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Article: P-Bodies: Cytosolic Droplets for Coordinated mRNA Storage.

Standart, Nancy / Weil, Dominique

2018 Volume 34, Issue 8, Page(s) 612–626

Abstract: P-bodies (PBs) are cytosolic RNP granules that are conserved among eukaryotic organisms. In the past few years, major progress has been made in understanding the biochemical and biophysical mechanisms that lead to their formation. However, whether they ... ...

Abstract	P-bodies (PBs) are cytosolic RNP granules that are conserved among eukaryotic organisms. In the past few years, major progress has been made in understanding the biochemical and biophysical mechanisms that lead to their formation. However, whether they play a role in mRNA storage or decay remains actively debated. P-bodies were recently isolated from human cells by a novel fluorescence-activated particle sorting (FAPS) approach that enabled the characterization of their protein and RNA content, providing new insights into their function. Together with recent innovative imaging studies, these new data show that mammalian PBs are primarily involved not in RNA decay but rather in the coordinated storage of mRNAs encoding regulatory functions. These small cytoplasmic droplets could thus be important for cell adaptation to the environment.
MeSH term(s)	Animals ; Chromatin/genetics ; Chromatin/metabolism ; Cytoplasmic Granules/genetics ; Cytoplasmic Granules/metabolism ; Cytoplasmic Granules/ultrastructure ; Humans ; Organelles/metabolism ; Organelles/ultrastructure ; RNA Stability ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; RNA, Messenger, Stored/genetics ; RNA, Messenger, Stored/metabolism ; Ribonucleoproteins/metabolism
Chemical Substances	Chromatin ; RNA, Messenger ; RNA, Messenger, Stored ; Ribonucleoproteins
Language	English
Publishing date	2018-06-13
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	619240-3
ISSN	1362-4555 ; 0168-9525 ; 0168-9479
ISSN (online)	1362-4555
ISSN	0168-9525 ; 0168-9479
DOI	10.1016/j.tig.2018.05.005
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Article ; Online: Mutations in genes encoding regulators of mRNA decapping and translation initiation: links to intellectual disability.

Weil, Dominique / Piton, Amélie / Lessel, Davor / Standart, Nancy

Biochemical Society transactions

2020 Volume 48, Issue 3, Page(s) 1199–1211

Abstract: Intellectual disability (ID) affects at least 1% of the population, and typically presents in the first few years of life. ID is characterized by impairments in cognition and adaptive behavior and is often accompanied by further delays in language and ... ...

Abstract	Intellectual disability (ID) affects at least 1% of the population, and typically presents in the first few years of life. ID is characterized by impairments in cognition and adaptive behavior and is often accompanied by further delays in language and motor skills, as seen in many neurodevelopmental disorders (NDD). Recent widespread high-throughput approaches that utilize whole-exome sequencing or whole-genome sequencing have allowed for a considerable increase in the identification of these pathogenic variants in monogenic forms of ID. Notwithstanding this progress, the molecular and cellular consequences of the identified mutations remain mostly unknown. This is particularly important as the associated protein dysfunctions are the prerequisite to the identification of targets for novel drugs of these rare disorders. Recent Next-Generation sequencing-based studies have further established that mutations in genes encoding proteins involved in RNA metabolism are a major cause of NDD. Here, we review recent studies linking germline mutations in genes encoding factors mediating mRNA decay and regulators of translation, namely DCPS, EDC3, DDX6 helicase and ID. These RNA-binding proteins have well-established roles in mRNA decapping and/or translational repression, and the mutations abrogate their ability to remove 5' caps from mRNA, diminish their interactions with cofactors and stabilize sub-sets of transcripts. Additional genes encoding RNA helicases with roles in translation including DDX3X and DHX30 have also been linked to NDD. Given the speed in the acquisition, analysis and sharing of sequencing data, and the importance of post-transcriptional regulation for brain development, we anticipate mutations in more such factors being identified and functionally characterized.
MeSH term(s)	Animals ; DEAD-box RNA Helicases/genetics ; Germ-Line Mutation ; High-Throughput Nucleotide Sequencing ; Homozygote ; Humans ; Intellectual Disability/genetics ; Mutation ; Mutation, Missense ; Neurodevelopmental Disorders/genetics ; Pedigree ; Peptide Chain Initiation, Translational ; Protein Binding ; Protein Biosynthesis ; RNA/metabolism ; RNA Helicases/genetics ; RNA Stability ; RNA, Messenger/genetics ; Whole Exome Sequencing
Chemical Substances	RNA, Messenger ; RNA (63231-63-0) ; DHX30 protein, human (EC 2.7.7.-) ; DDX3X protein, human (EC 3.6.1.-) ; DEAD-box RNA Helicases (EC 3.6.4.13) ; RNA Helicases (EC 3.6.4.13)
Language	English
Publishing date	2020-05-11
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	184237-7
ISSN	1470-8752 ; 0300-5127
ISSN (online)	1470-8752
ISSN	0300-5127
DOI	10.1042/BST20200109
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Article ; Online: Pat1 RNA-binding proteins: Multitasking shuttling proteins.

