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  1. Book: Long noncoding RNAs

    Kurokawa, Riki

    structures and functions

    2015  

    Author's details Riki Kurokawa, editor
    MeSH term(s) RNA, Long Noncoding/chemistry ; RNA, Long Noncoding/physiology
    Language English
    Size viii, 257 pages :, illustrations (chiefly color) ;, 25 cm
    Document type Book
    ISBN 9784431555759 ; 4431555757 ; 9784431555766 ; 4431555765
    Database Catalogue of the US National Library of Medicine (NLM)

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  2. Article ; Online: m

    Yoneda, Ryoma / Ueda, Naomi / Kurokawa, Riki

    International journal of molecular sciences

    2021  Volume 22, Issue 20

    Abstract: Translocated in LipoSarcoma/Fused in Sarcoma (TLS/FUS) is a nuclear RNA binding protein whose mutations cause amyotrophic lateral sclerosis. TLS/FUS undergoes LLPS and forms membraneless particles with other proteins and nucleic acids. Interaction with ... ...

    Abstract Translocated in LipoSarcoma/Fused in Sarcoma (TLS/FUS) is a nuclear RNA binding protein whose mutations cause amyotrophic lateral sclerosis. TLS/FUS undergoes LLPS and forms membraneless particles with other proteins and nucleic acids. Interaction with RNA alters conformation of TLS/FUS, which affects binding with proteins, but the effect of m
    MeSH term(s) Adenosine/analogs & derivatives ; Adenosine/chemistry ; Cell Line ; Cell Survival/drug effects ; Cytoplasm/metabolism ; Genetic Loci ; Humans ; Liquid-Liquid Extraction ; Mutagenesis, Site-Directed ; Protein Aggregates/drug effects ; Protein Binding ; RNA/chemistry ; RNA/metabolism ; RNA/pharmacology ; RNA, Long Noncoding/chemistry ; RNA-Binding Protein FUS/chemistry ; RNA-Binding Protein FUS/genetics ; RNA-Binding Protein FUS/metabolism ; Sorbitol/pharmacology
    Chemical Substances Protein Aggregates ; RNA, Long Noncoding ; RNA-Binding Protein FUS ; Sorbitol (506T60A25R) ; RNA (63231-63-0) ; N-methyladenosine (CLE6G00625) ; Adenosine (K72T3FS567)
    Language English
    Publishing date 2021-10-12
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms222011014
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Long noncoding RNA

    Yoneda, Ryoma / Ueda, Naomi / Uranishi, Kousuke / Hirasaki, Masataka / Kurokawa, Riki

    The Journal of biological chemistry

    2020  Volume 295, Issue 17, Page(s) 5626–5639

    Abstract: ... pncRNA- ... ...

    Abstract pncRNA-D
    MeSH term(s) Cell Cycle Checkpoints ; Cyclin D1/genetics ; Down-Regulation ; Epigenesis, Genetic ; Genes, bcl-1 ; HeLa Cells ; Humans ; Methylation ; Promoter Regions, Genetic ; RNA, Long Noncoding/genetics
    Chemical Substances CCND1 protein, human ; RNA, Long Noncoding ; Cyclin D1 (136601-57-5)
    Language English
    Publishing date 2020-03-12
    Publishing country United States
    Document type Journal Article ; 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.RA119.011556
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Long noncoding RNA as a regulator for transcription.

    Kurokawa, Riki

    Progress in molecular and subcellular biology

    2011  Volume 51, Page(s) 29–41

    Abstract: Investigation of noncoding RNAs is in rapid progress, especially regarding translational repression by small (short) noncoding RNAs like microRNAs with 20-25 nucleotide-lengths, while long noncoding RNAs with nucleotide length of more than two hundred ... ...

