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Article ; Online: Wt1 flip-flops chromatin in a CTCF domain.

Gurudatta, B V / Corces, Victor G

2011 Volume 21, Issue 3, Page(s) 389–390

Abstract: CTCF plays diverse roles in nuclear organization and transcriptional regulation. In this issue of Developmental Cell, Essafi et al. (2011) report a mechanism by which the repressive or active state of chromatin in a domain defined by CTCF can be switched ...

Abstract	CTCF plays diverse roles in nuclear organization and transcriptional regulation. In this issue of Developmental Cell, Essafi et al. (2011) report a mechanism by which the repressive or active state of chromatin in a domain defined by CTCF can be switched by the Wt1 transcription factor to regulate gene expression.
Language	English
Publishing date	2011-08-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	2054967-2
ISSN	1878-1551 ; 1534-5807
ISSN (online)	1878-1551
ISSN	1534-5807
DOI	10.1016/j.devcel.2011.08.022
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Article ; Online: Chromatin insulators: lessons from the fly.

Gurudatta, B V / Corces, Victor G

Briefings in functional genomics & proteomics

2009 Volume 8, Issue 4, Page(s) 276–282

Abstract: Chromatin insulators are DNA-protein complexes with broad functions in nuclear biology. Drosophila has at least five different types of insulators; recent results suggest that these different insulators share some components that may allow them to ... ...

Abstract	Chromatin insulators are DNA-protein complexes with broad functions in nuclear biology. Drosophila has at least five different types of insulators; recent results suggest that these different insulators share some components that may allow them to function through common mechanisms. Data from genome-wide localization studies of insulator proteins indicate a possible functional specialization, with different insulators playing distinct roles in nuclear biology. Cells have developed mechanisms to control insulator activity by recruiting specialized proteins or by covalent modification of core components. Current results suggest that insulators set up cell-specific blueprints of nuclear organization that may contribute to the establishment of different patterns of gene expression during cell differentiation and development.
MeSH term(s)	Animals ; Base Sequence ; Chromatin/genetics ; Drosophila Proteins/genetics ; Drosophila melanogaster/genetics ; Insulator Elements/genetics
Chemical Substances	Chromatin ; Drosophila Proteins
Language	English
Publishing date	2009-09-14
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	2138368-6
ISSN	1477-4062 ; 1473-9550
ISSN (online)	1477-4062
ISSN	1473-9550
DOI	10.1093/bfgp/elp032
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Article ; Online: The BEAF insulator regulates genes involved in cell polarity and neoplastic growth.

Gurudatta, B V / Ramos, Edward / Corces, Victor G

Developmental biology

2012 Volume 369, Issue 1, Page(s) 124–132

Abstract: Boundary Element Associated Factor-32 (BEAF-32) is an insulator protein predominantly found near gene promoters and thought to play a role in gene expression. We find that mutations in BEAF-32 are lethal, show loss of epithelial morphology in imaginal ... ...

Abstract	Boundary Element Associated Factor-32 (BEAF-32) is an insulator protein predominantly found near gene promoters and thought to play a role in gene expression. We find that mutations in BEAF-32 are lethal, show loss of epithelial morphology in imaginal discs and cause neoplastic growth defects. To investigate the molecular mechanisms underlying this phenotype, we carried out a genome-wide analysis of BEAF-32 localization in wing imaginal disc cells. Mutation of BEAF-32 results in miss-regulation of 3850 genes by at least 1.5-fold, 794 of which are bound by this protein in wing imaginal cells. Up-regulated genes encode proteins involved in cell polarity, cell proliferation and cell differentiation. Among the down-regulated genes are those encoding components of the wingless pathway, which is required for cell differentiation. Miss-regulation of these genes explains the unregulated cell growth and neoplastic phenotypes observed in imaginal tissues of BEAF-32 mutants.
MeSH term(s)	Animals ; Base Sequence ; Body Patterning/genetics ; Cell Differentiation/genetics ; Cell Polarity/genetics ; DNA-Binding Proteins/genetics ; DNA-Binding Proteins/metabolism ; Drosophila Proteins/genetics ; Drosophila Proteins/metabolism ; Drosophila melanogaster/cytology ; Drosophila melanogaster/genetics ; Epithelium/metabolism ; Epithelium/pathology ; Eye Proteins/genetics ; Eye Proteins/metabolism ; Gene Expression Regulation, Neoplastic ; Genes, Insect/genetics ; Imaginal Discs/metabolism ; Insulator Elements/genetics ; Molecular Sequence Data ; Mutation/genetics ; Neoplasms/genetics ; Neoplasms/pathology ; Signal Transduction/genetics ; Transcription Initiation Site ; Transcription, Genetic ; Up-Regulation/genetics ; Wings, Animal/metabolism
Chemical Substances	BEAF-32 protein, Drosophila ; DNA-Binding Proteins ; Drosophila Proteins ; Eye Proteins
Language	English
Publishing date	2012-06-26
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1114-9
ISSN	1095-564X ; 0012-1606
ISSN (online)	1095-564X
ISSN	0012-1606
DOI	10.1016/j.ydbio.2012.06.013
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Article: Wt1 Flip-Flops Chromatin in a CTCF Domain

