - Angela Yen
- 1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Alireza Heravi-Moussavi
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, British Columbia V5Z 1L3, Canada
| | - Pouya Kheradpour
- 1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Zhizhuo Zhang
- 1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Jianrong Wang
- 1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Michael J Ziller
- 1] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA. [2] Department of Stem Cell and Regenerative Biology, 7 Divinity Ave, Cambridge, Massachusetts 02138, USA
| | - Viren Amin
- Epigenome Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - John W Whitaker
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, Moores Cancer Center, Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Matthew D Schultz
- Genomic Analysis Laboratory, Howard Hughes Medical Institute &The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, California 92037, USA
| | - Lucas D Ward
- 1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Abhishek Sarkar
- 1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Gerald Quon
- 1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Richard S Sandstrom
- Department of Genome Sciences, University of Washington, 3720 15th Ave. NE, Seattle, Washington 98195, USA
| | - Matthew L Eaton
- 1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Yi-Chieh Wu
- 1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Andreas R Pfenning
- 1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Xinchen Wang
- 1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA. [3] Biology Department, Massachusetts Institute of Technology, 31 Ames St, Cambridge, Massachusetts 02142, USA
| | - Melina Claussnitzer
- 1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Yaping Liu
- 1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Cristian Coarfa
- Epigenome Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - R Alan Harris
- Epigenome Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Noam Shoresh
- The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Charles B Epstein
- The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Elizabeta Gjoneska
- 1] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA. [2] The Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, 43 Vassar St, Cambridge, Massachusetts 02139, USA
| | - Danny Leung
- 1] Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, Moores Cancer Center, Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA. [2] Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Wei Xie
- 1] Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, Moores Cancer Center, Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA. [2] Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - R David Hawkins
- 1] Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, Moores Cancer Center, Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA. [2] Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Ryan Lister
- Genomic Analysis Laboratory, Howard Hughes Medical Institute &The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, California 92037, USA
| | - Chibo Hong
- Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, 1450 3rd Street, San Francisco, California 94158, USA
| | - Philippe Gascard
- Department of Pathology, University of California San Francisco, 513 Parnassus Avenue, San Francisco, California 94143-0511, USA
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, British Columbia V5Z 1L3, Canada
| | - Richard Moore
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, British Columbia V5Z 1L3, Canada
| | - Eric Chuah
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, British Columbia V5Z 1L3, Canada
| | - Angela Tam
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, British Columbia V5Z 1L3, Canada
| | - Theresa K Canfield
- Department of Genome Sciences, University of Washington, 3720 15th Ave. NE, Seattle, Washington 98195, USA
| | - R Scott Hansen
- Department of Medicine, Division of Medical Genetics, University of Washington, 2211 Elliot Avenue, Seattle, Washington 98121, USA
| | - Rajinder Kaul
- Department of Medicine, Division of Medical Genetics, University of Washington, 2211 Elliot Avenue, Seattle, Washington 98121, USA
| | - Peter J Sabo
- Department of Genome Sciences, University of Washington, 3720 15th Ave. NE, Seattle, Washington 98195, USA
| | - Mukul S Bansal
- 1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA. [3] Department of Computer Science &Engineering, University of Connecticut, 371 Fairfield Way, Storrs, Connecticut 06269, USA
| | - Annaick Carles
- Department of Microbiology and Immunology and Centre for High-Throughput Biology, University of British Columbia, 2125 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
| | - Jesse R Dixon
- 1] Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, Moores Cancer Center, Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA. [2] Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Kai-How Farh
- The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Soheil Feizi
- 1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Rosa Karlic
- Bioinformatics Group, Department of Molecular Biology, Division of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Ah-Ram Kim
- 1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Ashwinikumar Kulkarni
- Department of Molecular and Cell Biology, Center for Systems Biology, The University of Texas, Dallas, NSERL, RL10, 800 W Campbell Road, Richardson, Texas 75080, USA
| | - Daofeng Li
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University in St Louis, 4444 Forest Park Ave, St Louis, Missouri 63108, USA
| | - Rebecca Lowdon
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University in St Louis, 4444 Forest Park Ave, St Louis, Missouri 63108, USA
| | - GiNell Elliott
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University in St Louis, 4444 Forest Park Ave, St Louis, Missouri 63108, USA
| | - Tim R Mercer
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland 4072, Australia
| | - Shane J Neph
- Department of Genome Sciences, University of Washington, 3720 15th Ave. NE, Seattle, Washington 98195, USA
| | - Vitor Onuchic
- Epigenome Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Paz Polak
- 1] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA. [2] Brigham &Women's Hospital, 75 Francis Street, Boston, Massachusetts 02115, USA
| | - Nisha Rajagopal
- 1] Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, Moores Cancer Center, Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA. [2] Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Pradipta Ray
- Department of Molecular and Cell Biology, Center for Systems Biology, The University of Texas, Dallas, NSERL, RL10, 800 W Campbell Road, Richardson, Texas 75080, USA
| | - Richard C Sallari
- 1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Kyle T Siebenthall
- Department of Genome Sciences, University of Washington, 3720 15th Ave. NE, Seattle, Washington 98195, USA
| | - Nicholas A Sinnott-Armstrong