    Abstract Investigation of noncoding RNAs is in rapid progress, especially regarding translational repression by small (short) noncoding RNAs like microRNAs with 20-25 nucleotide-lengths, while long noncoding RNAs with nucleotide length of more than two hundred are also emerging. Indeed, our analysis has revealed that a long noncoding RNA transcribed from cyclin D1 promoter of 200 and 300 nucleotides exerts transcriptional repression through its binding protein TLS instead of translational repression. Translational repression is executed by short noncoding RNAs, while transcriptional repression is mainly done by long noncoding RNAs. These long noncoding RNAs are heterogeneous molecules and employ divergent molecular mechanisms to exert transcriptional repression. In this review, I overview recent publications regarding the transcription regulation by long noncoding RNAs and explore their biological significance. In addition, the relation between a random transcriptional activity of RNA polymerase II and the origin of long noncoding RNAs is discussed.
    MeSH term(s) Gene Expression Regulation ; Promoter Regions, Genetic ; RNA Polymerase II/genetics ; RNA, Long Noncoding/genetics ; RNA, Untranslated/genetics
    Chemical Substances RNA, Long Noncoding ; RNA, Untranslated ; RNA Polymerase II (EC 2.7.7.-)
    Language English
    Publishing date 2011
    Publishing country United States
    Document type Journal Article ; Review
    ISSN 0079-6484
    ISSN 0079-6484
    DOI 10.1007/978-3-642-16502-3_2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Promoter-associated long noncoding RNAs repress transcription through a RNA binding protein TLS.

    Kurokawa, Riki

    Advances in experimental medicine and biology

    2011  Volume 722, Page(s) 196–208

    Abstract: The majority of the human genome is found to be transcribed and generates mostly noncoding (nc) RNAs that do not possess protein information. MicroRNAs are one of the well-identified small ncRNAs, but occupy merely a fraction of ncRNAs. Long (large) ... ...

    Abstract The majority of the human genome is found to be transcribed and generates mostly noncoding (nc) RNAs that do not possess protein information. MicroRNAs are one of the well-identified small ncRNAs, but occupy merely a fraction of ncRNAs. Long (large) ncRNAs are emerging as a novel class of ncRNAs, but knowledge of these ncRNAs is far less accumulated. Long ncRNAs are tentatively classified as an ncRNA species containing more than 200 nucleotides. Recently, a long promoter-associated ncRNA (pncRNA) has been identified to be transcribed from the cyclin D1 promoter upon induction by genotoxic factors like ionizing-irradiation. The cyclin D1 pncRNA is specifically bound with an RNA-binding protein TLS (Translocated in liposarcoma) and exerts transcriptional repression through histone acetyltransferase (HAT) inhibitory activity. Analysis of TLS and the pncRNAs could provide a model for elucidating their roles inregulation of mammalian transcriptional programs. The pncRNA binding to TLS turns out to be an essential event for the HAT inhibitory activity. A key consensus sequence of the pncRNA is composed of GGUG, while not every RNA sequence bearing GGUG is targeted by TLS, suggesting that a secondary structure of the GGUG-bearing RNAs is also involved in recognition by TLS. Taken together, TLS is a unique mediator between signals of the long ncRNAs and transcription, suggesting that RNA networking functions in living cells.(1-3).
    MeSH term(s) Amino Acid Sequence ; Base Sequence ; Binding Sites/genetics ; Cyclic AMP Response Element-Binding Protein/metabolism ; Cyclin D1/genetics ; DNA Damage ; Gene Expression Regulation ; Histone Acetyltransferases/metabolism ; Humans ; Models, Genetic ; Molecular Sequence Data ; Promoter Regions, Genetic/genetics ; Protein Binding ; RNA, Untranslated/genetics ; RNA, Untranslated/metabolism ; RNA-Binding Protein FUS/genetics ; RNA-Binding Protein FUS/metabolism ; Transcription, Genetic
    Chemical Substances Cyclic AMP Response Element-Binding Protein ; RNA, Untranslated ; RNA-Binding Protein FUS ; Cyclin D1 (136601-57-5) ; Histone Acetyltransferases (EC 2.3.1.48)
    Language English
    Publishing date 2011
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2214-8019 ; 0065-2598
    ISSN (online) 2214-8019
    ISSN 0065-2598
    DOI 10.1007/978-1-4614-0332-6_12
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Non-coding RNA suppresses FUS aggregation caused by mechanistic shear stress on pipetting in a sequence-dependent manner.

    Hamad, Nesreen / Yoneda, Ryoma / So, Masatomo / Kurokawa, Riki / Nagata, Takashi / Katahira, Masato

    Scientific reports

    2021  Volume 11, Issue 1, Page(s) 9523

    Abstract: Fused in sarcoma/translocated in liposarcoma (FUS/TLS) is a multitasking RNA/DNA binding protein. FUS aggregation is implicated in various neurodegenerative diseases. RNA was suggested to modulate phase transition of FUS. Here, we found that FUS ... ...

