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Scaffold attachments within the human genome
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of special interest. Chromosomes were painted by in situ hybridization using total 'attached' and 'loop' DNA fractions prepared from nuclei or metaphase chromosomes by the scaffold, matrix or nuclear skeleton protocols. Both types of scaffold DNA preparations indicated that gene-poor Q-bands are enriched ~2-fold for SARs relative to gene-rich R-bands. The ratios obtained for matrix and skeleton preparations varied depending on whether the DNA fractions were prepared from nuclei or chromosomes, indicating that these attachments are more dynamic.
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Craig JM, Boyle S, Perry P, Bickmore WA. Scaffold attachments within the human genome. of special interest J Cell Sci. 110:1997;2673-2682 Chromosomes were painted by in situ hybridization using total 'attached' and 'loop' DNA fractions prepared from nuclei or metaphase chromosomes by the scaffold, matrix or nuclear skeleton protocols. Both types of scaffold DNA preparations indicated that gene-poor Q-bands are enriched ~2-fold for SARs relative to gene-rich R-bands. The ratios obtained for matrix and skeleton preparations varied depending on whether the DNA fractions were prepared from nuclei or chromosomes, indicating that these attachments are more dynamic.
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Craig, J.M.1
Boyle, S.2
Perry, P.3
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Gasser SM, Laroche T, Falquet J, Boy de la Tour E, Laemmli UK. Metaphase chromosome structure. Involvement of topoisomerase II. J Mol Biol. 188:1986;613-629.
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Adachi Y, Käs E, Laemmli UK. Preferential, cooperative binding of DNA topoisomerase II to scaffold-associated regions. EMBO J. 13:1989;3997-4006.
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Adachi, Y.1
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Strick R, Laemmli UK. SARs are cis DNA elements of chromosome dynamics: synthesis of a SAR repressor protein. Cell. 83:1995;1137-1148.
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Strick, R.1
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0025196283
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The A.T-DNA-binding domain of mammalian high mobility group I chromosomal proteins. A novel peptide motif for recognizing DNA structure
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Reeves R, Nissen MS. The A.T-DNA-binding domain of mammalian high mobility group I chromosomal proteins. A novel peptide motif for recognizing DNA structure. J Biol Chem. 265:1990;8573-8582.
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Adachi Y, Luke M, Laemmli UK. Chromosome assembly in vitro: topoisomerase II is required for condensation. Cell. 64:1991;137-148.
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Adachi, Y.1
Luke, M.2
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0027943721
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A heterodimeric coiled-coil protein required for mitotic chromosome condensation in vitro
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Hirano T, Mitchison TJ. A heterodimeric coiled-coil protein required for mitotic chromosome condensation in vitro. Cell. 79:1994;449-458.
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Hirano, T.1
Mitchison, T.J.2
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19
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0030830639
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Condensins, chromosome condensation protein complexes containing XCAP-C, XCAP-E and a Xenopus homolog of the Drosophila Barren protein
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of outstanding interest. XCAP-C/E (ScII) and topoisopmerase II (ScI) were the most abundant proteins present in chromosome scaffolds as originally prepared by Laemmli and collaborators [13]. As was previously shown for topoisomerase II, this important paper demonstrates that XCAP-C/E, in a complex that includes a homolog of the Drosophila Barren protein, is required for chromosome condensation in Xenopus egg extracts. The targeting of condensin complexes to chromosomes is regulated during the cell cycle by phosphorylation. Condensin and topoisomerase II can be targetted to chromosomes independently of each other, but these results do not rule out a targeting of condensin to SARs by interactions with topoisomerase II. Such interactions could be mediated by the Barren protein (see [20]) and could be affected by phosphorylation and, hence, be transient.
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Hirano T, Kobayashi R, Hirano M. Condensins, chromosome condensation protein complexes containing XCAP-C, XCAP-E and a Xenopus homolog of the Drosophila Barren protein. of outstanding interest Cell. 89:1997;511-521 XCAP-C/E (ScII) and topoisopmerase II (ScI) were the most abundant proteins present in chromosome scaffolds as originally prepared by Laemmli and collaborators [13]. As was previously shown for topoisomerase II, this important paper demonstrates that XCAP-C/E, in a complex that includes a homolog of the Drosophila Barren protein, is required for chromosome condensation in Xenopus egg extracts. The targeting of condensin complexes to chromosomes is regulated during the cell cycle by phosphorylation. Condensin and topoisomerase II can be targetted to chromosomes independently of each other, but these results do not rule out a targeting of condensin to SARs by interactions with topoisomerase II. Such interactions could be mediated by the Barren protein (see [20]) and could be affected by phosphorylation and, hence, be transient.
