1
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Achom M, Sadagopan A, Bao C, McBride F, Xu Q, Konda P, Tourdot RW, Li J, Nakhoul M, Gallant DS, Ahmed UA, O’Toole J, Freeman D, Mary Lee GS, Hecht JL, Kauffman EC, Einstein DJ, Choueiri TK, Zhang CZ, Viswanathan SR. A genetic basis for cancer sex differences revealed in Xp11 translocation renal cell carcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.04.552029. [PMID: 37577497 PMCID: PMC10418269 DOI: 10.1101/2023.08.04.552029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Xp11 translocation renal cell carcinoma (tRCC) is a female-predominant kidney cancer driven by translocations between the TFE3 gene on chromosome Xp11.2 and partner genes located on either chrX or on autosomes. The rearrangement processes that underlie TFE3 fusions, and whether they are linked to the female sex bias of this cancer, are largely unexplored. Moreover, whether oncogenic TFE3 fusions arise from both the active and inactive X chromosomes in females remains unknown. Here we address these questions by haplotype-specific analyses of whole-genome sequences of 29 tRCC samples from 15 patients and by re-analysis of 145 published tRCC whole-exome sequences. We show that TFE3 fusions universally arise as reciprocal translocations with minimal DNA loss or insertion at paired break ends. Strikingly, we observe a near exact 2:1 female:male ratio in TFE3 fusions arising via X:autosomal translocation (but not via X inversion), which accounts for the female predominance of tRCC. This 2:1 ratio is at least partially attributable to oncogenic fusions involving the inactive X chromosome and is accompanied by partial re-activation of silenced chrX genes on the rearranged chromosome. Our results highlight how somatic alterations involving the X chromosome place unique constraints on tumor initiation and exemplify how genetic rearrangements of the sex chromosomes can underlie cancer sex differences.
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Affiliation(s)
- Mingkee Achom
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
- Department of Data Science, Dana-Farber Cancer Institute; Boston, MA, USA
- Department of Medicine, Harvard Medical School; Boston, MA, USA
| | - Ananthan Sadagopan
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
| | - Chunyang Bao
- Department of Data Science, Dana-Farber Cancer Institute; Boston, MA, USA
- Department of Pathology, Brigham and Women’s Hospital; Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard; Cambridge, MA, USA
| | - Fiona McBride
- Department of Biomedical Informatics, Blavatnik Institute, Harvard Medical School; Boston, MA, USA
| | - Qingru Xu
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
- Department of Data Science, Dana-Farber Cancer Institute; Boston, MA, USA
| | - Prathyusha Konda
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
- Department of Medicine, Harvard Medical School; Boston, MA, USA
| | - Richard W. Tourdot
- Department of Data Science, Dana-Farber Cancer Institute; Boston, MA, USA
- Department of Biomedical Informatics, Blavatnik Institute, Harvard Medical School; Boston, MA, USA
| | - Jiao Li
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
- Department of Medicine, Harvard Medical School; Boston, MA, USA
| | - Maria Nakhoul
- Department of Informatics & Analytics, Dana-Farber Cancer Institute; Boston, MA, USA
| | - Daniel S. Gallant
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
| | - Usman Ali Ahmed
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
| | - Jillian O’Toole
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
| | - Dory Freeman
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
| | - Gwo-Shu Mary Lee
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
| | - Jonathan L. Hecht
- Department of Pathology, Beth Israel Deaconess Medical Center; Boston, MA, USA
| | - Eric C Kauffman
- Department of Urology, Roswell Park Comprehensive Cancer Center; Buffalo, New York, USA
| | - David J Einstein
- Division of Medical Oncology, Beth Israel Deaconess Medical Center; Boston, MA, USA
| | - Toni K. Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
- Department of Medicine, Harvard Medical School; Boston, MA, USA
- Department of Medicine, Brigham and Women’s Hospital; Boston, MA, USA
| | - Cheng-Zhong Zhang
- Department of Data Science, Dana-Farber Cancer Institute; Boston, MA, USA
- Department of Pathology, Brigham and Women’s Hospital; Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard; Cambridge, MA, USA
| | - Srinivas R. Viswanathan
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
- Department of Medicine, Harvard Medical School; Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard; Cambridge, MA, USA
- Department of Medicine, Brigham and Women’s Hospital; Boston, MA, USA
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2
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Poonperm R, Ichihara S, Miura H, Tanigawa A, Nagao K, Obuse C, Sado T, Hiratani I. Replication dynamics identifies the folding principles of the inactive X chromosome. Nat Struct Mol Biol 2023; 30:1224-1237. [PMID: 37563439 PMCID: PMC10442229 DOI: 10.1038/s41594-023-01052-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 06/28/2023] [Indexed: 08/12/2023]
Abstract
Chromosome-wide late replication is an enigmatic hallmark of the inactive X chromosome (Xi). How it is established and what it represents remains obscure. By single-cell DNA replication sequencing, here we show that the entire Xi is reorganized to replicate rapidly and uniformly in late S-phase during X-chromosome inactivation (XCI), reflecting its relatively uniform structure revealed by 4C-seq. Despite this uniformity, only a subset of the Xi became earlier replicating in SmcHD1-mutant cells. In the mutant, these domains protruded out of the Xi core, contacted each other and became transcriptionally reactivated. 4C-seq suggested that they constituted the outermost layer of the Xi even before XCI and were rich in escape genes. We propose that this default positioning forms the basis for their inherent heterochromatin instability in cells lacking the Xi-binding protein SmcHD1 or exhibiting XCI escape. These observations underscore the importance of 3D genome organization for heterochromatin stability and gene regulation.
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Affiliation(s)
- Rawin Poonperm
- Laboratory for Developmental Epigenetics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
| | - Saya Ichihara
- Department of Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara, Japan
- Cell Architecture Laboratory, Department of Chromosome Science, National Institute of Genetics, Shizuoka, Japan
| | - Hisashi Miura
- Laboratory for Developmental Epigenetics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
| | - Akie Tanigawa
- Laboratory for Developmental Epigenetics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
| | - Koji Nagao
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Chikashi Obuse
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Takashi Sado
- Department of Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara, Japan
- Agricultural Technology and Innovation Research Institute, Kindai University, Nara, Japan
| | - Ichiro Hiratani
- Laboratory for Developmental Epigenetics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan.
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3
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Arroyo M, Hastert FD, Zhadan A, Schelter F, Zimbelmann S, Rausch C, Ludwig AK, Carell T, Cardoso MC. Isoform-specific and ubiquitination dependent recruitment of Tet1 to replicating heterochromatin modulates methylcytosine oxidation. Nat Commun 2022; 13:5173. [PMID: 36056023 PMCID: PMC9440122 DOI: 10.1038/s41467-022-32799-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 08/15/2022] [Indexed: 01/26/2023] Open
Abstract
Oxidation of the epigenetic DNA mark 5-methylcytosine by Tet dioxygenases is an established route to diversify the epigenetic information, modulate gene expression and overall cellular (patho-)physiology. Here, we demonstrate that Tet1 and its short isoform Tet1s exhibit distinct nuclear localization during DNA replication resulting in aberrant cytosine modification levels in human and mouse cells. We show that Tet1 is tethered away from heterochromatin via its zinc finger domain, which is missing in Tet1s allowing its targeting to these regions. We find that Tet1s interacts with and is ubiquitinated by CRL4(VprBP). The ubiquitinated Tet1s is then recognized by Uhrf1 and recruited to late replicating heterochromatin. This leads to spreading of 5-methylcytosine oxidation to heterochromatin regions, LINE 1 activation and chromatin decondensation. In summary, we elucidate a dual regulation mechanism of Tet1, contributing to the understanding of how epigenetic information can be diversified by spatio-temporal directed Tet1 catalytic activity.