Gurudatta, B.V / Corces, Victor G

Developmental cell. 2011 Sept. 13, v. 21, no. 3

2011

Abstract	CTCF plays diverse roles in nuclear organization and transcriptional regulation. In this issue of Developmental Cell, Essafi et al. (2011) report a mechanism by which the repressive or active state of chromatin in a domain defined by CTCF can be switched by the Wt1 transcription factor to regulate gene expression.
Keywords	chromatin ; gene expression ; transcription (genetics) ; transcription factors
Language	English
Dates of publication	2011-0913
Size	p. 389-390.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	2054967-2
ISSN	1878-1551 ; 1534-5807
ISSN (online)	1878-1551
ISSN	1534-5807
DOI	10.1016/j.devcel.2011.08.022
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Lamin C and chromatin organization in Drosophila.

Gurudatta, B V / Shashidhara, L S / Parnaik, Veena K

Journal of genetics

2010 Volume 89, Issue 1, Page(s) 37–49

Abstract: Drosophila lamin C (LamC) is a developmentally regulated component of the nuclear lamina. The lamC gene is situated in the fifth intron of the essential gene tout velu (ttv). We carried out genetic analysis of lamC during development. Phenotypic analyses ...

Abstract	Drosophila lamin C (LamC) is a developmentally regulated component of the nuclear lamina. The lamC gene is situated in the fifth intron of the essential gene tout velu (ttv). We carried out genetic analysis of lamC during development. Phenotypic analyses of RNAi-mediated downregulation of lamC expression as well as targeted misexpression of lamin C suggest a role for lamC in cell survival. Of particular interest in the context of laminopathies is the caspase-dependent apoptosis induced by the overexpression of lamin C. Interestingly, misexpression of lamin C in the central nervous system, where it is not normally expressed, did not affect organization of the nuclear lamina. lamC mutant alleles suppressed position effect variegation normally displayed at near-centromeric and telomeric regions. Further, both downregulation and misexpression of lamin C affected the distribution of heterochromatin protein 1. Our results suggest that Drosophila lamC has a tissue-specific role during development and is required for chromatin organization.
MeSH term(s)	Animals ; Apoptosis ; Chromatin/metabolism ; Chromosomal Position Effects/genetics ; Chromosomal Proteins, Non-Histone/metabolism ; Down-Regulation/genetics ; Drosophila Proteins/metabolism ; Drosophila melanogaster/cytology ; Drosophila melanogaster/genetics ; Drosophila melanogaster/metabolism ; Enhancer Elements, Genetic/genetics ; Genetic Loci/genetics ; Lamin Type A/genetics ; Larva/cytology ; Larva/metabolism ; Mutation/genetics ; Organ Specificity/genetics ; Phenotype ; Protein Transport ; RNA Interference ; Wings, Animal/cytology ; Wings, Animal/metabolism
Chemical Substances	Chromatin ; Chromosomal Proteins, Non-Histone ; Drosophila Proteins ; Lamin Type A ; heterochromatin protein 1, Drosophila ; lamin C
Language	English
Publishing date	2010-05-26
Publishing country	India
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	3039-9
ISSN	0973-7731 ; 0958-8361 ; 0022-1333
ISSN (online)	0973-7731
ISSN	0958-8361 ; 0022-1333
DOI	10.1007/s12041-010-0009-y
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Article ; Online: Dynamic changes in the genomic localization of DNA replication-related element binding factor during the cell cycle.

Gurudatta, B V / Yang, Jingping / Van Bortle, Kevin / Donlin-Asp, Paul G / Corces, Victor G

Cell cycle (Georgetown, Tex.)