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Cell
, vol.89
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Hirano, T.1
Kobayashi, R.2
Hirano, M.3
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20
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0030582717
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Chromatid segregation at anaphase requires the barren product, a novel chromosome-associated protein that interacts with Topoisomerase II
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Bhat MA, Philp AV, Glover DM, Bellen HJ. Chromatid segregation at anaphase requires the barren product, a novel chromosome-associated protein that interacts with Topoisomerase II. Cell. 87:1996;1103-1114.
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Bhat, M.A.1
Philp, A.V.2
Glover, D.M.3
Bellen, H.J.4
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21
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0031457326
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Interphase chromosomes undergo constrained diffusional motion in living cells
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of outstanding interest. This study used high-resolution confocal microscopy to observe the three dimensional motion of interphase chromatin in living cells. Consistent with the concept of a highly defined nuclear architecture, large-scale movement was not observed but segments of chromatin are free to move within their local region which represents ~1% of the nuclear volume. This constrained diffusion appears to be caused by Brownian motion rather than by an active process. The motion observed in Drosophila nuclei utilized chromatin labelled with microinjected, fluorescently labelled topoisomerase II which was found to concentrate on Satellite III sequences which are essentially an 11 megabase SAR. It is probably that topoisomerase II bound other SARs too but their sizes were too small to give a detectable fluorescent signal.
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Marshall WF, Straight A, Marko JF, Swedlow J, Dernburg A, Belmont A, Murray AW, Agard DA, Sedat JW. Interphase chromosomes undergo constrained diffusional motion in living cells. of outstanding interest Curr Biol. 7:1997;930-939 This study used high-resolution confocal microscopy to observe the three dimensional motion of interphase chromatin in living cells. Consistent with the concept of a highly defined nuclear architecture, large-scale movement was not observed but segments of chromatin are free to move within their local region which represents ~1% of the nuclear volume. This constrained diffusion appears to be caused by Brownian motion rather than by an active process. The motion observed in Drosophila nuclei utilized chromatin labelled with microinjected, fluorescently labelled topoisomerase II which was found to concentrate on Satellite III sequences which are essentially an 11 megabase SAR. It is probably that topoisomerase II bound other SARs too but their sizes were too small to give a detectable fluorescent signal.
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Curr Biol
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, pp. 930-939
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Marshall, W.F.1
Straight, A.2
Marko, J.F.3
Swedlow, J.4
Dernburg, A.5
Belmont, A.6
Murray, A.W.7
Agard, D.A.8
Sedat, J.W.9
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22
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Scaffold attachment regions increase reporter gene expression in stably transformed plant cells
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Allen GC, Hall GE Jr, Childs LC, Weissinger AK, Spiker S, Thompson WF. Scaffold attachment regions increase reporter gene expression in stably transformed plant cells. Plant Cell. 5:1993;603-613.
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Allen, G.C.1
Hall G.E., Jr.2
Childs, L.C.3
Weissinger, A.K.4
Spiker, S.5
Thompson, W.F.6
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23
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0025869479
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Scaffold-attached regions from the human interferon B domain can be used to enhance the stable expression of genes under the control of various promoters
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Klehr D, Maass K, Bode J. Scaffold-attached regions from the human interferon B domain can be used to enhance the stable expression of genes under the control of various promoters. Biochemistry. 30:1991;1264-1270.
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Biochemistry
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Klehr, D.1
Maass, K.2
Bode, J.3
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24
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SARs stimulate but do not confer position independent gene expression
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Poljak L, Seum C, Mattioni T, Laemmli UK. SARs stimulate but do not confer position independent gene expression. Nucleic Acids Res. 22:1994;4386-4394.
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Nucleic Acids Res
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Poljak, L.1
Seum, C.2
Mattioni, T.3
Laemmli, U.K.4
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25
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0027396087
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A model for chromatin opening: Stimulation of topoisomerase II and restriction enzyme cleavage of chromatin by distamycin
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Käs E, Poljak L, Adachi Y, Laemmli UK. A model for chromatin opening: stimulation of topoisomerase II and restriction enzyme cleavage of chromatin by distamycin. EMBO J. 12:1993;115-126.
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EMBO J
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Käs, E.1
Poljak, L.2
Adachi, Y.3
Laemmli, U.K.4
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26
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0027306750
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SAR-dependent mobilization of histone H1 by HMG-I/Y in vitro: HMG-I/Y is enriched in H1-depleted chromatin
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Zhao K, Käs E, Gonzalez E, Laemmli UK. SAR-dependent mobilization of histone H1 by HMG-I/Y in vitro: HMG-I/Y is enriched in H1-depleted chromatin. EMBO J. 12:1993;3237-3247.
