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Article ; Online: Direct observation of a condensate effect on super-enhancer controlled gene bursting.

Du, Manyu / Stitzinger, Simon Hendrik / Spille, Jan-Hendrik / Cho, Won-Ki / Lee, Choongman / Hijaz, Mohammed / Quintana, Andrea / Cissé, Ibrahim I

Cell

2024

Language	English
Publishing date	2024-04-12
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.2024.04.001
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Article ; Online: Direct observation of a condensate effect on super-enhancer controlled gene bursting.

Du, Manyu / Stitzinger, Simon Hendrik / Spille, Jan-Hendrik / Cho, Won-Ki / Lee, Choongman / Hijaz, Mohammed / Quintana, Andrea / Cissé, Ibrahim I

Cell

2024 Volume 187, Issue 2, Page(s) 331–344.e17

Abstract: Enhancers are distal DNA elements believed to loop and contact promoters to control gene expression. Recently, we found diffraction-sized transcriptional condensates at genes controlled by clusters of enhancers (super-enhancers). However, a direct ... ...

Abstract	Enhancers are distal DNA elements believed to loop and contact promoters to control gene expression. Recently, we found diffraction-sized transcriptional condensates at genes controlled by clusters of enhancers (super-enhancers). However, a direct function of endogenous condensates in controlling gene expression remains elusive. Here, we develop live-cell super-resolution and multi-color 3D-imaging approaches to investigate putative roles of endogenous condensates in the regulation of super-enhancer controlled gene Sox2. In contrast to enhancer distance, we find instead that the condensate's positional dynamics are a better predictor of gene expression. A basal gene bursting occurs when the condensate is far (>1 μm), but burst size and frequency are enhanced when the condensate moves in proximity (<1 μm). Perturbations of cohesin and local DNA elements do not prevent basal bursting but affect the condensate and its burst enhancement. We propose a three-way kissing model whereby the condensate interacts transiently with gene locus and regulatory DNA elements to control gene bursting.
MeSH term(s)	DNA/genetics ; Enhancer Elements, Genetic ; Gene Expression Regulation ; Super Enhancers ; Transcription, Genetic ; SOXB1 Transcription Factors/genetics ; Animals ; Mice ; Embryonic Stem Cells/metabolism ; Microscopy/methods
Chemical Substances	DNA (9007-49-2) ; SOXB1 Transcription Factors
Language	English
Publishing date	2024-01-08
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; 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.2023.12.005
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Article ; Online: Development of Scott Transformer Model in Electromagnetic Transients Programs for Real-Time Simulations

Choongman Lee / Gyu-Jung Cho / Joorak Kim

Applied Sciences, Vol 11, Iss 5752, p

2021 Volume 5752

Abstract: This paper presents a Scott transformer model to be applied in electromagnetic transients (EMT) programs, particularly in the absence of a detailed Scott transformer model for performing real-time simulations (RTS). Regarding a Scott transformer, a ... ...

Abstract	This paper presents a Scott transformer model to be applied in electromagnetic transients (EMT) programs, particularly in the absence of a detailed Scott transformer model for performing real-time simulations (RTS). Regarding a Scott transformer, a common topology for converting a three-phase network into two single-phase networks, the transformer model in EMT programs is essential to simulate large-scale electric railway systems. A code-based model has been developed to simulate the transformer in RTS directly and contain the transformer’s actual impedance characteristics. By establishing a mathematical foundation with the current injection method, we presented a matrix representation in conjunction with a network solution of EMT programs. The proposed model can handle more practical parameters of Scott transformers with a relatively low computational load. Thus, it supports the flexible computation of real-time simulators with a finite number of processor units. The accuracy of the model is verified by simulating it and comparing the simulation results with an industrial transformer’s certified performance. Furthermore, a case study involving a comparison of the results with the field measurement data of an actual Korean railway system demonstrated the efficacy of the model.
Keywords	Scott transformer ; electric railway system ; real-time simulation ; Technology ; T ; Engineering (General). Civil engineering (General) ; TA1-2040 ; Biology (General) ; QH301-705.5 ; Physics ; QC1-999 ; Chemistry ; QD1-999
Subject code	600
Language	English
Publishing date	2021-06-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A dual role for H2A.Z.1 in modulating the dynamics of RNA polymerase II initiation and elongation.

Mylonas, Constantine / Lee, Choongman / Auld, Alexander L / Cisse, Ibrahim I / Boyer, Laurie A

Nature structural & molecular biology

2021 Volume 28, Issue 5, Page(s) 435–442

Abstract: RNA polymerase II (RNAPII) pausing immediately downstream of the transcription start site is a critical rate-limiting step for the expression of most metazoan genes. During pause release, RNAPII encounters a highly conserved +1 H2A.Z nucleosome, yet how ... ...

