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Ogaki Y, Fukuma M, Shimizu N. Repeat induces not only gene silencing, but also gene activation in mammalian cells. PLoS One 2020; 15:e0235127. [PMID: 32579599 PMCID: PMC7313748 DOI: 10.1371/journal.pone.0235127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 06/08/2020] [Indexed: 11/19/2022] Open
Abstract
Repeat-induced gene silencing (RIGS) establishes the centromere structure, prevents the spread of transposons and silences transgenes, thereby limiting recombinant protein production. We previously isolated a sequence (B-3-31) that alleviates RIGS from the human genome. Here, we developed an assay system for evaluating the influence of repeat sequences on gene expression, based on in vitro ligation followed by our original gene amplification technology in animal cells. Using this assay, we found that the repeat of B-3-31, three core sequences of replication initiation regions (G5, C12, and D8) and two matrix attachment regions (AR1 and 32–3), activated the co-amplified plasmid-encoded d2EGFP gene in both human and hamster cell lines. This upregulation effect persisted for up to 82 days, which was confirmed to be repeat-induced, and was thus designated as a repeat-induced gene activation (RIGA). In clear contrast, the repeat of three bacterial sequences (lambda-phage, Amp, and ColE1) and three human retroposon sequences (Alu, 5’-untranslated region, and ORF1 of a long interspersed nuclear element) suppressed gene expression, thus reflecting RIGS. RIGS was CpG-independent. We suggest that RIGA might be associated with replication initiation. The discovery of RIGS and RIGA has implications for the repeat in mammalian genome, as well as practical value in recombinant production.
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Affiliation(s)
- Yusuke Ogaki
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Miki Fukuma
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Noriaki Shimizu
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
- * E-mail:
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2
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Asoshina M, Myo G, Tada N, Tajino K, Shimizu N. Targeted amplification of a sequence of interest in artificial chromosome in mammalian cells. Nucleic Acids Res 2019; 47:5998-6006. [PMID: 31062017 PMCID: PMC6582328 DOI: 10.1093/nar/gkz343] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 04/08/2019] [Accepted: 05/01/2019] [Indexed: 12/14/2022] Open
Abstract
A plasmid with a replication initiation region (IR) and a matrix attachment region (MAR) initiates gene amplification in mammalian cells at a random chromosomal location. A mouse artificial chromosome (MAC) vector can stably carry a large genomic region. In this study we combined these two technologies with the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated nuclease (Cas)9 strategy to achieve targeted amplification of a sequence of interest. We previously showed that the IR/MAR plasmid was amplified up to the extrachromosomal tandem repeat; here we demonstrate that cleavage of these tandem plasmids and MAC by Cas9 facilitates homologous recombination between them. The plasmid array on the MAC could be further extended to form a ladder structure with high gene expression by a breakage–fusion–bridge cycle involving breakage at mouse major satellites. Amplification of genes on the MAC has the advantage that the MAC can be transferred between cells. We visualized the MAC in live cells by amplifying the lactose operator array on the MAC in cells expressing lactose repressor-green fluorescent protein fusion protein. This targeted amplification strategy is in theory be applicable to any sequence at any chromosomal site, and provides a novel tool for animal cell technology.
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Affiliation(s)
- Manami Asoshina
- Graduate School of Biosphere Science, Hiroshima University, Higashi-hiroshima, Hiroshima 739-8521, Japan
| | - Genki Myo
- Graduate School of Biosphere Science, Hiroshima University, Higashi-hiroshima, Hiroshima 739-8521, Japan
| | - Natsuko Tada
- Chromocenter Inc., Yonago, Tottori 683-0823, Japan
| | - Koji Tajino
- Chromocenter Inc., Yonago, Tottori 683-0823, Japan
| | - Noriaki Shimizu
- Graduate School of Biosphere Science, Hiroshima University, Higashi-hiroshima, Hiroshima 739-8521, Japan
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3
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HP1 cooperates with CAF-1 to compact heterochromatic transgene repeats in mammalian cells. Sci Rep 2018; 8:14141. [PMID: 30237539 PMCID: PMC6147918 DOI: 10.1038/s41598-018-32381-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 09/04/2018] [Indexed: 11/19/2022] Open
Abstract
The nuclear organization of tightly condensed heterochromatin plays important roles in regulating gene transcription and genome integrity. Heterochromatic domains are usually present at chromosomal regions containing a large array of repeated DNA sequences. We previously showed that integration of a 1,000-copy tandem array of an inducible reporter gene into the genome of mammalian cells induces the formation of a highly compact heterochromatic domain enriched in heterochromatin protein 1 (HP1). It remains to be determined how these DNA repeats are packaged into a heterochromatic form and are silenced. Here, we show that HP1-mediated transgene condensation and silencing require the interaction with PxVxL motif-containing proteins. The chromatin assembly factor 1 (CAF-1) complex concentrates at the transgenic locus through the interaction of its PxVxL motif-containing p150 subunit with HP1. Knockdown of p150 relieves HP1-mediated transgene compaction and repression. When targeted to the transgenic locus, p150 mutants defective in binding HP1 cause transgene decondensation and activation. Taken together, these results suggest that HP1 cooperates with CAF-1 to compact transgene repeats. This study provides important insight into how heterochromatin is maintained at chromosomal regions with abundant DNA repeats.