Vindry, Caroline / Weil, Dominique / Standart, Nancy

Wiley interdisciplinary reviews. RNA

2019 Volume 10, Issue 6, Page(s) e1557

Abstract: Post-transcriptional regulation of gene expression is largely achieved at the level of splicing in the nucleus, and translation and mRNA decay in the cytosol. While the regulation may be global, through the direct inhibition of central factors, such as ... ...

Abstract	Post-transcriptional regulation of gene expression is largely achieved at the level of splicing in the nucleus, and translation and mRNA decay in the cytosol. While the regulation may be global, through the direct inhibition of central factors, such as the spliceosome, translation initiation factors and mRNA decay enzymes, in many instances transcripts bearing specific sequences or particular features are regulated by RNA-binding factors which mobilize or impede recruitment of these machineries. This review focuses on the Pat1 family of RNA-binding proteins, conserved from yeast to man, that enhance the removal of the 5' cap by the decapping enzyme Dcp1/2, leading to mRNA decay and also have roles in translational repression. Like Dcp1/2, other decapping coactivators, including DDX6 and Edc3, and translational repressor proteins, Pat1 proteins are enriched in cytoplasmic P-bodies, which have a principal role in mRNA storage. They also concentrate in nuclear Cajal-bodies and splicing speckles and in man, impact splice site choice in some pre-mRNAs. Pivotal to these functions is the association of Pat1 proteins with distinct heptameric Lsm complexes: the cytosolic Pat1/Lsm1-7 complex mediates mRNA decay and the nuclear Pat1/Lsm2-8 complex alternative splicing. This dual role of human Pat1b illustrates the power of paralogous complexes to impact distinct processes in separate compartments. The review highlights our recent findings that Pat1b mediates the decay of AU-rich mRNAs, which are particularly enriched in P-bodies, unlike the decapping activator DDX6, which acts on GC-rich mRNAs, that tend to be excluded from P-bodies, and discuss the implications for mRNA decay pathways. This article is categorized under: RNA Turnover and Surveillance > Regulation of RNA Stability RNRNA Processing > Splicing Regulation/Alternative Splicing Translation > Translation Regulation.
MeSH term(s)	Humans ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; RNA-Binding Proteins/genetics ; RNA-Binding Proteins/metabolism
Chemical Substances	RNA, Messenger ; RNA-Binding Proteins
Language	English
Publishing date	2019-06-24
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2634714-3
ISSN	1757-7012 ; 1757-7004
ISSN (online)	1757-7012
ISSN	1757-7004
DOI	10.1002/wrna.1557
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Article ; Online: The awesome power of ribosome profiling.

Jackson, Richard / Standart, Nancy

RNA (New York, N.Y.)

2015 Volume 21, Issue 4, Page(s) 652–654

MeSH term(s)	Crystallography, X-Ray ; Nucleic Acid Conformation ; Open Reading Frames ; RNA, Messenger/chemistry ; RNA, Messenger/genetics ; Ribosomes/metabolism
Chemical Substances	RNA, Messenger
Language	English
Publishing date	2015-04
Publishing country	United States
Document type	Journal Article
ZDB-ID	1241540-6
ISSN	1469-9001 ; 1355-8382
ISSN (online)	1469-9001
ISSN	1355-8382
DOI	10.1261/rna.049908.115
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Article: Pat1 proteins: regulating mRNAs from birth to death?

Standart, Nancy / Marnef, Aline

Biomolecular concepts

2012 Volume 3, Issue 4, Page(s) 295–306

Abstract: Abstract The Pat1 protein family has been the subject of several recent extensive investigations of diverse model systems ranging from yeast, flies and worms to man, using a variety of experimental approaches. Although some contradictions remain, the ... ...