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Affiliation(s)
- María Arroyo
- grid.6546.10000 0001 0940 1669Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
| | - Florian D. Hastert
- grid.6546.10000 0001 0940 1669Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany ,grid.425396.f0000 0001 1019 0926Section AIDS and newly emerging pathogens, Paul Ehrlich Institute, Paul-Ehrlich-Str. 51-59, 63225 Langen, Germany
| | - Andreas Zhadan
- grid.6546.10000 0001 0940 1669Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
| | - Florian Schelter
- grid.5252.00000 0004 1936 973XDepartment of Chemistry, Ludwig Maximilians University, Butenandstr. 5-13, 81377 Munich, Germany
| | - Susanne Zimbelmann
- grid.6546.10000 0001 0940 1669Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
| | - Cathia Rausch
- grid.6546.10000 0001 0940 1669Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany ,grid.16008.3f0000 0001 2295 9843Present Address: Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6, avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Anne K. Ludwig
- grid.6546.10000 0001 0940 1669Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany ,grid.5253.10000 0001 0328 4908Present Address: Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany
| | - Thomas Carell
- grid.5252.00000 0004 1936 973XDepartment of Chemistry, Ludwig Maximilians University, Butenandstr. 5-13, 81377 Munich, Germany
| | - M. Cristina Cardoso
- grid.6546.10000 0001 0940 1669Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
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4
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Trewin AJ, Silver J, Dillon HT, Della Gatta PA, Parker L, Hiam DS, Lee YP, Richardson M, Wadley GD, Lamon S. Long non-coding RNA Tug1 modulates mitochondrial and myogenic responses to exercise in skeletal muscle. BMC Biol 2022; 20:164. [PMID: 35850762 PMCID: PMC9295458 DOI: 10.1186/s12915-022-01366-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 07/05/2022] [Indexed: 11/17/2022] Open
Abstract
Background Mitochondria have an essential role in regulating metabolism and integrate environmental and physiological signals to affect processes such as cellular bioenergetics and response to stress. In the metabolically active skeletal muscle, mitochondrial biogenesis is one important component contributing to a broad set of mitochondrial adaptations occurring in response to signals, which converge on the biogenesis transcriptional regulator peroxisome proliferator-activated receptor coactivator 1-alpha (PGC-1α), and is central to the beneficial effects of exercise in skeletal muscle. We investigated the role of long non-coding RNA (lncRNA) taurine-upregulated gene 1 (TUG1), which interacts with PGC-1α in regulating transcriptional responses to exercise in skeletal muscle. Results In human skeletal muscle, TUG1 gene expression was upregulated post-exercise and was also positively correlated with the increase in PGC-1α gene expression (PPARGC1A). Tug1 knockdown (KD) in differentiating mouse myotubes led to decreased Ppargc1a gene expression, impaired mitochondrial respiration and morphology, and enhanced myosin heavy chain slow isoform protein expression. In response to a Ca2+-mediated stimulus, Tug1 KD prevented an increase in Ppargc1a expression. RNA sequencing revealed that Tug1 KD impacted mitochondrial Ca2+ transport genes and several downstream PGC-1α targets. Finally, Tug1 KD modulated the expression of ~300 genes that were upregulated in response to an in vitro model of exercise in myotubes, including genes involved in regulating myogenesis. Conclusions We found that TUG1 is upregulated in human skeletal muscle after a single session of exercise, and mechanistically, Tug1 regulates transcriptional networks associated with mitochondrial calcium handling, muscle differentiation and myogenesis. These data demonstrate that lncRNA Tug1 exerts regulation over fundamental aspects of skeletal muscle biology and response to exercise stimuli. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01366-4.
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Affiliation(s)
- Adam J Trewin
- Institute for Physical Activity and Nutrition, and School of Exercise and Nutrition Sciences, Deakin University, Geelong, Australia.
| | - Jessica Silver
- Institute for Physical Activity and Nutrition, and School of Exercise and Nutrition Sciences, Deakin University, Geelong, Australia
| | - Hayley T Dillon
- Institute for Physical Activity and Nutrition, and School of Exercise and Nutrition Sciences, Deakin University, Geelong, Australia.,Human Integrated Physiology and Sports Cardiology Laboratory, Baker Heart and Diabetes Institute, Melbourne, Australia
| | - Paul A Della Gatta
- Institute for Physical Activity and Nutrition, and School of Exercise and Nutrition Sciences, Deakin University, Geelong, Australia
| | - Lewan Parker
- Institute for Physical Activity and Nutrition, and School of Exercise and Nutrition Sciences, Deakin University, Geelong, Australia
| | - Danielle S Hiam
- Institute for Physical Activity and Nutrition, and School of Exercise and Nutrition Sciences, Deakin University, Geelong, Australia.,Institute for Health and Sport (iHeS), Victoria University, Melbourne, Australia
| | - Yin Peng Lee
- Genomics Centre, School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, Waurn Ponds, Victoria, Australia
| | - Mark Richardson
- Genomics Centre, School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, Waurn Ponds, Victoria, Australia
| | - Glenn D Wadley
- Institute for Physical Activity and Nutrition, and School of Exercise and Nutrition Sciences, Deakin University, Geelong, Australia
| | - Séverine Lamon
- Institute for Physical Activity and Nutrition, and School of Exercise and Nutrition Sciences, Deakin University, Geelong, Australia.
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5
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Rausch C, Weber P, Prorok P, Hörl D, Maiser A, Lehmkuhl A, Chagin VO, Casas-Delucchi CS, Leonhardt H, Cardoso MC. Developmental differences in genome replication program and origin activation. Nucleic Acids Res 2021; 48:12751-12777. [PMID: 33264404 PMCID: PMC7736824 DOI: 10.1093/nar/gkaa1124] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 10/09/2020] [Accepted: 11/04/2020] [Indexed: 12/17/2022] Open
Abstract
To ensure error-free duplication of all (epi)genetic information once per cell cycle, DNA replication follows a cell type and developmental stage specific spatio-temporal program. Here, we analyze the spatio-temporal DNA replication progression in (un)differentiated mouse embryonic stem (mES) cells. Whereas telomeres replicate throughout S-phase, we observe mid S-phase replication of (peri)centromeric heterochromatin in mES cells, which switches to late S-phase replication upon differentiation. This replication timing reversal correlates with and depends on an increase in condensation and a decrease in acetylation of chromatin. We further find synchronous duplication of the Y chromosome, marking the end of S-phase, irrespectively of the pluripotency state. Using a combination of single-molecule and super-resolution microscopy, we measure molecular properties of the mES cell replicon, the number of replication foci active in parallel and their spatial clustering. We conclude that each replication nanofocus in mES cells corresponds to an individual replicon, with up to one quarter representing unidirectional forks. Furthermore, with molecular combing and genome-wide origin mapping analyses, we find that mES cells activate twice as many origins spaced at half the distance than somatic cells. Altogether, our results highlight fundamental developmental differences on progression of genome replication and origin activation in pluripotent cells.
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Affiliation(s)
- Cathia Rausch
- Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Patrick Weber
- Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Paulina Prorok
- Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - David Hörl
- Department of Biology II, LMU Munich, 81377 Munich, Germany
| | - Andreas Maiser
- Department of Biology II, LMU Munich, 81377 Munich, Germany
| | - Anne Lehmkuhl
- Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Vadim O Chagin
- Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany.,Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | | | | | - M Cristina Cardoso
- Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
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6
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Strehle M, Guttman M. Xist drives spatial compartmentalization of DNA and protein to orchestrate initiation and maintenance of X inactivation. Curr Opin Cell Biol 2020; 64:139-147. [PMID: 32535328 DOI: 10.1016/j.ceb.2020.04.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 04/13/2020] [Accepted: 04/23/2020] [Indexed: 12/15/2022]
Abstract
X chromosome inactivation (XCI) is the process whereby one of the X chromosomes in female mammalian cells is silenced to equalize X-linked gene expression with males. XCI depends on the long noncoding RNA Xist, which coats the inactive X chromosome in cis and triggers a cascade of events that ultimately lead to chromosome-wide transcriptional silencing that is stable for the lifetime of an organism. In recent years, the discovery of proteins that interact with Xist have led to new insights into how the initiation of XCI occurs. Nevertheless, there are still various unknowns about the mechanisms by which Xist orchestrates and maintains stable X-linked silencing. Here, we review recent work elucidating the role of Xist and its protein partners in mediating chromosome-wide transcriptional repression, as well as discuss a model by which Xist may compartmentalize proteins across the inactive X chromosome to enable both the initiation and maintenance of XCI.
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Affiliation(s)
- Mackenzie Strehle
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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7
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Janssen KA, Coradin M, Lu C, Sidoli S, Garcia BA. Quantitation of Single and Combinatorial Histone Modifications by Integrated Chromatography of Bottom-up Peptides and Middle-down Polypeptide Tails. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:2449-2459. [PMID: 31512222 DOI: 10.1007/s13361-019-02303-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 07/03/2019] [Accepted: 07/08/2019] [Indexed: 06/10/2023]
Abstract
The analysis of histone post-translational modifications (PTMs) by mass spectrometry (MS) has been critical to the advancement of the field of epigenetics. The most sensitive and accurate workflow is similar to the canonical proteomics analysis workflow (bottom-up MS), where histones are digested into short peptides (4-20 aa) and quantitated in extracted ion chromatograms. However, this limits the ability to detect even very common co-occurrences of modifications on histone proteins, preventing biological interpretation of PTM crosstalk. By digesting with GluC rather than trypsin, it is possible to produce long polypeptides corresponding to intact histone N-terminal tails (50-60 aa), where most modifications reside. This middle-down MS approach is used to study distant PTM co-existence. However, the most sensitive middle-down workflow uses weak cation exchange-hydrophilic interaction chromatography (WCX-HILIC), which is less robust than conventional reversed-phase chromatography. Additionally, since the buffer systems for middle-down and bottom-up proteomics differ substantially, it is cumbersome to toggle back and forth between both experimental setups on the same LC system. Here, we present a new workflow using porous graphitic carbon (PGC) as a stationary phase for histone analysis where bottom-up and middle-down sized histone peptides can be analyzed simultaneously using the same reversed-phase buffer setup. By using this protocol for middle-down sized peptides, we identified 406 uniquely modified intact histone tails and achieved a correlation of 0.85 between PGC and WCX-HILIC LC methods. Together, our method facilitates the analysis of single and combinatorial histone PTMs with much simpler applicability for conventional proteomics labs than the state-of-the-art middle-down MS.