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Zhang Y, An J, Yang G, Zhang X, Xie Y, Chen L, Feng Y. Structure features of GH10 xylanase from Caldicellulosiruptor bescii: implication for its thermophilic adaption and substrate binding preference. Acta Biochim Biophys Sin (Shanghai) 2016; 48:948-957. [PMID: 27563004 DOI: 10.1093/abbs/gmw086] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 07/27/2016] [Indexed: 12/11/2022] Open
Abstract
Caldicellulosiruptor bescii is the most thermophilic cellulolytic species of organisms known to date. In our previous study, GH10 xylanase CbXyn10B from C. bescii displayed outstanding hydrolytic activity toward various xylans at high temperatures. To understand the structural basis for this protein's catalysis and thermostability, we solved the crystal structures of CbXyn10B and its complexes with xylooligosaccharides. These structural models were used to guide comparison with its mesophilic counterpart PbXyn10B. A distinctive structural feature is that thermophilic CbXyn10B presents a relatively stable interaction between the extended loops L7 and L8 in the catalytic cleft by an extensive hydrogen bonding network, which is mediated by Lys306, Arg314 and three well-ordered water molecules. Moreover, a unique aromatic cluster consisting of Try17, Phe20, Phe21, and Phe337 may enhance the interaction between the N- and C- terminus. Targeted mutagenesis demonstrated that these interactions substantially contribute to enzyme stabilization, as indicated by a considerable decrease in the melting temperature (Tm) of CbXyn10B by substituting critical residues with Ala. Therefore, it was shown that not only the aromatic interaction connecting protein termini but also the extensive hydrogen bonding network formed between surface loops could restrict the local structural flexibility and contribute significantly to the overall stability of enzymes. Furthermore, the xylooligosaccharides were found to tightly bind to the glycone subsites of xylanase, indicating higher affinities at these subsites and reflecting its substrate binding preference. Our results suggest that CbXyn10B is stabilized with distinct rigidity at the catalytic cleft as well as the terminal regions, which provides insights into the evolutionary strategy for accommodating the functional needs of GH10 enzymes to high temperature.
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Affiliation(s)
- Yong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jiao An
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Guangyu Yang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaofei Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuan Xie
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Liuqing Chen
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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Mitsuda SH, Shimizu N. Epigenetic Repeat-Induced Gene Silencing in the Chromosomal and Extrachromosomal Contexts in Human Cells. PLoS One 2016; 11:e0161288. [PMID: 27525955 PMCID: PMC4985131 DOI: 10.1371/journal.pone.0161288] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 08/02/2016] [Indexed: 02/06/2023] Open
Abstract
A plasmid bearing both a replication initiation region and a matrix attachment region is spontaneously amplified in transfected mammalian cells and generates plasmid repeats in the extrachromosomal double minutes (DMs) or the chromosomal homogeneously staining region (HSR). Generally, the repeat sequences are subject to repeat-induced gene silencing, the mechanism of which remains to be elucidated. Previous research showed that gene expression from the same plasmid repeat was higher from repeats located at DMs than at the HSR, which may reflect the extrachromosomal environment of the DMs. In the current study, plasmid repeats in both DMs and HSR were associated with repressive histone modifications (H3K9me3, H3K9me2), and the levels of repressive chromatin markers were higher in HSR than in DMs. Inactive chromatin is known to spread to neighboring regions in chromosome arm. Here, we found that such spreading also occurs in extrachromosomal DMs. Higher levels of active histone modifications (H3K9Ac, H3K4me3, and H3K79me2) were detected at plasmid repeats in DMs than in HSR. The level of DNA CpG methylation was generally low in both DMs and HSR; however, there were some hypermethylated copies within the population of repeated sequences, and the frequency of such copies was higher in DMs than in HSR. Together, these data suggest a “DNA methylation-core and chromatin-spread” model for repeat-induced gene silencing. The unique histone modifications at the extrachromosomal context are discussed with regard to the model.
