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Journal articles on the topic 'Scaffold matrix attachment region'

Author: Grafiati

Published: 4 June 2021

Last updated: 6 February 2022

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1

Martens, Joost H. A., Matty Verlaan, Eric Kalkhoven, Josephine C. Dorsman, and Alt Zantema. "Scaffold/Matrix Attachment Region Elements Interact with a p300-Scaffold Attachment Factor A Complex and Are Bound by Acetylated Nucleosomes." Molecular and Cellular Biology 22, no. 8 (2002): 2598–606. http://dx.doi.org/10.1128/mcb.22.8.2598-2606.2002.

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ABSTRACT The transcriptional coactivator p300 regulates transcription by binding to proteins involved in transcription and by acetylating histones and other proteins. These transcriptional effects are mainly at promoter and enhancer elements. Regulation of transcription also occurs through scaffold/matrix attachment regions (S/MARs), the chromatin regions that bind the nuclear matrix. Here we show that p300 binds to the S/MAR binding protein scaffold attachment factor A (SAF-A), a major constituent of the nuclear matrix. Using chromatin immunoprecipitations, we established that both p300 and S

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2

Fiorini, A., F. de S. Gouveia, and M. A. Fernandez. "Scaffold/matrix attachment regions and intrinsic DNA curvature." Biochemistry (Moscow) 71, no. 5 (2006): 481–88. http://dx.doi.org/10.1134/s0006297906050038.

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3

Iarovaia, O., R. Hancock, M. Lagarkova, R. Miassod, and S. V. Razin. "Mapping of genomic DNA loop organization in a 500-kilobase region of the Drosophila X chromosome by the topoisomerase II-mediated DNA loop excision protocol." Molecular and Cellular Biology 16, no. 1 (1996): 302–8. http://dx.doi.org/10.1128/mcb.16.1.302.

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The recently developed procedure of chromosomal DNA loop excision by topoisomerase II-mediated DNA cleavage at matrix attachment sites (S. V. Razin, R. Hancock, O. Iarovaia, O. Westergaard, I. Gromova, and G. P. Georgiev, Cold Spring Harbor Symp. Quant. Biol. 58:25-35, 1993; I. I. Gromova, B. Thompsen, and S. V. Razin, Proc. Natl. Acad. Sci. USA 92:102-106, 1995) has been employed for mapping the DNA loop anchorage sites in a 500-kb region of the Drosophila melanogaster X chromosome. Eleven anchorage sites delimiting 10 DNA loops ranging in size from 20 to 90 kb were found within this region.

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4

Sumer, H. "A Rapid Method of Genomic Array Analysis of Scaffold/Matrix Attachment Regions (S/MARs) Identifies a 2.5-Mb Region of Enhanced Scaffold/Matrix Attachment at a Human Neocentromere." Genome Research 13, no. 7 (2003): 1737–43. http://dx.doi.org/10.1101/gr.1095903.

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5

Kipp, Michael, Frank Göhring, Thorsten Ostendorp, et al. "SAF-Box, a Conserved Protein Domain That Specifically Recognizes Scaffold Attachment Region DNA." Molecular and Cellular Biology 20, no. 20 (2000): 7480–89. http://dx.doi.org/10.1128/mcb.20.20.7480-7489.2000.

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ABSTRACT SARs (scaffold attachment regions) are candidate DNA elements for partitioning eukaryotic genomes into independent chromatin loops by attaching DNA to proteins of a nuclear scaffold or matrix. The interaction of SARs with the nuclear scaffold is evolutionarily conserved and appears to be due to specific DNA binding proteins that recognize SARs by a mechanism not yet understood. We describe a novel, evolutionarily conserved protein domain that specifically binds to SARs but is not related to SAR binding motifs of other proteins. This domain was first identified in human scaffold attach

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6

von Kries, Jens P., Hartmut Buhrmester, and Wolf H. Strätling. "A matrix/scaffold attachment region binding protein: Identification, purification, and mode of binding." Cell 64, no. 1 (1991): 123–35. http://dx.doi.org/10.1016/0092-8674(91)90214-j.

