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Book: Argonaute proteins

Okamura, Katsutomo / Nakanishi, Kotaro

methods and protocols

(Methods in molecular biology ; 1680 ; Springer protocols)

2018

Author's details	edited by Katsutomo Okamura, Kotaro Nakanishi
Series title	Methods in molecular biology ; 1680 Springer protocols
Collection
Keywords	prokaryotes ; eukaryotes ; nucleic acids ; chaperon machinery ; Proteomics
Subject code	570
Language	English
Size	xiii, 260 Seiten, Illustrationen, 25.4 cm x 17.8 cm
Publisher	Humana Press
Publishing place	New York, NY
Publishing country	United States
Document type	Book
HBZ-ID	HT019480600
ISBN	978-1-4939-7338-5 ; 1-4939-7338-X ; 9781493973392 ; 1493973398
Database	Catalogue ZB MED Medicine, Health

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Zs A 7042 -1680-	verfügbar in Königswinter	Königswinter

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Article ; Online: Argonaute reformatting.

Okamura, Katsutomo

Molecular cell

2013 Volume 50, Issue 3, Page(s) 305–306

Abstract: In this issue of Molecular Cell, De et al. (2013) report that highly complementary targets promote release of small RNAs from effector Argonaute complexes, thus providing mechanistic insights into regulation of small RNA stability and implications for ... ...

Abstract	In this issue of Molecular Cell, De et al. (2013) report that highly complementary targets promote release of small RNAs from effector Argonaute complexes, thus providing mechanistic insights into regulation of small RNA stability and implications for siRNA design.
Language	English
Publishing date	2013-05-09
Publishing country	United States
Document type	Comment ; Journal Article
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2013.04.019
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Article ; Online: Hidden sequence specificity in loading of single-stranded RNAs onto Drosophila Argonautes.

Goh, Eling / Okamura, Katsutomo

Nucleic acids research

2019 Volume 47, Issue 6, Page(s) 3101–3116

Abstract: Argonaute proteins play important roles in gene regulation with small RNAs (sRNAs) serving as guides to targets. Argonautes are believed to bind sRNAs in a sequence non-specific manner. However, we recently discovered that Argonautes selectively load ... ...

Abstract	Argonaute proteins play important roles in gene regulation with small RNAs (sRNAs) serving as guides to targets. Argonautes are believed to bind sRNAs in a sequence non-specific manner. However, we recently discovered that Argonautes selectively load endogenous single-stranded (ss) RNAs, suggesting that Argonaute loading may conform to sequence specificity. To identify sequences preferred for Argonaute loading, we have developed HIgh-throughput Sequencing mediated Specificity Analysis (HISSA). HISSA allows massively parallel analysis of RNA binding efficiency by using randomized oligos in in vitro binding assays and quantifying RNAs by deep-sequencing. We chose Drosophila as a model system to take advantage of the presence of two biochemically distinct Argonautes, AGO1 and AGO2. Our results revealed AGO2 loading to be strongly favored by G-rich sequences. In contrast, AGO1 showed an enrichment of the 'GAC' motif in loaded species. Reanalysis of published sRNA sequencing data from fly tissues detected enrichment of the GAC motif in ssRNA-derived small RNAs in the immunopurified AGO1-complex under certain conditions, suggesting that the sequence preference of AGO1-loading may influence the repertoire of AGO1-bound endogenous sRNAs. Finally, we showed that human Ago2 also exhibited selectivity in loading ssRNAs in cell lysates. These findings may have implications for therapeutic ssRNA-mediated gene silencing.
MeSH term(s)	Animals ; Argonaute Proteins/genetics ; DNA, Single-Stranded/genetics ; Drosophila Proteins/genetics ; Drosophila melanogaster/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; RNA-Induced Silencing Complex/genetics
Chemical Substances	AGO1 protein, Drosophila ; AGO2 protein, Drosophila ; Argonaute Proteins ; DNA, Single-Stranded ; Drosophila Proteins ; RNA-Induced Silencing Complex
Language	English
Publishing date	2019-01-01
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gky1300
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Article ; Online: Diversity of animal small RNA pathways and their biological utility.

Okamura, Katsutomo

Wiley interdisciplinary reviews. RNA

2012 Volume 3, Issue 3, Page(s) 351–368

Abstract: Higher eukaryotes employ extensive post-transcriptional gene regulation to accomplish fine control of gene expression. The microRNA (miRNA) family plays important roles in the post-transcriptional gene regulation of broad networks of target mRNA ... ...

