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Article: A Chemical Genetic Method for Monitoring Genome-Wide Dynamics of

Liu, Ta-Wei / Myschyshyn, Mike / Sinclair, Donald A / Vocadlo, David J

ACS central science

2019 Volume 5, Issue 4, Page(s) 663–670

Abstract: Advances in DNA sequencing are enabling new experimental modalities for studying chromatin. One emerging area is to use high-throughput DNA sequencing to monitor dynamic changes occurring to chromatin. ...

Abstract	Advances in DNA sequencing are enabling new experimental modalities for studying chromatin. One emerging area is to use high-throughput DNA sequencing to monitor dynamic changes occurring to chromatin.
Language	English
Publishing date	2019-03-01
Publishing country	United States
Document type	Journal Article
ISSN	2374-7943
ISSN	2374-7943
DOI	10.1021/acscentsci.9b00044
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Article ; Online: Characterization of

Cotsworth, Shawn / Jackson, Catherine J / Hallson, Graham / Fitzpatrick, Kathleen A / Syrzycka, Monika / Coulthard, Alistair B / Bejsovec, Amy / Marchetti, Marcella / Pimpinelli, Sergio / Wang, Simon J H / Camfield, Robert G / Verheyen, Esther M / Sinclair, Donald A / Honda, Barry M / Hilliker, Arthur J

Cells

2022 Volume 11, Issue 3

Abstract: ... ...

Abstract	The
MeSH term(s)	Animals ; Biosynthetic Pathways/genetics ; Drosophila melanogaster/genetics ; Drosophila melanogaster/metabolism ; Euchromatin ; Glutamine/metabolism ; Glutamine-Fructose-6-Phosphate Transaminase (Isomerizing)/genetics ; Glutamine-Fructose-6-Phosphate Transaminase (Isomerizing)/metabolism ; Hexosamines
Chemical Substances	Euchromatin ; Hexosamines ; Glutamine (0RH81L854J) ; Glutamine-Fructose-6-Phosphate Transaminase (Isomerizing) (EC 2.6.1.16)
Language	English
Publishing date	2022-01-27
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2661518-6
ISSN	2073-4409 ; 2073-4409
ISSN (online)	2073-4409
ISSN	2073-4409
DOI	10.3390/cells11030448
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Article ; Online: The nutrient sensor OGT regulates Hipk stability and tumorigenic-like activities in

Wong, Kenneth Kin Lam / Liu, Ta-Wei / Parker, Jessica M / Sinclair, Donald A R / Chen, Yi-Yun / Khoo, Kay-Hooi / Vocadlo, David J / Verheyen, Esther M

Proceedings of the National Academy of Sciences of the United States of America

2020 Volume 117, Issue 4, Page(s) 2004–2013

Abstract: Environmental cues such as nutrients alter cellular behaviors by acting on a wide array of molecular sensors inside cells. Of emerging interest is the link observed between effects of dietary sugars on cancer proliferation. Here, we identify the ... ...

Abstract	Environmental cues such as nutrients alter cellular behaviors by acting on a wide array of molecular sensors inside cells. Of emerging interest is the link observed between effects of dietary sugars on cancer proliferation. Here, we identify the requirements of hexosamine biosynthetic pathway (HBP) and
MeSH term(s)	Acetylglucosamine/metabolism ; Animals ; Carcinogenesis/chemically induced ; Carcinogenesis/metabolism ; Carcinogenesis/pathology ; Carrier Proteins/genetics ; Carrier Proteins/metabolism ; Cell Proliferation ; Cells, Cultured ; Drosophila Proteins/genetics ; Drosophila Proteins/metabolism ; Drosophila melanogaster/drug effects ; Drosophila melanogaster/growth & development ; Drosophila melanogaster/metabolism ; Fibroblasts/drug effects ; Fibroblasts/metabolism ; Fibroblasts/pathology ; Glucose/pharmacology ; HEK293 Cells ; Humans ; MCF-7 Cells ; Mice ; N-Acetylglucosaminyltransferases/genetics ; N-Acetylglucosaminyltransferases/metabolism ; Phosphorylation ; Protein Kinases/genetics ; Protein Kinases/metabolism ; Protein Stability ; Protein-Serine-Threonine Kinases/genetics ; Protein-Serine-Threonine Kinases/metabolism ; Sweetening Agents/pharmacology
Chemical Substances	Carrier Proteins ; Drosophila Proteins ; Sweetening Agents ; N-Acetylglucosaminyltransferases (EC 2.4.1.-) ; O-GlcNAc transferase (EC 2.4.1.-) ; Protein Kinases (EC 2.7.-) ; HIPK2 protein, human (EC 2.7.1.-) ; HIPK protein, Drosophila (EC 2.7.11.1) ; Protein-Serine-Threonine Kinases (EC 2.7.11.1) ; Glucose (IY9XDZ35W2) ; Acetylglucosamine (V956696549)
Language	English
Publishing date	2020-01-13
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.1912894117
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Article ; Online: Homeodomain-interacting protein kinase (Hipk) plays roles in nervous system and muscle structure and function.

