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Article ; Online: Different means, same end-heterochromatin formation by RNAi and RNAi-independent RNA processing factors in fission yeast.

Reyes-Turcu, Francisca E / Grewal, Shiv Is

Current opinion in genetics & development

2012 Volume 22, Issue 2, Page(s) 156–163

Abstract: The assembly of heterochromatin in eukaryotic genomes is critical for diverse chromosomal events including regulation of gene expression, silencing of repetitive DNA elements, proper segregation of chromosomes and maintenance of genomic integrity. ... ...

Abstract	The assembly of heterochromatin in eukaryotic genomes is critical for diverse chromosomal events including regulation of gene expression, silencing of repetitive DNA elements, proper segregation of chromosomes and maintenance of genomic integrity. Previous studies have shown that noncoding RNAs and the RNA interference (RNAi) machinery promote the assembly of heterochromatin that serves as a multipurpose platform for targeting effectors involved in various chromosomal processes. Recent work has revealed that RNAi-independent mechanisms, involving RNA processing activities that utilize both noncoding and coding RNAs, operate in the assembly of heterochromatin. These findings have established that, in addition to coding for proteins, mRNAs also function as signaling molecules that modify chromatin structure by targeting heterochromatin assembly factors.
MeSH term(s)	Animals ; Heterochromatin ; Humans ; RNA Interference ; RNA, Fungal/genetics ; RNA, Messenger/genetics ; Schizosaccharomyces/genetics
Chemical Substances	Heterochromatin ; RNA, Fungal ; RNA, Messenger
Language	English
Publishing date	2012-01-11
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Intramural ; Review
ZDB-ID	1077312-5
ISSN	1879-0380 ; 0959-437X
ISSN (online)	1879-0380
ISSN	0959-437X
DOI	10.1016/j.gde.2011.12.004
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Article: Different means, same end—heterochromatin formation by RNAi and RNAi-independent RNA processing factors in fission yeast

Reyes-Turcu, Francisca E / Grewal, Shiv IS

Current Opinion in Genetics & Development. 2012 Apr., v. 22, no. 2

2012

Abstract	The assembly of heterochromatin in eukaryotic genomes is critical for diverse chromosomal events including regulation of gene expression, silencing of repetitive DNA elements, proper segregation of chromosomes and maintenance of genomic integrity. Previous studies have shown that noncoding RNAs and the RNA interference (RNAi) machinery promote the assembly of heterochromatin that serves as a multipurpose platform for targeting effectors involved in various chromosomal processes. Recent work has revealed that RNAi-independent mechanisms, involving RNA processing activities that utilize both noncoding and coding RNAs, operate in the assembly of heterochromatin. These findings have established that, in addition to coding for proteins, mRNAs also function as signaling molecules that modify chromatin structure by targeting heterochromatin assembly factors.
Keywords	DNA ; RNA interference ; Schizosaccharomyces pombe ; genome ; heterochromatin ; messenger RNA ; non-coding RNA
Language	English
Dates of publication	2012-04
Size	p. 156-163.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	1077312-5
ISSN	1879-0380 ; 0959-437X
ISSN (online)	1879-0380
ISSN	0959-437X
DOI	10.1016/j.gde.2011.12.004
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Article ; Online: Challenges and Strategies in the Development of Radiation Biodosimetry Tests for Patient Management.

Satyamitra, Merriline / Reyes Turcu, Francisca E / Pantoja-Galicia, Norberto / Wathen, Lynne

Radiation research

2021 Volume 196, Issue 5, Page(s) 455–467

Abstract: The public health and medical response to a radiological or nuclear incident requires the capability to sort, assess, treat, triage and ultimately discharge, as well as to refer or transport people to their next step in medical care. The Public Health ... ...