Abstract	Higher eukaryotes employ extensive post-transcriptional gene regulation to accomplish fine control of gene expression. The microRNA (miRNA) family plays important roles in the post-transcriptional gene regulation of broad networks of target mRNA expression. Most miRNAs are generated by a conserved mechanism involving two RNase III enzymes Drosha and Dicer. However, work from the past few years has uncovered diverse noncanonical miRNA pathways, which exploit a variety of other RNA processing enzymes. In addition, the discovery of another abundant small RNA family, endogenous short interfering RNAs (endo-siRNAs), has also broadened the catalogs of short regulatory RNAs. This review highlights recent studies that revealed novel small RNA biogenesis pathways, and discusses their relevance to gene regulatory networks.
MeSH term(s)	Animals ; Fungi/genetics ; Fungi/metabolism ; Gene Expression Regulation ; MicroRNAs/genetics ; MicroRNAs/metabolism ; RNA Interference ; RNA, Small Interfering/genetics ; RNA, Small Interfering/metabolism ; RNA, Untranslated/metabolism ; Ribonuclease III/metabolism
Chemical Substances	MicroRNAs ; RNA, Small Interfering ; RNA, Untranslated ; Ribonuclease III (EC 3.1.26.3)
Language	English
Publishing date	2012-05
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.113
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Article ; Online: A novel eukaryotic RdRP-dependent small RNA pathway represses antiviral immunity by controlling an ERK pathway component in the black-legged tick.

Feng, Canran / Torimaru, Kyosuke / Lim, Mandy Yu Theng / Chak, Li-Ling / Shiimori, Masami / Tsuji, Kosuke / Tanaka, Tetsuya / Iida, Junko / Okamura, Katsutomo

PloS one

2023 Volume 18, Issue 3, Page(s) e0281195

Abstract: Small regulatory RNAs (sRNAs) are involved in antiviral defense and gene regulation. Although roles of RNA-dependent RNA Polymerases (RdRPs) in sRNA biology are extensively studied in nematodes, plants and fungi, understanding of RdRP homologs in other ... ...

Abstract	Small regulatory RNAs (sRNAs) are involved in antiviral defense and gene regulation. Although roles of RNA-dependent RNA Polymerases (RdRPs) in sRNA biology are extensively studied in nematodes, plants and fungi, understanding of RdRP homologs in other animals is still lacking. Here, we study sRNAs in the ISE6 cell line, which is derived from the black-legged tick, an important vector of human and animal pathogens. We find abundant classes of ~22nt sRNAs that require specific combinations of RdRPs and sRNA effector proteins (Argonautes or AGOs). RdRP1-dependent sRNAs possess 5'-monophosphates and are mainly derived from RNA polymerase III-transcribed genes and repetitive elements. Knockdown of some RdRP homologs misregulates genes including RNAi-related genes and the regulator of immune response Dsor1. Sensor assays demonstrate that Dsor1 is downregulated by RdRP1 through the 3'UTR that contains a target site of RdRP1-dependent repeat-derived sRNAs. Consistent with viral gene repression by the RNAi mechanism using virus-derived small interfering RNAs, viral transcripts are upregulated by AGO knockdown. On the other hand, RdRP1 knockdown unexpectedly results in downregulation of viral transcripts. This effect is dependent on Dsor1, suggesting that antiviral immunity is enhanced by RdRP1 knockdown through Dsor1 upregulation. We propose that tick sRNA pathways control multiple aspects of immune response via RNAi and regulation of signaling pathways.
MeSH term(s)	Animals ; Humans ; Ixodes/genetics ; Ixodes/metabolism ; Eukaryota/genetics ; MAP Kinase Signaling System ; Antiviral Agents ; RNA, Small Interfering/genetics ; RNA, Small Interfering/metabolism ; RNA Interference ; RNA-Dependent RNA Polymerase/genetics ; RNA-Dependent RNA Polymerase/metabolism ; RNA, Small Untranslated/genetics ; RNA, Small Untranslated/metabolism
Chemical Substances	Antiviral Agents ; RNA, Small Interfering ; RNA-Dependent RNA Polymerase (EC 2.7.7.48) ; RNA, Small Untranslated
Language	English
Publishing date	2023-03-30
Publishing country	United States
Document type	Journal Article ; 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.0281195
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Article: Switches in Dicer Activity During Oogenesis and Early Development.

Lim, Mandy Yu Theng / Okamura, Katsutomo

Results and problems in cell differentiation

2017 Volume 63, Page(s) 325–351

Abstract: Dicer is a versatile protein regulating diverse biological processes via the production of multiple classes of small regulatory RNAs, including microRNAs (miRNAs) and small interfering RNAs (siRNAs). In this chapter, we will discuss roles for Dicer in ... ...