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Affiliation(s)
- Kevin A Janssen
- Biochemistry and Molecular Biophysics Graduate Group, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mariel Coradin
- Biochemistry and Molecular Biophysics Graduate Group, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Congcong Lu
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Simone Sidoli
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, USA
| | - Benjamin A Garcia
- Biochemistry and Molecular Biophysics Graduate Group, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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8
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Heinz KS, Casas-Delucchi CS, Török T, Cmarko D, Rapp A, Raska I, Cardoso MC. Peripheral re-localization of constitutive heterochromatin advances its replication timing and impairs maintenance of silencing marks. Nucleic Acids Res 2019; 46:6112-6128. [PMID: 29750270 PMCID: PMC6158597 DOI: 10.1093/nar/gky368] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 04/25/2018] [Indexed: 11/13/2022] Open
Abstract
The replication of the genome is a highly organized process, both spatially and temporally. Although a lot is known on the composition of the basic replication machinery, how its activity is regulated is mostly unknown. Several chromatin properties have been proposed as regulators, but a potential role of the nuclear DNA position remains unclear. We made use of the prominent structure and well-defined heterochromatic landscape of mouse pericentric chromosome domains as a well-studied example of late replicating constitutive heterochromatin. We established a method to manipulate its nuclear position and evaluated the effect on replication timing, DNA compaction and epigenetic composition. Using time-lapse microscopy, we observed that constitutive heterochromatin, known to replicate during late S-phase, was replicated in mid S-phase when repositioned to the nuclear periphery. Out-of-schedule replication resulted in deficient post-replicative maintenance of chromatin modifications, namely silencing marks. We propose that repositioned constitutive heterochromatin was activated in trans according to the domino model of origin firing by nearby (mid S) firing origins. In summary, our data provide, on the one hand, a novel approach to manipulate nuclear DNA position and, on the other hand, establish nuclear DNA position as a novel mechanism regulating DNA replication timing and epigenetic maintenance.
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Affiliation(s)
- Kathrin S Heinz
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Corella S Casas-Delucchi
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Timea Török
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Dusan Cmarko
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00 Prague, Czech Republic
| | - Alexander Rapp
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Ivan Raska
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00 Prague, Czech Republic
| | - M Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
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9
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Heinz KS, Rapp A, Casas-Delucchi CS, Lehmkuhl A, Romero-Fernández I, Sánchez A, Krämer OH, Marchal JA, Cardoso MC. DNA replication dynamics of vole genome and its epigenetic regulation. Epigenetics Chromatin 2019; 12:18. [PMID: 30871586 PMCID: PMC6416958 DOI: 10.1186/s13072-019-0262-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 03/07/2019] [Indexed: 01/19/2023] Open
Abstract
Background The genome of some vole rodents exhibit large blocks of heterochromatin coupled to their sex chromosomes. The DNA composition and transcriptional activity of these heterochromatin blocks have been studied, but little is known about their DNA replication dynamics and epigenetic composition. Results Here, we show prominent epigenetic marks of the heterochromatic blocks in the giant sex chromosomes of female Microtus cabrerae cells. While the X chromosomes are hypoacetylated and cytosine hypomethylated, they are either enriched for macroH2A and H3K27me3 typical for facultative heterochromatin or for H3K9me3 and HP1 beta typical for constitutive heterochromatin. Using pulse-chase replication labeling and time-lapse microscopy, we found that the heterochromatic block enriched for macroH2A/H3K27me3 of the X chromosome is replicated during mid-S-phase, prior to the heterochromatic block enriched for H3K9me3/HP1 beta, which is replicated during late S-phase. To test whether histone acetylation level regulates its replication dynamics, we induced either global hyperacetylation by pharmacological inhibition or by targeting a histone acetyltransferase to the heterochromatic region of the X chromosomes. Our data reveal that histone acetylation level affects DNA replication dynamics of the sex chromosomes’ heterochromatin and leads to a global reduction in replication fork rate genome wide. Conclusions In conclusion, we mapped major epigenetic modifications controlling the structure of the sex chromosome-associated heterochromatin and demonstrated the occurrence of differences in the molecular mechanisms controlling the replication timing of the heterochromatic blocks at the sex chromosomes in female Microtus cabrerae cells. Furthermore, we highlighted a conserved role of histone acetylation level on replication dynamics across mammalian species. Electronic supplementary material The online version of this article (10.1186/s13072-019-0262-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kathrin S Heinz
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287, Darmstadt, Germany
| | - Alexander Rapp
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287, Darmstadt, Germany
| | - Corella S Casas-Delucchi
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287, Darmstadt, Germany.,Chromosome Replication Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Anne Lehmkuhl
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287, Darmstadt, Germany
| | | | - Antonio Sánchez
- Department of Experimental Biology, University of Jaén, Jaén, Spain
| | - Oliver H Krämer
- Institute of Toxicology, Universitätsmedizin der Johannes Gutenberg-Universität Mainz, Mainz, Germany
| | | | - M Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287, Darmstadt, Germany.
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10
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Maintenance of epigenetic landscape requires CIZ1 and is corrupted in differentiated fibroblasts in long-term culture. Nat Commun 2019; 10:460. [PMID: 30692537 PMCID: PMC6484225 DOI: 10.1038/s41467-018-08072-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 12/04/2018] [Indexed: 01/09/2023] Open
Abstract
The inactive X chromosome (Xi) serves as a model for establishment and maintenance of repressed chromatin and the function of polycomb repressive complexes (PRC1/2). Here we show that Xi transiently relocates from the nuclear periphery towards the interior during its replication, in a process dependent on CIZ1. Compromised relocation of Xi in CIZ1-null primary mouse embryonic fibroblasts is accompanied by loss of PRC-mediated H2AK119Ub1 and H3K27me3, increased solubility of PRC2 catalytic subunit EZH2, and genome-wide deregulation of polycomb-regulated genes. Xi position in S phase is also corrupted in cells adapted to long-term culture (WT or CIZ1-null), and also accompanied by specific changes in EZH2 and its targets. The data are consistent with the idea that chromatin relocation during S phase contributes to maintenance of epigenetic landscape in primary cells, and that elevated soluble EZH2 is part of an error-prone mechanism by which modifying enzyme meets template when chromatin relocation is compromised. The inactive X chromosome (Xi) is a model for establishment and maintenance of repressed chromatin and the function of polycomb repressive complexes. Here the authors show that Xi transiently relocates from the nuclear periphery during replication in a CIZ1-dependent manner, which plays a role in maintaining PRC-mediated repressed chromatin.
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11
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Lou W, Reynolds CA, Li Y, Liu J, Hüttemann M, Schlame M, Stevenson D, Strathdee D, Greenberg ML. Loss of tafazzin results in decreased myoblast differentiation in C2C12 cells: A myoblast model of Barth syndrome and cardiolipin deficiency. Biochim Biophys Acta Mol Cell Biol Lipids 2018; 1863:857-865. [PMID: 29694924 DOI: 10.1016/j.bbalip.2018.04.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 04/17/2018] [Accepted: 04/19/2018] [Indexed: 12/25/2022]
Abstract
Barth syndrome (BTHS) is an X-linked genetic disorder resulting from mutations in the tafazzin gene (TAZ), which encodes the transacylase that remodels the mitochondrial phospholipid cardiolipin (CL). While most BTHS patients exhibit pronounced skeletal myopathy, the mechanisms linking defective CL remodeling and skeletal myopathy have not been determined. In this study, we constructed a CRISPR-generated stable tafazzin knockout (TAZ-KO) C2C12 myoblast cell line. TAZ-KO cells exhibit mitochondrial deficits consistent with other models of BTHS, including accumulation of monolyso-CL (MLCL), decreased mitochondrial respiration, and increased mitochondrial ROS production. Additionally, tafazzin deficiency was associated with impairment of myocyte differentiation. Future studies should determine whether alterations in myogenic determination contribute to the skeletal myopathy observed in BTHS patients. The BTHS myoblast model will enable studies to elucidate mechanisms by which defective CL remodeling interferes with normal myocyte differentiation and skeletal muscle ontogenesis.
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Affiliation(s)
- Wenjia Lou
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA
| | | | - Yiran Li
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA
| | - Jenney Liu
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
| | - Maik Hüttemann
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
| | - Michael Schlame
- Department of Anesthesiology and Cell Biology, New York University School of Medicine, New York, NY, USA
| | - David Stevenson
- Transgenic Technology Laboratory, Cancer Research UK Beatson Institute, Garscube Estate, Glasgow, United Kingdom
| | - Douglas Strathdee
- Transgenic Technology Laboratory, Cancer Research UK Beatson Institute, Garscube Estate, Glasgow, United Kingdom
| | - Miriam L Greenberg
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA.