Wang, Simon J H / Sinclair, Donald A R / Kim, Hae-Yoon / Kinsey, Stephen D / Yoo, Byoungjoo / Shih, Claire R Y / Wong, Kenneth K L / Krieger, Charles / Harden, Nicholas / Verheyen, Esther M

PloS one

2020 Volume 15, Issue 3, Page(s) e0221006

Abstract: Homeodomain-interacting protein kinases (Hipks) have been previously associated with cell proliferation and cancer, however, their effects in the nervous system are less well understood. We have used Drosophila melanogaster to evaluate the effects of ... ...

Abstract	Homeodomain-interacting protein kinases (Hipks) have been previously associated with cell proliferation and cancer, however, their effects in the nervous system are less well understood. We have used Drosophila melanogaster to evaluate the effects of altered Hipk expression on the nervous system and muscle. Using genetic manipulation of Hipk expression we demonstrate that knockdown and over-expression of Hipk produces early adult lethality, possibly due to the effects on the nervous system and muscle involvement. We find that optimal levels of Hipk are critical for the function of dopaminergic neurons and glial cells in the nervous system, as well as muscle. Furthermore, manipulation of Hipk affects the structure of the larval neuromuscular junction (NMJ) by promoting its growth. Hipk regulates the phosphorylation of the synapse-associated cytoskeletal protein Hu-li tai shao (Hts; adducin in mammals) and modulates the expression of two important protein kinases, Calcium-calmodulin protein kinase II (CaMKII) and Partitioning-defective 1 (PAR-1), all of which may alter neuromuscular structure/function and influence lethality. Hipk also modifies the levels of an important nuclear protein, TBPH, the fly orthologue of TAR DNA-binding protein 43 (TDP-43), which may have relevance for understanding motor neuron diseases.
MeSH term(s)	Animals ; Body Patterning ; Cell Nucleus/metabolism ; Drosophila Proteins/isolation & purification ; Drosophila Proteins/metabolism ; Drosophila melanogaster/anatomy & histology ; Drosophila melanogaster/enzymology ; Drosophila melanogaster/physiology ; Eye/embryology ; Larva/metabolism ; Male ; Muscles/anatomy & histology ; Muscles/cytology ; Muscles/metabolism ; Nervous System/anatomy & histology ; Nervous System/cytology ; Nervous System/metabolism ; Neuromuscular Junction/metabolism ; Organ Size ; Phosphorylation ; Protein Kinases/isolation & purification ; Synapses/metabolism
Chemical Substances	Drosophila Proteins ; Protein Kinases (EC 2.7.-) ; HIPK protein, Drosophila (EC 2.7.11.1)
Language	English
Publishing date	2020-03-18
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0221006
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Article ; Online: Genome-wide chemical mapping of O-GlcNAcylated proteins in Drosophila melanogaster.

Liu, Ta-Wei / Myschyshyn, Mike / Sinclair, Donald A / Cecioni, Samy / Beja, Kevin / Honda, Barry M / Morin, Ryan D / Vocadlo, David J

Nature chemical biology

2017 Volume 13, Issue 2, Page(s) 161–167

Abstract: N-Acetylglucosamine β-O-linked to nucleocytoplasmic proteins (O-GlcNAc) is implicated in the regulation of gene expression in organisms, from humans to Drosophila melanogaster. Within Drosophila, O-GlcNAc transferase (OGT) is one of the Polycomb group ... ...

