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  1. Article ; Online: Enhancer-promoter specificity in gene transcription: molecular mechanisms and disease associations.

    Friedman, Meyer J / Wagner, Tobias / Lee, Haram / Rosenfeld, Michael G / Oh, Soohwan

    Experimental & molecular medicine

    2024  Volume 56, Issue 4, Page(s) 772–787

    Abstract: Although often located at a distance from their target gene promoters, enhancers are the primary genomic determinants of temporal and spatial transcriptional specificity in metazoans. Since the discovery of the first enhancer element in simian virus 40, ... ...

    Abstract Although often located at a distance from their target gene promoters, enhancers are the primary genomic determinants of temporal and spatial transcriptional specificity in metazoans. Since the discovery of the first enhancer element in simian virus 40, there has been substantial interest in unraveling the mechanism(s) by which enhancers communicate with their partner promoters to ensure proper gene expression. These research efforts have benefited considerably from the application of increasingly sophisticated sequencing- and imaging-based approaches in conjunction with innovative (epi)genome-editing technologies; however, despite various proposed models, the principles of enhancer-promoter interaction have still not been fully elucidated. In this review, we provide an overview of recent progress in the eukaryotic gene transcription field pertaining to enhancer-promoter specificity. A better understanding of the mechanistic basis of lineage- and context-dependent enhancer-promoter engagement, along with the continued identification of functional enhancers, will provide key insights into the spatiotemporal control of gene expression that can reveal therapeutic opportunities for a range of enhancer-related diseases.
    MeSH term(s) Enhancer Elements, Genetic ; Promoter Regions, Genetic ; Humans ; Animals ; Transcription, Genetic ; Gene Expression Regulation
    Language English
    Publishing date 2024-04-25
    Publishing country United States
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 1328915-9
    ISSN 2092-6413 ; 1226-3613 ; 0378-8512
    ISSN (online) 2092-6413
    ISSN 1226-3613 ; 0378-8512
    DOI 10.1038/s12276-024-01233-y
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Transcriptional and Epigenetic Regulation of Context-Dependent Plasticity in T-Helper Lineages.

    Friedman, Meyer J / Lee, Haram / Lee, June-Yong / Oh, Soohwan

    Immune network

    2023  Volume 23, Issue 1, Page(s) e5

    Abstract: Th cell lineage determination and functional specialization are tightly linked to the activation of lineage-determining transcription factors (TFs) that ... ...

    Abstract Th cell lineage determination and functional specialization are tightly linked to the activation of lineage-determining transcription factors (TFs) that bind
    Language English
    Publishing date 2023-02-23
    Publishing country Korea (South)
    Document type Journal Article ; Review
    ZDB-ID 2536191-0
    ISSN 2092-6685 ; 1598-2629
    ISSN (online) 2092-6685
    ISSN 1598-2629
    DOI 10.4110/in.2023.23.e5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Dynamics of Viral and Host 3D Genome Structure upon Infection.

    Friedman, Meyer J / Lee, Haram / Kwon, Young-Chan / Oh, Soohwan

    Journal of microbiology and biotechnology

    2022  Volume 32, Issue 12, Page(s) 1515–1526

    Abstract: Eukaryotic chromatin is highly organized in the 3D nuclear space and dynamically regulated in response to environmental stimuli. This genomic organization is arranged in a hierarchical fashion to support various cellular functions, including ... ...

    Abstract Eukaryotic chromatin is highly organized in the 3D nuclear space and dynamically regulated in response to environmental stimuli. This genomic organization is arranged in a hierarchical fashion to support various cellular functions, including transcriptional regulation of gene expression. Like other host cellular mechanisms, viral pathogens utilize and modulate host chromatin architecture and its regulatory machinery to control features of their life cycle, such as lytic versus latent status. Combined with previous research focusing on individual loci, recent global genomic studies employing conformational assays coupled with high-throughput sequencing technology have informed models for host and, in some cases, viral 3D chromosomal structure re-organization during infection and the contribution of these alterations to virus-mediated diseases. Here, we review recent discoveries and progress in host and viral chromatin structural dynamics during infection, focusing on a subset of DNA (human herpesviruses and HPV) as well as RNA (HIV, influenza virus and SARS-CoV-2) viruses. An understanding of how host and viral genomic structure affect gene expression in both contexts and ultimately viral pathogenesis can facilitate the development of novel therapeutic strategies.
    MeSH term(s) Humans ; Gene Expression Regulation, Viral ; COVID-19 ; SARS-CoV-2/genetics ; Virus Diseases/genetics ; Chromatin/genetics ; Genome, Viral ; Virus Replication ; Herpesvirus 8, Human/genetics
    Chemical Substances Chromatin
    Language English
    Publishing date 2022-09-30
    Publishing country Korea (South)
    Document type Journal Article ; Review
    ZDB-ID 2412195-2
    ISSN 1738-8872 ; 1738-8872
    ISSN (online) 1738-8872
    ISSN 1738-8872
    DOI 10.4014/jmb.2208.08020
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  4. Article ; Online: Direct observation of surface charge and stiffness of human metaphase chromosomes.

