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  1. Article ; Online: Towards higher-resolution and in vivo understanding of lncRNA biogenesis and function.

    Chen, Ling-Ling

    Nature methods

    2022  Volume 19, Issue 10, Page(s) 1152–1155

    MeSH term(s) Cell Proliferation ; Gene Expression Regulation, Neoplastic ; RNA, Long Noncoding/genetics ; Signal Transduction
    Chemical Substances RNA, Long Noncoding
    Language English
    Publishing date 2022-09-25
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2169522-2
    ISSN 1548-7105 ; 1548-7091
    ISSN (online) 1548-7105
    ISSN 1548-7091
    DOI 10.1038/s41592-022-01626-9
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  2. Article ; Online: The Functional Circular RNA Screening via RfxCas13d/BSJ-gRNA System.

    Wu, Hao / Chen, Ling-Ling

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

    2024  Volume 2765, Page(s) 173–191

    Abstract: Although discovered decades ago, functions of circular RNAs (circRNAs) produced from exon(s) back-splicing of pre-mRNAs have only been unveiled recently. As circRNAs share overlapping sequences with their cognate linear RNAs, except for the back-splicing ...

    Abstract Although discovered decades ago, functions of circular RNAs (circRNAs) produced from exon(s) back-splicing of pre-mRNAs have only been unveiled recently. As circRNAs share overlapping sequences with their cognate linear RNAs, except for the back-splicing junction sites, it is difficult to distinguish circRNAs from cognate mRNAs in functional studies. In this chapter, we describe a programmable method for the large-scale functional circRNA screening based on the RNA-guided, RNA-targeting CRISPR-Cas13 (RfxCas13d) system. This method can be applied both in vivo and in cell to explore highly expressed circRNAs that may influence cell growth, either under natural conditions or in response to environmental stimulation, without disturbing cognate linear mRNAs.
    MeSH term(s) RNA, Circular ; RNA, Guide, CRISPR-Cas Systems ; RNA, Untranslated ; RNA/genetics ; Cell Cycle ; RNA, Messenger
    Chemical Substances RNA, Circular ; RNA, Guide, CRISPR-Cas Systems ; RNA, Untranslated ; RNA (63231-63-0) ; RNA, Messenger
    Language English
    Publishing date 2024-02-21
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-3678-7_10
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  3. Article ; Online: Unveiling the mystery of nuclear RNA homeostasis.

    Shan, Lin / Chen, Ling-Ling

    Cell stem cell

    2024  Volume 31, Issue 5, Page(s) 583–585

    Abstract: How nuclear RNA homeostasis impacts cellular functions remains elusive. In this issue of Cell Stem Cell, Han et al. ...

    Abstract How nuclear RNA homeostasis impacts cellular functions remains elusive. In this issue of Cell Stem Cell, Han et al.
    MeSH term(s) Animals ; Homeostasis ; Mice ; RNA, Nuclear/metabolism ; RNA, Nuclear/genetics ; Exosome Multienzyme Ribonuclease Complex/metabolism ; Exosome Multienzyme Ribonuclease Complex/genetics ; Cell Nucleus/metabolism ; Mouse Embryonic Stem Cells/metabolism ; Mouse Embryonic Stem Cells/cytology ; Humans ; RNA-Binding Proteins/metabolism ; RNA-Binding Proteins/genetics ; RNA/metabolism ; Pluripotent Stem Cells/metabolism ; Pluripotent Stem Cells/cytology
    Chemical Substances RNA, Nuclear ; Exosome Multienzyme Ribonuclease Complex (EC 3.1.-) ; RNA-Binding Proteins ; RNA (63231-63-0)
    Language English
    Publishing date 2024-04-23
    Publishing country United States
    Document type Journal Article ; Comment
    ZDB-ID 2375354-7
    ISSN 1875-9777 ; 1934-5909
    ISSN (online) 1875-9777
    ISSN 1934-5909
    DOI 10.1016/j.stem.2024.03.014
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  4. Article ; Online: The expanding regulatory mechanisms and cellular functions of circular RNAs.

    Chen, Ling-Ling

    Nature reviews. Molecular cell biology

    2020  Volume 21, Issue 8, Page(s) 475–490

    Abstract: Many protein-coding genes in higher eukaryotes can produce circular RNAs (circRNAs) through back-splicing of exons. CircRNAs differ from mRNAs in their production, structure and turnover and thereby have unique cellular functions and potential biomedical ...