Abstract	The public health and medical response to a radiological or nuclear incident requires the capability to sort, assess, treat, triage and ultimately discharge, as well as to refer or transport people to their next step in medical care. The Public Health Emergency Medical Countermeasures Enterprise (PHEMCE), directed by the U.S. Department of Health and Human Services (HHS), facilitates a comprehensive, multi-agency effort to develop and deploy radiation biodosimetry tests. Within HHS, discovery and development of biodosimetry tests includes the National Institute of Allergy and Infectious Diseases (NIAID) National Institutes of Health (NIH), the Office of the Assistant Secretary of Preparedness and Response (ASPR), Biomedical Advanced Research and Development Authority (BARDA), and the Food and Drug Administration (FDA) as primary partners in this endeavor. The study of radiation biodosimetry has advanced significantly, with expansion into the fields of cytogenetics, genomics, proteomics, metabolomics, lipidomics and transcriptomics. In addition, expansion of traditional cytogenetic assessment methods using automated platforms, and development of laboratory surge capacity networks have helped to advance biodefense preparedness. This article describes various programs and coordinating efforts between NIAID, BARDA and FDA in the development of radiation biodosimetry approaches to respond to radiological and nuclear threats.
MeSH term(s)	Disaster Planning ; Genomics ; Humans ; National Institute of Allergy and Infectious Diseases (U.S.) ; Radioactive Hazard Release ; Terrorism ; United States
Language	English
Publishing date	2021-06-17
Publishing country	United States
Document type	Journal Article
ZDB-ID	80322-4
ISSN	1938-5404 ; 0033-7587
ISSN (online)	1938-5404
ISSN	0033-7587
DOI	10.1667/RADE-21-00072.1
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Article ; Online: Polyubiquitin binding and disassembly by deubiquitinating enzymes.

Reyes-Turcu, Francisca E / Wilkinson, Keith D

Chemical reviews

2009 Volume 109, Issue 4, Page(s) 1495–1508

MeSH term(s)	Catalytic Domain ; Endopeptidases/metabolism ; Humans ; Protein Binding ; Protein Processing, Post-Translational ; Protein Structure, Tertiary ; Structure-Activity Relationship ; Ubiquitins/chemistry ; Ubiquitins/metabolism
Chemical Substances	Ubiquitins ; Endopeptidases (EC 3.4.-)
Language	English
Publishing date	2009-02-25
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	207949-5
ISSN	1520-6890 ; 0009-2665
ISSN (online)	1520-6890
ISSN	0009-2665
DOI	10.1021/cr800470j
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Article ; Online: Regulation and cellular roles of ubiquitin-specific deubiquitinating enzymes.

Reyes-Turcu, Francisca E / Ventii, Karen H / Wilkinson, Keith D

Annual review of biochemistry

2009 Volume 78, Page(s) 363–397

Abstract: Deubiquitinating enzymes (DUBs) are proteases that process ubiquitin or ubiquitin-like gene products, reverse the modification of proteins by a single ubiquitin(-like) protein, and remodel polyubiquitin(-like) chains on target proteins. The human genome ... ...

Abstract	Deubiquitinating enzymes (DUBs) are proteases that process ubiquitin or ubiquitin-like gene products, reverse the modification of proteins by a single ubiquitin(-like) protein, and remodel polyubiquitin(-like) chains on target proteins. The human genome encodes nearly 100 DUBs with specificity for ubiquitin in five gene families. Most DUB activity is cryptic, and conformational rearrangements often occur during the binding of ubiquitin and/or scaffold proteins. DUBs with specificity for ubiquitin contain insertions and extensions modulating DUB substrate specificity, protein-protein interactions, and cellular localization. Binding partners and multiprotein complexes with which DUBs associate modulate DUB activity and substrate specificity. Quantitative studies of activity and protein-protein interactions, together with genetic studies and the advent of RNAi, have led to new insights into the function of yeast and human DUBs. This review discusses ubiquitin-specific DUBs, some of the generalizations emerging from recent studies of the regulation of DUB activity, and their roles in various cellular processes.
MeSH term(s)	Animals ; Endopeptidases/chemistry ; Endopeptidases/genetics ; Endopeptidases/metabolism ; Humans ; Protein Structure, Tertiary ; Ubiquitin/genetics ; Ubiquitin/metabolism ; Ubiquitination
Chemical Substances	Ubiquitin ; Endopeptidases (EC 3.4.-)
Keywords	covid19
Language	English
Publishing date	2009-06-02
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	207924-0
ISSN	1545-4509 ; 0066-4154
ISSN (online)	1545-4509
ISSN	0066-4154
DOI	10.1146/annurev.biochem.78.082307.091526
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Article ; Online: Defects in RNA quality control factors reveal RNAi-independent nucleation of heterochromatin.