Abstract	Dicer is a versatile protein regulating diverse biological processes via the production of multiple classes of small regulatory RNAs, including microRNAs (miRNAs) and small interfering RNAs (siRNAs). In this chapter, we will discuss roles for Dicer in driving temporal changes in activity of individual small RNA classes to support oogenesis and early embryogenesis. Genetic strategies that perturb particular functions of Dicer family proteins, such as ablation of individual Dicer paralogs or their binding partners as well as introduction of point mutations to individual domains, allowed the dissection of Dicer functions in diverse small RNA pathways. Evolutionary conservation and divergence of the mechanisms highlight the importance of Dicer versatility in supporting rapid changes in gene expression during oogenesis and early development. Furthermore, we will discuss potential roles of Dicer in transgenerational inheritance of small RNA-mediated gene regulation.
MeSH term(s)	Animals ; Embryonic Development/genetics ; Female ; Oogenesis/genetics ; RNA, Small Untranslated/genetics ; RNA, Small Untranslated/metabolism ; Ribonuclease III/metabolism
Chemical Substances	RNA, Small Untranslated ; Ribonuclease III (EC 3.1.26.3)
Language	English
Publishing date	2017-08-04
Publishing country	Germany
Document type	Journal Article ; Review
ISSN	0080-1844
ISSN	0080-1844
DOI	10.1007/978-3-319-60855-6_14
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Article ; Online: Gateway to Understanding Argonaute Loading of Single-Stranded RNAs: Preparation of Deep Sequencing Libraries with In Vitro Loading Samples.

Goh, Eling / Okamura, Katsutomo

Methods in molecular biology (Clifton, N.J.)

2017 Volume 1680, Page(s) 41–63

Abstract: Identification of sequences preferred by individual RNA-binding proteins (RBPs) has been accelerated by recent advances in the quantitative analysis of protein-RNA interactions on a massive scale, and such experiments have even revealed hidden sequence ... ...

Abstract	Identification of sequences preferred by individual RNA-binding proteins (RBPs) has been accelerated by recent advances in the quantitative analysis of protein-RNA interactions on a massive scale, and such experiments have even revealed hidden sequence specificity of RBPs that were assumed to be non-specific. Argonaute (AGO) proteins bind diverse guide small RNAs and were believed to have no sequence specificity besides the preference for particular bases at the 5' nucleotide. However, we recently showed that short single-stranded RNAs (ssRNAs) are loaded to AGOs in vivo and in cell extracts with detectable sequence preferences. To study the sequence specificity, we established a protocol for preparing the oligo-specific deep-sequencing library. The protocol includes in vitro loading assay that uses RNA oligos containing randomized nucleotides at the first five positions and also splinted-ligation that specifically amplifies the introduced oligo RNA species from a complex mixture of endogenous small RNAs and exogenously introduced RNA oligos. With the current sequencing depth, this procedure will allow quantitative profiling of interactions between the AGO and ~1000 ssRNA species with different sequences. The method would aid in studying the mechanism behind the selective loading of ssRNAs to AGOs and may potentially be applied to study interactions between RNA and other RNA-binding proteins.
MeSH term(s)	Antibodies ; Argonaute Proteins/metabolism ; Gene Library ; High-Throughput Nucleotide Sequencing ; High-Throughput Screening Assays ; Immunoprecipitation ; In Vitro Techniques ; Isotope Labeling ; Protein Binding ; RNA, Small Untranslated/genetics ; RNA, Small Untranslated/metabolism
Chemical Substances	Antibodies ; Argonaute Proteins ; RNA, Small Untranslated
Language	English
Publishing date	2017-10-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-7339-2_3
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: A novel eukaryotic RdRP-dependent small RNA pathway represses antiviral immunity by controlling an ERK pathway component in the black-legged tick.