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12
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Takahashi S, Kobayashi S, Hiratani I. Epigenetic differences between naïve and primed pluripotent stem cells. Cell Mol Life Sci 2018; 75:1191-1203. [PMID: 29134247 PMCID: PMC5843680 DOI: 10.1007/s00018-017-2703-x] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 10/22/2017] [Accepted: 10/30/2017] [Indexed: 02/07/2023]
Abstract
It has been 8 years since the concept of naïve and primed pluripotent stem cell states was first proposed. Both are states of pluripotency, but exhibit slightly different properties. The naïve state represents the cellular state of the preimplantation mouse blastocyst inner cell mass, while the primed state is representative of the post-implantation epiblast cells. These two cell types exhibit clearly distinct developmental potential, as evidenced by the fact that naïve cells are able to contribute to blastocyst chimeras, while primed cells cannot. However, the epigenetic differences that underlie the distinct developmental potential of these cell types remain unclear, which is rather surprising given the large amount of active investigation over the years. Elucidating such epigenetic differences should lead to a better understanding of the fundamental properties of these states of pluripotency and the means by which the naïve-to-primed transition occurs, which may provide insights into the essence of stem cell commitment.
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Affiliation(s)
- Saori Takahashi
- Laboratory for Developmental Epigenetics, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Shin Kobayashi
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koutou-ku, Tokyo, 135-0064, Japan.
- Department of Epigenetics, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.
| | - Ichiro Hiratani
- Laboratory for Developmental Epigenetics, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan.
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13
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Zhao PA, Rivera-Mulia JC, Gilbert DM. Replication Domains: Genome Compartmentalization into Functional Replication Units. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1042:229-257. [DOI: 10.1007/978-981-10-6955-0_11] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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14
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Natarajan G, Perriotte-Olson C, Bhinderwala F, Powers R, Desouza CV, Talmon GA, Yuhang J, Zimmerman MC, Kabanov AV, Saraswathi V. Nanoformulated copper/zinc superoxide dismutase exerts differential effects on glucose vs lipid homeostasis depending on the diet composition possibly via altered AMPK signaling. Transl Res 2017; 188:10-26. [PMID: 28867395 PMCID: PMC5819896 DOI: 10.1016/j.trsl.2017.08.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 08/08/2017] [Accepted: 08/09/2017] [Indexed: 12/17/2022]
Abstract
Evidence suggests that superoxide dismutase 1 (SOD1) promotes glucose vs lipid metabolism depending on the diet type. We recently reported that nanoformulated SOD1 (Nano) improved lipid metabolism without altering glucose homeostasis in high-fat (HF) diet-fed mice. Here, we sought to determine the effects and potential mechanisms of Nano in modulating glucose and lipid homeostasis in mice fed a normal chow diet (CD) vs HF diet. Mice were fed a CD or a HF diet (45%) for 10 wk and injected with Nano once every 2 days for 15 days. The fasting glucose level was lower (P < 0.05) in CD + Nano-treated mice compared to control. Conversely, blood glucose was not altered but serum triglycerides were lower in HF + Nano-treated mice. Genes involved in fatty acid synthesis were reduced by Nano in the skeletal muscle of CD but not of HF diet-fed mice. Adenosine monophosphate-activated protein kinase (AMPK), which promotes both glucose and lipid metabolism depending on the fuel availability, is activated by Nano in CD-fed mice. Moreover, Nano increased phosphorylation of ACC, a downstream target of AMPK, in both CD and HF diet-fed mice. Nano increased mitochondrial respiration in C2C12 myocytes in the presence of glucose or fatty acid, and this effect is inhibited by Compound C, an AMPK inhibitor. Our data suggest that Nano promotes glucose and lipid metabolism in CD and HF diet-fed mice, respectively, and this effect is mediated partly via AMPK signaling.
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Affiliation(s)
- Gopalakrishnan Natarajan
- Department of Internal Medicine/Division of Diabetes, Endocrinology, and Metabolism, University of Nebraska Medical Center, Omaha, Neb
| | - Curtis Perriotte-Olson
- Department of Internal Medicine/Division of Diabetes, Endocrinology, and Metabolism, University of Nebraska Medical Center, Omaha, Neb
| | - Fatema Bhinderwala
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Neb; Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, Neb
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Neb; Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, Neb
| | - Cyrus V Desouza
- VA Nebraska-Western Iowa Health Care System, Omaha, Neb; Department of Internal Medicine/Division of Diabetes, Endocrinology, and Metabolism, University of Nebraska Medical Center, Omaha, Neb
| | - Geoffrey A Talmon
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Neb
| | - Jiang Yuhang
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Matthew C Zimmerman
- Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, Neb
| | - Alexander V Kabanov
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Viswanathan Saraswathi
- Department of Internal Medicine/Division of Diabetes, Endocrinology, and Metabolism, University of Nebraska Medical Center, Omaha, Neb; VA Nebraska-Western Iowa Health Care System, Omaha, Neb.
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15
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Han DS, Yang WS, Kao TW. Dexamethasone Treatment at the Myoblast Stage Enhanced C2C12 Myocyte Differentiation. Int J Med Sci 2017; 14:434-443. [PMID: 28539819 PMCID: PMC5441035 DOI: 10.7150/ijms.18427] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Accepted: 03/01/2017] [Indexed: 01/02/2023] Open
Abstract
Background: Glucocorticoids induce skeletal muscle atrophy in many clinical situations; however, their hypertrophic and pro-differentiation effects on myotubes have rarely been reported. We hypothesized that dexamethasone (DEX) has a dual effect on muscle differentiation, and aimed to develop a new differentiation protocol for C2C12 cell line. Methods: Dose- and time-dependent effect of DEX on C2C12 myoblast cell line was analyzed at myoblast and myotube stage, respectively. The level of differentiation was determined by myh1, pax7, atrogin-1, and myostatin mRNA expression and fusion index. Results: After differentiation and at the myotube stage, DEX treatment has an atrophic effect. Specifically, the myotube was thinner, the expression of atrogin-1 increased, and the protein content of myosin heavy chain decreased. In contrast, when DEX treatment was performed before the onset of differentiation, we observed an increase in myotube diameter and myosin heavy chain levels, and a decrease in the expression of atrogin-1. The ratio of multinuclear myotube cells increased in the DEX treatment group. The optimal treatment concentration and time was 100 μM and 48 h, respectively. Co-treatment with 10 μM DEX and 100 nM insulin further enhanced the process of myotube differentiation. Discussion: This novel finding contributed to the explanation on the stage-specific mechanism of glucocorticoid-induced myopathy. A new formula for myoblast differentiation, containing both DEX and insulin, is proposed. Further research is required to understand the complete mechanism of DEX-induced muscle hypertrophy.
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Affiliation(s)
- Der-Sheng Han
- Department of Physical Medicine and Rehabilitation.,Community and Geriatric Medicine Research Center, National Taiwan University Hospital, BeiHu Branch, Taipei.,Department of Physical Medicine and Rehabilitation
| | - Wei-Shiung Yang
- Department of Internal Medicine, National Taiwan University Hospital, Taipei.,Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei.,Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei
| | - Tung-Wei Kao
- Division of Geriatric Medicine, Department of Family and Community Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
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16
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Sato Y, Kujirai T, Arai R, Asakawa H, Ohtsuki C, Horikoshi N, Yamagata K, Ueda J, Nagase T, Haraguchi T, Hiraoka Y, Kimura A, Kurumizaka H, Kimura H. A Genetically Encoded Probe for Live-Cell Imaging of H4K20 Monomethylation. J Mol Biol 2016; 428:3885-3902. [PMID: 27534817 DOI: 10.1016/j.jmb.2016.08.010] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 08/04/2016] [Accepted: 08/05/2016] [Indexed: 01/28/2023]
Abstract
Eukaryotic gene expression is regulated in the context of chromatin. Dynamic changes in post-translational histone modification are thought to play key roles in fundamental cellular functions such as regulation of the cell cycle, development, and differentiation. To elucidate the relationship between histone modifications and cellular functions, it is important to monitor the dynamics of modifications in single living cells. A genetically encoded probe called mintbody (modification-specific intracellular antibody), which is a single-chain variable fragment tagged with a fluorescent protein, has been proposed as a useful visualization tool. However, the efficacy of intracellular expression of antibody fragments has been limited, in part due to different environmental conditions in the cytoplasm compared to the endoplasmic reticulum where secreted proteins such as antibodies are folded. In this study, we have developed a new mintbody specific for histone H4 Lys20 monomethylation (H4K20me1). The specificity of the H4K20me1-mintbody in living cells was verified using yeast mutants and mammalian cells in which this target modification was diminished. Expression of the H4K20me1-mintbody allowed us to monitor the oscillation of H4K20me1 levels during the cell cycle. Moreover, dosage-compensated X chromosomes were visualized using the H4K20me1-mintbody in mouse and nematode cells. Using X-ray crystallography and mutational analyses, we identified critical amino acids that contributed to stabilization and/or proper folding of the mintbody. Taken together, these data provide important implications for future studies aimed at developing functional intracellular antibodies. Specifically, the H4K20me1-mintbody provides a powerful tool to track this particular histone modification in living cells and organisms.
