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Article ; Online: Tet controls axon guidance in early brain development through glutamatergic signaling.

Tran, Hiep / Le, Le / Singh, Badri Nath / Kramer, Joseph / Steward, Ruth

iScience

2024 Volume 27, Issue 5, Page(s) 109634

Abstract: Mutations in ten-eleven translocation (TET) proteins are associated with human neurodevelopmental disorders. We find a function of Tet in ... ...

Abstract	Mutations in ten-eleven translocation (TET) proteins are associated with human neurodevelopmental disorders. We find a function of Tet in regulating
Language	English
Publishing date	2024-04-01
Publishing country	United States
Document type	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2024.109634
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Article: Tet Controls Axon Guidance in Early Brain Development through Glutamatergic Signaling.

Tran, Hiep / Le, Le / Singh, Badri Nath / Kramer, Joseph / Steward, Ruth

bioRxiv : the preprint server for biology

2023

Abstract: Mutations in human TET proteins have been found in individuals with neurodevelopmental disorders. Here we report a new function of Tet in ... ...

Abstract	Mutations in human TET proteins have been found in individuals with neurodevelopmental disorders. Here we report a new function of Tet in regulating
Language	English
Publishing date	2023-07-05
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.05.02.539069
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Article ; Online: Tet-dependent 5-hydroxymethyl-Cytosine modification of mRNA regulates axon guidance genes in Drosophila.

Singh, Badri Nath / Tran, Hiep / Kramer, Joseph / Kirichenko, Elmira / Changela, Neha / Wang, Fei / Feng, Yaping / Kumar, Dibyendu / Tu, Min / Lan, Jie / Bizet, Martin / Fuks, François / Steward, Ruth

PloS one

2024 Volume 19, Issue 2, Page(s) e0293894

Abstract: Modifications of mRNA, especially methylation of adenosine, have recently drawn much attention. The much rarer modification, 5-hydroxymethylation of cytosine (5hmC), is not well understood and is the subject of this study. Vertebrate Tet proteins are 5- ... ...

Abstract	Modifications of mRNA, especially methylation of adenosine, have recently drawn much attention. The much rarer modification, 5-hydroxymethylation of cytosine (5hmC), is not well understood and is the subject of this study. Vertebrate Tet proteins are 5-methylcytosine (5mC) hydroxylases and catalyze the transition of 5mC to 5hmC in DNA. These enzymes have recently been shown to have the same function in messenger RNAs in both vertebrates and in Drosophila. The Tet gene is essential in Drosophila as Tet knock-out animals do not reach adulthood. We describe the identification of Tet-target genes in the embryo and larval brain by mapping one, Tet DNA-binding sites throughout the genome and two, the Tet-dependent 5hmrC modifications transcriptome-wide. 5hmrC modifications are distributed along the entire transcript, while Tet DNA-binding sites are preferentially located at the promoter where they overlap with histone H3K4me3 peaks. The identified mRNAs are preferentially involved in neuron and axon development and Tet knock-out led to a reduction of 5hmrC marks on specific mRNAs. Among the Tet-target genes were the robo2 receptor and its slit ligand that function in axon guidance in Drosophila and in vertebrates. Tet knock-out embryos show overlapping phenotypes with robo2 and both Robo2 and Slit protein levels were markedly reduced in Tet KO larval brains. Our results establish a role for Tet-dependent 5hmrC in facilitating the translation of modified mRNAs primarily in cells of the nervous system.
MeSH term(s)	Animals ; Cytosine/metabolism ; Drosophila/genetics ; Drosophila/metabolism ; DNA Methylation ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Axon Guidance ; DNA-Binding Proteins/metabolism ; 5-Methylcytosine/metabolism ; DNA/metabolism ; Dioxygenases/genetics
Chemical Substances	Cytosine (8J337D1HZY) ; RNA, Messenger ; DNA-Binding Proteins ; 5-Methylcytosine (6R795CQT4H) ; DNA (9007-49-2) ; Dioxygenases (EC 1.13.11.-)
Language	English
Publishing date	2024-02-21
Publishing country	United States
Document type	Journal Article
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0293894
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Article: Tet-dependent 5-hydroxymethyl-Cytosine modification of mRNA regulates the axon guidance genes