- 1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Michael Stevens
- 1] Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University in St Louis, 4444 Forest Park Ave, St Louis, Missouri 63108, USA. [2] Department of Computer Science and Engineeering, Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | - Robert E Thurman
- Department of Genome Sciences, University of Washington, 3720 15th Ave. NE, Seattle, Washington 98195, USA
| | - Jie Wu
- 1] Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York 11794-3600, USA. [2] Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Bo Zhang
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University in St Louis, 4444 Forest Park Ave, St Louis, Missouri 63108, USA
| | - Xin Zhou
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University in St Louis, 4444 Forest Park Ave, St Louis, Missouri 63108, USA
| | - Arthur E Beaudet
- Molecular and Human Genetics Department, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Laurie A Boyer
- Biology Department, Massachusetts Institute of Technology, 31 Ames St, Cambridge, Massachusetts 02142, USA
| | - Philip L De Jager
- 1] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA. [2] Brigham &Women's Hospital, 75 Francis Street, Boston, Massachusetts 02115, USA. [3] Harvard Medical School, 25 Shattuck St, Boston, Massachusetts 02115, USA
| | - Peggy J Farnham
- Department of Biochemistry, Keck School of Medicine, University of Southern California, 1450 Biggy Street, Los Angeles, California 90089-9601, USA
| | - Susan J Fisher
- ObGyn, Reproductive Sciences, University of California San Francisco, 35 Medical Center Way, San Francisco, California 94143, USA
| | - David Haussler
- Center for Biomolecular Sciences and Engineering, University of Santa Cruz, 1156 High Street, Santa Cruz, California 95064, USA
| | - Steven J M Jones
- 1] Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, British Columbia V5Z 1L3, Canada. [2] Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada. [3] Department of Medical Genetics, University of British Columbia, 2329 West Mall, Vancouver, BC, Canada, V6T 1Z4
| | - Wei Li
- Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Marco A Marra
- 1] Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, British Columbia V5Z 1L3, Canada. [2] Department of Medical Genetics, University of British Columbia, 2329 West Mall, Vancouver, BC, Canada, V6T 1Z4
| | - Michael T McManus
- Department of Microbiology and Immunology, Diabetes Center, University of California, San Francisco, 513 Parnassus Ave, San Francisco, California 94143-0534, USA
| | - Shamil Sunyaev
- 1] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA. [2] Brigham &Women's Hospital, 75 Francis Street, Boston, Massachusetts 02115, USA. [3] Harvard Medical School, 25 Shattuck St, Boston, Massachusetts 02115, USA
| | - James A Thomson
- 1] University of Wisconsin, Madison, Wisconsin 53715, USA. [2] Morgridge Institute for Research, 330 N. Orchard Street, Madison, Wisconsin 53707, USA
| | - Thea D Tlsty
- Department of Pathology, University of California San Francisco, 513 Parnassus Avenue, San Francisco, California 94143-0511, USA
| | - Li-Huei Tsai
- 1] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA. [2] The Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, 43 Vassar St, Cambridge, Massachusetts 02139, USA
| | - Wei Wang
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, Moores Cancer Center, Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Robert A Waterland
- USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, 1100 Bates Street, Houston, Texas 77030, USA
| | - Michael Q Zhang
- 1] Department of Molecular and Cell Biology, Center for Systems Biology, The University of Texas, Dallas, NSERL, RL10, 800 W Campbell Road, Richardson, Texas 75080, USA. [2] Bioinformatics Division, Center for Synthetic and Systems Biology, TNLIST, Tsinghua University, Beijing 100084, China
| | - Lisa H Chadwick
- National Institute of Environmental Health Sciences, 111 T.W. Alexander Drive, Research Triangle Park, North Carolina 27709, USA
| | - Bradley E Bernstein
- 1] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA. [2] Massachusetts General Hospital, 55 Fruit St, Boston, Massachusetts 02114, USA. [3] Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, Maryland 20815-6789, USA
| | - Joseph F Costello
- Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, 1450 3rd Street, San Francisco, California 94158, USA
| | - Joseph R Ecker
- Genomic Analysis Laboratory, Howard Hughes Medical Institute &The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, California 92037, USA
| | - Martin Hirst
- 1] Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver, British Columbia V5Z 1L3, Canada. [2] Department of Microbiology and Immunology and Centre for High-Throughput Biology, University of British Columbia, 2125 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
| | - Alexander Meissner
- 1] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA. [2] Department of Stem Cell and Regenerative Biology, 7 Divinity Ave, Cambridge, Massachusetts 02138, USA
| | | | - Bing Ren
- 1] Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, Moores Cancer Center, Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA. [2] Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - John A Stamatoyannopoulos
- Department of Genome Sciences, University of Washington, 3720 15th Ave. NE, Seattle, Washington 98195, USA
| | - Ting Wang
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University in St Louis, 4444 Forest Park Ave, St Louis, Missouri 63108, USA
| | - Manolis Kellis
- 1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
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284
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Lee ST, Muench MO, Fomin ME, Xiao J, Zhou M, de Smith A, Martín-Subero JI, Heath S, Houseman EA, Roy R, Wrensch M, Wiencke J, Metayer C, Wiemels JL. Epigenetic remodeling in B-cell acute lymphoblastic leukemia occurs in two tracks and employs embryonic stem cell-like signatures. Nucleic Acids Res 2015; 43:2590-602. [PMID: 25690899 PMCID: PMC4357708 DOI: 10.1093/nar/gkv103] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
We investigated DNA methylomes of pediatric B-cell acute lymphoblastic leukemias (B-ALLs) using whole-genome bisulfite sequencing and high-definition microarrays, along with RNA expression profiles. Epigenetic alteration of B-ALLs occurred in two tracks: de novo methylation of small functional compartments and demethylation of large inter-compartmental backbones. The deviations were exaggerated in lamina-associated domains, with differences corresponding to methylation clusters and/or cytogenetic groups. Our data also suggested a pivotal role of polycomb and CTBP2 in de novo methylation, which may be traced back to bivalency status of embryonic stem cells. Driven by these potent epigenetic modulations, suppression of polycomb target genes was observed along with disruption of developmental fate and cell cycle and mismatch repair pathways and altered activities of key upstream regulators.