Abstract	Abstract The Pat1 protein family has been the subject of several recent extensive investigations of diverse model systems ranging from yeast, flies and worms to man, using a variety of experimental approaches. Although some contradictions remain, the emerging consensus view is that these RNA-binding proteins act in mRNA decay by physically linking deadenylation with decapping and by regulating gene expression as translational repressors. These multiple functions are present in the single invertebrate Pat1 proteins, whereas, in vertebrates, one Pat1 variant represses translation in early development, while a somatic version synthesised in embrogenesis and in adults acts in mRNA decay. At steady state, Pat1 proteins are found enriched in cytoplasmic P(rocessing)-bodies, and related mRNP complexes and granules. Evidence recently obtained from mammalian tissue culture cells shows that Pat1 shuttles in and out of the nucleus, where it localises to nuclear speckles, PML bodies and nucleolar caps, which suggests RNA-related nuclear functions. Less well understood, Pat1 proteins may play additional roles in miRNA silencing and/or biogenesis, as well in the regulation of viral gene expression. Due to the relatively low level of sequence conservation between Pat1 proteins from different species and lacking any discernable motifs, determining their functional domains has proved difficult, as is obtaining a simple unified view of the location of the binding sites of their interacting proteins in all examined species. Questions that remain to be addressed include the following: 1) What are their roles in the nucleus? 2) What is the link, if one exists, between their cytoplasmic and nuclear roles? 3) Do they have specific mRNA targets? 4) Which signalling pathways regulate their P-body localisation in mammalian cells, which may affect quiescent cell survival?
Language	English
Publishing date	2012-08
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2557908-3
ISSN	1868-503X ; 1868-5021
ISSN (online)	1868-503X
ISSN	1868-5021
DOI	10.1515/bmc-2012-0005
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Article ; Online: CPEB and miR-15/16 Co-Regulate Translation of Cyclin E1 mRNA during Xenopus Oocyte Maturation.

Wilczynska, Ania / Git, Anna / Argasinska, Joanna / Belloc, Eulàlia / Standart, Nancy

PloS one

2016 Volume 11, Issue 2, Page(s) e0146792

Abstract: Cell cycle transitions spanning meiotic maturation of the Xenopus oocyte and early embryogenesis are tightly regulated at the level of stored inactive maternal mRNA. We investigated here the translational control of cyclin E1, required for metaphase II ... ...

Abstract	Cell cycle transitions spanning meiotic maturation of the Xenopus oocyte and early embryogenesis are tightly regulated at the level of stored inactive maternal mRNA. We investigated here the translational control of cyclin E1, required for metaphase II arrest of the unfertilised egg and the initiation of S phase in the early embryo. We show that the cyclin E1 mRNA is regulated by both cytoplasmic polyadenylation elements (CPEs) and two miR-15/16 target sites within its 3'UTR. Moreover, we provide evidence that maternal miR-15/16 microRNAs co-immunoprecipitate with CPE-binding protein (CPEB), and that CPEB interacts with the RISC component Ago2. Experiments using competitor RNA and mutated cyclin E1 3'UTRs suggest cooperation of the regulatory elements to sustain repression of the cyclin E1 mRNA during early stages of maturation when CPEB becomes limiting and cytoplasmic polyadenylation of repressed mRNAs begins. Importantly, injection of anti-miR-15/16 LNA results in the early polyadenylation of endogenous cyclin E1 mRNA during meiotic maturation, and an acceleration of GVBD, altogether strongly suggesting that the proximal CPEB and miRNP complexes act to mutually stabilise each other. We conclude that miR-15/16 and CPEB co-regulate cyclin E1 mRNA. This is the first demonstration of the co-operation of these two pathways.
MeSH term(s)	Animals ; Base Sequence ; Cyclin E/genetics ; Cyclin E/metabolism ; Female ; Meiosis ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Models, Biological ; Molecular Sequence Data ; Oocytes/metabolism ; Oogenesis/genetics ; Protein Biosynthesis/genetics ; RNA 3' Polyadenylation Signals/genetics ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; RNA-Induced Silencing Complex/metabolism ; Transcription Factors/metabolism ; Xenopus Proteins/genetics ; Xenopus Proteins/metabolism ; Xenopus laevis/metabolism ; mRNA Cleavage and Polyadenylation Factors/metabolism
Chemical Substances	Cpeb1 protein, Xenopus ; Cyclin E ; MIRN15 microRNA, Xenopus ; MIRN16 microRNA, Xenopus ; MicroRNAs ; RNA, Messenger ; RNA-Induced Silencing Complex ; Transcription Factors ; Xenopus Proteins ; cyclin E1, Xenopus ; mRNA Cleavage and Polyadenylation Factors
Language	English
Publishing date	2016-02-01
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.0146792
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Article ; Online: eIF4E-binding proteins: new factors, new locations, new roles.