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EMBO J
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Zhao, K.1
Käs, E.2
Gonzalez, E.3
Laemmli, U.K.4
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0027963309
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Dependence of enhancer-mediated transcription of the immunoglobulin μ gene on nuclear matrix attachment regions
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Forrester WC, van Genderen C, Jenuwein T, Grosschedl R. Dependence of enhancer-mediated transcription of the immunoglobulin μ gene on nuclear matrix attachment regions. Science. 265:1994;1221-1225.
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Science
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Forrester, W.C.1
Van Genderen, C.2
Jenuwein, T.3
Grosschedl, R.4
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28
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0031030535
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Extension of chromatin accessibility by nuclear matrix attachment regions
-
of outstanding interest. The members of this laboratory demonstrated previously that an intronic enhancer plus its associated SAR function together to allow developmentally regulated gene activation. Here they extend this work by utilizing bacteriophage T3 and T7 RNA polymerases to probe the accessibility of chromatin in isolated nuclei. They show that an intronic enhancer can only open chromatin locally to allow access to an adjacent T3 promoter. In contrast, the enhancer plus its normally associated SAR opens a larger region of chromatin to allow access to a 1 kb distant T7 promoter.
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Jenuwein T, Forrester WC, Fernandez-Herrero LA, Laible G, Dull M, Grosschedl R. Extension of chromatin accessibility by nuclear matrix attachment regions. of outstanding interest Nature. 385:1997;269-272 The members of this laboratory demonstrated previously that an intronic enhancer plus its associated SAR function together to allow developmentally regulated gene activation. Here they extend this work by utilizing bacteriophage T3 and T7 RNA polymerases to probe the accessibility of chromatin in isolated nuclei. They show that an intronic enhancer can only open chromatin locally to allow access to an adjacent T3 promoter. In contrast, the enhancer plus its normally associated SAR opens a larger region of chromatin to allow access to a 1 kb distant T7 promoter.
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Nature
, vol.385
, pp. 269-272
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Jenuwein, T.1
Forrester, W.C.2
Fernandez-Herrero, L.A.3
Laible, G.4
Dull, M.5
Grosschedl, R.6
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29
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0028328632
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B cell-specific demethylation: A novel role for the intronic κ chain enhancer sequence
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Lichtenstein M, Keini G, Cedar H, Bergman Y. B cell-specific demethylation: a novel role for the intronic κ chain enhancer sequence. Cell. 76:1994;913-923.
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Cell
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Lichtenstein, M.1
Keini, G.2
Cedar, H.3
Bergman, Y.4
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30
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0030038608
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A role for nuclear NF-κB in B-cell-specific demethylation of the Igκ locus
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Kirillov A, Kistler B, Mostoslavsky R, Cedar H, Wirth T, Bergman Y. A role for nuclear NF-κB in B-cell-specific demethylation of the Igκ locus. Nat Genet. 13:1996;435-441.
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Kirillov, A.1
Kistler, B.2
Mostoslavsky, R.3
Cedar, H.4
Wirth, T.5
Bergman, Y.6
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31
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0023050122
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Cohabitation of scaffold binding regions with upstream/enhancer elements of three developmentally regulated genes of D. melanogaster
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Gasser SM, Laemmli UK. Cohabitation of scaffold binding regions with upstream/enhancer elements of three developmentally regulated genes of D. melanogaster. Cell. 46:1986;521-530.
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Gasser, S.M.1
Laemmli, U.K.2
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32
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0032055120
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In vivo analysis of scaffold-associated regions in Drosophila: A synthetic high-affinity SAR binding protein suppresses position effect variegation
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of outstanding interest. Using an artificial SAR-specific DNA binding protein (MATH-20) composed of reiterated AT-hooks derived from HMG I/Y, inactivation of a gene placed next to heterochromatin is suppressed. A major component of this heterochromatin is an SAR-like satellite of 11 megabases that is a target for MATH-20. Binding by MATH-20 apparently interferes with heterochromatinization of satellite III sequences, and presumably prevents spreading of this inactive chromatin state of encompass the rearranged gene.
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Girard F, Bello B, Laemmli UK, Gehring WJ. In vivo analysis of scaffold-associated regions in Drosophila: a synthetic high-affinity SAR binding protein suppresses position effect variegation. of outstanding interest EMBO J. 17:1998;2079-2085 Using an artificial SAR-specific DNA binding protein (MATH-20) composed of reiterated AT-hooks derived from HMG I/Y, inactivation of a gene placed next to heterochromatin is suppressed. A major component of this heterochromatin is an SAR-like satellite of 11 megabases that is a target for MATH-20. Binding by MATH-20 apparently interferes with heterochromatinization of satellite III sequences, and presumably prevents spreading of this inactive chromatin state of encompass the rearranged gene.