Abstract	N-Acetylglucosamine β-O-linked to nucleocytoplasmic proteins (O-GlcNAc) is implicated in the regulation of gene expression in organisms, from humans to Drosophila melanogaster. Within Drosophila, O-GlcNAc transferase (OGT) is one of the Polycomb group proteins (PcGs) that act through Polycomb group response elements (PREs) to silence homeotic (HOX) and other PcG target genes. Using Drosophila, we identify new O-GlcNAcylated PcG proteins and develop an antibody-free metabolic feeding approach to chemoselectively map genomic loci enriched in O-GlcNAc using next-generation sequencing. We find that O-GlcNAc is distributed to specific genomic loci both in cells and in vivo. Many of these loci overlap with PREs, but O-GlcNAc is also present at other loci lacking PREs. Loss of OGT leads to altered gene expression not only at loci containing PREs but also at loci lacking PREs, including several heterochromatic genes. These data suggest that O-GlcNAc acts through multiple mechanisms to regulate gene expression in Drosophila.
MeSH term(s)	Acetylglucosamine/metabolism ; Animals ; Drosophila melanogaster/enzymology ; Drosophila melanogaster/genetics ; Genome, Insect ; Polycomb-Group Proteins/chemistry ; Polycomb-Group Proteins/genetics ; Polycomb-Group Proteins/metabolism
Chemical Substances	Polycomb-Group Proteins ; Acetylglucosamine (V956696549)
Language	English
Publishing date	2017-02
Publishing country	United States
Document type	Journal Article
ZDB-ID	2202962-X
ISSN	1552-4469 ; 1552-4450
ISSN (online)	1552-4469
ISSN	1552-4450
DOI	10.1038/nchembio.2247
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Article ; Online: Genetic and Molecular Analysis of Essential Genes in Centromeric Heterochromatin of the Left Arm of Chromosome 3 in

Syrzycka, Monika / Hallson, Graham / Fitzpatrick, Kathleen A / Kim, Inho / Cotsworth, Shawn / Hollebakken, Rob E / Simonetto, Kevin / Yang, Linda / Luongo, Stephanie / Beja, Kevin / Coulthard, Alistair B / Hilliker, Arthur J / Sinclair, Donald A / Honda, Barry M

G3 (Bethesda, Md.)

2019 Volume 9, Issue 5, Page(s) 1581–1595

Abstract: A large portion of ... ...

Abstract	A large portion of the
MeSH term(s)	Animals ; Centromere/genetics ; Chromosome Mapping ; Chromosomes, Insect ; Drosophila melanogaster/genetics ; Gene Knockdown Techniques ; Genes, Essential ; Genes, Lethal ; Genetic Complementation Test ; Genetic Testing ; Genomics/methods ; Genotype ; Heterochromatin/genetics ; Models, Genetic ; Mutagenesis/radiation effects ; Mutation ; RNA Interference ; X-Rays
Chemical Substances	Heterochromatin
Language	English
Publishing date	2019-05-07
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2629978-1
ISSN	2160-1836 ; 2160-1836
ISSN (online)	2160-1836
ISSN	2160-1836
DOI	10.1534/g3.119.0003
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Article: Different patterns of gene silencing in position-effect variegation.

Lloyd, Vett K / Dyment, David / Sinclair, Donald A R / Grigliatti, Thomas A

Genome

2003 Volume 46, Issue 6, Page(s) 1104–1117

Abstract: Position-effect variegation (PEV) results when a fully functional gene is moved from its normal position to a position near to a broken heterochromatic-euchromatic boundary. In this new position, the gene, while remaining unaltered at the DNA level, is ... ...

Abstract	Position-effect variegation (PEV) results when a fully functional gene is moved from its normal position to a position near to a broken heterochromatic-euchromatic boundary. In this new position, the gene, while remaining unaltered at the DNA level, is transcriptionally silenced in some cells but active in others, producing a diagnostic mosaic phenotype. Many variegating stocks show phenotypic instability, in that the level of variegation is dramatically different in different isolates or when out crossed. To test if this phenotypic instability was due to segregation of spontaneously accumulated mutations that suppress variegation, four different and well-characterized strains showing PEV for the white+ gene (wm4, wmMc, wm51b, and wmJ) and representing both large and small spot variegators were repeatedly out crossed to a strain free of modifiers, and the phenotypes of these variegators were monitored for 30 generations. Once free of modifiers, these variegating strains were then allowed to reaccumulate modifiers. The spontaneous suppressors of variegation were found to include both dominant and recessive, autosomal and X-linked alleles selected to reduce the detrimental effects of silencing white+ and adjacent genes. The time of peak sensitivity to temperature during development was also determined for these four variegators. Although large and small spot variegators have previously been attributed to early and late silencing events, respectively, the variegators we examined all shared a common early period of peak sensitivity to temperature. Once free of their variegation suppressors, the different variegating strains showed considerable differences in the frequency of inactivation at a cellular level (the number of cells showing silencing of a given gene) and the extent of variegation within the cell (the number of silenced genes). These results suggest that large and small spot variegation may be a superficial consequence of spontaneous variegation suppressors. The nature and number of these spontaneous variegation suppressors depends on the number of genes silenced in a given variegating rearrangement. These results are interpreted in the context of a model that proposes that the different underlying patterns of gene silencing seen in PEV can be attributed directly to the formation of heterochromatin domains possessing different properties of propagation during cell division.
MeSH term(s)	Animals ; Crosses, Genetic ; Drosophila melanogaster/genetics ; Drosophila melanogaster/growth & development ; Euchromatin/genetics ; Eye Color/genetics ; Female ; Gene Expression Regulation, Developmental ; Gene Rearrangement ; Gene Silencing ; Genes, Insect/genetics ; Heterochromatin/genetics ; Male ; Mutation ; Phenotype ; Temperature
Chemical Substances	Euchromatin ; Heterochromatin
Language	English
Publishing date	2003-12
Publishing country	Canada
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	639031-6
ISSN	1480-3321 ; 0831-2796
ISSN (online)	1480-3321
ISSN	0831-2796
DOI	10.1139/g03-070
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Article ; Online: Drosophila O-GlcNAc transferase (OGT) is encoded by the Polycomb group (PcG) gene, super sex combs (sxc).

