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  1. Article: Editorial: Circadian desynchrony: Consequences, mechanisms, and Open Issues.

    Gutman, Roee / Pendergast, Julie S / Nakamura, Wataru / Kojima, Shihoko

    Frontiers in physiology

    2023  Volume 14, Page(s) 1177643

    Language English
    Publishing date 2023-03-17
    Publishing country Switzerland
    Document type Editorial
    ZDB-ID 2564217-0
    ISSN 1664-042X
    ISSN 1664-042X
    DOI 10.3389/fphys.2023.1177643
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Coordination of rhythmic RNA synthesis and degradation orchestrates 24- and 12-h RNA expression patterns in mouse fibroblasts.

    Unruh, Benjamin A / Weidemann, Douglas E / Miao, Lin / Kojima, Shihoko

    Proceedings of the National Academy of Sciences of the United States of America

    2024  Volume 121, Issue 7, Page(s) e2314690121

    Abstract: Circadian RNA expression is essential to ultimately regulate a plethora of downstream rhythmic biochemical, physiological, and behavioral processes. Both transcriptional and posttranscriptional mechanisms are considered important to drive rhythmic RNA ... ...

    Abstract Circadian RNA expression is essential to ultimately regulate a plethora of downstream rhythmic biochemical, physiological, and behavioral processes. Both transcriptional and posttranscriptional mechanisms are considered important to drive rhythmic RNA expression; however, the extent to which each regulatory process contributes to the rhythmic RNA expression remains controversial. To systematically address this, we monitored RNA dynamics using metabolic RNA labeling technology during a circadian cycle in mouse fibroblasts. We find that rhythmic RNA synthesis is the primary contributor of 24-h RNA rhythms, while rhythmic degradation is more important for 12-h RNA rhythms. These rhythms were predominantly regulated by
    MeSH term(s) Mice ; Animals ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Circadian Rhythm/genetics ; Fibroblasts/metabolism ; Circadian Clocks/genetics
    Chemical Substances RNA, Messenger
    Language English
    Publishing date 2024-02-05
    Publishing country United States
    Document type Journal Article
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2314690121
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1148: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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    Jg. 1995 - 2021: Lesesall (1.OG)
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  3. Article: Coordination of rhythmic RNA synthesis and degradation orchestrates 24-hour and 12-hour RNA expression patterns in mouse fibroblasts.

    Unruh, Benjamin A / Weidemann, Douglas E / Kojima, Shihoko

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Circadian RNA expression is essential to ultimately regulate a plethora of downstream rhythmic biochemical, physiological, and behavioral processes. Both transcriptional and post-transcriptional mechanisms are considered important to drive rhythmic RNA ... ...

    Abstract Circadian RNA expression is essential to ultimately regulate a plethora of downstream rhythmic biochemical, physiological, and behavioral processes. Both transcriptional and post-transcriptional mechanisms are considered important to drive rhythmic RNA expression, however, the extent to which each regulatory process contributes to the rhythmic RNA expression remains controversial. To systematically address this, we monitored RNA dynamics using metabolic RNA labeling technology during a circadian cycle in mouse fibroblasts. We find that rhythmic RNA synthesis is the primary contributor of 24 hr RNA rhythms, while rhythmic degradation is more important for 12 hr RNA rhythms. These rhythms were predominantly regulated by
    Language English
    Publishing date 2023-07-26
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.07.26.550672
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Timing without coding: How do long non-coding RNAs regulate circadian rhythms?

    Mosig, Rebecca A / Kojima, Shihoko

    Seminars in cell & developmental biology

    2021  Volume 126, Page(s) 79–86

    Abstract: Long non-coding RNAs (lncRNAs) are a new class of regulatory RNAs that play important roles in disease development and a variety of biological processes. Recent studies have underscored the importance of lncRNAs in the circadian clock system and ... ...