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7

Rudd, Stephen, Matthias Frisch, Korbinian Grote, Blake C. Meyers, Klaus Mayer, and Thomas Werner. "Genome-Wide in Silico Mapping of Scaffold/Matrix Attachment Regions in Arabidopsis Suggests Correlation of Intragenic Scaffold/Matrix Attachment Regions with Gene Expression." Plant Physiology 135, no. 2 (2004): 715–22. http://dx.doi.org/10.1104/pp.103.037861.

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8

Chavali, Pavithra Lakshminarasimhan, Keiko Funa, and Sreenivas Chavali. "Cis -regulation of microRNA expression by scaffold/matrix-attachment regions." Nucleic Acids Research 39, no. 16 (2011): 6908–18. http://dx.doi.org/10.1093/nar/gkr303.

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9

Heng, H. H. Q. "Chromatin loops are selectively anchored using scaffold/matrix-attachment regions." Journal of Cell Science 117, no. 7 (2004): 999–1008. http://dx.doi.org/10.1242/jcs.00976.

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10

Benham, Craig, Terumi Kohwi-Shigematsu, and Jürgen Bode. "Stress-induced duplex DNA destabilization in scaffold/matrix attachment regions." Journal of Molecular Biology 274, no. 2 (1997): 181–96. http://dx.doi.org/10.1006/jmbi.1997.1385.

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11

van Drunen, C. "A bipartite sequence element associated with matrix/scaffold attachment regions." Nucleic Acids Research 27, no. 14 (1999): 2924–30. http://dx.doi.org/10.1093/nar/27.14.2924.

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12

Amati, B., and S. M. Gasser. "Drosophila scaffold-attached regions bind nuclear scaffolds and can function as ARS elements in both budding and fission yeasts." Molecular and Cellular Biology 10, no. 10 (1990): 5442–54. http://dx.doi.org/10.1128/mcb.10.10.5442.

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Histone-depleted nuclei maintain sequence-specific interactions with genomic DNA at sites known as scaffold attachment regions (SARs) or matrix attachment regions. We have previously shown that in Saccharomyces cerevisiae, autonomously replicating sequence elements bind the nuclear scaffold. Here, we extend these observations to the fission yeast Schizosaccharomyces pombe. In addition, we show that four SARs previously mapped in the genomic DNA of Drosophila melanogaster bind in vitro to nuclear scaffolds from both yeast species. In view of these results, we have assayed the ability of the Dro

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13

Amati, B., and S. M. Gasser. "Drosophila scaffold-attached regions bind nuclear scaffolds and can function as ARS elements in both budding and fission yeasts." Molecular and Cellular Biology 10, no. 10 (1990): 5442–54. http://dx.doi.org/10.1128/mcb.10.10.5442-5454.1990.

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Histone-depleted nuclei maintain sequence-specific interactions with genomic DNA at sites known as scaffold attachment regions (SARs) or matrix attachment regions. We have previously shown that in Saccharomyces cerevisiae, autonomously replicating sequence elements bind the nuclear scaffold. Here, we extend these observations to the fission yeast Schizosaccharomyces pombe. In addition, we show that four SARs previously mapped in the genomic DNA of Drosophila melanogaster bind in vitro to nuclear scaffolds from both yeast species. In view of these results, we have assayed the ability of the Dro

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14

D'UGO, EMILIO, ROBERTO BRUNI, CLAUDIO ARGENTINI, ROBERTO GIUSEPPETTI, and MARIA RAPICETTA. "Identification of Scaffold/Matrix Attachment Region in Recurrent Site of Woodchuck Hepatitis Virus Integration." DNA and Cell Biology 17, no. 6 (1998): 519–27. http://dx.doi.org/10.1089/dna.1998.17.519.

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15

Nabirochkin, Serguei, Marina Ossokina, and Thierry Heidmann. "A Nuclear Matrix/Scaffold Attachment Region Co-localizes with the Gypsy Retrotransposon Insulator Sequence." Journal of Biological Chemistry 273, no. 4 (1998): 2473–79. http://dx.doi.org/10.1074/jbc.273.4.2473.

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16

Kisseljova, Natalia P., Petr Dmitriev, Alexey Katargin, et al. "DNA polymorphism and epigenetic marks modulate the affinity of a scaffold/matrix attachment region to the nuclear matrix." European Journal of Human Genetics 22, no. 9 (2014): 1117–23. http://dx.doi.org/10.1038/ejhg.2013.306.