Sinclair, Donald A R / Syrzycka, Monika / Macauley, Matthew S / Rastgardani, Tara / Komljenovic, Ivana / Vocadlo, David J / Brock, Hugh W / Honda, Barry M

Proceedings of the National Academy of Sciences of the United States of America

2009 Volume 106, Issue 32, Page(s) 13427–13432

Abstract: O-linked N-acetylglucosamine transferase (OGT) reversibly modifies serine and threonine residues of many intracellular proteins with a single beta-O-linked N-acetylglucosamine residue (O-GlcNAc), and has been implicated in insulin signaling, ... ...

Abstract	O-linked N-acetylglucosamine transferase (OGT) reversibly modifies serine and threonine residues of many intracellular proteins with a single beta-O-linked N-acetylglucosamine residue (O-GlcNAc), and has been implicated in insulin signaling, neurodegenerative disease, cellular stress response, and other important processes in mammals. OGT also glycosylates RNA polymerase II and various transcription factors, which suggests that it might be directly involved in transcriptional regulation. We report here that the Drosophila OGT is encoded by the Polycomb group (PcG) gene, super sex combs (sxc). Furthermore, major sites of O-GlcNAc modification on polytene chromosomes correspond to PcG protein binding sites. Our results thus suggest a direct role for O-linked glycosylation by OGT in PcG-mediated epigenetic gene silencing, which is important in developmental regulation, stem cell maintenance, genomic imprinting, and cancer. In addition, we observe rescue of sxc lethality by a human Ogt cDNA transgene; thus Drosophila may provide an ideal model to study important functional roles of OGT in mammals.
MeSH term(s)	Animals ; Binding Sites ; Chromatin Immunoprecipitation ; Chromosome Mapping ; Chromosomes/metabolism ; Drosophila Proteins/genetics ; Drosophila Proteins/metabolism ; Drosophila melanogaster/enzymology ; Drosophila melanogaster/genetics ; Genes, Insect ; Humans ; Mutation/genetics ; N-Acetylglucosaminyltransferases/genetics ; N-Acetylglucosaminyltransferases/metabolism ; Polycomb-Group Proteins ; Protein Binding ; Protein Processing, Post-Translational ; Protein Transport ; Repressor Proteins/genetics ; Transgenes
Chemical Substances	Drosophila Proteins ; Polycomb-Group Proteins ; Repressor Proteins ; N-Acetylglucosaminyltransferases (EC 2.4.1.-) ; O-GlcNAc transferase (EC 2.4.1.-) ; UDP-N-acetylglucosamine-peptide beta-N-acetylglucosaminyltransferase (EC 2.4.1.-)
Language	English
Publishing date	2009-07-28
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.0904638106
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Article: A genetic and molecular characterization of two proximal heterochromatic genes on chromosome 3 of Drosophila melanogaster.

Schulze, Sandra R / Sinclair, Donald A R / Fitzpatrick, Kathleen A / Honda, Barry M

Genetics

2005 Volume 169, Issue 4, Page(s) 2165–2177

Abstract: Heterochromatin comprises a transcriptionally repressive chromosome compartment in the eukaryotic nucleus; this is exemplified by the silencing effect it has on euchromatic genes that have been relocated nearby, a phenomenon known as position-effect ... ...