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Affiliation(s)
- Sho-Hei Mitsuda
- Graduate School of Biosphere Science, Hiroshima University, Higashi-hiroshima, Hiroshima, 739-8521, Japan
| | - Noriaki Shimizu
- Graduate School of Biosphere Science, Hiroshima University, Higashi-hiroshima, Hiroshima, 739-8521, Japan
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Fukuma M, Ganmyo Y, Miura O, Ohyama T, Shimizu N. Cloning and Characterization of a Human Genomic Sequence that Alleviates Repeat-Induced Gene Silencing. PLoS One 2016; 11:e0153338. [PMID: 27078685 PMCID: PMC4831671 DOI: 10.1371/journal.pone.0153338] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 03/28/2016] [Indexed: 01/06/2023] Open
Abstract
Plasmids bearing a mammalian replication initiation region (IR) and a nuclear matrix attachment region (MAR) are spontaneously amplified in transfected mammalian cells, and such amplification generates chromosomal homogeneously staining regions (HSRs) or extrachromosomal double minutes (DMs). This method provides a novel, efficient, and rapid way to establish cells that stably produce high levels of recombinant proteins. However, because IR/MAR plasmids are amplified as repeats, they are frequently targeted by repeat-induced gene silencing (RIGS), which silences a variety of repeated sequences in transgenes and the genome. To address this problem, we developed a novel screening system using the IR/MAR plasmid to isolate human genome sequences that alleviate RIGS. The screen identified a 3,271 bp sequence (B-3-31) that elevated transgene expression without affecting the amplification process. Neither non-B structure (i.e., the inverted repeats or bending) nor known epigenetic modifier elements such as MARs, insulators, UCOEs, or STARs could explain the anti-silencing activity of B-3-31. Instead, the activity was distributed throughout the entire B-3-31 sequence, which was extremely A/T-rich and CpG-poor. Because B-3-31 effectively and reproducibly alleviated RIGS of repeated genes, it could be used to increase recombinant protein production.
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Affiliation(s)
- Miki Fukuma
- Graduate School of Biosphere Science, Hiroshima University, Higashi-hiroshima, Hiroshima, Japan
| | - Yuto Ganmyo
- Graduate School of Biosphere Science, Hiroshima University, Higashi-hiroshima, Hiroshima, Japan
| | - Osamu Miura
- Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Takashi Ohyama
- Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Noriaki Shimizu
- Graduate School of Biosphere Science, Hiroshima University, Higashi-hiroshima, Hiroshima, Japan
- * E-mail:
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7
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Okada N, Shimizu N. Dissection of the beta-globin replication-initiation region reveals specific requirements for replicator elements during gene amplification. PLoS One 2013; 8:e77350. [PMID: 24124615 PMCID: PMC3790722 DOI: 10.1371/journal.pone.0077350] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 09/06/2013] [Indexed: 11/18/2022] Open
Abstract
Gene amplification plays a pivotal role in malignant transformation of human cells. A plasmid with both a mammalian replication-initiation region (IR)/origin/replicator and a nuclear matrix-attachment region (MAR) is spontaneously amplified in transfected cells by a mechanism that involves amplification at the extrachromosomal site, followed by amplification at the chromosomal arm, ultimately generating a long homogeneously staining region (HSR). Several observations suggest that replication initiation from IR sequences might mediate amplification. To test this idea, we previously dissected c-myc and DHFR IRs to identify the minimum sequence required to support amplification. In this study, we applied an improved analysis that discriminates between two amplification steps to the ß-globin RepP IR, which contains separate elements already known to be essential for initiation on the chromosome arm. The IR sequence was required at least for the extrachromosomal amplification step. In addition to the vector-encoded MAR, amplification also required an AT-rich region and a MAR-like element, consistent with the results regarding replicator activity on the chromosome. However, amplification did not require the AG-rich tract necessary for replicator activity, but instead required a novel sequence containing another AG-rich tract. The differential sequence requirement might be a consequence of extrachromosomal replication.