Reyes-Turcu, Francisca E / Zhang, Ke / Zofall, Martin / Chen, Eesin / Grewal, Shiv I S

Nature structural & molecular biology

2011 Volume 18, Issue 10, Page(s) 1132–1138

Abstract: Heterochromatin assembly at Schizosaccharomyces pombe centromeres involves a self-reinforcing loop mechanism wherein chromatin-bound RNAi factors facilitate targeting of Clr4-Rik1 methyltransferase. However, the initial nucleation of heterochromatin has ... ...

Abstract	Heterochromatin assembly at Schizosaccharomyces pombe centromeres involves a self-reinforcing loop mechanism wherein chromatin-bound RNAi factors facilitate targeting of Clr4-Rik1 methyltransferase. However, the initial nucleation of heterochromatin has remained elusive. We show that cells lacking Mlo3, a protein involved in mRNP biogenesis and RNA quality control, assemble functional heterochromatin in RNAi-deficient cells. Heterochromatin restoration is linked to RNA surveillance because loss of Mlo3-associated TRAMP also rescues heterochromatin defects of RNAi mutants. mlo3Δ, which causes accumulation of bidirectional repeat-transcripts, restores Rik1 enrichment at repeats and triggers de novo heterochromatin formation in the absence of RNAi. RNAi-independent heterochromatin nucleation occurs at selected euchromatic loci that show upregulation of antisense RNAs in mlo3Δ cells. We find that the exosome RNA degradation machinery acts parallel to RNAi to promote heterochromatin formation at centromeres. These results suggest that RNAi-independent mechanisms exploit transcription and non-coding RNAs to nucleate heterochromatin.
MeSH term(s)	Centromere ; Heterochromatin/chemistry ; Heterochromatin/genetics ; Mutation ; Quality Control ; RNA Interference ; Schizosaccharomyces/genetics
Chemical Substances	Heterochromatin
Language	English
Publishing date	2011-09-04
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Intramural
ZDB-ID	2126708-X
ISSN	1545-9985 ; 1545-9993
ISSN (online)	1545-9985
ISSN	1545-9993
DOI	10.1038/nsmb.2122
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Article: Recognition of Polyubiquitin Isoforms by the Multiple Ubiquitin Binding Modules of Isopeptidase T

Reyes-Turcu, Francisca E / Shanks, John R / Komander, David / Wilkinson, Keith D

Journal of biological chemistry. 2008 July 11, v. 283, no. 28

2008

Abstract: The conjugation of polyubiquitin to target proteins acts as a signal that regulates target stability, localization, and function. Several ubiquitin binding domains have been described, and while much is known about ubiquitin binding to the isolated ... ...

Abstract	The conjugation of polyubiquitin to target proteins acts as a signal that regulates target stability, localization, and function. Several ubiquitin binding domains have been described, and while much is known about ubiquitin binding to the isolated domains, little is known with regard to how the domains interact with polyubiquitin in the context of full-length proteins. Isopeptidase T (IsoT/USP5) is a deubiquitinating enzyme that is largely responsible for the disassembly of unanchored polyubiquitin in the cell. IsoT has four ubiquitin binding domains: a zinc finger domain (ZnF UBP), which binds the proximal ubiquitin, a UBP domain that forms the active site, and two ubiquitin-associated (UBA) domains whose roles are unknown. Here, we show that the UBA domains are involved in binding two different polyubiquitin isoforms, linear and K48-linked. Using isothermal titration calorimetry, we show that IsoT has at least four ubiquitin binding sites for both polyubiquitin isoforms. The thermodynamics of the interactions reveal that the binding is enthalpy-driven. Mutation of the UBA domains suggests that UBA1 and UBA2 domains of IsoT interact with the third and fourth ubiquitins in both polyubiquitin isoforms, respectively. These data suggest that recognition of the polyubiquitin isoforms by IsoT involves considerable conformational mobility in the polyubiquitin ligand, in the enzyme, or in both.
Language	English
Dates of publication	2008-0711
Size	p. 19581-19592.
Publishing place	American Society for Biochemistry and Molecular Biology
Document type	Article
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
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Article ; Online: RNAi triggered by specialized machinery silences developmental genes and retrotransposons.