2013 Volume 12, Issue 10, Page(s) 1605–1615

Abstract: DREF was first characterized for its role in the regulation of transcription of genes encoding proteins involved in DNA replication and found to interact with sequences similar to the DNA recognition motif of the BEAF-32 insulator protein. Insulators are ...

Abstract	DREF was first characterized for its role in the regulation of transcription of genes encoding proteins involved in DNA replication and found to interact with sequences similar to the DNA recognition motif of the BEAF-32 insulator protein. Insulators are DNA-protein complexes that mediate intra- and inter-chromosome interactions. Several DNA-binding insulator proteins have been described in Drosophila, including BEAF-32, dCTCF and Su(Hw). Here we find that DREF and BEAF-32 co-localize at the same genomic sites, but their enrichment shows an inverse correlation. Furthermore, DREF co-localizes in the genome with other insulator proteins, suggesting that the function of this protein may require components of Drosophila insulators. This is supported by the finding that mutations in insulator proteins modulate DREF-induced cell proliferation. DREF persists bound to chromatin during mitosis at a subset of sites where it also co-localizes with dCTCF, BEAF-32 and CP190. These sites are highly enriched for sites where Orc2 and Mcm2 are present during interphase and at the borders of topological domains of chromosomes defined by Hi-C. The results suggest that DREF and insulator proteins may help maintain chromosome organization during the cell cycle and mark a subset of genomic sites for the assembly of pre-replication complexes and gene bookmarking during the M/G1 transition.
MeSH term(s)	Animals ; Cell Proliferation ; Cells, Cultured ; Chromatin/metabolism ; DNA-Binding Proteins/analysis ; DNA-Binding Proteins/genetics ; DNA-Binding Proteins/metabolism ; Drosophila ; Drosophila Proteins/analysis ; Drosophila Proteins/genetics ; Drosophila Proteins/metabolism ; Eye Proteins/analysis ; Eye Proteins/genetics ; Eye Proteins/metabolism ; Genome ; Insulator Elements/genetics ; Interphase ; Microtubule-Associated Proteins/analysis ; Microtubule-Associated Proteins/genetics ; Microtubule-Associated Proteins/metabolism ; Minichromosome Maintenance Proteins/metabolism ; Mitosis ; Mutation ; Nuclear Proteins/analysis ; Nuclear Proteins/genetics ; Nuclear Proteins/metabolism ; Origin Recognition Complex/metabolism ; Transcription Factors/analysis ; Transcription Factors/genetics ; Transcription Factors/metabolism
Chemical Substances	BEAF-32 protein, Drosophila ; CP190 protein, Drosophila ; Chromatin ; DNA-Binding Proteins ; Dref protein, Drosophila ; Drosophila Proteins ; Eye Proteins ; Microtubule-Associated Proteins ; Nuclear Proteins ; Orc2 protein, Drosophila ; Origin Recognition Complex ; Transcription Factors ; MCM2 protein, Drosophila (EC 3.6.4.12) ; Minichromosome Maintenance Proteins (EC 3.6.4.12)
Language	English
Publishing date	2013-04-25
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2146183-1
ISSN	1551-4005 ; 1538-4101 ; 1554-8627
ISSN (online)	1551-4005
ISSN	1538-4101 ; 1554-8627
DOI	10.4161/cc.24742
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Article: Lamin C and chromatin organization in drosophila

Gurudatta, B. V. / Shashidhara, L. S. / Parnaik, Veena K.

Journal of Genetics (INDIA)

(Apr 2010) Volume v. 89, Issue (1)

Abstract	Drosophila lamin C (LamC) is a developmentally regulated component of the nuclear lamina. The lamC gene is situated in the fifth intron of the essential gene tout velu (ttv). We carried out genetic analysis of lamC during development. Phenotypic analyses of RNAi-mediated downregulation of lamC expression as well as targeted misexpression of lamin C suggest a role for lamC in cell survival. Of particular interest in the context of laminopathies is the caspase-dependent apoptosis induced by the overexpression of lamin C. Interestingly, misexpression of lamin C in the central nervous system, where it is not normally expressed, did not affect organization of the nuclear lamina. lamC mutant alleles suppressed position effect variegation normally displayed at near-centromeric and telomeric regions. Further, both downregulation and misexpression of lamin C affected the distribution of heterochromatin protein 1. Our results suggest that Drosophila lamC has a tissue-specific role during development and is required for chromatin organization.
Keywords	HETEROCHROMATIN ; DROSOPHILA ; HETEROCHROMATINE ; DROSOPHILA ; HETEROCROMATINA ; DROSOPHILA ; http://www.fao.org/aos/agrovoc#c_26786 ; http://www.fao.org/aos/agrovoc#c_2390
Language	English
Document type	Article
ISSN	0022-1333
Database	AGRIS - International Information System for the Agricultural Sciences and Technology

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Article ; Online: DNA topoisomerase II modulates insulator function in Drosophila.