    Abstract Long non-coding RNAs (lncRNAs) are a new class of regulatory RNAs that play important roles in disease development and a variety of biological processes. Recent studies have underscored the importance of lncRNAs in the circadian clock system and demonstrated that lncRNAs regulate core clock genes and the core clock machinery in mammals. In this review, we provide an overview of our current understanding of how lncRNAs regulate the circadian clock without coding a protein. We also offer additional insights into the challenges in understanding the functions of lncRNAs and other unresolved questions in the field. We do not cover other regulatory ncRNAs even though they also play important roles; readers are highly encouraged to refer to other excellent reviews on this topic.
    MeSH term(s) Animals ; Circadian Clocks/genetics ; Circadian Rhythm/genetics ; Mammals/genetics ; RNA, Long Noncoding/genetics ; RNA, Long Noncoding/metabolism ; RNA, Untranslated
    Chemical Substances RNA, Long Noncoding ; RNA, Untranslated
    Language English
    Publishing date 2021-06-09
    Publishing country England
    Document type Journal Article ; Review ; Research Support, N.I.H., Extramural
    ZDB-ID 1312473-0
    ISSN 1096-3634 ; 1084-9521
    ISSN (online) 1096-3634
    ISSN 1084-9521
    DOI 10.1016/j.semcdb.2021.04.020
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2918: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  5. Article ; Online: Correction: Critical role of deadenylation in regulating poly(A) rhythms and circadian gene expression.

    Yao, Xiangyu / Kojima, Shihoko / Chen, Jing

    PLoS computational biology

    2021  Volume 17, Issue 5, Page(s) e1009065

    Abstract: This corrects the article DOI: 10.1371/journal.pcbi.1007842.]. ...

    Abstract [This corrects the article DOI: 10.1371/journal.pcbi.1007842.].
    Language English
    Publishing date 2021-05-26
    Publishing country United States
    Document type Published Erratum
    ZDB-ID 2193340-6
    ISSN 1553-7358 ; 1553-734X
    ISSN (online) 1553-7358
    ISSN 1553-734X
    DOI 10.1371/journal.pcbi.1009065
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  6. Article ; Online: Correction

    Xiangyu Yao / Shihoko Kojima / Jing Chen

    PLoS Computational Biology, Vol 17, Iss 5, p e

    Critical role of deadenylation in regulating poly(A) rhythms and circadian gene expression.

    2021  Volume 1009065

    Abstract: This corrects the article DOI:10.1371/journal.pcbi.1007842.]. ...

    Abstract [This corrects the article DOI:10.1371/journal.pcbi.1007842.].
    Keywords Biology (General) ; QH301-705.5
    Language English
    Publishing date 2021-05-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: The Making and Breaking of RNAs: Dynamics of Rhythmic RNA Expression in Mammals.

    Unruh, Benjamin A / Kojima, Shihoko

    Journal of biological rhythms

    2020  Volume 35, Issue 6, Page(s) 519–529

    Abstract: The identification and characterization of rhythmically expressed mRNAs have been an active area of research over the past 20 years, as these mRNAs are believed to produce the daily rhythms in a wide range of biological processes. Circadian transcriptome ...

    Abstract The identification and characterization of rhythmically expressed mRNAs have been an active area of research over the past 20 years, as these mRNAs are believed to produce the daily rhythms in a wide range of biological processes. Circadian transcriptome studies have used mature mRNA as a primary readout and focused largely on rhythmic RNA synthesis as a regulatory mechanism underlying rhythmic mRNA expression. However, RNA synthesis, RNA degradation, or a combination of both must be rhythmic to drive rhythmic RNA profiles, and it is still unclear to what extent rhythmic synthesis leads to rhythmic RNA profiles. In addition, circadian RNA expression is also often tissue specific. Although a handful of genes cycle in all or most tissues, others are rhythmic only in certain tissues, even though the same core clock mechanism is believed to control the rhythmic RNA profiles in all tissues. This review focuses on the dynamics of rhythmic RNA synthesis and degradation and discusses how these steps collectively determine the rhythmicity, phase, and amplitude of RNA accumulation. In particular, we highlight a possible role of RNA degradation in driving tissue-specific RNA rhythms. By unifying findings from experimental and theoretical studies, we will provide a comprehensive overview of how rhythmic gene expression can be achieved and how each regulatory step contributes to tissue-specific circadian transcriptome output in mammals.
    MeSH term(s) Animals ; Circadian Clocks/genetics ; Circadian Rhythm/genetics ; Humans ; Mammals/metabolism ; RNA, Messenger/analysis ; RNA, Messenger/genetics ; Transcriptome/genetics
    Chemical Substances RNA, Messenger
    Language English
    Publishing date 2020-09-23
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Review
    ZDB-ID 896387-3
    ISSN 1552-4531 ; 0748-7304
    ISSN (online) 1552-4531
    ISSN 0748-7304
    DOI 10.1177/0748730420957498
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2872: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  8. Article: A comparative study of algorithms detecting differential rhythmicity in transcriptomic data.