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Affiliation(s)
- Seung-Tae Lee
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA 94158, USA Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul 120752, Republic of Korea
| | - Marcus O Muench
- Blood Systems Research Institute, University of California at San Francisco, San Francisco, CA 94158, USA Liver Center and Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA 94158, USA
| | - Marina E Fomin
- Blood Systems Research Institute, University of California at San Francisco, San Francisco, CA 94158, USA
| | - Jianqiao Xiao
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA 94158, USA
| | - Mi Zhou
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA 94158, USA
| | - Adam de Smith
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA 94158, USA
| | - José I Martín-Subero
- Unidad de Hematopatología, Servicio de Anatomía Patológica, Hospital Clínic, Universitat de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Simon Heath
- Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, Barcelona 08036, Spain
| | - E Andres Houseman
- Department of Public Health, Oregon State University, Corvallis, OR, 97331 USA
| | - Ritu Roy
- Cancer Research Institute, University of California at San Francisco, San Francisco, CA 94158, USA
| | - Margaret Wrensch
- Department of Neurological Surgery, University of California at San Francisco, San Francisco, CA 94158, USA
| | - John Wiencke
- Department of Neurological Surgery, University of California at San Francisco, San Francisco, CA 94158, USA
| | - Catherine Metayer
- Division of Epidemiology, School of Public Health, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Joseph L Wiemels
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA 94158, USA Department of Neurological Surgery, University of California at San Francisco, San Francisco, CA 94158, USA
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285
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Gavrilov AA, Razin SV. Compartmentalization of the cell nucleus and spatial organization of the genome. Mol Biol 2015. [DOI: 10.1134/s0026893315010033] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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286
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Artemov G, Bondarenko S, Sapunov G, Stegniy V. Tissue-specific differences in the spatial interposition of X-chromosome and 3R chromosome regions in the malaria mosquito Anopheles messeae Fall. PLoS One 2015; 10:e0115281. [PMID: 25671311 PMCID: PMC4324937 DOI: 10.1371/journal.pone.0115281] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Accepted: 11/22/2014] [Indexed: 11/19/2022] Open
Abstract
Spatial organization of a chromosome in a nucleus is very important in biology but many aspects of it are still generally unresolved. We focused on tissue-specific features of chromosome architecture in closely related malaria mosquitoes, which have essential inter-specific differences in polytene chromosome attachments in nurse cells. We showed that the region responsible for X-chromosome attachment interacts with nuclear lamina stronger in nurse cells, then in salivary glands cells in Anopheles messeae Fall. The inter-tissue differences were demonstrated more convincingly in an experiment of two distinct chromosomes interposition in the nucleus space of cells from four tissues. Microdissected DNA-probes from nurse cells X-chromosome (2BC) and 3R chromosomes (32D) attachment regions were hybridized with intact nuclei of nurse cells, salivary gland cells, follicle epithelium cells and imaginal disсs cells in 3D-FISH experiments. We showed that only salivary gland cells and follicle epithelium cells have no statistical differences in the interposition of 2BC and 32D. Generally, the X-chromosome and 3R chromosome are located closer to each other in cells of the somatic system in comparison with nurse cells on average. The imaginal disсs cell nuclei have an intermediate arrangement of chromosome interposition, similar to other somatic cells and nurse cells. In spite of species-specific chromosome attachments there are no differences in interposition of nurse cells chromosomes in An. messeae and An. atroparvus Thiel. Nurse cells have an unusual chromosome arrangement without a chromocenter, which could be due to the special mission of generative system cells in ontogenesis and evolution.