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Affiliation(s)
- Yuko Sato
- Cell Biology Unit, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.
| | - Tomoya Kujirai
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Ritsuko Arai
- Cell Architecture Laboratory, Structural Biology Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Haruhiko Asakawa
- Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Chizuru Ohtsuki
- Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Naoki Horikoshi
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Kazuo Yamagata
- Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa City, Wakayama 649-6493, Japan
| | - Jun Ueda
- Center for Education in Laboratory Animal Research, Chubu University, Kasugai, Aichi 487-8501, Japan
| | - Takahiro Nagase
- Public Relations Team, Kazusa DNA Research Institute, Chiba 292-0818, Japan
| | - Tokuko Haraguchi
- Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan; Advanced ICT Research Institute, National Institute of Information and Communications Technology (NICT), Kobe 651-2492, Japan
| | - Yasushi Hiraoka
- Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan; Advanced ICT Research Institute, National Institute of Information and Communications Technology (NICT), Kobe 651-2492, Japan
| | - Akatsuki Kimura
- Cell Architecture Laboratory, Structural Biology Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Hiroshi Kimura
- Cell Biology Unit, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.
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17
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Ilaiwy A, Quintana MT, Bain JR, Muehlbauer MJ, Brown DI, Stansfield WE, Willis MS. Cessation of biomechanical stretch model of C2C12 cells models myocyte atrophy and anaplerotic changes in metabolism using non-targeted metabolomics analysis. Int J Biochem Cell Biol 2016; 79:80-92. [PMID: 27515590 DOI: 10.1016/j.biocel.2016.08.012] [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] [Received: 04/11/2016] [Revised: 07/20/2016] [Accepted: 08/07/2016] [Indexed: 12/18/2022]
Abstract
Studies of skeletal muscle disuse, either in patients on bed rest or experimentally in animals (immobilization), have demonstrated that decreased protein synthesis is common, with transient parallel increases in protein degradation. Muscle disuse atrophy involves a process of transition from slow to fast myosin fiber types. A shift toward glycolysis, decreased capacity for fat oxidation, and substrate accumulation in atrophied muscles have been reported, as has accommodation of the liver with an increased gluconeogenic capacity. Recent studies have modeled skeletal muscle disuse by using cyclic stretch of differentiated myotubes (C2C12), which mimics the loading pattern of mature skeletal muscle, followed by cessation of stretch. We utilized this model to determine the metabolic changes using non-targeted metabolomics analysis of the media. We identified increases in amino acids resulting from muscle atrophy-induced protein degradation (largely sarcomere) that occurs with muscle atrophy that are involved in feeding the Kreb's cycle through anaplerosis. Specifically, we identified increased alanine/proline metabolism (significantly elevated proline, alanine, glutamine, and asparagine) and increased α-ketoglutaric acid, the proposed Kreb's cycle intermediate being fed by the alanine/proline metabolic anaplerotic mechanism. Additionally, several unique pathways not clearly delineated in previous studies of muscle unloading were seen, including: (1) elevated keto-acids derived from branched chain amino acids (i.e. 2-ketoleucine and 2-keovaline), which feed into a metabolic pathway supplying acetyl-CoA and 2-hydroxybutyrate (also significantly increased); and (2) elevated guanine, an intermediate of purine metabolism, was seen at 12h unloading. Given the interest in targeting different aspects of the ubiquitin proteasome system to inhibit protein degradation, this C2C12 system may allow the identification of direct and indirect alterations in metabolism due to anaplerosis or through other yet to be identified mechanisms using a non-targeted metabolomics approach.
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Affiliation(s)
- Amro Ilaiwy
- Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA; Division of Endocrinology, Metabolism, and Nutrition, Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Megan T Quintana
- Department of Surgery, University of North Carolina, Chapel Hill, NC, USA
| | - James R Bain
- Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA; Division of Endocrinology, Metabolism, and Nutrition, Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Michael J Muehlbauer
- Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
| | - David I Brown
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC, USA
| | | | - Monte S Willis
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC, USA; Department of Pathology & Laboratory Medicine, University of North Carolina, Chapel Hill, NC, USA; Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA.
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18
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Abstract
X chromosome inactivation (XCI) is the dosage compensation mechanism that evolved in female mammals to correct the genetic imbalance of X-linked genes between sexes. X chromosome inactivation occurs in early development when one of the two X chromosomes of females is nearly-completely silenced. Differentiating Embryonic Stem cells (ESC) are regarded as a useful tool to study XCI, since they recapitulate many events occurring during early development. In this review we aim to summarise the advances in the field and to discuss the close connection between cell differentiation and X chromosome inactivation, with a particular focus on mouse ESCs.
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Affiliation(s)
- Greta Pintacuda
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
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19
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Insights into the activation mechanism of class I HDAC complexes by inositol phosphates. Nat Commun 2016; 7:11262. [PMID: 27109927 PMCID: PMC4848466 DOI: 10.1038/ncomms11262] [Citation(s) in RCA: 154] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 03/07/2016] [Indexed: 02/07/2023] Open
Abstract
Histone deacetylases (HDACs) 1, 2 and 3 form the catalytic subunit of several large transcriptional repression complexes. Unexpectedly, the enzymatic activity of HDACs in these complexes has been shown to be regulated by inositol phosphates, which bind in a pocket sandwiched between the HDAC and co-repressor proteins. However, the actual mechanism of activation remains poorly understood. Here we have elucidated the stereochemical requirements for binding and activation by inositol phosphates, demonstrating that activation requires three adjacent phosphate groups and that other positions on the inositol ring can tolerate bulky substituents. We also demonstrate that there is allosteric communication between the inositol-binding site and the active site. The crystal structure of the HDAC1:MTA1 complex bound to a novel peptide-based inhibitor and to inositol hexaphosphate suggests a molecular basis of substrate recognition, and an entropically driven allosteric mechanism of activation.
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20
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Rivera-Mulia JC, Gilbert DM. Replication timing and transcriptional control: beyond cause and effect-part III. Curr Opin Cell Biol 2016; 40:168-178. [PMID: 27115331 DOI: 10.1016/j.ceb.2016.03.022] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 03/24/2016] [Accepted: 03/29/2016] [Indexed: 11/17/2022]
Abstract
DNA replication is essential for faithful transmission of genetic information and is intimately tied to chromosome structure and function. Genome duplication occurs in a defined temporal order known as the replication-timing (RT) program, which is regulated during the cell cycle and development in discrete units referred to as replication domains (RDs). RDs correspond to topologically-associating domains (TADs) and are spatio-temporally compartmentalized in the nucleus. While improvements in experimental tools have begun to reveal glimpses of causality, they have also unveiled complex context-dependent relationships that challenge long recognized correlations of RT to chromatin organization and gene regulation. In particular, RDs/TADs that switch RT during development march to the beat of a different drummer.
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Affiliation(s)
| | - David M Gilbert
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA; Center for Genomics and Personalized Medicine, Florida State University, Tallahassee, FL, USA.
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21
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Pinter SF. A Tale of Two Cities: How Xist and its partners localize to and silence the bicompartmental X. Semin Cell Dev Biol 2016; 56:19-34. [PMID: 27072488 DOI: 10.1016/j.semcdb.2016.03.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 03/30/2016] [Accepted: 03/30/2016] [Indexed: 10/22/2022]
Abstract
Sex chromosomal dosage compensation in mammals takes the form of X chromosome inactivation (XCI), driven by the non-coding RNA Xist. In contrast to dosage compensation systems of flies and worms, mammalian XCI has to restrict its function to the Xist-producing X chromosome, while leaving autosomes and active X untouched. The mechanisms behind the long-range yet cis-specific localization and silencing activities of Xist have long been enigmatic, but genomics, proteomics, super-resolution microscopy, and innovative genetic approaches have produced significant new insights in recent years. In this review, I summarize and integrate these findings with a particular focus on the redundant yet mutually reinforcing pathways that enable long-term transcriptional repression throughout the soma. This includes an exploration of concurrent epigenetic changes acting in parallel within two distinct compartments of the inactive X. I also examine how Polycomb repressive complexes 1 and 2 and macroH2A may bridge XCI establishment and maintenance. XCI is a remarkable phenomenon that operates across multiple scales, combining changes in nuclear architecture, chromosome topology, chromatin compaction, and nucleosome/nucleotide-level epigenetic cues. Learning how these pathways act in concert likely holds the answer to the riddle posed by Cattanach's and other autosomal translocations: What makes the X especially receptive to XCI?
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Affiliation(s)
- Stefan F Pinter
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, 263 Farmington Ave, Farmington, CT 06030-6403, USA.
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22
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4D Visualization of replication foci in mammalian cells corresponding to individual replicons. Nat Commun 2016; 7:11231. [PMID: 27052570 PMCID: PMC4829660 DOI: 10.1038/ncomms11231] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 03/03/2016] [Indexed: 01/05/2023] Open
Abstract
Since the pioneering proposal of the replicon model of DNA replication 50 years ago, the predicted replicons have not been identified and quantified at the cellular level. Here, we combine conventional and super-resolution microscopy of replication sites in live and fixed cells with computational image analysis. We complement these data with genome size measurements, comprehensive analysis of S-phase dynamics and quantification of replication fork speed and replicon size in human and mouse cells. These multidimensional analyses demonstrate that replication foci (RFi) in three-dimensional (3D) preserved somatic mammalian cells can be optically resolved down to single replicons throughout S-phase. This challenges the conventional interpretation of nuclear RFi as replication factories, that is, the complex entities that process multiple clustered replicons. Accordingly, 3D genome organization and duplication can be now followed within the chromatin context at the level of individual replicons.