Kamenska, Anastasiia / Simpson, Clare / Standart, Nancy

Biochemical Society transactions

2014 Volume 42, Issue 4, Page(s) 1238–1245

Abstract: The cap-binding translation initiation factor eIF4E (eukaryotic initiation factor 4E) is central to protein synthesis in eukaryotes. As an integral component of eIF4F, a complex also containing the large bridging factor eIF4G and eIF4A RNA helicase, ... ...

Abstract	The cap-binding translation initiation factor eIF4E (eukaryotic initiation factor 4E) is central to protein synthesis in eukaryotes. As an integral component of eIF4F, a complex also containing the large bridging factor eIF4G and eIF4A RNA helicase, eIF4E enables the recruitment of the small ribosomal subunit to the 5' end of mRNAs. The interaction between eIF4E and eIF4G via a YXXXXLϕ motif is regulated by small eIF4E-binding proteins, 4E-BPs, which use the same sequence to competitively bind eIF4E thereby inhibiting cap-dependent translation. Additional eIF4E-binding proteins have been identified in the last 10-15 years, characterized by the YXXXXLϕ motif, and by interactions (many of which remain to be detailed) with RNA-binding proteins, or other factors in complexes that recognize the specific mRNAs. In the present article, we focus on the metazoan 4E-T (4E-transporter)/Cup family of eIF4E-binding proteins, and also discuss very recent examples in yeast, fruitflies and humans, some of which predictably inhibit translation, while others may result in mRNA decay or even enhance translation; altogether considerably expanding our understanding of the roles of eIF4E-binding proteins in gene expression regulation.
MeSH term(s)	Animals ; Eukaryotic Initiation Factor-4E/genetics ; Eukaryotic Initiation Factor-4E/metabolism ; Humans ; RNA Stability/genetics ; RNA Stability/physiology ; RNA-Binding Proteins/genetics ; RNA-Binding Proteins/metabolism
Chemical Substances	Eukaryotic Initiation Factor-4E ; RNA-Binding Proteins
Language	English
Publishing date	2014-08
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	184237-7
ISSN	1470-8752 ; 0300-5127
ISSN (online)	1470-8752
ISSN	0300-5127
DOI	10.1042/BST20140063
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Article ; Online: Pat1 proteins: a life in translation, translation repression and mRNA decay.

Marnef, Aline / Standart, Nancy

Biochemical Society transactions

2010 Volume 38, Issue 6, Page(s) 1602–1607

Abstract: Pat1 proteins are conserved across eukaryotes. Vertebrates have evolved two Pat1 proteins paralogues, whereas invertebrates and yeast only possess one such protein. Despite their lack of known domains or motifs, Pat1 proteins are involved in several key ... ...

Abstract	Pat1 proteins are conserved across eukaryotes. Vertebrates have evolved two Pat1 proteins paralogues, whereas invertebrates and yeast only possess one such protein. Despite their lack of known domains or motifs, Pat1 proteins are involved in several key post-transcriptional mechanisms of gene expression control. In yeast, Pat1p interacts with translating mRNPs (messenger ribonucleoproteins), and is responsible for translational repression and decapping activation, ultimately leading to mRNP degradation. Drosophila HPat and human Pat1b (PatL1) proteins also have conserved roles in the 5'→3' mRNA decay pathway. Consistent with their functions in silencing gene expression, Pat1 proteins localize to P-bodies (processing bodies) in yeast, Drosophila, Caenorhabditis elegans and human cells. Altogether, Pat1 proteins may act as scaffold proteins allowing the sequential binding of repression and decay factors on mRNPs, eventually leading to their degradation. In the present mini-review, we present the current knowledge on Pat1 proteins in the context of their multiple functions in post-transcriptional control.
MeSH term(s)	Animals ; DNA-Binding Proteins/classification ; DNA-Binding Proteins/genetics ; DNA-Binding Proteins/metabolism ; Evolution, Molecular ; Fungal Proteins/genetics ; Fungal Proteins/metabolism ; Gene Expression Regulation ; Humans ; Phylogeny ; Protein Biosynthesis ; Protein Isoforms/genetics ; Protein Isoforms/metabolism ; RNA Stability ; RNA-Binding Proteins/classification ; RNA-Binding Proteins/genetics ; RNA-Binding Proteins/metabolism
Chemical Substances	DNA-Binding Proteins ; Fungal Proteins ; Protein Isoforms ; RNA-Binding Proteins
Language	English
Publishing date	2010-12
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	184237-7
ISSN	1470-8752 ; 0300-5127
ISSN (online)	1470-8752
ISSN	0300-5127
DOI	10.1042/BST0381602
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Article ; Online: Pat1 proteins

Standart Nancy / Marnef Aline

Biomolecular Concepts, Vol 3, Iss 4, Pp 295-

regulating mRNAs from birth to death?