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Affiliation(s)
| | - Semen Bondarenko
- Institute of Theoretical and Experimental Biophysics of RAS, Pushchino, Moscow region, Russia
| | - Gleb Sapunov
- Institute for Biological Instrumentation of RAS, Pushchino, Moscow region, Russia
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287
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Chromatin-Driven Behavior of Topologically Associating Domains. J Mol Biol 2015; 427:608-25. [DOI: 10.1016/j.jmb.2014.09.013] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 09/17/2014] [Accepted: 09/23/2014] [Indexed: 12/19/2022]
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288
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Topologically associating domains are stable units of replication-timing regulation. Nature 2015; 515:402-5. [PMID: 25409831 PMCID: PMC4251741 DOI: 10.1038/nature13986] [Citation(s) in RCA: 589] [Impact Index Per Article: 65.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 10/22/2014] [Indexed: 02/06/2023]
Abstract
Eukaryotic chromosomes replicate in a temporal order known as the replication-timing program. In mammals, replication timing is cell-type-specific with at least half the genome switching replication timing during development, primarily in units of 400-800 kilobases ('replication domains'), whose positions are preserved in different cell types, conserved between species, and appear to confine long-range effects of chromosome rearrangements. Early and late replication correlate, respectively, with open and closed three-dimensional chromatin compartments identified by high-resolution chromosome conformation capture (Hi-C), and, to a lesser extent, late replication correlates with lamina-associated domains (LADs). Recent Hi-C mapping has unveiled substructure within chromatin compartments called topologically associating domains (TADs) that are largely conserved in their positions between cell types and are similar in size to replication domains. However, TADs can be further sub-stratified into smaller domains, challenging the significance of structures at any particular scale. Moreover, attempts to reconcile TADs and LADs to replication-timing data have not revealed a common, underlying domain structure. Here we localize boundaries of replication domains to the early-replicating border of replication-timing transitions and map their positions in 18 human and 13 mouse cell types. We demonstrate that, collectively, replication domain boundaries share a near one-to-one correlation with TAD boundaries, whereas within a cell type, adjacent TADs that replicate at similar times obscure replication domain boundaries, largely accounting for the previously reported lack of alignment. Moreover, cell-type-specific replication timing of TADs partitions the genome into two large-scale sub-nuclear compartments revealing that replication-timing transitions are indistinguishable from late-replicating regions in chromatin composition and lamina association and accounting for the reduced correlation of replication timing to LADs and heterochromatin. Our results reconcile cell-type-specific sub-nuclear compartmentalization and replication timing with developmentally stable structural domains and offer a unified model for large-scale chromosome structure and function.
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289
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Ulianov SV, Gavrilov AA, Razin SV. Nuclear Compartments, Genome Folding, and Enhancer-Promoter Communication. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015; 315:183-244. [DOI: 10.1016/bs.ircmb.2014.11.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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290
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Bianchi A, Lanzuolo C. Into the chromatin world: Role of nuclear architecture in epigenome regulation. AIMS BIOPHYSICS 2015. [DOI: 10.3934/biophy.2015.4.585] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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291
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Lemaître C, Soutoglou E. DSB (Im)mobility and DNA repair compartmentalization in mammalian cells. J Mol Biol 2014; 427:652-8. [PMID: 25463437 DOI: 10.1016/j.jmb.2014.11.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Chromosomal translocations are considered as causal in approximately 20% of cancers. Therefore, understanding their mechanisms of formation is crucial in the prevention of carcinogenesis. The first step of translocation formation is the concomitant occurrence of double-strand DNA breaks (DSBs) in two different chromosomes. DSBs can be repaired by different repair mechanisms, including error-free homologous recombination (HR), potentially error-prone non-homologous end joining (NHEJ) and the highly mutagenic alternative end joining (alt-EJ) pathways. Regulation of DNA repair pathway choice is crucial to avoid genomic instability. In yeast, DSBs are mobile and can scan the entire nucleus to be repaired in specialized DNA repair centers or if they are persistent, in order to associate with the nuclear pores or the nuclear envelope where they can be repaired by specialized repair pathways. DSB mobility is limited in mammals; therefore, raising the question of whether the position at which a DSB occurs influences its repair. Here, we review the recent literature addressing this question. We first present the reports describing the extent of DSB mobility in mammalian cells. In a second part, we discuss the consequences of non-random gene positioning on chromosomal translocations formation. In the third part, we discuss the mobility of heterochromatic DSBs in light of our recent data on DSB repair at the nuclear lamina, and finally, we show that DSB repair compartmentalization at the nuclear periphery is conserved from yeast to mammals, further pointing to a role for gene positioning in the outcome of DSB repair. When regarded as a whole, the different studies reviewed here demonstrate the importance of nuclear architecture on DSB repair and reveal gene positioning as an important parameter in the study of tumorigenesis.
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Affiliation(s)
- Charlène Lemaître
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, CEDEX, France; Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France; Centre National de Recherche Scientifique, UMR7104, Illkirch, France; Université de Strasbourg, 67404, Illkirch, CEDEX, France
| | - Evi Soutoglou
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, CEDEX, France; Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France; Centre National de Recherche Scientifique, UMR7104, Illkirch, France; Université de Strasbourg, 67404, Illkirch, CEDEX, France.