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23
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Löb D, Lengert N, Chagin VO, Reinhart M, Casas-Delucchi CS, Cardoso MC, Drossel B. 3D replicon distributions arise from stochastic initiation and domino-like DNA replication progression. Nat Commun 2016; 7:11207. [PMID: 27052359 PMCID: PMC4829661 DOI: 10.1038/ncomms11207] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 03/02/2016] [Indexed: 01/02/2023] Open
Abstract
DNA replication dynamics in cells from higher eukaryotes follows very complex but highly efficient mechanisms. However, the principles behind initiation of potential replication origins and emergence of typical patterns of nuclear replication sites remain unclear. Here, we propose a comprehensive model of DNA replication in human cells that is based on stochastic, proximity-induced replication initiation. Critical model features are: spontaneous stochastic firing of individual origins in euchromatin and facultative heterochromatin, inhibition of firing at distances below the size of chromatin loops and a domino-like effect by which replication forks induce firing of nearby origins. The model reproduces the empirical temporal and chromatin-related properties of DNA replication in human cells. We advance the one-dimensional DNA replication model to a spatial model by taking into account chromatin folding in the nucleus, and we are able to reproduce the spatial and temporal characteristics of the replication foci distribution throughout S-phase.
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Affiliation(s)
- D. Löb
- Department of Physics, Institute for Condensed Matter Physics, Technische Universität Darmstadt, 64289 Darmstadt, Germany
| | - N. Lengert
- Department of Physics, Institute for Condensed Matter Physics, Technische Universität Darmstadt, 64289 Darmstadt, Germany
| | - V. O. Chagin
- Laboratory of Chromosome Stability, Institute of Cytology, St Petersburg 194064, Russia
- Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - M. Reinhart
- Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - C. S. Casas-Delucchi
- Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - M. C. Cardoso
- Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - B. Drossel
- Department of Physics, Institute for Condensed Matter Physics, Technische Universität Darmstadt, 64289 Darmstadt, Germany
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Dixon-McDougall T, Brown C. The making of a Barr body: the mosaic of factors that eXIST on the mammalian inactive X chromosome. Biochem Cell Biol 2015; 94:56-70. [PMID: 26283003 DOI: 10.1139/bcb-2015-0016] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
During X-chromosome inactivation (XCI), nearly an entire X chromosome is permanently silenced and converted into a Barr body, providing dosage compensation for eutherians between the sexes. XCI is facilitated by the upregulation of the long non-coding RNA gene, XIST, which coats its chromosome of origin, recruits heterochromatin factors, and silences gene expression. During XCI, at least two distinct types of heterochromatin are established, and in this review we discuss the enrichment of facultative heterochromatin marks such as H3K27me3, H2AK119ub, and macroH2A as well as pericentric heterochromatin marks such as HP1, H3K9me3, and H4K20me3. The extremely stable maintenance of silencing is a product of reinforcing interactions within and between these domains. This paper "Xplores" the current knowledge of the pathways involved in XCI, how the pathways interact, and the gaps in our understanding that need to be filled.
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Affiliation(s)
- Thomas Dixon-McDougall
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Carolyn Brown
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
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25
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Harada A, Mallappa C, Okada S, Butler JT, Baker SP, Lawrence JB, Ohkawa Y, Imbalzano AN. Spatial re-organization of myogenic regulatory sequences temporally controls gene expression. Nucleic Acids Res 2015; 43:2008-21. [PMID: 25653159 PMCID: PMC4344497 DOI: 10.1093/nar/gkv046] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 11/05/2014] [Accepted: 01/13/2015] [Indexed: 12/14/2022] Open
Abstract
During skeletal muscle differentiation, the activation of some tissue-specific genes occurs immediately while others are delayed. The molecular basis controlling temporal gene regulation is poorly understood. We show that the regulatory sequences, but not other regions of genes expressed at late times of myogenesis, are in close physical proximity in differentiating embryonic tissue and in differentiating culture cells, despite these genes being located on different chromosomes. Formation of these inter-chromosomal interactions requires the lineage-determinant MyoD and functional Brg1, the ATPase subunit of SWI/SNF chromatin remodeling enzymes. Ectopic expression of myogenin and a specific Mef2 isoform induced myogenic differentiation without activating endogenous MyoD expression. Under these conditions, the regulatory sequences of late gene loci were not in close proximity, and these genes were prematurely activated. The data indicate that the spatial organization of late genes contributes to temporal regulation of myogenic transcription by restricting late gene expression during the early stages of myogenesis.
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Affiliation(s)
- Akihito Harada
- Department of Advanced Medical Initiatives, JST-CREST, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan
| | - Chandrashekara Mallappa
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Seiji Okada
- Department of Advanced Medical Initiatives, JST-CREST, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan
| | - John T Butler
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Stephen P Baker
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA Department of Quantitative Health Sciences, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Jeanne B Lawrence
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Yasuyuki Ohkawa
- Department of Advanced Medical Initiatives, JST-CREST, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Anthony N Imbalzano
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
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26
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Minkovsky A, Sahakyan A, Rankin-Gee E, Bonora G, Patel S, Plath K. The Mbd1-Atf7ip-Setdb1 pathway contributes to the maintenance of X chromosome inactivation. Epigenetics Chromatin 2014; 7:12. [PMID: 25028596 PMCID: PMC4099106 DOI: 10.1186/1756-8935-7-12] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Accepted: 06/05/2014] [Indexed: 01/08/2023] Open
Abstract
Background X chromosome inactivation (XCI) is a developmental program of heterochromatin formation that initiates during early female mammalian embryonic development and is maintained through a lifetime of cell divisions in somatic cells. Despite identification of the crucial long non-coding RNA Xist and involvement of specific chromatin modifiers in the establishment and maintenance of the heterochromatin of the inactive X chromosome (Xi), interference with known pathways only partially reactivates the Xi once silencing has been established. Here, we studied ATF7IP (MCAF1), a protein previously characterized to coordinate DNA methylation and histone H3K9 methylation through interactions with the methyl-DNA binding protein MBD1 and the histone H3K9 methyltransferase SETDB1, as a candidate maintenance factor of the Xi. Results We found that siRNA-mediated knockdown of Atf7ip in mouse embryonic fibroblasts (MEFs) induces the activation of silenced reporter genes on the Xi in a low number of cells. Additional inhibition of two pathways known to contribute to Xi maintenance, DNA methylation and Xist RNA coating of the X chromosome, strongly increased the number of cells expressing Xi-linked genes upon Atf7ip knockdown. Despite its functional importance in Xi maintenance, ATF7IP does not accumulate on the Xi in MEFs or differentiating mouse embryonic stem cells. However, we found that depletion of two known repressive biochemical interactors of ATF7IP, MBD1 and SETDB1, but not of other unrelated H3K9 methyltransferases, also induces the activation of an Xi-linked reporter in MEFs. Conclusions Together, these data indicate that Atf7ip acts in a synergistic fashion with DNA methylation and Xist RNA to maintain the silent state of the Xi in somatic cells, and that Mbd1 and Setdb1, similar to Atf7ip, play a functional role in Xi silencing. We therefore propose that ATF7IP links DNA methylation on the Xi to SETDB1-mediated H3K9 trimethylation via its interaction with MBD1, and that this function is a crucial feature of the stable silencing of the Xi in female mammalian cells.
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Affiliation(s)
- Alissa Minkovsky
- David Geffen School of Medicine, Department of Biological Chemistry, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA 90095, USA
| | - Anna Sahakyan
- David Geffen School of Medicine, Department of Biological Chemistry, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA 90095, USA
| | - Elyse Rankin-Gee
- David Geffen School of Medicine, Department of Biological Chemistry, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA 90095, USA
| | - Giancarlo Bonora
- David Geffen School of Medicine, Department of Biological Chemistry, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA 90095, USA
| | - Sanjeet Patel
- David Geffen School of Medicine, Department of Biological Chemistry, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA 90095, USA
| | - Kathrin Plath
- David Geffen School of Medicine, Department of Biological Chemistry, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA 90095, USA
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Smeets D, Markaki Y, Schmid VJ, Kraus F, Tattermusch A, Cerase A, Sterr M, Fiedler S, Demmerle J, Popken J, Leonhardt H, Brockdorff N, Cremer T, Schermelleh L, Cremer M. Three-dimensional super-resolution microscopy of the inactive X chromosome territory reveals a collapse of its active nuclear compartment harboring distinct Xist RNA foci. Epigenetics Chromatin 2014; 7:8. [PMID: 25057298 PMCID: PMC4108088 DOI: 10.1186/1756-8935-7-8] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 04/11/2014] [Indexed: 12/31/2022] Open
Abstract
Background A Xist RNA decorated Barr body is the structural hallmark of the compacted inactive X territory in female mammals. Using super-resolution three-dimensional structured illumination microscopy (3D-SIM) and quantitative image analysis, we compared its ultrastructure with active chromosome territories (CTs) in human and mouse somatic cells, and explored the spatio-temporal process of Barr body formation at onset of inactivation in early differentiating mouse embryonic stem cells (ESCs). Results We demonstrate that all CTs are composed of structurally linked chromatin domain clusters (CDCs). In active CTs the periphery of CDCs harbors low-density chromatin enriched with transcriptionally competent markers, called the perichromatin region (PR). The PR borders on a contiguous channel system, the interchromatin compartment (IC), which starts at nuclear pores and pervades CTs. We propose that the PR and macromolecular complexes in IC channels together form the transcriptionally permissive active nuclear compartment (ANC). The Barr body differs from active CTs by a partially collapsed ANC with CDCs coming significantly closer together, although a rudimentary IC channel system connected to nuclear pores is maintained. Distinct Xist RNA foci, closely adjacent to the nuclear matrix scaffold attachment factor-A (SAF-A) localize throughout Xi along the rudimentary ANC. In early differentiating ESCs initial Xist RNA spreading precedes Barr body formation, which occurs concurrent with the subsequent exclusion of RNA polymerase II (RNAP II). Induction of a transgenic autosomal Xist RNA in a male ESC triggers the formation of an ‘autosomal Barr body’ with less compacted chromatin and incomplete RNAP II exclusion. Conclusions 3D-SIM provides experimental evidence for profound differences between the functional architecture of transcriptionally active CTs and the Barr body. Basic structural features of CT organization such as CDCs and IC channels are however still recognized, arguing against a uniform compaction of the Barr body at the nucleosome level. The localization of distinct Xist RNA foci at boundaries of the rudimentary ANC may be considered as snap-shots of a dynamic interaction with silenced genes. Enrichment of SAF-A within Xi territories and its close spatial association with Xist RNA suggests their cooperative function for structural organization of Xi.
