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  1. Article ; Online: SUMO pathway is required for ribosome biogenesis.

    Ryu, Hong-Yeoul

    BMB reports

    2022  Volume 55, Issue 11, Page(s) 535–540

    Abstract: Ribosomes, acting as the cellular factories for protein production, are essential for all living organisms. Ribosomes are composed of both proteins and RNAs and are established through the coordination of several steps, including transcription, ... ...

    Abstract Ribosomes, acting as the cellular factories for protein production, are essential for all living organisms. Ribosomes are composed of both proteins and RNAs and are established through the coordination of several steps, including transcription, maturation of ribosomal RNA (rRNA), and assembly of ribosomal proteins. In particular, diverse factors required for ribosome biogenesis, such as transcription factors, small nucleolar RNA (snoRNA)-associated proteins, and assembly factors, are tightly regulated by various post-translational modifications. Among these modifications, small ubiquitin-related modifier (SUMO) targets lots of proteins required for gene expression of ribosomal proteins, rRNA, and snoRNAs, rRNA processing, and ribosome assembly. The tight control of SUMOylation affects functions and locations of substrates. This review summarizes current studies and recent progress of SUMOylation-mediated regulation of ribosome biogenesis. [BMB Reports 2022; 55(11): 535-540].
    MeSH term(s) Ubiquitin/metabolism ; Ribosomes/metabolism ; RNA Processing, Post-Transcriptional ; RNA, Small Nucleolar/genetics ; RNA, Small Nucleolar/metabolism ; Ribosomal Proteins/genetics ; Ribosomal Proteins/metabolism
    Chemical Substances Ubiquitin ; RNA, Small Nucleolar ; Ribosomal Proteins
    Language English
    Publishing date 2022-10-04
    Publishing country Korea (South)
    Document type Review ; News
    ZDB-ID 2410389-5
    ISSN 1976-670X ; 1976-6696
    ISSN (online) 1976-670X
    ISSN 1976-6696
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    Zs.A 4202: Show issues Location:
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  2. Article ; Online: SUMO: a novel target for anti-coronavirus therapy.

    Ryu, Hong-Yeoul

    Pathogens and global health

    2021  Volume 115, Issue 5, Page(s) 292–299

    Abstract: Over the past 20 years, humankind has encountered three severe coronavirus outbreaks. Currently ongoing, COVID-19 (coronavirus disease 2019) was declared a pandemic due to its massive impact on global health and the economy. Numerous scientists are ... ...

    Abstract Over the past 20 years, humankind has encountered three severe coronavirus outbreaks. Currently ongoing, COVID-19 (coronavirus disease 2019) was declared a pandemic due to its massive impact on global health and the economy. Numerous scientists are working to identify efficacious therapeutic agents for COVID-19, although treatment ability has yet to be demonstrated. The SUMO (small ubiquitin-like modifier) system has diverse roles in viral manipulation, but the function of SUMO in coronaviruses is still unknown. The objective of this review article is to present recently published data suggesting contributions of the host SUMO system to coronavirus infection. These findings underscore the potential of SUMO as a novel target for anti-coronavirus therapy, and the need for a deeper understanding of coronavirus pathology to prepare and prevail against the current and emerging coronavirus outbreaks.
    MeSH term(s) COVID-19 ; Disease Outbreaks ; Humans ; Pandemics ; SARS-CoV-2
    Language English
    Publishing date 2021-03-26
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 2625162-0
    ISSN 2047-7732 ; 2047-7724
    ISSN (online) 2047-7732
    ISSN 2047-7724
    DOI 10.1080/20477724.2021.1906562
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  3. Article ; Online: Histone sumoylation and chromatin dynamics.

    Ryu, Hong-Yeoul / Hochstrasser, Mark

    Nucleic acids research

    2021  Volume 49, Issue 11, Page(s) 6043–6052

    Abstract: Chromatin structure and gene expression are dynamically controlled by post-translational modifications (PTMs) on histone proteins, including ubiquitylation, methylation, acetylation and small ubiquitin-like modifier (SUMO) conjugation. It was initially ... ...