    Miao, Lin / Weidemann, Douglas E / Ngo, Katherine / Unruh, Benjamin A / Kojima, Shihoko

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Rhythmic transcripts play pivotal roles in driving the daily oscillations of various biological processes. Genetic or environmental disruptions can lead to alterations in the rhythmicity of transcripts, ultimately impacting downstream circadian outputs, ... ...

    Abstract Rhythmic transcripts play pivotal roles in driving the daily oscillations of various biological processes. Genetic or environmental disruptions can lead to alterations in the rhythmicity of transcripts, ultimately impacting downstream circadian outputs, including metabolic processes and even behavior. To statistically compare the differences in transcript rhythms between two or more conditions, several algorithms have been developed to analyze circadian transcriptomic data, each with distinct features. In this study, we compared the performance of seven algorithms that were specifically designed to detect differential rhythmicity. We found that even when applying the same statistical threshold, these algorithms yielded varying numbers of differentially rhythmic transcripts. Nevertheless, the set of transcripts commonly identified as differentially rhythmic exhibited substantial overlap among algorithms. Furthermore, the phase and amplitude differences calculated by these algorithms displayed significant correlations. In summary, our study highlights a high degree of similarity in the results produced by these algorithms. Furthermore, when selecting an algorithm for analysis, it is crucial to ensure the compatibility of input data with the specific requirements of the chosen algorithm and to assess whether the algorithm's output fits the needs of the user.
    Language English
    Publishing date 2023-10-17
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.10.12.562079
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Genetic and environmental perturbations alter the rhythmic expression pattern of a circadian long non-coding RNA,

    Miao, Lin / Batty, Kyle R / Jackson, Ayana N / Pieno, Heather A / Rhoades, Maisy W / Kojima, Shihoko

    F1000Research

    2022  Volume 11, Page(s) 1073

    Abstract: ... ...

    Abstract Background
    MeSH term(s) Mice ; Animals ; RNA, Long Noncoding/genetics ; Circadian Clocks/genetics ; Circadian Rhythm/genetics ; Transcription Factors/metabolism ; Liver
    Chemical Substances RNA, Long Noncoding ; Transcription Factors
    Language English
    Publishing date 2022-09-20
    Publishing country England
    Document type Journal Article
    ZDB-ID 2699932-8
    ISSN 2046-1402 ; 2046-1402
    ISSN (online) 2046-1402
    ISSN 2046-1402
    DOI 10.12688/f1000research.125628.2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Aneuploidy and gene expression: is there dosage compensation?

    Kojima, Shihoko / Cimini, Daniela

    Epigenomics

    2019  Volume 11, Issue 16, Page(s) 1827–1837

    Abstract: Aneuploidy (i.e., abnormal chromosome number) is the leading cause of miscarriage and congenital defects in humans. Moreover, aneuploidy is ubiquitous in cancer. The deleterious phenotypes associated with aneuploidy are likely a result of the imbalance ... ...

    Abstract Aneuploidy (i.e., abnormal chromosome number) is the leading cause of miscarriage and congenital defects in humans. Moreover, aneuploidy is ubiquitous in cancer. The deleterious phenotypes associated with aneuploidy are likely a result of the imbalance in the levels of gene products derived from the additional chromosome(s). Here, we summarize the current knowledge on how the presence of extra chromosomes impacts gene expression. We describe studies that have found a strict correlation between gene dosage and transcript levels as wells as studies that have found a less stringent correlation, hinting at the possible existence of dosage compensation mechanisms. We conclude by peering into the epigenetic changes found in aneuploid cells and outlining current knowledge gaps and potential areas of future investigation.
    MeSH term(s) Aneuploidy ; Animals ; Dosage Compensation, Genetic ; Gene Dosage ; Gene Expression ; Humans
    Language English
    Publishing date 2019-11-22
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Review
    ISSN 1750-192X
    ISSN (online) 1750-192X
    DOI 10.2217/epi-2019-0135
    Database MEDical Literature Analysis and Retrieval System OnLINE

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