Ramos, Edward / Torre, Eduardo A / Bushey, Ashley M / Gurudatta, B V / Corces, Victor G

PloS one

2011 Volume 6, Issue 1, Page(s) e16562

Abstract: Insulators are DNA sequences thought to be important for the establishment and maintenance of cell-type specific nuclear architecture. In Drosophila there are several classes of insulators that appear to have unique roles in gene expression. The ... ...

Abstract	Insulators are DNA sequences thought to be important for the establishment and maintenance of cell-type specific nuclear architecture. In Drosophila there are several classes of insulators that appear to have unique roles in gene expression. The mechanisms involved in determining and regulating the specific roles of these insulator classes are not understood. Here we report that DNA Topoisomerase II modulates the activity of the Su(Hw) insulator. Downregulation of Topo II by RNAi or mutations in the Top2 gene result in disruption of Su(Hw) insulator function. This effect is mediated by the Mod(mdg4)2.2 protein, which is a unique component of the Su(Hw) insulator complex. Co-immunoprecipitation and yeast two-hybrid experiments show that Topo II and Mod(mdg4)2.2 proteins directly interact. In addition, mutations in Top2 cause a slight decrease of Mod(mdg4)2.2 transcript but have a dramatic effect on Mod(mdg4)2.2 protein levels. In the presence of proteasome inhibitors, normal levels of Mod(mdg4)2.2 protein and its binding to polytene chromosomes are restored. Thus, Topo II is required to prevent Mod(mdg4)2.2 degradation and, consequently, to stabilize Su(Hw) insulator-mediated chromatin organization.
MeSH term(s)	Animals ; Chromatin/metabolism ; Chromosomes/metabolism ; DNA Topoisomerases, Type II/chemistry ; DNA Topoisomerases, Type II/genetics ; DNA Topoisomerases, Type II/physiology ; Drosophila Proteins/genetics ; Drosophila Proteins/metabolism ; Drosophila melanogaster/enzymology ; Drosophila melanogaster/genetics ; Gene Expression Regulation/genetics ; Insulator Elements ; Repressor Proteins/genetics ; Transcription Factors/metabolism
Chemical Substances	Chromatin ; Drosophila Proteins ; Repressor Proteins ; Transcription Factors ; mod(mdg4) protein, Drosophila ; su(Hw) protein, Drosophila ; DNA Topoisomerases, Type II (EC 5.99.1.3)
Language	English
Publishing date	2011-01-27
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0016562
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Article ; Online: Identification and characterization of proteins involved in nuclear organization using Drosophila GFP protein trap lines.

Rohrbaugh, Margaret / Clore, Alyssia / Davis, Julia / Johnson, Sharonta / Jones, Brian / Jones, Keith / Kim, Joanne / Kithuka, Bramwel / Lunsford, Krystal / Mitchell, Joy / Mott, Brian / Ramos, Edward / Tchedou, Maza R / Acosta, Gilbert / Araujo, Mark / Cushing, Stuart / Duffy, Gabriel / Graves, Felicia / Griffin, Kyler /

Gurudatta, B V / Jackson, Deaundra / Jaimes, Denis / Jamison, Kendall / Jones, Khali / Kelley, Dhaujee / Kilgore, Marquita / Laramore, Derica / Le, Thuy / Mazhar, Bakhtawar / Mazhar, Muhammad M / McCrary, Britney / Miller, Teanndras / Moreland, Celethia / Mullins, Alex / Munye, Elyas / Okoorie, Sheila / Pittman, Elisha / Roberts, Nikkita / Rose, De'Warren / Rowland, Alex / Shagarabi, Anwar / Smith, Jamela / Stallworth, Tayler / Stroud, Nicole / Sung, Elizabeth / Sung, Kai / Takenaka, Naomi / Torre, Eduardo / Veira, Jarvis / Vu, Kim / Wagstaff, William / Wood, Ashley M / Wu, Karen / Yang, Jingping / Corces, Victor G

PloS one

2013 Volume 8, Issue 1, Page(s) e53091

Abstract: Background: Strains from a collection of Drosophila GFP protein trap lines express GFP in the normal tissues where the endogenous protein is present. This collection can be used to screen for proteins distributed in the nucleus in a non-uniform pattern.! ...