    Roh, Seokbeom / Lee, Taeha / Cheong, Da Yeon / Kim, Yeonjin / Oh, Soohwan / Lee, Gyudo

    Nanoscale advances

    2022  Volume 5, Issue 2, Page(s) 368–377

    Abstract: Metaphase chromosomes in which both polynucleotides and proteins are condensed with hierarchies are closely related to life phenomena such as cell division, cancer development, and cellular senescence. Nevertheless, their nature is rarely revealed, owing ...

    Abstract Metaphase chromosomes in which both polynucleotides and proteins are condensed with hierarchies are closely related to life phenomena such as cell division, cancer development, and cellular senescence. Nevertheless, their nature is rarely revealed, owing to their structural complexity and technical limitations in analytical methods. In this study, we used surface potential and nanomechanics mapping technology based on atomic force microscopy to measure the surface charge and intrinsic stiffness of metaphase chromosomes. We found that extra materials covering the chromosomes after the extraction process were positively charged. With the covering materials, the chromosomes were positively charged (
    Language English
    Publishing date 2022-12-20
    Publishing country England
    Document type Journal Article
    ISSN 2516-0230
    ISSN (online) 2516-0230
    DOI 10.1039/d2na00620k
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Long-distance association of topological boundaries through nuclear condensates.

    Gamliel, Amir / Meluzzi, Dario / Oh, Soohwan / Jiang, Nan / Destici, Eugin / Rosenfeld, Michael G / Nair, Sreejith J

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

    2022  Volume 119, Issue 32, Page(s) e2206216119

    Abstract: The eukaryotic genome is partitioned into distinct topological domains separated by boundary elements. Emerging data support the concept that several well-established nuclear compartments are ribonucleoprotein condensates assembled through the physical ... ...

    Abstract The eukaryotic genome is partitioned into distinct topological domains separated by boundary elements. Emerging data support the concept that several well-established nuclear compartments are ribonucleoprotein condensates assembled through the physical process of phase separation. Here, based on our demonstration that chemical disruption of nuclear condensate assembly weakens the insulation properties of a specific subset (∼20%) of topologically associated domain (TAD) boundaries, we report that the disrupted boundaries are characterized by a high level of transcription and striking spatial clustering. These topological boundary regions tend to be spatially associated, even interchromosomally, segregate with nuclear speckles, and harbor a specific subset of "housekeeping" genes widely expressed in diverse cell types. These observations reveal a previously unappreciated mode of genome organization mediated by conserved boundary elements harboring highly and widely expressed transcription units and associated transcriptional condensates.
    MeSH term(s) Cell Compartmentation ; Cell Nucleus/chemistry ; Cell Nucleus/genetics ; Cell Nucleus/metabolism ; Chromosomes/genetics ; Eukaryota/cytology ; Eukaryota/genetics ; Genes, Essential ; Genome/genetics ; Nuclear Speckles/genetics ; Ribonucleoproteins/metabolism ; Transcription, Genetic
    Chemical Substances Ribonucleoproteins
    Language English
    Publishing date 2022-08-01
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2206216119
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Association Between Tic Aggravation and Methylphenidate in Youth With Attention-Deficit/Hyperactivity Disorder.

    Cha, Jung Yoon / Joung, Yoo-Sook / Oh, Soohwan / Kim, Byung Wook / Song, In Mok / Ahn, Bo Mi

    Psychiatry investigation

    2021  Volume 18, Issue 9, Page(s) 818–824

    Abstract: Objective: This study aimed to determine the tic aggravation event rate and cumulative incidence rate in the use of methylphenidate (MPH) treatment in attention-deficit/hyperactivity disorder (ADHD) and the factors that influence tic aggravation.: ... ...