Yamanaka, Soichiro / Mehta, Sameet / Reyes-Turcu, Francisca E / Zhuang, Fanglei / Fuchs, Ryan T / Rong, Yikang / Robb, Gregory B / Grewal, Shiv I S

Nature

2012 Volume 493, Issue 7433, Page(s) 557–560

Abstract: RNA interference (RNAi) is a conserved mechanism in which small interfering RNAs (siRNAs) guide the degradation of cognate RNAs, but also promote heterochromatin assembly at repetitive DNA elements such as centromeric repeats. However, the full extent of ...

Abstract	RNA interference (RNAi) is a conserved mechanism in which small interfering RNAs (siRNAs) guide the degradation of cognate RNAs, but also promote heterochromatin assembly at repetitive DNA elements such as centromeric repeats. However, the full extent of RNAi functions and its endogenous targets have not been explored. Here we show that, in the fission yeast Schizosaccharomyces pombe, RNAi and heterochromatin factors cooperate to silence diverse loci, including sexual differentiation genes, genes encoding transmembrane proteins, and retrotransposons that are also targeted by the exosome RNA degradation machinery. In the absence of the exosome, transcripts are processed preferentially by the RNAi machinery, revealing siRNA clusters and a corresponding increase in heterochromatin modifications across large domains containing genes and retrotransposons. We show that the generation of siRNAs and heterochromatin assembly by RNAi is triggered by a mechanism involving the canonical poly(A) polymerase Pla1 and an associated RNA surveillance factor Red1, which also activate the exosome. Notably, siRNA production and heterochromatin modifications at these target loci are regulated by environmental growth conditions, and by developmental signals that induce gene expression during sexual differentiation. Our analyses uncover an interaction between RNAi and the exosome that is conserved in Drosophila, and show that differentiation signals modulate RNAi silencing to regulate developmental genes.
MeSH term(s)	Animals ; Drosophila melanogaster/genetics ; Exome/genetics ; Gene Expression Regulation, Fungal/genetics ; Genes, Fungal/genetics ; Heterochromatin/genetics ; Multigene Family/genetics ; Polynucleotide Adenylyltransferase/genetics ; RNA Interference ; RNA Stability/genetics ; RNA, Fungal/genetics ; RNA, Small Interfering/genetics ; Retroelements/genetics ; Schizosaccharomyces/cytology ; Schizosaccharomyces/enzymology ; Schizosaccharomyces/genetics ; Schizosaccharomyces/growth & development ; Schizosaccharomyces pombe Proteins/genetics ; Schizosaccharomyces pombe Proteins/metabolism ; Sex Differentiation/genetics
Chemical Substances	Heterochromatin ; RNA, Fungal ; RNA, Small Interfering ; Retroelements ; Schizosaccharomyces pombe Proteins ; Polynucleotide Adenylyltransferase (EC 2.7.7.19)
Language	English
Publishing date	2012-11-14
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Intramural
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/nature11716
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Article: Recognition of polyubiquitin isoforms by the multiple ubiquitin binding modules of isopeptidase T.

Reyes-Turcu, Francisca E / Shanks, John R / Komander, David / Wilkinson, Keith D

The Journal of biological chemistry

2008 Volume 283, Issue 28, Page(s) 19581–19592

Abstract	The conjugation of polyubiquitin to target proteins acts as a signal that regulates target stability, localization, and function. Several ubiquitin binding domains have been described, and while much is known about ubiquitin binding to the isolated domains, little is known with regard to how the domains interact with polyubiquitin in the context of full-length proteins. Isopeptidase T (IsoT/USP5) is a deubiquitinating enzyme that is largely responsible for the disassembly of unanchored polyubiquitin in the cell. IsoT has four ubiquitin binding domains: a zinc finger domain (ZnF UBP), which binds the proximal ubiquitin, a UBP domain that forms the active site, and two ubiquitin-associated (UBA) domains whose roles are unknown. Here, we show that the UBA domains are involved in binding two different polyubiquitin isoforms, linear and K48-linked. Using isothermal titration calorimetry, we show that IsoT has at least four ubiquitin binding sites for both polyubiquitin isoforms. The thermodynamics of the interactions reveal that the binding is enthalpy-driven. Mutation of the UBA domains suggests that UBA1 and UBA2 domains of IsoT interact with the third and fourth ubiquitins in both polyubiquitin isoforms, respectively. These data suggest that recognition of the polyubiquitin isoforms by IsoT involves considerable conformational mobility in the polyubiquitin ligand, in the enzyme, or in both.
MeSH term(s)	Animals ; Binding Sites/physiology ; Endopeptidases/chemistry ; Endopeptidases/genetics ; Endopeptidases/metabolism ; Humans ; Mutation ; Protein Binding/physiology ; Protein Isoforms/chemistry ; Protein Isoforms/genetics ; Protein Isoforms/metabolism ; Protein Structure, Tertiary/physiology ; Recombinant Fusion Proteins/chemistry ; Recombinant Fusion Proteins/genetics ; Recombinant Fusion Proteins/metabolism ; Ubiquitin/chemistry ; Ubiquitin/genetics ; Ubiquitin/metabolism ; Ubiquitination/physiology ; Zinc Fingers/physiology
Chemical Substances	Protein Isoforms ; Recombinant Fusion Proteins ; Ubiquitin ; Endopeptidases (EC 3.4.-) ; ubiquitin isopeptidase (EC 3.4.99.-)
Language	English
Publishing date	2008-05-15
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1074/jbc.M800947200
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Article ; Online: RNA elimination machinery targeting meiotic mRNAs promotes facultative heterochromatin formation.