2012 Volume 306

Abstract: The Pat1 protein family has been the subject of several recent extensive investigations of diverse model systems ranging from yeast, flies and worms to man, using a variety of experimental approaches. Although some contradictions remain, the emerging ... ...

Abstract	The Pat1 protein family has been the subject of several recent extensive investigations of diverse model systems ranging from yeast, flies and worms to man, using a variety of experimental approaches. Although some contradictions remain, the emerging consensus view is that these RNA-binding proteins act in mRNA decay by physically linking deadenylation with decapping and by regulating gene expression as translational repressors. These multiple functions are present in the single invertebrate Pat1 proteins, whereas, in vertebrates, one Pat1 variant represses translation in early development, while a somatic version synthesised in embrogenesis and in adults acts in mRNA decay. At steady state, Pat1 proteins are found enriched in cytoplasmic P(rocessing)-bodies, and related mRNP complexes and granules. Evidence recently obtained from mammalian tissue culture cells shows that Pat1 shuttles in and out of the nucleus, where it localises to nuclear speckles, PML bodies and nucleolar caps, which suggests RNA-related nuclear functions. Less well understood, Pat1 proteins may play additional roles in miRNA silencing and/or biogenesis, as well in the regulation of viral gene expression. Due to the relatively low level of sequence conservation between Pat1 proteins from different species and lacking any discernable motifs, determining their functional domains has proved difficult, as is obtaining a simple unified view of the location of the binding sites of their interacting proteins in all examined species. Questions that remain to be addressed include the following: 1) What are their roles in the nucleus? 2) What is the link, if one exists, between their cytoplasmic and nuclear roles? 3) Do they have specific mRNA targets? 4) Which signalling pathways regulate their P-body localisation in mammalian cells, which may affect quiescent cell survival?
Keywords	4e-t ; hela cells ; pat1b ; rck/p54/dhh1 ; xenopus oocytes ; Biology (General) ; QH301-705.5
Subject code	570
Language	English
Publishing date	2012-08-01T00:00:00Z
Publisher	De Gruyter
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: CPEB and miR-15/16 Co-Regulate Translation of Cyclin E1 mRNA during Xenopus Oocyte Maturation.

Ania Wilczynska / Anna Git / Joanna Argasinska / Eulàlia Belloc / Nancy Standart

PLoS ONE, Vol 11, Iss 2, p e

2016 Volume 0146792

Abstract	Cell cycle transitions spanning meiotic maturation of the Xenopus oocyte and early embryogenesis are tightly regulated at the level of stored inactive maternal mRNA. We investigated here the translational control of cyclin E1, required for metaphase II arrest of the unfertilised egg and the initiation of S phase in the early embryo. We show that the cyclin E1 mRNA is regulated by both cytoplasmic polyadenylation elements (CPEs) and two miR-15/16 target sites within its 3'UTR. Moreover, we provide evidence that maternal miR-15/16 microRNAs co-immunoprecipitate with CPE-binding protein (CPEB), and that CPEB interacts with the RISC component Ago2. Experiments using competitor RNA and mutated cyclin E1 3'UTRs suggest cooperation of the regulatory elements to sustain repression of the cyclin E1 mRNA during early stages of maturation when CPEB becomes limiting and cytoplasmic polyadenylation of repressed mRNAs begins. Importantly, injection of anti-miR-15/16 LNA results in the early polyadenylation of endogenous cyclin E1 mRNA during meiotic maturation, and an acceleration of GVBD, altogether strongly suggesting that the proximal CPEB and miRNP complexes act to mutually stabilise each other. We conclude that miR-15/16 and CPEB co-regulate cyclin E1 mRNA. This is the first demonstration of the co-operation of these two pathways.
Keywords	Medicine ; R ; Science ; Q
Subject code	571
Language	English
Publishing date	2016-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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