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Affiliation(s)
- Naoya Okada
- Graduate School of Biosphere Science, Hiroshima University, Higashi-hiroshima, Hiroshima, Japan
| | - Noriaki Shimizu
- Graduate School of Biosphere Science, Hiroshima University, Higashi-hiroshima, Hiroshima, Japan
- * E-mail:
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8
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Zhou X, Jin X, Sun G, Wu X. A Sensitive and Selective Fluorescent Probe for Cysteine Based on a New Response-Assisted Electrostatic Attraction Strategy: The Role of Spatial Charge Configuration. Chemistry 2013; 19:7817-24. [DOI: 10.1002/chem.201300078] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 03/11/2013] [Indexed: 12/22/2022]
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9
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Efficient recombinant production in mammalian cells using a novel IR/MAR gene amplification method. PLoS One 2012; 7:e41787. [PMID: 22844523 PMCID: PMC3402416 DOI: 10.1371/journal.pone.0041787] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 06/25/2012] [Indexed: 01/21/2023] Open
Abstract
We previously found that plasmids bearing a mammalian replication initiation region (IR) and a nuclear matrix attachment region (MAR) efficiently initiate gene amplification and spontaneously increase their copy numbers in animal cells. In this study, this novel method was applied to the establishment of cells with high recombinant antibody production. The level of recombinant antibody expression was tightly correlated with the efficiency of plasmid amplification and the cytogenetic appearance of the amplified genes, and was strongly dependent on cell type. By using a widely used cell line for industrial protein production, CHO DG44, clones expressing very high levels of antibody were easily obtained. High-producer clones stably expressed the antibody over several months without eliciting changes in both the protein expression level and the cytogenetic appearance of the amplified genes. The integrity and reactivity of the protein produced by this method was fine. In serum-free suspension culture, the specific protein production rate in high-density cultures was 29.4 pg/cell/day. In conclusion, the IR/MAR gene amplification method is a novel and efficient platform for recombinant antibody production in mammalian cells, which rapidly and easily enables the establishment of stable high-producer cell clone.
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Shimizu N. Molecular mechanisms of the origin of micronuclei from extrachromosomal elements. Mutagenesis 2011; 26:119-23. [PMID: 21164192 DOI: 10.1093/mutage/geq053] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In addition to micronuclei that are formed from chromosomal material (the chromosome-type micronuclei), there are also micronuclei formed from extrachromosomal elements [the double minute (DM)-type micronuclei]. These two types of micronuclei are distinct entities, which exist and arise independently in a cell. A DM is a large extrachromosomal element that consists of amplified genes that are commonly seen in cancer cells; the aggregates of DMs can eventually be expressed as DM-type micronuclei. The question of how the DM-type micronuclei arise was answered by uncovering the quite unique intracellular behaviour of DMs during the cell cycle progression. This behaviour of DMs appeared to be common among the broad spectrum of extrachromosomal elements of endogenous, exogenous or artificial origin. Therefore, studying the biology of DM-type micronuclei will enable us to understand how these extrachromosomal structures may be retained within a cell or expelled from the nucleus and eliminated from the cell. This knowledge could also be used for the treatment of cancers and the development of a new mammalian host-vector system.
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Affiliation(s)
- Noriaki Shimizu
- Graduate School of Biosphere Science, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima 739-8521 Japan.
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11
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Harada S, Sekiguchi N, Shimizu N. Amplification of a plasmid bearing a mammalian replication initiation region in chromosomal and extrachromosomal contexts. Nucleic Acids Res 2010; 39:958-69. [PMID: 20929873 PMCID: PMC3035466 DOI: 10.1093/nar/gkq882] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Amplified genes in cancer cells reside on extrachromosomal double minutes (DMs) or chromosomal homogeneously staining regions (HSRs). We used a plasmid bearing a mammalian replication initiation region to model gene amplification. Recombination junctions in the amplified region were comprehensively identified and sequenced. The junctions consisted of truncated direct repeats (type 1) or inverted repeats (type 2) with or without spacing. All of these junctions were frequently detected in HSRs, whereas there were few type 1 or a unique type 2 flanked by a short inverted repeat in DMs. The junction sequences suggested a model in which the inverted repeats were generated by sister chromatid fusion. We were consistently able to detect anaphase chromatin bridges connected by the plasmid repeat, which were severed in the middle during mitosis. De novo HSR generation was observed in live cells, and each HSR was lengthened more rapidly than expected from the classical breakage/fusion/bridge model. Importantly, we found massive DNA synthesis at the broken anaphase bridge during the G1 to S phase, which could explain the rapid lengthening of the HSR. This mechanism may not operate in acentric DMs, where most of the junctions are eliminated and only those junctions produced through stable intermediates remain.