    Abstract Objective: This study aimed to determine the tic aggravation event rate and cumulative incidence rate in the use of methylphenidate (MPH) treatment in attention-deficit/hyperactivity disorder (ADHD) and the factors that influence tic aggravation.
    Methods: We conducted a retrospective chart review of children and adolescents aged between 6 to 15 years, who were diagnosed with ADHD from January 2017 to December 2019. A total of 121 subjects were included. The MPH dosage, psychiatric family history, comorbidity and past history of tics were assessed through chart review and the psychological examinations data were included. Collected data were analyzed using Cox regression and Kaplan-Meier survival analysis.
    Results: Tic aggravation event rates without a past history of tics were 2.9% with MPH treatment in ADHD. Past history of tics, total MPH dosage and age were the factors associated with tic aggravation ([HR 21.46, p<0.001], [HR 0.94, p=0.023], [HR 0.79, p=0.021] for each). Cumulative incidence of tic aggravation was different between groups with or without past tic history. When treated with MPH, all tic aggravation appeared within approximately eight months but for subjects with a past history of tic, aggravation showed within approximately six months (p<0.001).
    Conclusion: Tic aggravation event rate was significantly low especially in the group without a past history of tics with the use of MPH in ADHD. However, a thorough assessment of past history of tics, and close monitoring during the first six-eight months of treatment with MPH is needed to avert a potential worsening of tics.
    Language English
    Publishing date 2021-09-10
    Publishing country Korea (South)
    Document type Journal Article
    ZDB-ID 2414364-9
    ISSN 1976-3026 ; 1738-3684
    ISSN (online) 1976-3026
    ISSN 1738-3684
    DOI 10.30773/pi.2021.0047
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  7. Article ; Online: Resting-state alpha and gamma activity in affective disorder with ADHD symptoms: Comparison between bipolar disorder and major depressive disorder.

    Kim, Ji Sun / Oh, Soohwan / Jeon, Hong Jin / Hong, Kyung Sue / Baek, Ji Hyun

    International journal of psychophysiology : official journal of the International Organization of Psychophysiology

    2019  Volume 143, Page(s) 57–63

    Abstract: Although comorbid attention deficit/hyperactivity disorder (ADHD) symptoms are very common in mood disorder, its neurophysiological correlates have not been explored. This study aimed to examine clinical and neurophysiological correlates of ADHD symptoms ...

    Abstract Although comorbid attention deficit/hyperactivity disorder (ADHD) symptoms are very common in mood disorder, its neurophysiological correlates have not been explored. This study aimed to examine clinical and neurophysiological correlates of ADHD symptoms in major depressive disorder (MDD) and bipolar disorder (BP). A total of 67 subjects with mood disorder, current depressive episode (38 subjects with MDD and 29 subjects with BP depression) were included in the analysis. Resting quantitative electroencephalography (qEEG) recordings were collected under eyes closed condition. ADHD symptoms, depression, anxiety, and lifetime hypomania were evaluated using self-report questionnaires. In MDD, ADHD symptoms did not show significant associations with anxiety and depression. In BP, ADHD symptoms showed significant associations with depression, anxiety and lifetime hypomania. Significant correlations with Adult ADHD self-report scales (ASRS) inattention score and total score were detected in left and right frontal alpha powers in MDD while significant correlation with ASRS hyperactivity score and ASRS total score were detected in right frontal gamma power in BP. Linear regression analyses revealed that left and right frontal alpha powers, depression and lifetime hypomania showed significant association with ASRS inattention score and ASRS total score in MDD. In BP, linear regression analysis showed ASRS hyperactivity score was associated with lifetime hypomania and the right frontal gamma power. MDD and BP showed different correlation patterns between frontal qEEG measures and ADHD symptoms. This might be associated with distinct neurobiological underpinnings of co-occurring ADHD symptoms in MDD and BP.
    MeSH term(s) Adult ; Alpha Rhythm/physiology ; Attention Deficit Disorder with Hyperactivity/epidemiology ; Attention Deficit Disorder with Hyperactivity/physiopathology ; Bipolar Disorder/epidemiology ; Bipolar Disorder/physiopathology ; Comorbidity ; Depressive Disorder, Major/epidemiology ; Depressive Disorder, Major/physiopathology ; Female ; Frontal Lobe/physiopathology ; Gamma Rhythm/physiology ; Humans ; Male ; Retrospective Studies ; Young Adult
    Language English
    Publishing date 2019-06-27
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 605645-3
    ISSN 1872-7697 ; 0167-8760
    ISSN (online) 1872-7697
    ISSN 0167-8760
    DOI 10.1016/j.ijpsycho.2019.06.009
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  8. Article ; Online: Global epigenomic analysis of KSHV-infected primary effusion lymphoma identifies functional

    Park, Angela / Oh, Soohwan / Jung, Kyle L / Choi, Un Yung / Lee, Hye-Ra / Rosenfeld, Michael G / Jung, Jae U

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

    2020  Volume 117, Issue 35, Page(s) 21618–21627

    Abstract: Enhancers play indispensable roles in cell proliferation and survival through spatiotemporally regulating gene transcription. Active enhancers and superenhancers often produce noncoding enhancer RNAs (eRNAs) that precisely control RNA polymerase II ... ...