Zofall, Martin / Yamanaka, Soichiro / Reyes-Turcu, Francisca E / Zhang, Ke / Rubin, Chanan / Grewal, Shiv I S

Science (New York, N.Y.)

2011 Volume 335, Issue 6064, Page(s) 96–100

Abstract: Facultative heterochromatin that changes during cellular differentiation coordinates regulated gene expression, but its assembly is poorly understood. Here, we describe facultative heterochromatin islands in fission yeast and show that their formation at ...

Abstract	Facultative heterochromatin that changes during cellular differentiation coordinates regulated gene expression, but its assembly is poorly understood. Here, we describe facultative heterochromatin islands in fission yeast and show that their formation at meiotic genes requires factors that eliminate meiotic messenger RNAs (mRNAs) during vegetative growth. Blocking production of meiotic mRNA or loss of RNA elimination factors, including Mmi1 and Red1 proteins, abolishes heterochromatin islands. RNA elimination machinery is enriched at meiotic loci and interacts with Clr4/SUV39h, a methyltransferase involved in heterochromatin assembly. Heterochromatin islands disassemble in response to nutritional signals that induce sexual differentiation. This process involves the antisilencing factor Epe1, the loss of which causes dramatic increase in heterochromatic loci. Our analyses uncover unexpected regulatory roles for mRNA-processing factors that assemble dynamic heterochromatin to modulate gene expression.
MeSH term(s)	Cell Cycle Proteins/metabolism ; Chromatin Assembly and Disassembly ; Chromatin Immunoprecipitation ; Dynactin Complex ; Gene Expression Regulation, Fungal ; Genes, Fungal ; Heterochromatin/metabolism ; Histone-Lysine N-Methyltransferase ; Histones/metabolism ; Meiosis/genetics ; Methyltransferases/metabolism ; Microtubule Proteins/genetics ; Microtubule Proteins/metabolism ; Nitrogen/metabolism ; Nuclear Proteins/genetics ; Nuclear Proteins/metabolism ; RNA Interference ; RNA, Fungal/genetics ; RNA, Fungal/metabolism ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Schizosaccharomyces/genetics ; Schizosaccharomyces/growth & development ; Schizosaccharomyces/metabolism ; Schizosaccharomyces pombe Proteins/genetics ; Schizosaccharomyces pombe Proteins/metabolism ; mRNA Cleavage and Polyadenylation Factors/metabolism
Chemical Substances	Cell Cycle Proteins ; Dynactin Complex ; Heterochromatin ; Histones ; Microtubule Proteins ; Mmi1 protein, S pombe ; Nuclear Proteins ; RNA, Fungal ; RNA, Messenger ; Schizosaccharomyces pombe Proteins ; Ssm4 protein, S pombe ; epe1 protein, S pombe ; mRNA Cleavage and Polyadenylation Factors ; mei4 protein, S pombe ; Methyltransferases (EC 2.1.1.-) ; Histone-Lysine N-Methyltransferase (EC 2.1.1.43) ; clr4 protein, S pombe (EC 2.1.1.43) ; Nitrogen (N762921K75)
Language	English
Publishing date	2011-12-01
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Intramural
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.1211651
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