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17

Tsutsui, K., K. Tsutsui, S. Okada, et al. "Identification and characterization of a nuclear scaffold protein that binds the matrix attachment region DNA." Journal of Biological Chemistry 268, no. 17 (1993): 12886–94. http://dx.doi.org/10.1016/s0021-9258(18)31469-8.

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18

Bode, Jürgen, Silke Winkelmann, Sandra Götze, et al. "Correlations between Scaffold/Matrix Attachment Region (S/MAR) Binding Activity and DNA Duplex Destabilization Energy." Journal of Molecular Biology 358, no. 2 (2006): 597–613. http://dx.doi.org/10.1016/j.jmb.2005.11.073.

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19

Frisch, M., K. Frech, A. Klingenhoff, K. Cartharius, I. Liebich, and T. Werner. "In Silico Prediction of Scaffold/Matrix Attachment Regions in Large Genomic Sequences." Genome Research 12, no. 2 (2003): 349–54. http://dx.doi.org/10.1101/gr.206602.

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20

Frisch, M. "In Silico Prediction of Scaffold/Matrix Attachment Regions in Large Genomic Sequences." Genome Research 12, no. 2 (2002): 349–54. http://dx.doi.org/10.1101/gr.206602.

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21

Li, Ming, and Zhong-can Ou-Yang. "Predicting the function of eukaryotic scaffold/matrix attachment regions via DNA mechanics." Journal of Physics: Condensed Matter 17, no. 31 (2005): S2853—S2860. http://dx.doi.org/10.1088/0953-8984/17/31/011.

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22

Wong, S., D. Tracey-White, O. Argyros, and R. Harbottle. "761 Genetic Modification of Cancer Cells Using Non-viral Vectors Harbouring a Scaffold/Matrix Attachment Region." European Journal of Cancer 48 (July 2012): S180. http://dx.doi.org/10.1016/s0959-8049(12)71397-7.

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23

Craig, J. M., S. Boyle, P. Perry, and W. A. Bickmore. "Scaffold attachments within the human genome." Journal of Cell Science 110, no. 21 (1997): 2673–82. http://dx.doi.org/10.1242/jcs.110.21.2673.

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It is generally agreed that, above the level of the 30 nm fibre, eukaryotic chromatin is constrained into loops, but there is disagreement about the nature of the substructure that serves to anchor loops and the DNA sequences that act as the attachment sites. This problem may stem from the very different methods that all purport to separate loop and attached DNAs. We have tested ideas about how the genome is arranged into loops by analysing the average loop size over different cytologically resolvable regions of human chromosomes using fluorescence in situ hybridisation with loop and attached

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24

Narwade, Nitin, Sonal Patel, Aftab Alam, Samit Chattopadhyay, Smriti Mittal, and Abhijeet Kulkarni. "Mapping of scaffold/matrix attachment regions in human genome: a data mining exercise." Nucleic Acids Research 47, no. 14 (2019): 7247–61. http://dx.doi.org/10.1093/nar/gkz562.

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AbstractScaffold/matrix attachment regions (S/MARs) are DNA elements that serve to compartmentalize the chromatin into structural and functional domains. These elements are involved in control of gene expression which governs the phenotype and also plays role in disease biology. Therefore, genome-wide understanding of these elements holds great therapeutic promise. Several attempts have been made toward identification of S/MARs in genomes of various organisms including human. However, a comprehensive genome-wide map of human S/MARs is yet not available. Toward this objective, ChIP-Seq data of

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25

Argyros, O., S. P. Wong, M. Niceta, et al. "Persistent episomal transgene expression in liver following delivery of a scaffold/matrix attachment region containing non-viral vector." Gene Therapy 15, no. 24 (2008): 1593–605. http://dx.doi.org/10.1038/gt.2008.113.

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26

Tetko, Igor V., Georg Haberer, Stephen Rudd, Blake Meyers, Hans-Werner Mewes, and Klaus F. X. Mayer. "Spatiotemporal Expression Control Correlates with Intragenic Scaffold Matrix Attachment Regions (S/MARs) in Arabidopsis thaliana." PLoS Computational Biology 2, no. 3 (2006): e21. http://dx.doi.org/10.1371/journal.pcbi.0020021.