    Abstract Chromatin structure and gene expression are dynamically controlled by post-translational modifications (PTMs) on histone proteins, including ubiquitylation, methylation, acetylation and small ubiquitin-like modifier (SUMO) conjugation. It was initially thought that histone sumoylation exclusively suppressed gene transcription, but recent advances in proteomics and genomics have uncovered its diverse functions in cotranscriptional processes, including chromatin remodeling, transcript elongation, and blocking cryptic initiation. Histone sumoylation is integral to complex signaling codes that prime additional histone PTMs as well as modifications of the RNA polymerase II carboxy-terminal domain (RNAPII-CTD) during transcription. In addition, sumoylation of histone variants is critical for the DNA double-strand break (DSB) response and for chromosome segregation during mitosis. This review describes recent findings on histone sumoylation and its coordination with other histone and RNAPII-CTD modifications in the regulation of chromatin dynamics.
    MeSH term(s) Centromere/metabolism ; Chromatin/chemistry ; Chromatin/metabolism ; DNA Repair ; Gene Expression Regulation ; Histone Code ; Histones/metabolism ; Sumoylation ; Transcription, Genetic
    Chemical Substances Chromatin ; Histones
    Language English
    Publishing date 2021-04-22
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
    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/gkab280
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    Zs.A 1067: Show issues Location:
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  4. Article: Histone modification in

    Chou, Kwon Young / Lee, Jun-Yeong / Kim, Kee-Beom / Kim, Eunjeong / Lee, Hyun-Shik / Ryu, Hong-Yeoul

    Computational and structural biotechnology journal

    2023  Volume 21, Page(s) 1843–1850

    Abstract: The budding ... ...

    Abstract The budding yeast
    Language English
    Publishing date 2023-02-24
    Publishing country Netherlands
    Document type Journal Article ; Review
    ZDB-ID 2694435-2
    ISSN 2001-0370
    ISSN 2001-0370
    DOI 10.1016/j.csbj.2023.02.037
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  5. Article ; Online: SUMO and cellular adaptive mechanisms

    Hong-Yeoul Ryu / Seong Hoon Ahn / Mark Hochstrasser

    Experimental and Molecular Medicine, Vol 52, Iss 6, Pp 931-

    2020  Volume 939

    Abstract: Stress response: how cells wrestle with SUMO disruption Cellular stress caused by disrupting attachment of the ubiquitous small ubiquitin-like modifier (SUMO) proteins, which are present in most organisms and regulate numerous DNA processes and stress ... ...

    Abstract Stress response: how cells wrestle with SUMO disruption Cellular stress caused by disrupting attachment of the ubiquitous small ubiquitin-like modifier (SUMO) proteins, which are present in most organisms and regulate numerous DNA processes and stress responses by attaching to key proteins, results in some remarkable adaptations. Mark Hochstrasser at Yale University, New Haven, USA, and co-workers review how this “sumoylation” is reversed by protease enzymes, and how imbalances between sumoylation and desumoylation may be linked to diseases including cancer. When certain SUMO proteases are deliberately disrupted, the cells quickly become aneuploid, i.e., carry an abnormal number of chromosomes. These cells show severe growth defects, but over many generations they regain the normal number of chromosomes. They also undergo genetic changes that promote alternative mechanisms that compensate for losing the SUMO protease and facilitate the same efficient stress responses as the original cells.
    Keywords Medicine ; R ; Biochemistry ; QD415-436
    Language English
    Publishing date 2020-06-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Nuclear mRNA Export and Aging

    Hyun-Sun Park / Jongbok Lee / Hyun-Shik Lee / Seong Hoon Ahn / Hong-Yeoul Ryu

    International Journal of Molecular Sciences, Vol 23, Iss 5451, p

    2022  Volume 5451

    Abstract: The relationship between transcription and aging is one that has been studied intensively and experimentally with diverse attempts. However, the impact of the nuclear mRNA export on the aging process following its transcription is still poorly understood, ...