Abstract	Heterochromatin comprises a transcriptionally repressive chromosome compartment in the eukaryotic nucleus; this is exemplified by the silencing effect it has on euchromatic genes that have been relocated nearby, a phenomenon known as position-effect variegation (PEV), first demonstrated in Drosophila melanogaster. However, the expression of essential heterochromatic genes within these apparently repressive regions of the genome presents a paradox, an understanding of which could provide key insights into the effects of chromatin structure on gene expression. To date, very few of these resident heterochromatic genes have been characterized to any extent, and their expression and regulation remain poorly understood. Here we report the cloning and characterization of two proximal heterochromatic genes in D. melanogaster, located deep within the centric heterochromatin of the left arm of chromosome 3. One of these genes, RpL15, is uncharacteristically small, is highly expressed, and encodes an essential ribosomal protein. Its expression appears to be compromised in a genetic background deficient for heterochromatin protein 1 (HP1), a protein associated with gene silencing in these regions. The second gene in this study, Dbp80, is very large and also appears to show a transcriptional dependence upon HP1; however, it does not correspond to any known lethal complementation group and is likely to be a nonessential gene.
MeSH term(s)	Alleles ; Animals ; Base Sequence ; Binding Sites ; Blotting, Northern ; Blotting, Southern ; Cell Survival ; Chromatin/genetics ; Chromosome Mapping ; Cloning, Molecular ; Crosses, Genetic ; DNA, Complementary/metabolism ; Drosophila Proteins/biosynthesis ; Drosophila Proteins/genetics ; Drosophila melanogaster/genetics ; Exons ; Female ; Gene Silencing ; Genetic Complementation Test ; Germ-Line Mutation ; Heterochromatin/chemistry ; Heterochromatin/genetics ; Heterozygote ; Introns ; Male ; Models, Genetic ; Molecular Sequence Data ; Mutation ; Phenotype ; Polymerase Chain Reaction ; Ribosomal Proteins/biosynthesis ; Ribosomal Proteins/genetics ; Sequence Analysis, DNA ; Sex Factors ; Transcription Factors/biosynthesis ; Transcription Factors/genetics ; Transcription, Genetic ; Transgenes ; Wings, Animal/embryology ; Wings, Animal/pathology
Chemical Substances	Chromatin ; DNA, Complementary ; Dbp80 protein, Drosophila ; Drosophila Proteins ; Heterochromatin ; Ribosomal Proteins ; RpL15 protein, Drosophila ; Transcription Factors
Language	English
Publishing date	2005-04
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2167-2
ISSN	1943-2631 ; 0016-6731
ISSN (online)	1943-2631
ISSN	0016-6731
DOI	10.1534/genetics.103.023341
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Article: Drosophila O-GlcNAc transferase (OGT) is encoded by the Polycomb group (PcG) gene, super sex combs (sxc)

Sinclair, Donald A.R / Syrzycka, Monika / Macauley, Matthew S / Rastgardani, Tara / Komljenovic, Ivana / Vocadlo, David J / Brock, Hugh W / Honda, Barry M

Proceedings of the National Academy of Sciences of the United States of America. 2009 Aug. 11, v. 106, no. 32

2009

Abstract: O-linked N-acetylglucosamine transferase (OGT) reversibly modifies serine and threonine residues of many intracellular proteins with a single Î²-O-linked N-acetylglucosamine residue (O-GlcNAc), and has been implicated in insulin signaling, ... ...

Abstract	O-linked N-acetylglucosamine transferase (OGT) reversibly modifies serine and threonine residues of many intracellular proteins with a single Î²-O-linked N-acetylglucosamine residue (O-GlcNAc), and has been implicated in insulin signaling, neurodegenerative disease, cellular stress response, and other important processes in mammals. OGT also glycosylates RNA polymerase II and various transcription factors, which suggests that it might be directly involved in transcriptional regulation. We report here that the Drosophila OGT is encoded by the Polycomb group (PcG) gene, super sex combs (sxc). Furthermore, major sites of O-GlcNAc modification on polytene chromosomes correspond to PcG protein binding sites. Our results thus suggest a direct role for O-linked glycosylation by OGT in PcG-mediated epigenetic gene silencing, which is important in developmental regulation, stem cell maintenance, genomic imprinting, and cancer. In addition, we observe rescue of sxc lethality by a human Ogt cDNA transgene; thus Drosophila may provide an ideal model to study important functional roles of OGT in mammals.
Keywords	DNA-directed RNA polymerase ; Drosophila ; N-acetylglucosamine ; binding proteins ; binding sites ; complementary DNA ; gene silencing ; genomic imprinting ; glycosylation ; humans ; insulin ; models ; neoplasms ; neurodegenerative diseases ; polytene chromosomes ; serine ; stem cells ; stress response ; threonine ; transcription (genetics) ; transcription factors ; transgenes
Language	English
Dates of publication	2009-0811
Size	p. 13427-13432.
Publishing place	National Academy of Sciences
Document type	Article
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.0904638106
Database	NAL-Catalogue (AGRICOLA)

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