    Abstract Fused in sarcoma/translocated in liposarcoma (FUS/TLS) is a multitasking RNA/DNA binding protein. FUS aggregation is implicated in various neurodegenerative diseases. RNA was suggested to modulate phase transition of FUS. Here, we found that FUS transforms into the amorphous aggregation state as an instant response to the shear stress caused by usual pipetting even at a low FUS concentration, 100 nM. It was revealed that non-coding RNA can suppress the transformation of FUS into aggregates. The suppressive effect of RNA on FUS aggregation is sequence-dependent. These results suggested that the non-coding RNA could be a prospective suppressor of FUS aggregation caused by mechanistic stress in cells. Our finding might pave the way for more research on the role of RNAs as aggregation inhibitors, which could facilitate the development of therapies for neurodegenerative diseases.
    MeSH term(s) DNA-Binding Proteins/genetics ; Protein Aggregates/genetics ; RNA, Untranslated/genetics ; RNA-Binding Protein FUS/genetics ; RNA-Binding Proteins/genetics ; Shear Strength/physiology
    Chemical Substances DNA-Binding Proteins ; Protein Aggregates ; RNA, Untranslated ; RNA-Binding Protein FUS ; RNA-Binding Proteins
    Language English
    Publishing date 2021-05-04
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-021-89075-w
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Non-coding RNA suppresses FUS aggregation caused by mechanistic shear stress on pipetting in a sequence-dependent manner

    Nesreen Hamad / Ryoma Yoneda / Masatomo So / Riki Kurokawa / Takashi Nagata / Masato Katahira

    Scientific Reports, Vol 11, Iss 1, Pp 1-

    2021  Volume 11

    Abstract: Abstract Fused in sarcoma/translocated in liposarcoma (FUS/TLS) is a multitasking RNA/DNA binding protein. FUS aggregation is implicated in various neurodegenerative diseases. RNA was suggested to modulate phase transition of FUS. Here, we found that FUS ...

    Abstract Abstract Fused in sarcoma/translocated in liposarcoma (FUS/TLS) is a multitasking RNA/DNA binding protein. FUS aggregation is implicated in various neurodegenerative diseases. RNA was suggested to modulate phase transition of FUS. Here, we found that FUS transforms into the amorphous aggregation state as an instant response to the shear stress caused by usual pipetting even at a low FUS concentration, 100 nM. It was revealed that non-coding RNA can suppress the transformation of FUS into aggregates. The suppressive effect of RNA on FUS aggregation is sequence-dependent. These results suggested that the non-coding RNA could be a prospective suppressor of FUS aggregation caused by mechanistic stress in cells. Our finding might pave the way for more research on the role of RNAs as aggregation inhibitors, which could facilitate the development of therapies for neurodegenerative diseases.
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2021-05-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Arginine methylation of translocated in liposarcoma (TLS) inhibits its binding to long noncoding RNA, abrogating TLS-mediated repression of CBP/p300 activity.

    Cui, Wei / Yoneda, Ryoma / Ueda, Naomi / Kurokawa, Riki

    The Journal of biological chemistry

    2018  Volume 293, Issue 28, Page(s) 10937–10948

    Abstract: Translocated in liposarcoma (TLS) is an RNA-binding protein and a transcription-regulatory sensor of DNA damage. TLS binds promoter-associated noncoding RNA (pncRNA) and inhibits histone acetyltransferase (HAT) activity of CREB-binding protein (CBP)/E1A- ... ...