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292
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Lemaître C, Grabarz A, Tsouroula K, Andronov L, Furst A, Pankotai T, Heyer V, Rogier M, Attwood KM, Kessler P, Dellaire G, Klaholz B, Reina-San-Martin B, Soutoglou E. Nuclear position dictates DNA repair pathway choice. Genes Dev 2014; 28:2450-63. [PMID: 25366693 PMCID: PMC4233239 DOI: 10.1101/gad.248369.114] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Faithful DNA repair is essential to avoid chromosomal rearrangements and promote genome integrity. Lemaitre et al. demonstrate that double-strand breaks (DSBs) induced at the nuclear membrane fail to rapidly activate the DNA damage response and repair by homologous recombination (HR). DNA DSBs within lamina-associated domains do not migrate to more permissive environments for HR, like the nuclear pores or the nuclear interior, but instead are repaired in situ by alternative end-joining. Faithful DNA repair is essential to avoid chromosomal rearrangements and promote genome integrity. Nuclear organization has emerged as a key parameter in the formation of chromosomal translocations, yet little is known as to whether DNA repair can efficiently occur throughout the nucleus and whether it is affected by the location of the lesion. Here, we induce DNA double-strand breaks (DSBs) at different nuclear compartments and follow their fate. We demonstrate that DSBs induced at the nuclear membrane (but not at nuclear pores or nuclear interior) fail to rapidly activate the DNA damage response (DDR) and repair by homologous recombination (HR). Real-time and superresolution imaging reveal that DNA DSBs within lamina-associated domains do not migrate to more permissive environments for HR, like the nuclear pores or the nuclear interior, but instead are repaired in situ by alternative end-joining. Our results are consistent with a model in which nuclear position dictates the choice of DNA repair pathway, thus revealing a new level of regulation in DSB repair controlled by spatial organization of DNA within the nucleus.
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Affiliation(s)
- Charlène Lemaître
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch CEDEX, France; U964, Institut National de la Santé et de la Recherche Médicale (INSERM), 67404 Illkirch CEDEX, France; UMR7104, Centre National de Recherche Scientifique (CNRS), 67404 Illkirch CEDEX, France; Université de Strasbourg (UDS), 67404 Illkirch CEDEX, France
| | - Anastazja Grabarz
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch CEDEX, France; U964, Institut National de la Santé et de la Recherche Médicale (INSERM), 67404 Illkirch CEDEX, France; UMR7104, Centre National de Recherche Scientifique (CNRS), 67404 Illkirch CEDEX, France; Université de Strasbourg (UDS), 67404 Illkirch CEDEX, France
| | - Katerina Tsouroula
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch CEDEX, France; U964, Institut National de la Santé et de la Recherche Médicale (INSERM), 67404 Illkirch CEDEX, France; UMR7104, Centre National de Recherche Scientifique (CNRS), 67404 Illkirch CEDEX, France; Université de Strasbourg (UDS), 67404 Illkirch CEDEX, France
| | - Leonid Andronov
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch CEDEX, France; U964, Institut National de la Santé et de la Recherche Médicale (INSERM), 67404 Illkirch CEDEX, France; UMR7104, Centre National de Recherche Scientifique (CNRS), 67404 Illkirch CEDEX, France; Université de Strasbourg (UDS), 67404 Illkirch CEDEX, France
| | - Audrey Furst
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch CEDEX, France; U964, Institut National de la Santé et de la Recherche Médicale (INSERM), 67404 Illkirch CEDEX, France; UMR7104, Centre National de Recherche Scientifique (CNRS), 67404 Illkirch CEDEX, France; Université de Strasbourg (UDS), 67404 Illkirch CEDEX, France
| | - Tibor Pankotai
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch CEDEX, France; U964, Institut National de la Santé et de la Recherche Médicale (INSERM), 67404 Illkirch CEDEX, France; UMR7104, Centre National de Recherche Scientifique (CNRS), 67404 Illkirch CEDEX, France; Université de Strasbourg (UDS), 67404 Illkirch CEDEX, France
| | - Vincent Heyer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch CEDEX, France; U964, Institut National de la Santé et de la Recherche Médicale (INSERM), 67404 Illkirch CEDEX, France; UMR7104, Centre National de Recherche Scientifique (CNRS), 67404 Illkirch CEDEX, France; Université de Strasbourg (UDS), 67404 Illkirch CEDEX, France
| | - Mélanie Rogier
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch CEDEX, France; U964, Institut National de la Santé et de la Recherche Médicale (INSERM), 67404 Illkirch CEDEX, France; UMR7104, Centre National de Recherche Scientifique (CNRS), 67404 Illkirch CEDEX, France; Université de Strasbourg (UDS), 67404 Illkirch CEDEX, France
| | - Kathleen M Attwood
- Department of Pathology, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Pascal Kessler
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch CEDEX, France; U964, Institut National de la Santé et de la Recherche Médicale (INSERM), 67404 Illkirch CEDEX, France; UMR7104, Centre National de Recherche Scientifique (CNRS), 67404 Illkirch CEDEX, France; Université de Strasbourg (UDS), 67404 Illkirch CEDEX, France
| | - Graham Dellaire
- Department of Pathology, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Bruno Klaholz