    Abstract Enhancers play indispensable roles in cell proliferation and survival through spatiotemporally regulating gene transcription. Active enhancers and superenhancers often produce noncoding enhancer RNAs (eRNAs) that precisely control RNA polymerase II activity. Kaposi's sarcoma-associated herpesvirus (KSHV) is a human oncogenic gamma-2 herpesvirus that causes Kaposi's sarcoma and primary effusion lymphoma (PEL). It is well characterized that KSHV utilizes host epigenetic machineries to control the switch between two lifecycles, latency and lytic replication. However, how KSHV impacts host epigenome at different stages of viral lifecycle is not well understood. Using global run-on sequencing (GRO-seq) and chromatin-immunoprecipitation sequencing (ChIP-seq), we profiled the dynamics of host transcriptional regulatory elements during latency and lytic replication of KSHV-infected PEL cells. This revealed that a number of critical host genes for KSHV latency, including
    MeSH term(s) Cell Line ; Epigenomics/methods ; Gene Expression Regulation, Viral/genetics ; Genes, myc/genetics ; Herpesvirus 8, Human/genetics ; Herpesvirus 8, Human/pathogenicity ; Humans ; Immediate-Early Proteins/genetics ; Lymphoma, Primary Effusion/genetics ; Lymphoma, Primary Effusion/metabolism ; Lymphoma, Primary Effusion/virology ; Nuclear Proteins/metabolism ; Proto-Oncogene Mas ; RNA/metabolism ; Sarcoma, Kaposi/virology ; Trans-Activators/metabolism ; Transcription, Genetic/genetics ; Viral Proteins/metabolism ; Virus Activation/genetics ; Virus Latency/genetics ; Virus Replication/genetics
    Chemical Substances Immediate-Early Proteins ; MAS1 protein, human ; Nuclear Proteins ; Proto-Oncogene Mas ; Trans-Activators ; Viral Proteins ; RNA (63231-63-0)
    Language English
    Publishing date 2020-08-18
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.1922216117
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  9. Article: Running the COVID-19 marathon: the behavioral adaptations in mobility and facemask over 27 weeks of pandemic in Seoul, South Korea

    Cho, Jungwoo / Shin, Yuyol / Kim, Seyun / Kim, Namwoo / Oh, Soohwan / Cho, Haechan / Yoon, Yoonjin

    Abstract: Battle with COVID-19 turned out to be a marathon, not a sprint, and behavioral adjustments have been unavoidable to stay viable. In this paper, we employ a data-centric approach to investigate individual mobility adaptations and mask-wearing in Seoul, ... ...

    Abstract Battle with COVID-19 turned out to be a marathon, not a sprint, and behavioral adjustments have been unavoidable to stay viable. In this paper, we employ a data-centric approach to investigate individual mobility adaptations and mask-wearing in Seoul, South Korea. We first identify six epidemic phases and two waves based on COVID-19 case count and its geospatial dispersion. The phase-specific linear models reveal the strong, self-driven mobility reductions in the first escalation and peak with a common focus on public transit use and less-essential weekend/afternoon trips. However, comparable reduction was not present in the second wave, as the shifted focus from mobility to mask-wearing was evident. Although no lockdowns and gentle nudge to wear mask seemed counter-intuitive, simple and persistent communication on personal safety has been effective and sustainable to induce cooperative behavioral adaptations. Our phase-specific analyses and interpretation highlight the importance of targeted response consistent with the fluctuating epidemic risk.
    Keywords covid19
    Publisher ArXiv
    Document type Article
    Database COVID19

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  10. Article ; Online: COVID-19 Mobility Data Collection of Seoul, South Korea

    Cho, Jungwoo / Oh, Soohwan / Kim, Seyun / Kim, Namwoo / Shin, Yuyol / Cho, Haechan / Yoon, Yoonjin

    Abstract: The relationship between pandemic and human mobility has received considerable attention from scholars, as it can provide an indication of how mobility patterns change in response to a public health crisis or whether reduced mobility contributes to ... ...

    Abstract The relationship between pandemic and human mobility has received considerable attention from scholars, as it can provide an indication of how mobility patterns change in response to a public health crisis or whether reduced mobility contributes to preventing the spread of an infectious disease. While several studies attempted to unveil such relationship, no studies have focused on changes in human mobility at a finer scale utilizing comprehensive, high-resolution data. To address the complex association between pandemic's spread and human mobility, this paper presents two categories of mobility datasets - trip mode and trip purpose - that concern nearly 10 million citizens' movements during COVID-19 in the capital city of South Korea, Seoul, where no lockdowns has been imposed. We curate hourly data of subway ridership, traffic volume and population present count at selected points of interests. The results to be derived from the presented datasets can be used as an important reference for public health decision making in the post COVID-19 era.
    Keywords covid19
    Publisher ArXiv
    Document type Article ; Online
    DOI 10.6084/m9.figshare.12462515
    Database COVID19

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