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Affiliation(s)
- Daniel Smeets
- Biocenter, Department of Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany ; Department of Biochemistry, University of Oxford, Oxford, UK
| | - Yolanda Markaki
- Biocenter, Department of Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
| | - Volker J Schmid
- Institute of Statistics, Ludwig Maximilians University (LMU), Munich, Germany
| | - Felix Kraus
- Biocenter, Department of Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany ; Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - Andrea Cerase
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Michael Sterr
- Biocenter, Department of Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
| | - Susanne Fiedler
- Biocenter, Department of Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
| | - Justin Demmerle
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Jens Popken
- Biocenter, Department of Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
| | - Heinrich Leonhardt
- Biocenter, Department of Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
| | - Neil Brockdorff
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Thomas Cremer
- Biocenter, Department of Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
| | - Lothar Schermelleh
- Biocenter, Department of Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany ; Department of Biochemistry, University of Oxford, Oxford, UK
| | - Marion Cremer
- Biocenter, Department of Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
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28
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Abstract
While large portions of the mammalian genome are known to replicate sequentially in a distinct, tissue-specific order, recent studies suggest that the inactive X chromosome is duplicated rapidly via random, synchronous DNA synthesis at numerous adjacent regions. The rapid duplication of the inactive X chromosome was observed in high-resolution studies visualizing DNA replication patterns in the nucleus, and by allele-specific DNA sequencing studies measuring the extent of DNA synthesis. These studies conclude that inactive X chromosomes complete replication earlier than previously thought and suggest that the strict order of DNA replication detected in the majority of genomic regions is not preserved in non-transcribed, "silent" chromatin. These observations alter current concepts about the regulation of DNA replication in non-transcribed portions of the genome in general and in the inactive X-chromosome in particular.
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Affiliation(s)
- Mirit I Aladjem
- Developmental Therapeutic Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
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29
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Bogomazova AN, Lagarkova MA, Panova AV, Nekrasov ED, Kiselev SL. Reactivation of Х chromosome upon reprogramming leads to changes in the replication pattern and 5hmC accumulation. Chromosoma 2014; 123:117-28. [PMID: 23982752 DOI: 10.1007/s00412-013-0433-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 07/30/2013] [Accepted: 08/09/2013] [Indexed: 02/07/2023]
Abstract
Once set, the inactive status of the X chromosome in female somatic cells is preserved throughout subsequent cell divisions. The inactive status of the X chromosome is characterized by many features, including late replication. In contrast to induced pluripotent stem cells (iPSCs) in mice, the X chromosome in human female iPSCs usually remains inactive after reprogramming of somatic cells to the pluripotent state, although recent studies point to the possibility of reactivation of the X chromosome. Here, we demonstrated that, during reprogramming, the inactive X chromosome switches from late to synchronous replication, with restoration of the transcription of previously silenced genes. This process is accompanied by accumulation of a new epigenetic mark or intermediate of the DNA demethylation pathway, 5-hydroxymethylcytosine (5hmC), on the activated X chromosome. Our results indicate that the active status of the X chromosome is better confirmed by early replication and the reappearance of 5hmC, rather than by appearance of histone marks of active chromatin, removal of histone marks of inactive chromatin, or an absence of XIST coating.
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Affiliation(s)
- Alexandra N Bogomazova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 3, Gubkina St, Moscow, 119991, Russia
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30
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Culver-Cochran AE, Chadwick BP. Loss of WSTF results in spontaneous fluctuations of heterochromatin formation and resolution, combined with substantial changes to gene expression. BMC Genomics 2013; 14:740. [PMID: 24168170 PMCID: PMC3870985 DOI: 10.1186/1471-2164-14-740] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 10/26/2013] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Williams syndrome transcription factor (WSTF) is a multifaceted protein that is involved in several nuclear processes, including replication, transcription, and the DNA damage response. WSTF participates in a chromatin-remodeling complex with the ISWI ATPase, SNF2H, and is thought to contribute to the maintenance of heterochromatin, including at the human inactive X chromosome (Xi). WSTF is encoded by BAZ1B, and is one of twenty-eight genes that are hemizygously deleted in the genetic disorder Williams-Beuren syndrome (WBS). RESULTS To explore the function of WSTF, we performed zinc finger nuclease-assisted targeting of the BAZ1B gene and isolated several independent knockout clones in human cells. Our results show that, while heterochromatin at the Xi is unaltered, new inappropriate areas of heterochromatin spontaneously form and resolve throughout the nucleus, appearing as large DAPI-dense staining blocks, defined by histone H3 lysine-9 trimethylation and association of the proteins heterochromatin protein 1 and structural maintenance of chromosomes flexible hinge domain containing 1. In three independent mutants, the expression of a large number of genes were impacted, both up and down, by WSTF loss. CONCLUSIONS Given the inappropriate appearance of regions of heterochromatin in BAZ1B knockout cells, it is evident that WSTF performs a critical role in maintaining chromatin and transcriptional states, a property that is likely compromised by WSTF haploinsufficiency in WBS patients.
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Affiliation(s)
| | - Brian P Chadwick
- Department of Biological Science, Florida State University, Tallahassee, FL, USA.
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31
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Legartová S, Stixová L, Strnad H, Kozubek S, Martinet N, Dekker FJ, Franek M, Bártová E. Basic nuclear processes affected by histone acetyltransferases and histone deacetylase inhibitors. Epigenomics 2013; 5:379-96. [DOI: 10.2217/epi.13.38] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: The optimal balance between histone acetylation and deacetylation is important for proper gene function. Therefore, we addressed how inhibitors of histone-modifying enzymes can modulate nuclear events, including replication, transcription, splicing and DNA repair. Materials & methods: Changes in cell signaling pathways upon treatment with histone acetyltransferases and/or histone deacetylase inhibitors were studied by cDNA microarrays and western blots. Results: We analyzed the effects of the histone deacetylase inhibitor suberoylanilide hydroxamic acid (SAHA) and the histone acetylase inhibitor MG149. SAHA altered the expression of factors involved in DNA replication complexes, basal transcription and the spliceosome pathway. DNA repair-related genes, including Rad51, Rad54 and BRCA2, were significantly downregulated by SAHA. However, MG149 had no effect on the investigated nuclear processes, with the exception of the spliceosome network and Sestrins, involved in DNA repair. Conclusion: Based on our results, we propose that the studied epigenetic drugs have the distinct potential to affect specific cell signaling pathways depending on their respective molecular targets.
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Affiliation(s)
- Soňa Legartová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 65, Brno, Czech Republic
| | - Lenka Stixová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 65, Brno, Czech Republic
| | - Hynek Strnad
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, 142 20, Prague, Czech Republic
| | - Stanislav Kozubek
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 65, Brno, Czech Republic
| | - Nadine Martinet
- Institut de Chimie, Université de Nice Sophia Antipolis-UMR CNRS 7272, Parc Valrose, 06100, Nice, France
| | - Frank J Dekker
- Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Michal Franek
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 65, Brno, Czech Republic
| | - Eva Bártová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 65, Brno, Czech Republic.