    Abstract Many protein-coding genes in higher eukaryotes can produce circular RNAs (circRNAs) through back-splicing of exons. CircRNAs differ from mRNAs in their production, structure and turnover and thereby have unique cellular functions and potential biomedical applications. In this Review, I discuss recent progress in our understanding of the biogenesis of circRNAs and the regulation of their abundance and of their biological functions, including in transcription and splicing, sequestering or scaffolding of macromolecules to interfere with microRNA activities or signalling pathways, and serving as templates for translation. I further discuss the emerging roles of circRNAs in regulating immune responses and cell proliferation, and the possibilities of applying circRNA technologies in biomedical research.
    MeSH term(s) Alternative Splicing/genetics ; Animals ; Exons/genetics ; Gene Expression/genetics ; Gene Expression Regulation/genetics ; Humans ; MicroRNAs/metabolism ; RNA/genetics ; RNA Splicing/genetics ; RNA, Circular/genetics ; RNA, Circular/metabolism ; RNA, Circular/physiology ; RNA, Messenger/metabolism
    Chemical Substances MicroRNAs ; RNA, Circular ; RNA, Messenger ; RNA (63231-63-0)
    Language English
    Publishing date 2020-05-04
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2031313-5
    ISSN 1471-0080 ; 1471-0072
    ISSN (online) 1471-0080
    ISSN 1471-0072
    DOI 10.1038/s41580-020-0243-y
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  5. Article ; Online: Circular RNAs: Characterization, cellular roles, and applications.

    Liu, Chu-Xiao / Chen, Ling-Ling

    Cell

    2022  Volume 185, Issue 12, Page(s) 2016–2034

    Abstract: Most circular RNAs are produced from the back-splicing of exons of precursor mRNAs. Recent technological advances have in part overcome problems with their circular conformation and sequence overlap with linear cognate mRNAs, allowing a better ... ...

    Abstract Most circular RNAs are produced from the back-splicing of exons of precursor mRNAs. Recent technological advances have in part overcome problems with their circular conformation and sequence overlap with linear cognate mRNAs, allowing a better understanding of their cellular roles. Depending on their localization and specific interactions with DNA, RNA, and proteins, circular RNAs can modulate transcription and splicing, regulate stability and translation of cytoplasmic mRNAs, interfere with signaling pathways, and serve as templates for translation in different biological and pathophysiological contexts. Emerging applications of RNA circles to interfere with cellular processes, modulate immune responses, and direct translation into proteins shed new light on biomedical research. In this review, we discuss approaches used in circular RNA studies and the current understanding of their regulatory roles and potential applications.
    MeSH term(s) Proteins/metabolism ; RNA/metabolism ; RNA Precursors/metabolism ; RNA Splicing ; RNA, Circular ; RNA, Messenger/metabolism
    Chemical Substances Proteins ; RNA Precursors ; RNA, Circular ; RNA, Messenger ; RNA (63231-63-0)
    Language English
    Publishing date 2022-05-17
    Publishing country United States
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2022.04.021
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  6. Article ; Online: Circular RNAs: Characterization, cellular roles, and applications.

    Liu, Chu-Xiao / Chen, Ling-Ling

    Cell

    2022  Volume 185, Issue 13, Page(s) 2390

    Language English
    Publishing date 2022-06-21
    Publishing country United States
    Document type Published Erratum
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2022.06.001
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  7. Article ; Online: Expanded regulation of circular RNA translation.

    Liu, Chu-Xiao / Chen, Ling-Ling

    Molecular cell

    2021  Volume 81, Issue 20, Page(s) 4111–4113

    Abstract: Chen et al. (2021) have identified many internal ribosome entry site-like elements that can potentially drive circRNA translation. Dozens of such element-containing circRNAs-encoded peptides are validated, among which a circFGFR1-encoded protein acts as ... ...

    Abstract Chen et al. (2021) have identified many internal ribosome entry site-like elements that can potentially drive circRNA translation. Dozens of such element-containing circRNAs-encoded peptides are validated, among which a circFGFR1-encoded protein acts as an antagonist of FGFR1.
    MeSH term(s) Gene Expression Regulation ; Internal Ribosome Entry Sites ; RNA, Circular
    Chemical Substances Internal Ribosome Entry Sites ; RNA, Circular
    Language English
    Publishing date 2021-10-22
    Publishing country United States
    Document type Journal Article ; Comment
    ZDB-ID 1415236-8
    ISSN 1097-4164 ; 1097-2765
    ISSN (online) 1097-4164
    ISSN 1097-2765
    DOI 10.1016/j.molcel.2021.09.023
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  8. Article ; Online: Methods for circular RNAs.