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27

Banerjee, Sulagna, Ohad Fisher, Anuradha Lohia, and Serge Ankri. "Entamoeba histolytica DNA methyltransferase (Ehmeth) is a nuclear matrix protein that binds EhMRS2, a DNA that includes a scaffold/matrix attachment region (S/MAR)." Molecular and Biochemical Parasitology 139, no. 1 (2005): 91–97. http://dx.doi.org/10.1016/j.molbiopara.2004.10.003.

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28

Dietz-Pfeilstetter, Antje, Nicola Arndt, and Ulrike Manske. "Effects of a petunia scaffold/matrix attachment region on copy number dependency and stability of transgene expression in Nicotiana tabacum." Transgenic Research 25, no. 2 (2016): 149–62. http://dx.doi.org/10.1007/s11248-015-9924-2.

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29

Tetko, Igor V., Georg Haberer, Stephen Rudd, Blake C. Meyers, Hans-Werner Mewes, and Klaus F. X. Mayer. "Correction: Spatiotemporal Expression Control Correlates with Intragenic Scaffold Matrix Attachment Regions (S/MARs) in Arabidopsis thaliana." PLoS Computational Biology 2, no. 6 (2006): e67. http://dx.doi.org/10.1371/journal.pcbi.0020067.

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30

Honda, Michiyo, Ryo Hariya, Morio Matsumoto, and Mamoru Aizawa. "Acceleration of Osteogenesis via Stimulation of Angiogenesis by Combination with Scaffold and Connective Tissue Growth Factor." Materials 12, no. 13 (2019): 2068. http://dx.doi.org/10.3390/ma12132068.

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In bone regeneration, there are some important cellular biological processes, such as mineralization, cell organization, and differentiation. In particular, vascularization into regenerative tissues is a key step for the survival of cells and tissues. In this study, to fabricate biomimetic-engineered bone, including vascular networks, we focused on connective tissue growth factor (CTGF), a multifunctional protein which could regulate the extracellular matrix remodeling. By combination with CTGF and hydroxyapatite (HAp) ceramics (2D) or apatite-fiber scaffold (AFS, 3D), we have fabricated bioac

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31

Pascuzzi, Pete E., Miguel A. Flores-Vergara, Tae-Jin Lee, et al. "In Vivo Mapping of Arabidopsis Scaffold/Matrix Attachment Regions Reveals Link to Nucleosome-Disfavoring Poly(dA:dT) Tracts." Plant Cell 26, no. 1 (2014): 102–20. http://dx.doi.org/10.1105/tpc.113.121194.

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32

Mohd Pilus, Nur Shazwani, Azrin Ahmad, and Nurul Yuziana Mohd Yusof. "Sequence Analysis of Scaffold/Matrix Attachment Regions (S/MARs) From Human Embryonic Kidney and Chinese Hamster Ovary Cells." OnLine Journal of Biological Sciences 18, no. 4 (2018): 387–400. http://dx.doi.org/10.3844/ojbsci.2018.387.400.

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33

Thompson, E. M., E. Christians, M. G. Stinnakre, and J. P. Renard. "Scaffold attachment regions stimulate HSP70.1 expression in mouse preimplantation embryos but not in differentiated tissues." Molecular and Cellular Biology 14, no. 7 (1994): 4694–703. http://dx.doi.org/10.1128/mcb.14.7.4694.

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Eukaryotic interphase chromatin is thought to be organized into topologically discrete, independent domains acting as units upon which differential patterns of gene expression are established. Sequences which attach chromatin to in vitro preparations of a nucleoprotein matrix (scaffold attachment regions [SARs]) may act as domain boundaries, but their role remains poorly defined compared with those of other elements such as locus control regions. We have produced mice homozygous for a transgene which is transcribed as early as the activation of the embryonic genome at the two-cell stage and wh

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34

Thompson, E. M., E. Christians, M. G. Stinnakre, and J. P. Renard. "Scaffold attachment regions stimulate HSP70.1 expression in mouse preimplantation embryos but not in differentiated tissues." Molecular and Cellular Biology 14, no. 7 (1994): 4694–703. http://dx.doi.org/10.1128/mcb.14.7.4694-4703.1994.