Singh, Badri Nath / Tran, Hiep / Kramer, Joseph / Kirishenko, Elmira / Changela, Neha / Wang, Fei / Feng, Yaping / Kumar, Dibyendu / Tu, Min / Lan, Jie / Bizet, Martin / Fuks, François / Steward, Ruth

Research square

2023

Abstract	Modifications of mRNA, especially methylation of adenosine, have recently drawn much attention. The much rarer modification, 5-hydroxymethylation of cytosine (5hmC), is not well understood and is the subject of this study. Vertebrate Tet proteins are 5-methylcytosine (5mC) hydroxylases enzymes catalyzing the transition of 5mC to 5hmC in DNA and have recently been shown to have the same function in messenger RNAs in both vertebrates and in Drosophila. The
Language	English
Publishing date	2023-02-14
Publishing country	United States
Document type	Preprint
DOI	10.21203/rs.3.rs-2511705/v1
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Article: Tet-dependent 5-hydroxymethyl-Cytosine modification of mRNA regulates axon guidance genes in Drosophila.

bioRxiv : the preprint server for biology

2023

Abstract	Modifications of mRNA, especially methylation of adenosine, have recently drawn much attention. The much rarer modification, 5-hydroxymethylation of cytosine (5hmC), is not well understood and is the subject of this study. Vertebrate Tet proteins are 5-methylcytosine (5mC) hydroxylases and catalyze the transition of 5mC to 5hmC in DNA. These enzymes have recently been shown to have the same function in messenger RNAs in both vertebrates and in Drosophila. The Tet gene is essential in Drosophila as Tet knock-out animals do not reach adulthood. We describe the identification of Tet-target genes in the embryo and larval brain by mapping one, Tet DNA-binding sites throughout the genome and two, the Tet-dependent 5hmrC modifications transcriptome-wide. 5hmrC modifications are distributed along the entire transcript, while Tet DNA-binding sites are preferentially located at the promoter where they overlap with histone H3K4me3 peaks. The identified mRNAs are preferentially involved in neuron and axon development and Tet knock-out led to a reduction of 5hmrC marks on specific mRNAs. Among the Tet-target genes were the robo2 receptor and its slit ligand that function in axon guidance in Drosophila and in vertebrates. Tet knock-out embryos show overlapping phenotypes with robo2 and both Robo2 and Slit protein levels were markedly reduced in Tet KO larval brains. Our results establish a role for Tet-dependent 5hmrC in facilitating the translation of modified mRNAs primarily in cells of the nervous system.
Language	English
Publishing date	2023-08-04
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.01.03.522592
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Article ; Online: Tet protein function during Drosophila development.

Wang, Fei / Minakhina, Svetlana / Tran, Hiep / Changela, Neha / Kramer, Joseph / Steward, Ruth

PloS one

2018 Volume 13, Issue 1, Page(s) e0190367

Abstract: The TET (Ten-eleven translocation) 1, 2 and 3 proteins have been shown to function as DNA hydroxymethylases in vertebrates and their requirements have been documented extensively. Recently, the Tet proteins have been shown to also hydroxylate 5- ... ...