    Chen, Ling-Ling / Wilusz, Jeremy E

    Methods (San Diego, Calif.)

    2021  Volume 196, Page(s) 1–2

    MeSH term(s) MicroRNAs ; RNA/genetics ; RNA, Circular
    Chemical Substances MicroRNAs ; RNA, Circular ; RNA (63231-63-0)
    Language English
    Publishing date 2021-10-01
    Publishing country United States
    Document type Editorial
    ZDB-ID 1066584-5
    ISSN 1095-9130 ; 1046-2023
    ISSN (online) 1095-9130
    ISSN 1046-2023
    DOI 10.1016/j.ymeth.2021.09.011
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  9. Article ; Online: Emerging roles of nuclear bodies in genome spatial organization.

    Shan, Lin / Li, Pan / Yu, Hongtao / Chen, Ling-Ling

    Trends in cell biology

    2023  

    Abstract: Nuclear bodies (NBs) are biomolecular condensates that participate in various cellular processes and respond to cellular stimuli in the nucleus. The assembly and function of these protein- and RNA-rich bodies, such as nucleoli, nuclear speckles, and ... ...

    Abstract Nuclear bodies (NBs) are biomolecular condensates that participate in various cellular processes and respond to cellular stimuli in the nucleus. The assembly and function of these protein- and RNA-rich bodies, such as nucleoli, nuclear speckles, and promyelocytic leukemia (PML) NBs, contribute to the spatial organization of the nucleus, regulating chromatin activities locally and globally. Recent technological advancements, including spatial multiomics approaches, have revealed novel roles of nucleoli in modulating ribosomal DNA (rDNA) and adjacent non-rDNA chromatin activity, nuclear speckles in scaffolding active genome architecture, and PML NBs in maintaining genome stability during stress conditions. In this review, we summarize emerging functions of these important NBs in the spatial organization of the genome, aided by recently developed spatial multiomics approaches toward this direction.
    Language English
    Publishing date 2023-11-21
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 30122-x
    ISSN 1879-3088 ; 0962-8924
    ISSN (online) 1879-3088
    ISSN 0962-8924
    DOI 10.1016/j.tcb.2023.10.012
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  10. Article ; Online: Screening circular RNAs with functional potential using the RfxCas13d/BSJ-gRNA system.

    Li, Siqi / Wu, Hao / Chen, Ling-Ling

    Nature protocols

    2022  Volume 17, Issue 9, Page(s) 2085–2107

    Abstract: Circular RNAs (circRNAs) are covalently enclosed, single-stranded RNAs produced by back-splicing of pre-mRNA exons that have recently emerged as an important class of molecules in gene expression regulation. circRNAs share overlapping sequences with ... ...

    Abstract Circular RNAs (circRNAs) are covalently enclosed, single-stranded RNAs produced by back-splicing of pre-mRNA exons that have recently emerged as an important class of molecules in gene expression regulation. circRNAs share overlapping sequences with their cognate linear mRNAs except the back-splicing junction (BSJ) sites. This feature makes it difficult to discriminate between the functions of circRNAs and their cognate mRNAs. We previously reported that the programmable RNA-guided, RNA-targeting CRISPR-Cas13 (RfxCas13d) system effectively and specifically discriminates circRNAs from mRNAs by using guide RNAs (gRNAs) targeting sequences across BSJ sites. Here, we describe a detailed protocol based on this RfxCas13d/BSJ-gRNA system for large-scale functional circRNA screening in human cell lines. The protocol includes gRNA library design, construction and transduction, analysis of screening results and validation of functional circRNA candidates. In total, it takes ~3-4 months of collaborative work between a well-trained molecular biologist and a bioinformatic expert. This protocol can be applied both in cells and in vivo to identify highly expressed circRNAs affecting cell growth, either in unperturbed conditions or under environmental stimulation, without disturbing their cognate linear mRNAs.
    MeSH term(s) Humans ; RNA/genetics ; RNA/metabolism ; RNA Splicing ; RNA, Circular ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Sequence Analysis, RNA/methods ; RNA, Guide, CRISPR-Cas Systems
    Chemical Substances RNA, Circular ; RNA, Messenger ; RNA (63231-63-0) ; RNA, Guide, CRISPR-Cas Systems
    Language English
    Publishing date 2022-07-13
    Publishing country England
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 2244966-8
    ISSN 1750-2799 ; 1754-2189
    ISSN (online) 1750-2799
    ISSN 1754-2189
    DOI 10.1038/s41596-022-00715-5
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