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Eukaryotic interphase chromatin is thought to be organized into topologically discrete, independent domains acting as units upon which differential patterns of gene expression are established. Sequences which attach chromatin to in vitro preparations of a nucleoprotein matrix (scaffold attachment regions [SARs]) may act as domain boundaries, but their role remains poorly defined compared with those of other elements such as locus control regions. We have produced mice homozygous for a transgene which is transcribed as early as the activation of the embryonic genome at the two-cell stage and wh

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35

Göhring, Frank, and Frank O. Fackelmayer. "The Scaffold/Matrix Attachment Region Binding Protein hnRNP-U (SAF-A) Is Directly Bound to Chromosomal DNAin Vivo: A Chemical Cross-Linking Study†." Biochemistry 36, no. 27 (1997): 8276–83. http://dx.doi.org/10.1021/bi970480f.

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36

Reyes, Jose C., Christian Muchardt, and Moshe Yaniv. "Components of the Human SWI/SNF Complex Are Enriched in Active Chromatin and Are Associated with the Nuclear Matrix." Journal of Cell Biology 137, no. 2 (1997): 263–74. http://dx.doi.org/10.1083/jcb.137.2.263.

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Biochemical and genetic evidence suggest that the SWI/SNF complex is involved in the remodeling of chromatin during gene activation. We have used antibodies specific against three human subunits of this complex to study its subnuclear localization, as well as its potential association with active chromatin and the nuclear skeleton. Immunofluorescence studies revealed a punctate nuclear labeling pattern that was excluded from the nucleoli and from regions of condensed chromatin. Dual labeling failed to reveal significant colocalization of BRG1 or hBRM proteins with RNA polymerase II or with nuc

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37

Jenke, Andreas C. W., Andreas D. Wilhelm, Valerie Orth, Hans Joachim Lipps, Ulrike Protzer, and Stefan Wirth. "Long-Term Suppression of Hepatitis B Virus Replication by Short Hairpin RNA Expression Using the Scaffold/Matrix Attachment Region-Based Replicating Vector System pEPI-1." Antimicrobial Agents and Chemotherapy 52, no. 7 (2008): 2355–59. http://dx.doi.org/10.1128/aac.00067-08.

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ABSTRACT Since the emergence of viral resistance of hepatitis B virus (HBV) during treatment is becoming an important issue even with newer drugs, there is a need for alternative treatment options such as, for example, RNA interference (RNAi) technology. While short-term suppression of HBV replication is easily achieved with small interfering RNA oligonucleotides, this is not the case for long-term suppression due to the lack of an optimal vector system. Based on the nonviral scaffold/matrix attachment region (S/MAR)-based vector system pEPI-1, which is free of common side effects and is stabl

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38

Scott, Kristin C., Aaron D. Taubman, and Pamela K. Geyer. "Enhancer Blocking by the Drosophila gypsy Insulator Depends Upon Insulator Anatomy and Enhancer Strength." Genetics 153, no. 2 (1999): 787–98. http://dx.doi.org/10.1093/genetics/153.2.787.

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Abstract Insulators are specialized DNA sequences that prevent enhancer-activated transcription only when interposed between an enhancer and its target promoter. The Drosophila gypsy retrotransposon contains an insulator composed of 12 degenerate binding sites for the Suppressor of Hairy-wing [Su(Hw)] protein that are separated by AT-rich DNA possessing sequence motifs common to matrix/scaffold attachment regions (MARs/SARs). To further understand mechanisms of insulator function, the parameters required for the gypsy insulator to prevent enhancer-activated transcription were examined. Synthet

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Hibino, Yasuhide, Hiromitsu Ohzeki, Nobuhiko Sugano, and Koichi Hiraga. "Transcription Modulation by a Rat Nuclear Scaffold Protein, P130, and a Rat Highly Repetitive DNA Component or Various Types of Animal and Plant Matrix or Scaffold Attachment Regions." Biochemical and Biophysical Research Communications 279, no. 1 (2000): 282–87. http://dx.doi.org/10.1006/bbrc.2000.3938.

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40

Chang, Ming, Ruijie Liu, Qingzhe Jin, Yuanfa Liu, and Xingguo Wang. "Scaffold/matrix attachment regions from CHO cell chromosome enhanced the stable transfection efficiency and the expression of transgene in CHO cells." Biotechnology and Applied Biochemistry 61, no. 5 (2014): 510–16. http://dx.doi.org/10.1002/bab.1204.