    Abstract The relationship between transcription and aging is one that has been studied intensively and experimentally with diverse attempts. However, the impact of the nuclear mRNA export on the aging process following its transcription is still poorly understood, although the nuclear events after transcription are coupled closely with the transcription pathway because the essential factors required for mRNA transport, namely TREX, TREX-2, and nuclear pore complex (NPC), physically and functionally interact with various transcription factors, including the activator/repressor and pre-mRNA processing factors. Dysregulation of the mediating factors for mRNA export from the nucleus generally leads to the aberrant accumulation of nuclear mRNA and further impairment in the vegetative growth and normal lifespan and the pathogenesis of neurodegenerative diseases. The optimal stoichiometry and density of NPC are destroyed during the process of cellular aging, and their damage triggers a defect of function in the nuclear permeability barrier. This review describes recent findings regarding the role of the nuclear mRNA export in cellular aging and age-related neurodegenerative disorders.
    Keywords mRNA export ; TREX ; TREX-2 ; NPC ; lifespan ; neurodegenerative diseases ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Language English
    Publishing date 2022-05-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
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  7. Article: Auto-sumoylation of the Ubc9 E2 SUMO-conjugating Enzyme Extends Cellular Lifespan.

    Ryu, Hong-Yeoul / Jeong, Dong-Won / Kim, Seung Yeon / Jeoung, Seok-Won / Zhao, Dejian / Knight, James / Lam, TuKiet / Jin, Jong Hwa / Lee, Hyun-Shik / Hochstrasser, Mark

    Research square

    2024  

    Abstract: Calorie restriction (CR) provides anti-aging benefits through diverse processes, such as reduced metabolism and growth and increased mitochondrial activity. Although controversy still exists regarding CR-mediated lifespan effects, many researchers are ... ...

    Abstract Calorie restriction (CR) provides anti-aging benefits through diverse processes, such as reduced metabolism and growth and increased mitochondrial activity. Although controversy still exists regarding CR-mediated lifespan effects, many researchers are seeking interventions that mimic the effects of CR. Yeast has proven to be a useful model system for aging studies, including CR effects. We report here that yeast adapted through
    Language English
    Publishing date 2024-03-21
    Publishing country United States
    Document type Preprint
    DOI 10.21203/rs.3.rs-4016606/v1
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  8. Article ; Online: Epigenetic Targeting of Histone Deacetylases in Diagnostics and Treatment of Depression.

    Park, Hyun-Sun / Kim, Jongmin / Ahn, Seong Hoon / Ryu, Hong-Yeoul

    International journal of molecular sciences

    2021  Volume 22, Issue 10

    Abstract: Depression is a highly prevalent, disabling, and often chronic illness that places substantial burdens on patients, families, healthcare systems, and the economy. A substantial minority of patients are unresponsive to current therapies, so there is an ... ...

    Abstract Depression is a highly prevalent, disabling, and often chronic illness that places substantial burdens on patients, families, healthcare systems, and the economy. A substantial minority of patients are unresponsive to current therapies, so there is an urgent need to develop more broadly effective, accessible, and tolerable therapies. Pharmacological regulation of histone acetylation level has been investigated as one potential clinical strategy. Histone acetylation status is considered a potential diagnostic biomarker for depression, while inhibitors of histone deacetylases (HDACs) have garnered interest as novel therapeutics. This review describes recent advances in our knowledge of histone acetylation status in depression and the therapeutic potential of HDAC inhibitors.
    MeSH term(s) Acetylation/drug effects ; Animals ; Depression/genetics ; Epigenesis, Genetic/genetics ; Epigenomics/methods ; Histone Deacetylase Inhibitors/pharmacology ; Histone Deacetylases/genetics ; Humans
    Chemical Substances Histone Deacetylase Inhibitors ; Histone Deacetylases (EC 3.5.1.98)
    Language English
    Publishing date 2021-05-20
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms22105398
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  9. Article ; Online: SUMO and cellular adaptive mechanisms.

    Ryu, Hong-Yeoul / Ahn, Seong Hoon / Hochstrasser, Mark

    Experimental & molecular medicine

    2020  Volume 52, Issue 6, Page(s) 931–939

    Abstract: The ubiquitin family member SUMO is a covalent regulator of proteins that functions in response to various stresses, and defects in SUMO-protein conjugation or deconjugation have been implicated in multiple diseases. The loss of the Ulp2 SUMO protease, ... ...