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch CEDEX, France; U964, Institut National de la Santé et de la Recherche Médicale (INSERM), 67404 Illkirch CEDEX, France; UMR7104, Centre National de Recherche Scientifique (CNRS), 67404 Illkirch CEDEX, France; Université de Strasbourg (UDS), 67404 Illkirch CEDEX, France
| | - Bernardo Reina-San-Martin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch CEDEX, France; U964, Institut National de la Santé et de la Recherche Médicale (INSERM), 67404 Illkirch CEDEX, France; UMR7104, Centre National de Recherche Scientifique (CNRS), 67404 Illkirch CEDEX, France; Université de Strasbourg (UDS), 67404 Illkirch CEDEX, France
| | - Evi Soutoglou
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch CEDEX, France; U964, Institut National de la Santé et de la Recherche Médicale (INSERM), 67404 Illkirch CEDEX, France; UMR7104, Centre National de Recherche Scientifique (CNRS), 67404 Illkirch CEDEX, France; Université de Strasbourg (UDS), 67404 Illkirch CEDEX, France
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293
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Dowen JM, Fan ZP, Hnisz D, Ren G, Abraham BJ, Zhang LN, Weintraub AS, Schujiers J, Lee TI, Zhao K, Young RA. Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes. Cell 2014; 159:374-387. [PMID: 25303531 PMCID: PMC4197132 DOI: 10.1016/j.cell.2014.09.030] [Citation(s) in RCA: 640] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 08/18/2014] [Accepted: 09/15/2014] [Indexed: 12/31/2022]
Abstract
The pluripotent state of embryonic stem cells (ESCs) is produced by active transcription of genes that control cell identity and repression of genes encoding lineage-specifying developmental regulators. Here, we use ESC cohesin ChIA-PET data to identify the local chromosomal structures at both active and repressed genes across the genome. The results produce a map of enhancer-promoter interactions and reveal that super-enhancer-driven genes generally occur within chromosome structures that are formed by the looping of two interacting CTCF sites co-occupied by cohesin. These looped structures form insulated neighborhoods whose integrity is important for proper expression of local genes. We also find that repressed genes encoding lineage-specifying developmental regulators occur within insulated neighborhoods. These results provide insights into the relationship between transcriptional control of cell identity genes and control of local chromosome structure.
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Affiliation(s)
- Jill M Dowen
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142
| | - Zi Peng Fan
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142
- Computational and Systems Biology Program
| | - Denes Hnisz
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142
| | - Gang Ren
- Systems Biology Center, NHLBI, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
- College of Animal Science and Technology, Northwest A&F University, Xi'An, P. R. China
| | - Brian J Abraham
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142
| | - Lyndon N Zhang
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139
| | - Abraham S Weintraub
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139
| | - Jurian Schujiers
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142
| | - Tong Ihn Lee
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142
| | - Keji Zhao
- Systems Biology Center, NHLBI, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139
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294
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Jost D, Carrivain P, Cavalli G, Vaillant C. Modeling epigenome folding: formation and dynamics of topologically associated chromatin domains. Nucleic Acids Res 2014; 42:9553-61. [PMID: 25092923 PMCID: PMC4150797 DOI: 10.1093/nar/gku698] [Citation(s) in RCA: 260] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Genomes of eukaryotes are partitioned into domains of functionally distinct chromatin states. These domains are stably inherited across many cell generations and can be remodeled in response to developmental and external cues, hence contributing to the robustness and plasticity of expression patterns and cell phenotypes. Remarkably, recent studies indicate that these 1D epigenomic domains tend to fold into 3D topologically associated domains forming specialized nuclear chromatin compartments. However, the general mechanisms behind such compartmentalization including the contribution of epigenetic regulation remain unclear. Here, we address the question of the coupling between chromatin folding and epigenome. Using polymer physics, we analyze the properties of a block copolymer model that accounts for local epigenomic information. Considering copolymers build from the epigenomic landscape of Drosophila, we observe a very good agreement with the folding patterns observed in chromosome conformation capture experiments. Moreover, this model provides a physical basis for the existence of multistability in epigenome folding at sub-chromosomal scale. We show how experiments are fully consistent with multistable conformations where topologically associated domains of the same epigenomic state interact dynamically with each other. Our approach provides a general framework to improve our understanding of chromatin folding during cell cycle and differentiation and its relation to epigenetics.