Abstract	The TET (Ten-eleven translocation) 1, 2 and 3 proteins have been shown to function as DNA hydroxymethylases in vertebrates and their requirements have been documented extensively. Recently, the Tet proteins have been shown to also hydroxylate 5-methylcytosine in RNA. 5-hydroxymethylcytosine (5hmrC) is enriched in messenger RNA but the function of this modification has yet to be elucidated. Because Cytosine methylation in DNA is barely detectable in Drosophila, it serves as an ideal model to study the biological function of 5hmrC. Here, we characterized the temporal and spatial expression and requirement of Tet throughout Drosophila development. We show that Tet is essential for viability as Tet complete loss-of-function animals die at the late pupal stage. Tet is highly expressed in neuronal tissues and at more moderate levels in somatic muscle precursors in embryos and larvae. Depletion of Tet in muscle precursors at early embryonic stages leads to defects in larval locomotion and late pupal lethality. Although Tet knock-down in neuronal tissue does not cause lethality, it is essential for neuronal function during development through its affects upon locomotion in larvae and the circadian rhythm of adult flies. Further, we report the function of Tet in ovarian morphogenesis. Together, our findings provide basic insights into the biological function of Tet in Drosophila, and may illuminate observed neuronal and muscle phenotypes observed in vertebrates.
MeSH term(s)	Animals ; Circadian Rhythm ; DNA Methylation ; DNA-Binding Proteins/physiology ; Drosophila/embryology ; Drosophila/growth & development ; Female ; Locomotion ; Muscles/physiology ; Neurons/physiology ; Ovary/embryology ; Ovary/growth & development
Chemical Substances	DNA-Binding Proteins
Language	English
Publishing date	2018
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.0190367
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Article ; Online: Zfrp8/PDCD2 Interacts with RpS2 Connecting Ribosome Maturation and Gene-Specific Translation.

Minakhina, Svetlana / Naryshkina, Tatyana / Changela, Neha / Tan, William / Steward, Ruth

PloS one

2016 Volume 11, Issue 1, Page(s) e0147631

Abstract: Zfrp8/PDCD2 is a highly conserved protein essential for stem cell maintenance in both flies and mammals. It is also required in fast proliferating cells such as cancer cells. Our previous studies suggested that Zfrp8 functions in the formation of mRNP ( ... ...

Abstract	Zfrp8/PDCD2 is a highly conserved protein essential for stem cell maintenance in both flies and mammals. It is also required in fast proliferating cells such as cancer cells. Our previous studies suggested that Zfrp8 functions in the formation of mRNP (mRNA ribonucleoprotein) complexes and also controls RNA of select Transposable Elements (TEs). Here we show that in Zfrp8/PDCD2 knock down (KD) ovaries, specific mRNAs and TE transcripts show increased nuclear accumulation. We also show that Zfrp8/PDCD2 interacts with the (40S) small ribosomal subunit through direct interaction with RpS2 (uS5). By studying the distribution of endogenous and transgenic fluorescently tagged ribosomal proteins we demonstrate that Zfrp8/PDCD2 regulates the cytoplasmic levels of components of the small (40S) ribosomal subunit, but does not control nuclear/nucleolar localization of ribosomal proteins. Our results suggest that Zfrp8/PDCD2 functions at late stages of ribosome assembly and may regulate the binding of specific mRNA-RNPs to the small ribosomal subunit ultimately controlling their cytoplasmic localization and translation.
MeSH term(s)	Animals ; Animals, Genetically Modified ; Apoptosis Regulatory Proteins/genetics ; Apoptosis Regulatory Proteins/metabolism ; Drosophila Proteins/genetics ; Drosophila Proteins/metabolism ; Drosophila melanogaster ; Protein Biosynthesis ; Ribosomal Proteins/genetics ; Ribosomal Proteins/metabolism ; Ribosomes/genetics ; Ribosomes/metabolism
Chemical Substances	Apoptosis Regulatory Proteins ; Drosophila Proteins ; Ribosomal Proteins ; Zfrp8 protein, Drosophila ; ribosomal protein S2
Language	English
Publishing date	2016-01-25
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0147631
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Article ; Online: Zfrp8 forms a complex with fragile-X mental retardation protein and regulates its localization and function.

Tan, William / Schauder, Curtis / Naryshkina, Tatyana / Minakhina, Svetlana / Steward, Ruth

Developmental biology

2016 Volume 410, Issue 2, Page(s) 202–212

Abstract: Fragile-X syndrome is the most commonly inherited cause of autism and mental disabilities. The Fmr1 (Fragile-X Mental Retardation 1) gene is essential in humans and Drosophila for the maintenance of neural stem cells, and Fmr1 loss results in ... ...