    Abstract The ubiquitin family member SUMO is a covalent regulator of proteins that functions in response to various stresses, and defects in SUMO-protein conjugation or deconjugation have been implicated in multiple diseases. The loss of the Ulp2 SUMO protease, which reverses SUMO-protein modifications, in the model eukaryote Saccharomyces cerevisiae is severely detrimental to cell fitness and has emerged as a useful model for studying how cells adapt to SUMO system dysfunction. Both short-term and long-term adaptive mechanisms are triggered depending on the length of time cells spend without this SUMO chain-cleaving enzyme. Such short-term adaptations include a highly specific multichromosome aneuploidy and large changes in ribosomal gene transcription. While aneuploid ulp2Δ cells survive, they suffer severe defects in growth and stress resistance. Over many generations, euploidy is restored, transcriptional programs are adjusted, and specific genetic changes that compensate for the loss of the SUMO protease are observed. These long-term adapted cells grow at normal rates with no detectable defects in stress resistance. In this review, we examine the connections between SUMO and cellular adaptive mechanisms more broadly.
    MeSH term(s) Aneuploidy ; Animals ; Humans ; SUMO-1 Protein/genetics ; SUMO-1 Protein/metabolism
    Chemical Substances SUMO-1 Protein
    Language English
    Publishing date 2020-06-26
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 1328915-9
    ISSN 2092-6413 ; 1226-3613 ; 0378-8512
    ISSN (online) 2092-6413
    ISSN 1226-3613 ; 0378-8512
    DOI 10.1038/s12276-020-0457-2
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    Zs.A 4775: Show issues Location:
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  10. Article ; Online: Sus1 maintains a normal lifespan through regulation of TREX-2 complex-mediated mRNA export.

    Lim, Suji / Liu, Yan / Rhie, Byung-Ho / Kim, Chun / Ryu, Hong-Yeoul / Ahn, Seong Hoon

    Aging

    2022  Volume 14, Issue 12, Page(s) 4990–5012

    Abstract: Eukaryotic gene expression requires multiple cellular events, including transcription and RNA processing and transport. Sus1, a common subunit in both the Spt-Ada-Gcn5 acetyltransferase (SAGA) and transcription and export complex-2 (TREX-2) complexes, is ...

    Abstract Eukaryotic gene expression requires multiple cellular events, including transcription and RNA processing and transport. Sus1, a common subunit in both the Spt-Ada-Gcn5 acetyltransferase (SAGA) and transcription and export complex-2 (TREX-2) complexes, is a key factor in coupling transcription activation to mRNA nuclear export. Here, we report that the SAGA DUB module and TREX-2 distinctly regulate yeast replicative lifespan in a Sir2-dependent and -independent manner, respectively. The growth and lifespan impaired by
    MeSH term(s) Active Transport, Cell Nucleus ; DEAD-box RNA Helicases/genetics ; Exodeoxyribonucleases/metabolism ; Gene Expression Regulation, Fungal ; Longevity ; Nuclear Proteins/genetics ; Nuclear Proteins/metabolism ; Nucleocytoplasmic Transport Proteins/genetics ; Nucleocytoplasmic Transport Proteins/metabolism ; Phosphoproteins/metabolism ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; RNA-Binding Proteins/genetics ; RNA-Binding Proteins/metabolism ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism
    Chemical Substances MEX67 protein, S cerevisiae ; Nuclear Proteins ; Nucleocytoplasmic Transport Proteins ; Phosphoproteins ; RNA, Messenger ; RNA-Binding Proteins ; Saccharomyces cerevisiae Proteins ; Sus1 protein, S cerevisiae ; Exodeoxyribonucleases (EC 3.1.-) ; DBP5 protein, S cerevisiae (EC 3.6.1.-) ; DEAD-box RNA Helicases (EC 3.6.4.13)
    Language English
    Publishing date 2022-06-29
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1945-4589
    ISSN (online) 1945-4589
    DOI 10.18632/aging.204146
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