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Affiliation(s)
- Daniel Jost
- Laboratoire de Physique, Ecole Normale Supérieure de Lyon, CNRS UMR 5672, Lyon 69007, France
| | - Pascal Carrivain
- Institute of Human Genetics, CNRS UPR 1142, Montpellier 34000, France
| | - Giacomo Cavalli
- Institute of Human Genetics, CNRS UPR 1142, Montpellier 34000, France
| | - Cédric Vaillant
- Laboratoire de Physique, Ecole Normale Supérieure de Lyon, CNRS UMR 5672, Lyon 69007, France
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295
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Re A, Workman CT, Waldron L, Quattrone A, Brunak S. Lineage-specific interface proteins match up the cell cycle and differentiation in embryo stem cells. Stem Cell Res 2014; 13:316-28. [PMID: 25173649 DOI: 10.1016/j.scr.2014.07.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 07/25/2014] [Accepted: 07/26/2014] [Indexed: 11/25/2022] Open
Abstract
The shortage of molecular information on cell cycle changes along embryonic stem cell (ESC) differentiation prompts an in silico approach, which may provide a novel way to identify candidate genes or mechanisms acting in coordinating the two programs. We analyzed germ layer specific gene expression changes during the cell cycle and ESC differentiation by combining four human cell cycle transcriptome profiles with thirteen in vitro human ESC differentiation studies. To detect cross-talk mechanisms we then integrated the transcriptome data that displayed differential regulation with protein interaction data. A new class of non-transcriptionally regulated genes was identified, encoding proteins which interact systematically with proteins corresponding to genes regulated during the cell cycle or cell differentiation, and which therefore can be seen as interface proteins coordinating the two programs. Functional analysis gathered insights in fate-specific candidates of interface functionalities. The non-transcriptionally regulated interface proteins were found to be highly regulated by post-translational ubiquitylation modification, which may synchronize the transition between cell proliferation and differentiation in ESCs.
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Affiliation(s)
- Angela Re
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Via delle Regole 101, I38123 Trento, Italy; Center for Biological Sequence Analysis, Technical University of Denmark, Kemitorvet, DK2800 Lyngby, Denmark
| | - Christopher T Workman
- Center for Biological Sequence Analysis, Technical University of Denmark, Kemitorvet, DK2800 Lyngby, Denmark
| | - Levi Waldron
- City University of New York School of Public Health, Hunter College, 2180 3rd Avenue, NY 10035, USA
| | - Alessandro Quattrone
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Via delle Regole 101, I38123 Trento, Italy.
| | - Søren Brunak
- Center for Biological Sequence Analysis, Technical University of Denmark, Kemitorvet, DK2800 Lyngby, Denmark; Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, DK2200 Copenhagen, Denmark.
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296
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Yoshihara M, Jiang L, Akatsuka S, Suyama M, Toyokuni S. Genome-wide profiling of 8-oxoguanine reveals its association with spatial positioning in nucleus. DNA Res 2014; 21:603-12. [PMID: 25008760 PMCID: PMC4263294 DOI: 10.1093/dnares/dsu023] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
8-Oxoguanine (8-oxoG) is one of the most common DNA lesions generated by reactive oxygen species. In this study, we analysed the genome-wide distribution profile of 8-oxoG by combining immunoprecipitation by antibodies specific for the DNA fragments containing 8-oxoG with a microarray that covers rat genome. Genome-wide mapping of 8-oxoG in normal rat kidney revealed that 8-oxoG is preferentially located at gene deserts. We did not observe differences in 8-oxoG levels between groups of genes with high and low expression, possibly because of the generally low 8-oxoG levels in genic regions compared with gene deserts. The distribution of 8-oxoG and lamina-associated domains (LADs) were strongly correlated, suggesting that the spatial location of genomic DNA in the nucleus determines the susceptibility to oxidative modifications. One possible explanation for high 8-oxoG levels in LADs is that the nuclear periphery is more susceptible to the oxidative damage caused by the extra-nuclear factors. Moreover, LADs have a rather compact conformation, which may limit the recruitment of repair components to the modified bases.
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Affiliation(s)
- Minako Yoshihara
- Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan Department of Pathology and Biology of Diseases, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Li Jiang
- Department of Pathology and Biology of Diseases, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan Department of Pathology and Biological Responses, Nagoya University Graduate School of Medicine, Tsurumai-cho 65, Showa-ku, Nagoya 466-8550, Japan
| | - Shinya Akatsuka
- Department of Pathology and Biology of Diseases, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan Department of Pathology and Biological Responses, Nagoya University Graduate School of Medicine, Tsurumai-cho 65, Showa-ku, Nagoya 466-8550, Japan
| | - Mikita Suyama
- Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan Japan Science and Technology Agency, CREST, Fukuoka 812-8582, Japan
| | - Shinya Toyokuni
- Department of Pathology and Biology of Diseases, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan Department of Pathology and Biological Responses, Nagoya University Graduate School of Medicine, Tsurumai-cho 65, Showa-ku, Nagoya 466-8550, Japan
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297
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Swift J, Discher DE. The nuclear lamina is mechano-responsive to ECM elasticity in mature tissue. J Cell Sci 2014; 127:3005-15. [PMID: 24963133 DOI: 10.1242/jcs.149203] [Citation(s) in RCA: 144] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
How cells respond to physical cues in order to meet and withstand the physical demands of their immediate surroundings has been of great interest for many years, with current research efforts focused on mechanisms that transduce signals into gene expression. Pathways that mechano-regulate the entry of transcription factors into the cell nucleus are emerging, and our most recent studies show that the mechanical properties of the nucleus itself are actively controlled in response to the elasticity of the extracellular matrix (ECM) in both mature and developing tissue. In this Commentary, we review the mechano-responsive properties of nuclei as determined by the intermediate filament lamin proteins that line the inside of the nuclear envelope and that also impact upon transcription factor entry and broader epigenetic mechanisms. We summarize the signaling pathways that regulate lamin levels and cell-fate decisions in response to a combination of ECM mechanics and molecular cues. We will also discuss recent work that highlights the importance of nuclear mechanics in niche anchorage and cell motility during development, hematopoietic differentiation and cancer metastasis, as well as emphasizing a role for nuclear mechanics in protecting chromatin from stress-induced damage.