    Abstract Translocated in liposarcoma (TLS) is an RNA-binding protein and a transcription-regulatory sensor of DNA damage. TLS binds promoter-associated noncoding RNA (pncRNA) and inhibits histone acetyltransferase (HAT) activity of CREB-binding protein (CBP)/E1A-binding protein P300 (p300) on the cyclin D1 (
    MeSH term(s) Arginine/chemistry ; Cyclin D1/genetics ; Cyclin D1/metabolism ; E1A-Associated p300 Protein/genetics ; E1A-Associated p300 Protein/metabolism ; Gene Expression Regulation ; Humans ; Methylation ; Promoter Regions, Genetic ; Protein-Arginine N-Methyltransferases/genetics ; Protein-Arginine N-Methyltransferases/metabolism ; RNA, Long Noncoding/genetics ; RNA, Long Noncoding/metabolism ; RNA-Binding Protein FUS/genetics ; RNA-Binding Protein FUS/metabolism ; Transcription, Genetic
    Chemical Substances CCND1 protein, human ; RNA, Long Noncoding ; RNA-Binding Protein FUS ; Cyclin D1 (136601-57-5) ; Arginine (94ZLA3W45F) ; Protein-Arginine N-Methyltransferases (EC 2.1.1.319) ; E1A-Associated p300 Protein (EC 2.3.1.48) ; EP300 protein, human (EC 2.3.1.48)
    Language English
    Publishing date 2018-05-21
    Publishing country United States
    Document type Journal Article ; 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.RA117.000598
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Direct visualization of the conformational change of FUS/TLS upon binding to promoter-associated non-coding RNA.

    Hamad, Nesreen / Watanabe, Hiroki / Uchihashi, Takayuki / Kurokawa, Riki / Nagata, Takashi / Katahira, Masato

    Chemical communications (Cambridge, England)

    2020  Volume 56, Issue 64, Page(s) 9134–9137

    Abstract: High-speed AFM revealed the conformational change of fused in sarcoma (FUS) from a compact to an extended structure upon binding of non-coding RNA, which is supposed to allow FUS to bind to CBP/p300 for transcriptional interference. Thus, a mechanistic ... ...

    Abstract High-speed AFM revealed the conformational change of fused in sarcoma (FUS) from a compact to an extended structure upon binding of non-coding RNA, which is supposed to allow FUS to bind to CBP/p300 for transcriptional interference. Thus, a mechanistic insight into transcription regulation by FUS and non-coding RNA is provided.
    MeSH term(s) Green Fluorescent Proteins/chemistry ; Intrinsically Disordered Proteins/chemistry ; Intrinsically Disordered Proteins/metabolism ; Maltose-Binding Proteins/chemistry ; Microscopy, Atomic Force ; Promoter Regions, Genetic ; Protein Binding ; Protein Conformation ; RNA, Untranslated/metabolism ; RNA-Binding Protein FUS/chemistry ; RNA-Binding Protein FUS/metabolism
    Chemical Substances Intrinsically Disordered Proteins ; Maltose-Binding Proteins ; RNA, Untranslated ; RNA-Binding Protein FUS ; Green Fluorescent Proteins (147336-22-9)
    Language English
    Publishing date 2020-07-22
    Publishing country England
    Document type Journal Article ; Video-Audio Media
    ZDB-ID 1472881-3
    ISSN 1364-548X ; 1359-7345 ; 0009-241X
    ISSN (online) 1364-548X
    ISSN 1359-7345 ; 0009-241X
    DOI 10.1039/d0cc03776a
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: Direct visualization of the conformational change of FUS/TLS upon binding to promoter-associated non-coding RNA

    Hamad, Nesreen / Watanabe, Hiroki / Uchihashi, Takayuki / Kurokawa, Riki / Nagata, Takashi / Katahira, Masato

    Chemical communications. 2020 Aug. 11, v. 56, no. 64

    2020  

    Abstract: High-speed AFM revealed the conformational change of fused in sarcoma (FUS) from a compact to an extended structure upon binding of non-coding RNA, which is supposed to allow FUS to bind to CBP/p300 for transcriptional interference. Thus, a mechanistic ... ...

    Abstract High-speed AFM revealed the conformational change of fused in sarcoma (FUS) from a compact to an extended structure upon binding of non-coding RNA, which is supposed to allow FUS to bind to CBP/p300 for transcriptional interference. Thus, a mechanistic insight into transcription regulation by FUS and non-coding RNA is provided.
    Keywords non-coding RNA ; sarcoma ; transcription (genetics)
    Language English
    Dates of publication 2020-0811
    Size p. 9134-9137.
    Publishing place The Royal Society of Chemistry
    Document type Article
    Note NAL-AP-2-clean
    ZDB-ID 1472881-3
    ISSN 1364-548X ; 1359-7345 ; 0009-241X
    ISSN (online) 1364-548X
    ISSN 1359-7345 ; 0009-241X
    DOI 10.1039/d0cc03776a
    Database NAL-Catalogue (AGRICOLA)

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