Canran Feng / Kyosuke Torimaru / Mandy Yu Theng Lim / Li-Ling Chak / Masami Shiimori / Kosuke Tsuji / Tetsuya Tanaka / Junko Iida / Katsutomo Okamura

PLoS ONE, Vol 18, Iss 3, p e

2023 Volume 0281195

Abstract	Small regulatory RNAs (sRNAs) are involved in antiviral defense and gene regulation. Although roles of RNA-dependent RNA Polymerases (RdRPs) in sRNA biology are extensively studied in nematodes, plants and fungi, understanding of RdRP homologs in other animals is still lacking. Here, we study sRNAs in the ISE6 cell line, which is derived from the black-legged tick, an important vector of human and animal pathogens. We find abundant classes of ~22nt sRNAs that require specific combinations of RdRPs and sRNA effector proteins (Argonautes or AGOs). RdRP1-dependent sRNAs possess 5'-monophosphates and are mainly derived from RNA polymerase III-transcribed genes and repetitive elements. Knockdown of some RdRP homologs misregulates genes including RNAi-related genes and the regulator of immune response Dsor1. Sensor assays demonstrate that Dsor1 is downregulated by RdRP1 through the 3'UTR that contains a target site of RdRP1-dependent repeat-derived sRNAs. Consistent with viral gene repression by the RNAi mechanism using virus-derived small interfering RNAs, viral transcripts are upregulated by AGO knockdown. On the other hand, RdRP1 knockdown unexpectedly results in downregulation of viral transcripts. This effect is dependent on Dsor1, suggesting that antiviral immunity is enhanced by RdRP1 knockdown through Dsor1 upregulation. We propose that tick sRNA pathways control multiple aspects of immune response via RNAi and regulation of signaling pathways.
Keywords	Medicine ; R ; Science ; Q
Subject code	570
Language	English
Publishing date	2023-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A novel eukaryotic RdRP-dependent small RNA pathway represses antiviral immunity by controlling an ERK pathway component in the black-legged tick

Canran Feng / Kyosuke Torimaru / Mandy Yu Theng Lim / Li-Ling Chak / Masami Shiimori / Kosuke Tsuji / Tetsuya Tanaka / Junko Iida / Katsutomo Okamura

PLoS ONE, Vol 18, Iss

2023 Volume 3

Abstract	Small regulatory RNAs (sRNAs) are involved in antiviral defense and gene regulation. Although roles of RNA-dependent RNA Polymerases (RdRPs) in sRNA biology are extensively studied in nematodes, plants and fungi, understanding of RdRP homologs in other animals is still lacking. Here, we study sRNAs in the ISE6 cell line, which is derived from the black-legged tick, an important vector of human and animal pathogens. We find abundant classes of ~22nt sRNAs that require specific combinations of RdRPs and sRNA effector proteins (Argonautes or AGOs). RdRP1-dependent sRNAs possess 5’-monophosphates and are mainly derived from RNA polymerase III-transcribed genes and repetitive elements. Knockdown of some RdRP homologs misregulates genes including RNAi-related genes and the regulator of immune response Dsor1. Sensor assays demonstrate that Dsor1 is downregulated by RdRP1 through the 3’UTR that contains a target site of RdRP1-dependent repeat-derived sRNAs. Consistent with viral gene repression by the RNAi mechanism using virus-derived small interfering RNAs, viral transcripts are upregulated by AGO knockdown. On the other hand, RdRP1 knockdown unexpectedly results in downregulation of viral transcripts. This effect is dependent on Dsor1, suggesting that antiviral immunity is enhanced by RdRP1 knockdown through Dsor1 upregulation. We propose that tick sRNA pathways control multiple aspects of immune response via RNAi and regulation of signaling pathways.
Keywords	Medicine ; R ; Science ; Q
Subject code	570
Language	English
Publishing date	2023-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Regulatory RNAs discovered in unexpected places.

Pek, Jun Wei / Okamura, Katsutomo

Wiley interdisciplinary reviews. RNA

2015 Volume 6, Issue 6, Page(s) 671–686

Abstract: Recent studies have discovered both small and long noncoding RNAs (ncRNAs) encoded in unexpected places. These ncRNA genes were surprises at the time of their discovery, but many quickly became well-accepted families of functional regulatory RNA species. ...

Abstract	Recent studies have discovered both small and long noncoding RNAs (ncRNAs) encoded in unexpected places. These ncRNA genes were surprises at the time of their discovery, but many quickly became well-accepted families of functional regulatory RNA species. Even after years of extensive gene annotation studies using high-throughput sequencing technologies, new types of ncRNA genes continue to be discovered in unexpected places. We highlight ncRNAs that have atypical structures and that are encoded in what are generally considered 'junk' sequences, such as spacers and introns. We also discuss current bottlenecks in the approaches for identifying novel ncRNAs and the possibility that many remain to be discovered.
MeSH term(s)	Animals ; Humans ; Introns ; RNA, Untranslated ; Viroids/genetics
Chemical Substances	RNA, Untranslated
Language	English
Publishing date	2015-11
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.1309
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