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Affiliation(s)
- Seiyu Harada
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima 739-8521, Japan
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12
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Joffe B, Leonhardt H, Solovei I. Differentiation and large scale spatial organization of the genome. Curr Opin Genet Dev 2010; 20:562-9. [PMID: 20561778 DOI: 10.1016/j.gde.2010.05.009] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Revised: 05/18/2010] [Accepted: 05/24/2010] [Indexed: 12/22/2022]
Abstract
The spatial organization of the genome plays an important role in the regulation of nuclear functions and undergoes large scale changes during differentiation. These changes in the nuclear distribution of chromatin are, in a complex way, related to transcriptional status and epigenetic modifications. Recent studies emphasize the roles that gene promoters and alterations in replication timing play in the spatial reorganization of chromatin during cell differentiation. Changes in the association of chromatin regions with the nuclear lamina also emerge as a significant factor of transcriptional regulation. New results suggest that the spatial organization of chromatin in embryonic stem cells may be important for maintenance of the pluripotent state, whereas the nuclear architecture of differentiated cells facilitates formation of transcriptionally active zones with shared transcription and splicing machinery.
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Affiliation(s)
- Boris Joffe
- Biocenter, Department of Biology II, Ludwig Maximilian University of Munich, 82152, Planegg-Martinsried, Germany
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Harada S, Uchida M, Shimizu N. Episomal high copy number maintenance of hairpin-capped DNA bearing a replication initiation region in human cells. J Biol Chem 2009; 284:24320-7. [PMID: 19617622 DOI: 10.1074/jbc.m109.008128] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
We previously found that a plasmid bearing a replication initiation region efficiently initiates gene amplification in mammalian cells and that it generates extrachromosomal double minutes and/or chromosomal homogeneously staining regions. During analysis of the underlying mechanism, we serendipitously found that hairpin-capped linear DNA was stably maintained as numerous extrachromosomal tiny episomes for more than a few months in a human cancer cell line. Generation of such episomes depended on the presence of the replication initiation region in the original plasmid. Despite extrachromosomal maintenance, episomal gene expression was epigenetically suppressed. The Southern blot analysis of the DNA of cloned cells revealed that the region around the hairpin end was diversified between the clones. Furthermore, the bisulfite-modified PCR and the sequencing analyses revealed that the palindrome sequence that derived from the original hairpin end or its end-resected structure were well preserved during clonal long term growth. From these data, we propose a model that explains the formation and maintenance of these episomes, in which replication of the hairpin-capped DNA and cruciform formation and its resolution play central roles. Our findings may be relevant for the dissection of mammalian replicator sequences.
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Affiliation(s)
- Seiyu Harada
- Graduate School of Biosphere Science, Hiroshima University, Higashi-hiroshima 739-8521, Japan
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Rose A, Lorenzen S, Goede A, Gruening B, Hildebrand PW. RHYTHM--a server to predict the orientation of transmembrane helices in channels and membrane-coils. Nucleic Acids Res 2009; 37:W575-80. [PMID: 19465378 PMCID: PMC2703963 DOI: 10.1093/nar/gkp418] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
RHYTHM is a web server that predicts buried versus exposed residues of helical membrane proteins. Starting from a given protein sequence, secondary and tertiary structure information is calculated by RHYTHM within only a few seconds. The prediction applies structural information from a growing data base of precalculated packing files and evolutionary information from sequence patterns conserved in a representative dataset of membrane proteins ('Pfam-domains'). The program uses two types of position specific matrices to account for the different geometries of packing in channels and transporters ('channels') or other membrane proteins ('membrane-coils'). The output provides information on the secondary structure and topology of the protein and specifically on the contact type of each residue and its conservation. This information can be downloaded as a graphical file for illustration, a text file for analysis and statistics and a PyMOL file for modeling purposes. The server can be freely accessed at: URL: http://proteinformatics.de/rhythm.
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Affiliation(s)
- Alexander Rose
- Institute for Medical Physics and Biophysics, Charité, University Medicine Berlin, Ziegelstrasse 5-9, 10098 Berlin, Germany
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