Abstract	Fragile-X syndrome is the most commonly inherited cause of autism and mental disabilities. The Fmr1 (Fragile-X Mental Retardation 1) gene is essential in humans and Drosophila for the maintenance of neural stem cells, and Fmr1 loss results in neurological and reproductive developmental defects in humans and flies. FMRP (Fragile-X Mental Retardation Protein) is a nucleo-cytoplasmic shuttling protein, involved in mRNA silencing and translational repression. Both Zfrp8 and Fmr1 have essential functions in the Drosophila ovary. In this study, we identified FMRP, Nufip (Nuclear Fragile-X Mental Retardation Protein-interacting Protein) and Tral (Trailer Hitch) as components of a Zfrp8 protein complex. We show that Zfrp8 is required in the nucleus, and controls localization of FMRP in the cytoplasm. In addition, we demonstrate that Zfrp8 genetically interacts with Fmr1 and tral in an antagonistic manner. Zfrp8 and FMRP both control heterochromatin packaging, also in opposite ways. We propose that Zfrp8 functions as a chaperone, controlling protein complexes involved in RNA processing in the nucleus.
MeSH term(s)	Animals ; Apoptosis Regulatory Proteins/genetics ; Apoptosis Regulatory Proteins/metabolism ; Apoptosis Regulatory Proteins/physiology ; Cell Nucleus/metabolism ; Drosophila ; Drosophila Proteins/genetics ; Drosophila Proteins/metabolism ; Drosophila Proteins/physiology ; Female ; Fragile X Mental Retardation Protein/genetics ; Fragile X Mental Retardation Protein/metabolism ; Fragile X Mental Retardation Protein/physiology ; Infertility, Female/genetics ; Male ; Oogenesis ; Ovary/abnormalities
Chemical Substances	Apoptosis Regulatory Proteins ; Drosophila Proteins ; FMR1 protein, Drosophila ; Zfrp8 protein, Drosophila ; Fragile X Mental Retardation Protein (139135-51-6)
Language	English
Publishing date	2016-02-15
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.2015.12.008
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Article ; Online: Discs large 5, an Essential Gene in Drosophila, Regulates Egg Chamber Organization.

Reilly, Eve / Changela, Neha / Naryshkina, Tatyana / Deshpande, Girish / Steward, Ruth

G3 (Bethesda, Md.)

2015 Volume 5, Issue 5, Page(s) 943–952

Abstract: Discs large 5 (Dlg5) is a member of the MAGUK family of proteins that typically serve as molecular scaffolds and mediate signaling complex formation and localization. In vertebrates, Dlg5 has been shown to be responsible for polarization of neural ... ...

Abstract	Discs large 5 (Dlg5) is a member of the MAGUK family of proteins that typically serve as molecular scaffolds and mediate signaling complex formation and localization. In vertebrates, Dlg5 has been shown to be responsible for polarization of neural progenitors and to associate with Rab11-positive vesicles in epithelial cells. In Drosophila, however, the function of Dlg5 is not well-documented. We have identified dlg5 as an essential gene that shows embryonic lethality. dlg5 embryos display partial loss of primordial germ cells (PGCs) during gonad coalescence between stages 12 and 15 of embryogenesis. Loss of Dlg5 in germline and somatic stem cells in the ovary results in the depletion of both cell lineages. Reduced expression of Dlg5 in the follicle cells of the ovary leads to a number of distinct phenotypes, including defects in egg chamber budding, stalk cell overgrowth, and ectopic polar cell induction. Interestingly, loss of Dlg5 in follicle cells results in abnormal distribution of a critical component of cell adhesion, E-cadherin, shown to be essential for proper organization of egg chambers.
MeSH term(s)	Alleles ; Animals ; Cadherins/genetics ; Cadherins/metabolism ; Cell Movement/genetics ; Chromosome Mapping ; Drosophila/genetics ; Drosophila Proteins/genetics ; Drosophila Proteins/metabolism ; Female ; Gene Deletion ; Gene Knockout Techniques ; Genes, Essential ; Genetic Association Studies ; Germ Cells/metabolism ; Oogenesis/genetics ; Ovarian Follicle/cytology ; Ovarian Follicle/metabolism ; Phenotype ; Protein Transport
Chemical Substances	Cadherins ; Drosophila Proteins
Language	English
Publishing date	2015-03-19
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; 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/g3.115.017558
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Article ; Online: Zfrp8/PDCD2 is required in ovarian stem cells and interacts with the piRNA pathway machinery.