Abstract	Background: Strains from a collection of Drosophila GFP protein trap lines express GFP in the normal tissues where the endogenous protein is present. This collection can be used to screen for proteins distributed in the nucleus in a non-uniform pattern. Methodology/principal findings: We analyzed four lines that show peripheral or punctate nuclear staining. One of these lines affects an uncharacterized gene named CG11138. The CG11138 protein shows a punctate distribution in the nuclear periphery similar to that of Drosophila insulator proteins but does not co-localize with known insulators. Interestingly, mutations in Lamin proteins result in alterations in CG11138 localization, suggesting that this protein may be a novel component of the nuclear lamina. A second line affects the Decondensation factor 31 (Df31) gene, which encodes a protein with a unique nuclear distribution that appears to segment the nucleus into four different compartments. The X-chromosome of males is confined to one of these compartments. We also find that Drosophila Nucleoplasmin (dNlp) is present in regions of active transcription. Heat shock leads to loss of dNlp from previously transcribed regions of polytene chromosome without redistribution to the heat shock genes. Analysis of Stonewall (Stwl), a protein previously found to be necessary for the maintenance of germline stem cells, shows that Stwl is present in a punctate pattern in the nucleus that partially overlaps with that of known insulator proteins. Finally we show that Stwl, dNlp, and Df31 form part of a highly interactive network. The properties of other components of this network may help understand the role of these proteins in nuclear biology. Conclusions/significance: These results establish screening of GFP protein trap alleles as a strategy to identify factors with novel cellular functions. Information gained from the analysis of CG11138 Stwl, dNlp, and Df31 sets the stage for future studies of these proteins.
MeSH term(s)	Animals ; Cell Differentiation ; Cell Nucleus/metabolism ; Diploidy ; Drosophila Proteins/metabolism ; Drosophila melanogaster/cytology ; Drosophila melanogaster/enzymology ; Drosophila melanogaster/metabolism ; Germ Cells/cytology ; Germ Cells/metabolism ; Green Fluorescent Proteins/metabolism ; Heat-Shock Response ; Lamin Type A/metabolism ; Male ; Models, Biological ; Nuclear Lamina/enzymology ; Nucleoplasmins ; Polytene Chromosomes/metabolism ; Protein Interaction Maps ; Ubiquitin-Protein Ligases/metabolism
Chemical Substances	Drosophila Proteins ; Lamin Type A ; Nucleoplasmins ; lamin C ; Green Fluorescent Proteins (147336-22-9) ; Ubiquitin-Protein Ligases (EC 2.3.2.27)
Language	English
Publishing date	2013-01-16
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0053091
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Article: BEAF insulator regulates genes involved in cell polarity and neoplastic growth

Gurudatta, B.V. / Ramos, Edward / Corces, Victor G

Developmental biology

Volume v. 369,, Issue no. 1

Abstract	Boundary Element Associated Factor-32 (BEAF-32) is an insulator protein predominantly found near gene promoters and thought to play a role in gene expression. We find that mutations in BEAF-32 are lethal, show loss of epithelial morphology in imaginal discs and cause neoplastic growth defects. To investigate the molecular mechanisms underlying this phenotype, we carried out a genome-wide analysis of BEAF-32 localization in wing imaginal disc cells. Mutation of BEAF-32 results in miss-regulation of 3850 genes by at least 1.5-fold, 794 of which are bound by this protein in wing imaginal cells. Up-regulated genes encode proteins involved in cell polarity, cell proliferation and cell differentiation. Among the down-regulated genes are those encoding components of the wingless pathway, which is required for cell differentiation. Miss-regulation of these genes explains the unregulated cell growth and neoplastic phenotypes observed in imaginal tissues of BEAF-32 mutants.
Keywords	imaginal discs ; cell proliferation ; cell polarity ; genes ; mutation ; gene expression ; phenotype ; cell growth ; cell differentiation ; proteins ; gene expression regulation ; mutants
Language	English
Document type	Article
ISSN	0012-1606
Database	AGRIS - International Information System for the Agricultural Sciences and Technology

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