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Herce HD, Casas-Delucchi CS, Cardoso MC. New image colocalization coefficient for fluorescence microscopy to quantify (bio-)molecular interactions. J Microsc 2013; 249:184-94. [PMID: 23301670 PMCID: PMC3599484 DOI: 10.1111/jmi.12008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 12/03/2012] [Indexed: 11/26/2022]
Abstract
The spatial relationship, or degree of colocalization, between two or more types of molecules in live cells is commonly detected using fluorescence microscopy. This spatial distribution can be used to estimate the interaction between fluorescently labelled molecules. These interactions are usually quantified by analysing the correlation and/or the overlap between images, using the Pearson's and Manders' coefficients, respectively. However, the correlation and overlap coefficients are parameters not designed to quantify molecular interactions. Here we propose a new colocalization coefficient specifically designed to quantify the interactions between molecules. In well-defined thermodynamic ensembles, this coefficient can in principle be used to calculate relevant statistical thermodynamic quantities such as binding free energies.
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Affiliation(s)
- HD Herce
- Department of Biology, Technische Universität DarmstadtDarmstadt, Germany
- Instituto de Física de Líquidos y Sistemas Biológicos (CONICET)La Plata
| | - CS Casas-Delucchi
- Department of Biology, Technische Universität DarmstadtDarmstadt, Germany
| | - MC Cardoso
- Department of Biology, Technische Universität DarmstadtDarmstadt, Germany
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33
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Reinhart M, Casas-Delucchi CS, Cardoso MC. Spatiotemporal visualization of DNA replication dynamics. Methods Mol Biol 2013; 1042:213-225. [PMID: 23980010 DOI: 10.1007/978-1-62703-526-2_15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The ability of cells to copy their DNA allows them to transmit their genetic information to their progeny. In such, this central biological process preserves the instructions that direct the entire development of a cell. Earlier biochemical analysis in vitro and genetic analysis in yeast laid the basis of our understanding of the highly conserved mechanism of DNA replication. Recent advances on labeling and live-cell microscopy permit now the dissection of this fundamental process in vivo within the context of intact cells. In this chapter, we describe in detail how to perform multiple DNA replication labeling and detection allowing high spatial resolution imaging, as well as how to follow DNA replication in living cells allowing high temporal resolution imaging.
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Affiliation(s)
- Marius Reinhart
- Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
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Obligate ligation-gated recombination (ObLiGaRe): custom-designed nuclease-mediated targeted integration through nonhomologous end joining. Genome Res 2012; 23:539-46. [PMID: 23152450 PMCID: PMC3589542 DOI: 10.1101/gr.145441.112] [Citation(s) in RCA: 232] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Custom-designed nucleases (CDNs) greatly facilitate genetic engineering by generating a targeted DNA double-strand break (DSB) in the genome. Once a DSB is created, specific modifications can be introduced around the breakage site during its repair by two major DNA damage repair (DDR) mechanisms: the dominant but error-prone nonhomologous end joining (NHEJ) pathway, and the less-frequent but precise homologous recombination (HR) pathway. Here we describe ObLiGaRe, a new method for site-specific gene insertions that uses the efficient NHEJ pathway and acts independently of HR. This method is applicable with both zinc finger nucleases (ZFNs) and Tale nucleases (TALENs), and has enabled us to insert a 15-kb inducible gene expression cassette at a defined locus in human cell lines. In addition, our experiments have revealed the previously underestimated error-free nature of NHEJ and provided new tools to further characterize this pathway under physiological and pathological conditions.
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35
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Casas-Delucchi CS, Becker A, Bolius JJ, Cardoso MC. Targeted manipulation of heterochromatin rescues MeCP2 Rett mutants and re-establishes higher order chromatin organization. Nucleic Acids Res 2012; 40:e176. [PMID: 22923521 PMCID: PMC3526307 DOI: 10.1093/nar/gks784] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Heterochromatic regions represent a significant portion of the mammalian genome and have been implied in several important cellular processes, including cell division and genomic stability. However, its composition and dynamics remain largely unknown. To better understand how heterochromatin functions and how it is organized within the context of the cell nucleus, we have developed molecular tools allowing the targeting of virtually any nuclear factor specifically to heterochromatic regions and, thereby, the manipulation, also in a temporally controlled manner, of its composition. To validate our approach, we have ectopically targeted MeCP2 chromatin binding deficient Rett mutants to constitutive heterochromatic regions and analyze its functional consequences. We could show that, once bound to their endogenous target regions, their ability to re-organize higher order chromatin structure is restored. Furthermore, a temporally controlled targeting strategy allowed us to monitor MeCP2-mediated chromatin rearrangements in vivo and to visualize large-scale chromatin movements over several micrometers, as well as heterochromatic foci fusion events. This novel strategy enables specific tethering of any protein to heterochromatin and lays the ground for controlled manipulation of its composition and organization.
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36
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Markaki Y, Smeets D, Fiedler S, Schmid VJ, Schermelleh L, Cremer T, Cremer M. The potential of 3D-FISH and super-resolution structured illumination microscopy for studies of 3D nuclear architecture: 3D structured illumination microscopy of defined chromosomal structures visualized by 3D (immuno)-FISH opens new perspectives for studies of nuclear architecture. Bioessays 2012; 34:412-26. [PMID: 22508100 DOI: 10.1002/bies.201100176] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Three-dimensional structured illumination microscopy (3D-SIM) has opened up new possibilities to study nuclear architecture at the ultrastructural level down to the ~100 nm range. We present first results and assess the potential using 3D-SIM in combination with 3D fluorescence in situ hybridization (3D-FISH) for the topographical analysis of defined nuclear targets. Our study also deals with the concern that artifacts produced by FISH may counteract the gain in resolution. We address the topography of DAPI-stained DNA in nuclei before and after 3D-FISH, nuclear pores and the lamina, chromosome territories, chromatin domains, and individual gene loci. We also look at the replication patterns of chromocenters and the topographical relationship of Xist-RNA within the inactive X-territory. These examples demonstrate that an appropriately adapted 3D-FISH/3D-SIM approach preserves key characteristics of the nuclear ultrastructure and that the gain in information obtained by 3D-SIM yields new insights into the functional nuclear organization.
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Affiliation(s)
- Yolanda Markaki
- Biocenter, Department Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
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37
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Structure, function and dynamics of nuclear subcompartments. Curr Opin Cell Biol 2012; 24:79-85. [DOI: 10.1016/j.ceb.2011.12.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Revised: 12/09/2011] [Accepted: 12/15/2011] [Indexed: 01/09/2023]
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38
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Evolutionary diversity and developmental regulation of X-chromosome inactivation. Hum Genet 2011; 130:307-27. [PMID: 21687993 PMCID: PMC3132430 DOI: 10.1007/s00439-011-1029-2] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2011] [Accepted: 05/31/2011] [Indexed: 12/26/2022]
Abstract
X-chromosome inactivation (XCI) results in the transcriptional silencing of one X-chromosome in females to attain gene dosage parity between XX female and XY male mammals. Mammals appear to have developed rather diverse strategies to initiate XCI in early development. In placental mammals XCI depends on the regulatory noncoding RNA X-inactive specific transcript (Xist), which is absent in marsupials and monotremes. Surprisingly, even placental mammals show differences in the initiation of XCI in terms of Xist regulation and the timing to acquire dosage compensation. Despite this, all placental mammals achieve chromosome-wide gene silencing at some point in development, and this is maintained by epigenetic marks such as chromatin modifications and DNA methylation. In this review, we will summarise recent findings concerning the events that occur downstream of Xist RNA coating of the inactive X-chromosome (Xi) to ensure its heterochromatinization and the maintenance of the inactive state in the mouse and highlight similarities and differences between mammals.
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Pasque V, Gillich A, Garrett N, Gurdon JB. Histone variant macroH2A confers resistance to nuclear reprogramming. EMBO J 2011; 30:2373-87. [PMID: 21552206 PMCID: PMC3116279 DOI: 10.1038/emboj.2011.144] [Citation(s) in RCA: 121] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Accepted: 04/13/2011] [Indexed: 01/31/2023] Open
Abstract
Gurdon and collaborators report reversible X chromosome inactivation in epiblast stem cells (EpiSCs) that seems to be determined by macroH2A1 deposition. These findings are of rather general interest as they highlight the epigenetic state of repressed loci as determinant for reprogramming efficiency. How various layers of epigenetic repression restrict somatic cell nuclear reprogramming is poorly understood. The transfer of mammalian somatic cell nuclei into Xenopus oocytes induces transcriptional reprogramming of previously repressed genes. Here, we address the mechanisms that restrict reprogramming following nuclear transfer by assessing the stability of the inactive X chromosome (Xi) in different stages of inactivation. We find that the Xi of mouse post-implantation-derived epiblast stem cells (EpiSCs) can be reversed by nuclear transfer, while the Xi of differentiated or extraembryonic cells is irreversible by nuclear transfer to oocytes. After nuclear transfer, Xist RNA is lost from chromatin of the Xi. Most epigenetic marks such as DNA methylation and Polycomb-deposited H3K27me3 do not explain the differences between reversible and irreversible Xi. Resistance to reprogramming is associated with incorporation of the histone variant macroH2A, which is retained on the Xi of differentiated cells, but absent from the Xi of EpiSCs. Our results uncover the decreased stability of the Xi in EpiSCs, and highlight the importance of combinatorial epigenetic repression involving macroH2A in restricting transcriptional reprogramming by oocytes.
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Affiliation(s)
- Vincent Pasque
- Wellcome Trust Cancer Research UK Gurdon Institute, Cambridge, UK.
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