Minakhina, Svetlana / Changela, Neha / Steward, Ruth

Development (Cambridge, England)

2013 Volume 141, Issue 2, Page(s) 259–268

Abstract: The maintenance of stem cells is central to generating diverse cell populations in many tissues throughout the life of an animal. Elucidating the mechanisms involved in how stem cells are formed and maintained is crucial to understanding both normal ... ...

Abstract	The maintenance of stem cells is central to generating diverse cell populations in many tissues throughout the life of an animal. Elucidating the mechanisms involved in how stem cells are formed and maintained is crucial to understanding both normal developmental processes and the growth of many cancers. Previously, we showed that Zfrp8/PDCD2 is essential for the maintenance of Drosophila hematopoietic stem cells. Here, we show that Zfrp8/PDCD2 is also required in both germline and follicle stem cells in the Drosophila ovary. Expression of human PDCD2 fully rescues the Zfrp8 phenotype, underlining the functional conservation of Zfrp8/PDCD2. The piRNA pathway is essential in early oogenesis, and we find that nuclear localization of Zfrp8 in germline stem cells and their offspring is regulated by some piRNA pathway genes. We also show that Zfrp8 forms a complex with the piRNA pathway protein Maelstrom and controls the accumulation of Maelstrom in the nuage. Furthermore, Zfrp8 regulates the activity of specific transposable elements also controlled by Maelstrom and Piwi. Our results suggest that Zfrp8/PDCD2 is not an integral member of the piRNA pathway, but has an overlapping function, possibly competing with Maelstrom and Piwi.
MeSH term(s)	Animals ; Animals, Genetically Modified ; Apoptosis Regulatory Proteins/antagonists & inhibitors ; Apoptosis Regulatory Proteins/genetics ; Apoptosis Regulatory Proteins/metabolism ; Argonaute Proteins/genetics ; Argonaute Proteins/metabolism ; DNA Transposable Elements/genetics ; Drosophila Proteins/antagonists & inhibitors ; Drosophila Proteins/genetics ; Drosophila Proteins/metabolism ; Drosophila melanogaster/genetics ; Drosophila melanogaster/growth & development ; Drosophila melanogaster/metabolism ; Female ; Germ Cells/cytology ; Germ Cells/metabolism ; Humans ; Oocytes/cytology ; Oocytes/metabolism ; Oogenesis/genetics ; Oogenesis/physiology ; Ovary/cytology ; Ovary/growth & development ; Ovary/metabolism ; RNA Interference ; RNA, Small Interfering/genetics ; RNA, Small Interfering/metabolism ; Stem Cells/cytology ; Stem Cells/metabolism
Chemical Substances	Apoptosis Regulatory Proteins ; Argonaute Proteins ; DNA Transposable Elements ; Drosophila Proteins ; PDCD2 protein, human ; RNA, Small Interfering ; Zfrp8 protein, Drosophila ; mael protein, Drosophila ; piwi protein, Drosophila
Language	English
Publishing date	2013-12-30
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	90607-4
ISSN	1477-9129 ; 0950-1991
ISSN (online)	1477-9129
ISSN	0950-1991
DOI	10.1242/dev.101410
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