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Affiliation(s)
- Joe Swift
- Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Dennis E Discher
- Molecular and Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
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298
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Lund E, Oldenburg AR, Collas P. Enriched domain detector: a program for detection of wide genomic enrichment domains robust against local variations. Nucleic Acids Res 2014; 42:e92. [PMID: 24782521 PMCID: PMC4066758 DOI: 10.1093/nar/gku324] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 04/03/2014] [Accepted: 04/07/2014] [Indexed: 12/31/2022] Open
Abstract
Nuclear lamins contact the genome at the nuclear periphery through large domains and are involved in chromatin organization. Among broad peak calling algorithms available to date, none are suited for mapping lamin-genome interactions genome wide. We disclose a novel algorithm, enriched domain detector (EDD), for analysis of broad enrichment domains from chromatin immunoprecipitation (ChIP)-seq data. EDD enables discovery of genomic domains interacting with broadly distributed proteins, such as A- and B-type lamins affinity isolated by ChIP. The advantages of EDD over existing broad peak callers are sensitivity to domain width rather than enrichment strength at a particular site, and robustness against local variations.
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Affiliation(s)
- Eivind Lund
- Stem Cell Epigenetics Laboratory, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, and Norwegian Center for Stem Cell Research, PO Box 1112 Blindern, 0317 Oslo, Norway
| | - Anja R Oldenburg
- Stem Cell Epigenetics Laboratory, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, and Norwegian Center for Stem Cell Research, PO Box 1112 Blindern, 0317 Oslo, Norway
| | - Philippe Collas
- Stem Cell Epigenetics Laboratory, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, and Norwegian Center for Stem Cell Research, PO Box 1112 Blindern, 0317 Oslo, Norway
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299
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Olins AL, Ishaque N, Chotewutmontri S, Langowski J, Olins DE. Retrotransposon Alu is enriched in the epichromatin of HL-60 cells. Nucleus 2014; 5:237-46. [PMID: 24824428 DOI: 10.4161/nucl.29141] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Epichromatin, the surface of chromatin facing the nuclear envelope in an interphase nucleus, reveals a "rim" staining pattern with specific mouse monoclonal antibodies against histone H2A/H2B/DNA and phosphatidylserine epitopes. Employing a modified ChIP-Seq procedure on undifferentiated and differentiated human leukemic (HL-60/S4) cells,>95% of assembled epichromatin regions overlapped with Alu retrotransposons. They also exhibited enrichment of the AluS subfamily and of Alu oligomers. Furthermore, mapping epichromatin regions to the human chromosomes revealed highly similar localization patterns in the various cell states and with the different antibodies. Comparisons with available epigenetic databases suggested that epichromatin is neither "classical" heterochromatin nor highly expressing genes, implying another function at the surface of interphase chromatin. A modified chromatin immunoprecipitation procedure (xxChIP) was developed because the studied antibodies react generally with mononucleosomes and lysed chromatin. A second fixation is necessary to securely attach the antibodies to the epichromatin epitopes of the intact nucleus.
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Affiliation(s)
- Ada L Olins
- Department of Pharmaceutical Sciences; College of Pharmacy; University of New England; Portland, ME USA
| | - Naveed Ishaque
- Division of Theoretical Bioinformatics; German Cancer Research Center (DKFZ); Heidelberg, Germany; Heidelberg Center for Personalized Oncology; German Cancer Research Center (DKFZ); Heidelberg, Germany
| | - Sasithorn Chotewutmontri
- German Cancer Research Center; Genomics and Proteomics Core Facility, High Throughput Sequencing Unit; Heidelberg, Germany
| | - Jörg Langowski
- Biophysik der Makromoleküle; German Cancer Research Center; Heidelberg, Germany
| | - Donald E Olins
- Department of Pharmaceutical Sciences; College of Pharmacy; University of New England; Portland, ME USA
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300
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Kind J, van Steensel B. Stochastic genome-nuclear lamina interactions: modulating roles of Lamin A and BAF. Nucleus 2014; 5:124-30. [PMID: 24717229 PMCID: PMC4049918 DOI: 10.4161/nucl.28825] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The nuclear lamina (NL) is thought to aid in the spatial organization of interphase chromosomes by providing an anchoring platform for hundreds of large genomic regions named lamina associated domains (LADs). Recently, a new live-cell imaging approach demonstrated directly that LAD-NL interactions are dynamic and in part stochastic. Here we discuss implications of these new findings and introduce Lamin A and BAF as potential modulators of stochastic LAD positioning.
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Affiliation(s)
- Jop Kind
- Division of Gene Regulation; Netherlands Cancer Institute; Amsterdam, the Netherlands
| | - Bas van Steensel
- Division of Gene Regulation; Netherlands Cancer Institute; Amsterdam, the Netherlands
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