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41

Toualbi, Lyes, Maria Toms, and Mariya Moosajee. "The Landscape of Non-Viral Gene Augmentation Strategies for Inherited Retinal Diseases." International Journal of Molecular Sciences 22, no. 5 (2021): 2318. http://dx.doi.org/10.3390/ijms22052318.

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Inherited retinal diseases (IRDs) are a heterogeneous group of disorders causing progressive loss of vision, affecting approximately one in 1000 people worldwide. Gene augmentation therapy, which typically involves using adeno-associated viral vectors for delivery of healthy gene copies to affected tissues, has shown great promise as a strategy for the treatment of IRDs. However, the use of viruses is associated with several limitations, including harmful immune responses, genome integration, and limited gene carrying capacity. Here, we review the advances in non-viral gene augmentation strate

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42

Tan, Joseph-Anthony T., Jing Song, Yuan Chen, and Linda K. Durrin. "Phosphorylation-Dependent Interaction of SATB1 and PIAS1 Directs SUMO-Regulated Caspase Cleavage of SATB1." Molecular and Cellular Biology 30, no. 11 (2010): 2823–36. http://dx.doi.org/10.1128/mcb.01603-09.

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ABSTRACT Special AT-rich sequence-binding protein 1 (SATB1) is a tissue-restricted genome organizer that provides a key link between DNA loop organization, chromatin modification/remodeling, and transcription factor association at matrix attachment regions (MARs). The SUMO E3 ligase PIAS1 enhances SUMO conjugation to SATB1 lysine-744, and this modification regulates caspase-6 mediated cleavage of SATB1 at promyelocytic leukemia nuclear bodies (PML NBs). Since this regulated caspase cleavage occurs on only a subset of SATB1, and the products are relatively stable, proteolysis likely mediates ce

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MacDonald, William A., Saqib S. Sachani, Carlee R. White, and Mellissa R. W. Mann. "A role for chromatin topology in imprinted domain regulation." Biochemistry and Cell Biology 94, no. 1 (2016): 43–55. http://dx.doi.org/10.1139/bcb-2015-0032.

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Recently, many advancements in genome-wide chromatin topology and nuclear architecture have unveiled the complex and hidden world of the nucleus, where chromatin is organized into discrete neighbourhoods with coordinated gene expression. This includes the active and inactive X chromosomes. Using X chromosome inactivation as a working model, we utilized publicly available datasets together with a literature review to gain insight into topologically associated domains, lamin-associated domains, nucleolar-associating domains, scaffold/matrix attachment regions, and nucleoporin-associated chromati

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Haviernik, Peter, Stephen M. Festin, Rene Opavsky, et al. "Linkage on chromosome 10 of several murine retroviral integration loci associated with leukaemia." Journal of General Virology 83, no. 4 (2002): 819–27. http://dx.doi.org/10.1099/0022-1317-83-4-819.

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Mml loci have been identified as provirus integration sites among a subset of monocytic tumours induced by murine leukaemia virus (MuLV) infection of BALB/c and DBA/2 mice. These myeloid leukaemias contain a retrovirus integrated on chromosome 10 in proximity to the c-myb locus; however, c-myb expression was not altered. Detailed physical mapping enabled placement of the retroviral integration sites ∼25 kb (Mml1), ∼51 kb (Mml2), and ∼70 kb (Mml3) upstream of the c-myb locus. Furthermore, the Fti1 (fit-1) locus, a common integration site in feline leukaemia virus-induced T cell lymphomas, was m

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45

Fallaux, F. J., R. C. Hoeben, S. J. Cramer, et al. "The human clotting factor VIII cDNA contains an autonomously replicating sequence consensus- and matrix attachment region-like sequence that binds a nuclear factor, represses heterologous gene expression, and mediates the transcriptional effects of sodium butyrate." Molecular and Cellular Biology 16, no. 8 (1996): 4264–72. http://dx.doi.org/10.1128/mcb.16.8.4264.