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EMBO J
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Girard, F.1
Bello, B.2
Laemmli, U.K.3
Gehring, W.J.4
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33
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0027261149
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Mapping simple repeated DNA sequences in heterochromatin of Drosophila melanogaster
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Lohe AR, Hilliker AJ, Roberts PA. Mapping simple repeated DNA sequences in heterochromatin of Drosophila melanogaster. Genetics. 134:1993;1149-1174.
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Genetics
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Lohe, A.R.1
Hilliker, A.J.2
Roberts, P.A.3
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34
-
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0026597313
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Biological significance of unwinding capability of nuclear matrix-associating DNAs
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Bode J, Kohwi Y, Dickinson L, Joh T, Klehr D, Mielke C, Kohwi-Shigematsu T. Biological significance of unwinding capability of nuclear matrix-associating DNAs. Science. 255:1992;195-197.
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Science
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Bode, J.1
Kohwi, Y.2
Dickinson, L.3
Joh, T.4
Klehr, D.5
Mielke, C.6
Kohwi-Shigematsu, T.7
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35
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0030876432
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A thymocyte factor SATB1 suppresses transcription of stably integrated matrix-attachment region-linked reporter genes
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of special interest. The authors of this paper claim that a cell-type specific protein, SATB1, targets a SAR to the nuclear matrix - resulting in gene inactivation.
-
Kohwi-Shigematsu T, Maass K, Bode J. A thymocyte factor SATB1 suppresses transcription of stably integrated matrix-attachment region-linked reporter genes. of special interest Biochemistry. 36:1997;12005-12010 The authors of this paper claim that a cell-type specific protein, SATB1, targets a SAR to the nuclear matrix - resulting in gene inactivation.
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Biochemistry
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Kohwi-Shigematsu, T.1
Maass, K.2
Bode, J.3
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36
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0028943215
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Nucleolin is a matrix attachment region DNA-binding protein that specifically recognizes a region with high base-unpairing potential
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Dickinson LA, Kohwi-Shigematsu T. Nucleolin is a matrix attachment region DNA-binding protein that specifically recognizes a region with high base-unpairing potential. Mol Cell Biol. 15:1995;456-465.
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Dickinson, L.A.1
Kohwi-Shigematsu, T.2
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37
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0029610034
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The immunoglobulin heavy-chain matrix-associating regions are bound by Bright: A B cell-specific trans-activator that describes a new DNA-binding protein family
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Herrscher RF, Kaplan MH, Lelsz DL, Das C, Scheuermann R, Tucker PW. The immunoglobulin heavy-chain matrix-associating regions are bound by Bright: a B cell-specific trans-activator that describes a new DNA-binding protein family. Genes Dev. 9:1995;3067-3082.
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Herrscher, R.F.1
Kaplan, M.H.2
Lelsz, D.L.3
Das, C.4
Scheuermann, R.5
Tucker, P.W.6
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38
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Mutually exclusive interaction of a novel matrix attachment region binding protein and the NF-μNR enhancer repressor. Implications for regulation of immunoglobulin heavy chain expression
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Zong RT, Scheuermann RH. Mutually exclusive interaction of a novel matrix attachment region binding protein and the NF-μNR enhancer repressor. Implications for regulation of immunoglobulin heavy chain expression. J Biol Chem. 270:1995;24010-24018.
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A tissue-specific MAR/SAR DNA-binding protein with unusual binding site recognition
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Dickinson LA, Joh T, Kohwi Y, Kohwi-Shigematsu T. A tissue-specific MAR/SAR DNA-binding protein with unusual binding site recognition. Cell. 70:1992;631-645.
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Dickinson, L.A.1
Joh, T.2
Kohwi, Y.3
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40
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A developmental-specific factor binds to suppressor sites flanking the immunoglobulin heavy-chain enhancer
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Scheuermann RH, Chen U. A developmental-specific factor binds to suppressor sites flanking the immunoglobulin heavy-chain enhancer. Genes Dev. 3:1989;1255-1266.
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Scheuermann, R.H.1
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41
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A position-effect assay for boundaries of higher order chromosomal domains
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Kellum R, Schedl P. A position-effect assay for boundaries of higher order chromosomal domains. Cell. 64:1991;941-950.
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Kellum R, Schedl P. A group of scs elements function as domain boundaries in an enhancer-blocking assay. Mol Cell Biol. 12:1992;2424-2431.
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