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Expression of the human blood-clotting factor VIII (FVIII) cDNA is hampered by the presence of sequences located in the coding region that repress transcription. We have previously identified a 305-bp fragment within the FVIII cDNA that is involved in the repression (R.C. Hoeben, F.J. Fallaux, S.J. Cramer, D.J.M. van den Wollenberg, H. van Ormondt, E. Briet, and A.J. van der Eb, Blood 85:2447-2454, 1995). Here, we show that this 305-bp region of FVIII cDNA contains sequences that resemble the yeast (Saccharomyces cerevisiae) autonomously replicating sequence consensus. Two of these DNA element

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46

Milligan, Erin D., Stephen J. Langer, Travis S. Hughes, et al. "259. Plasmid DNA Encoding the Anti-Inflammatory Cytokine Gene, Interleukin-10 (IL-10) for Chronic Pain Control: Taking Advantage of Nuclear Scaffold/Matrix Attachment Regions." Molecular Therapy 13 (2006): S99. http://dx.doi.org/10.1016/j.ymthe.2006.08.286.

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47

Szyman, Kinga, Bartek Wilczyński, and Michał Dąbrowski. "K-mer Content Changes with Node Degree in Promoter–Enhancer Network of Mouse ES Cells." International Journal of Molecular Sciences 22, no. 15 (2021): 8067. http://dx.doi.org/10.3390/ijms22158067.

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Maps of Hi-C contacts between promoters and enhancers can be analyzed as networks, with cis-regulatory regions as nodes and their interactions as edges. We checked if in the published promoter–enhancer network of mouse embryonic stem (ES) cells the differences in the node type (promoter or enhancer) and the node degree (number of regions interacting with a given promoter or enhancer) are reflected by sequence composition or sequence similarity of the interacting nodes. We used counts of all k-mers (k = 4) to analyze the sequence composition and the Euclidean distance between the k-mer count ve

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48

Goetze, Sandra, Alexandra Baer, Silke Winkelmann, et al. "Performance of Genomic Bordering Elements at Predefined Genomic Loci." Molecular and Cellular Biology 25, no. 6 (2005): 2260–72. http://dx.doi.org/10.1128/mcb.25.6.2260-2272.2005.

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ABSTRACT Eukaryotic DNA is organized into chromatin domains that regulate gene expression and chromosome behavior. Insulators and/or scaffold-matrix attachment regions (S/MARs) mark the boundaries of these chromatin domains where they delimit enhancing and silencing effects from the outside. By recombinase-mediated cassette exchange (RMCE), we were able to compare these two types of bordering elements at a number of predefined genomic loci. Flanking an expression vector with either S/MARs or two copies of the non-S/MAR chicken hypersensitive site 4 insulator demonstrates that while these borde

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Naghneh, Ehsan, Es'hagh Pourmaleki, and Azam Rahimpour. "Evaluation of the Effects of Human Beta-Interferon Scaffold Attachment Region (IFN-SAR) on Expression of Vascular Endothelial Growth Factor-Fc (VEGF-Fc) Fusion Protein Expression in Chinese Hamster Ovary (CHO) Cells." Pharmaceutical Sciences 26, no. 4 (2020): 393–98. http://dx.doi.org/10.34172/ps.2020.37.

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Background: Recombinant anti-vascular endothelial growth factor (VEGF) monoclonal antibodies and Fc-fusion proteins have been widely used for the effective treatment of retinal neovascular diseases. In this regard, VEGFR-Fc fusions, which act as strong VEGF inhibitors, have been approved for the treatment of age-related macular degeneration (AMD) and diabetic macular edema (DME). Production of monoclonal antibodies and Fc-fusion proteins relies on mammalian host systems such as Chinese hamster ovary (CHO) cells. Application of genomic regulatory elements including scaffold/matrix attachment re

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Cim, Abdullah, Greta J. Sawyer, Xiaohong Zhang та ін. "In vivo studies on non-viral transdifferentiation of liver cells towards pancreatic β cells". Journal of Endocrinology 214, № 3 (2012): 277–88. http://dx.doi.org/10.1530/joe-12-0033.

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Transdifferentiation in vivo is an attractive option for autologous replacement of pancreatic β cells in patients with type 1 diabetes. It has been achieved by adenoviral delivery of genes for transcription factors in the liver and pancreas of hyperglycaemic mice. However, these viral approaches are not clinically applicable. We used the hydrodynamic approach to deliver genes Pdx1, Ngn3 (Neurog3) and MafA singly and in combination to livers of normoglycaemic rats. Five expression plasmids were evaluated. Livers were removed 1, 3, 7, 14 and 28 days after gene delivery and assayed by quantitativ

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