Abstract	RNA polymerase II (RNAPII) pausing immediately downstream of the transcription start site is a critical rate-limiting step for the expression of most metazoan genes. During pause release, RNAPII encounters a highly conserved +1 H2A.Z nucleosome, yet how this histone variant contributes to transcription is poorly understood. Here, using an inducible protein degron system combined with genomic approaches and live cell super-resolution microscopy, we show that H2A.Z.1 modulates RNAPII dynamics across most genes in murine embryonic stem cells. Our quantitative analysis shows that H2A.Z.1 slows the rate of RNAPII pause release and consequently impacts negative elongation factor dynamics as well as nascent transcription. Consequently, H2A.Z.1 also impacts re-loading of the pre-initiation complex components TFIIB and TBP. Altogether, this work provides a critical mechanistic link between H2A.Z.1 and the proper induction of mammalian gene expression programs through the regulation of RNAPII dynamics and pause release.
MeSH term(s)	Animals ; Histones/metabolism ; Mice ; Mice, Inbred C57BL ; Mouse Embryonic Stem Cells/cytology ; Mouse Embryonic Stem Cells/metabolism ; Nucleosomes/metabolism ; RNA Polymerase II/metabolism ; Transcription, Genetic
Chemical Substances	H2az1 protein, mouse ; Histones ; Nucleosomes ; RNA Polymerase II (EC 2.7.7.-)
Language	English
Publishing date	2021-05-10
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2126708-X
ISSN	1545-9985 ; 1545-9993
ISSN (online)	1545-9985
ISSN	1545-9993
DOI	10.1038/s41594-021-00589-3
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Article: Reserve replacement from governor to energy storage system on conventional generator for operating-cost reduction

Shin, Wooyoung / Lee, Choongman / Chung, In-Young / Lim, Jingon / Youn, Juyoung / Rhie, Younghoon / Hur, Kyeon / Shim, Jae Woong

Applied energy. 2022 July 15,

2022

Abstract: This paper proposes an operation strategy for a steam turbine generator (GEN) with a built-in energy storage system (ESS) that replaces the role of the governor. The proposed strategy cuts the operating cost of GEN by minimizing the throttling loss and ... ...

Abstract	This paper proposes an operation strategy for a steam turbine generator (GEN) with a built-in energy storage system (ESS) that replaces the role of the governor. The proposed strategy cuts the operating cost of GEN by minimizing the throttling loss and the amount of fuel with the harmonious operation of ESS. For the conventional governor droop control, the valve cannot be fully open for emergency release; it causes losses in the throttle valve and fuel cost due to the reserve. Beyond these limitations, in the proposed coordinated operation between GEN and ESS, the GEN can operate in the natural sliding pressure mode, which fully opens the steam turbine valves, reduces the steam pressure, and improves the efficiency of the turbine by minimizing the throttling loss. In this method, while a generator produces constant power without the reserve for an emergency condition in the proposed coordinated operation, an ESS is in charge of fast primary frequency control. Subsequently, the GEN can achieve a replaced reserve operation by ESS, which removes the constant operational loss by reserved steam and provides economic advantages by reducing operation costs. We theoretically demonstrate that the proposed operation provides a quick and reliable frequency control performance through frequency- and time-domain analysis compared with the conventional operation. Using a power generation simulator practically installed at Korea Western Power Co., Ltd., we also proved that the proposed operation can yield the economic benefit based on the cost reduction by minimizing losses of GEN, and provide an improved frequency regulation performance with the coordinating operation.
Keywords	cost effectiveness ; energy ; energy costs ; financial economics ; power generation ; steam ; turbines ; Korean Peninsula
Language	English
Dates of publication	2022-0715
Publishing place	Elsevier Ltd
Document type	Article
Note	Pre-press version
ZDB-ID	2000772-3
ISSN	0306-2619
ISSN	0306-2619
DOI	10.1016/j.apenergy.2022.119697
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: A CRISPR/Cas9 platform for MS2-labelling of single mRNA in live stem cells.

Spille, Jan-Hendrik / Hecht, Micca / Grube, Valentin / Cho, Won-Ki / Lee, Choongman / Cissé, Ibrahim I

Methods (San Diego, Calif.)

2018 Volume 153, Page(s) 35–45

Abstract: The MS2 system is a powerful tool for investigating transcription dynamics at the single molecule directly in live cells. In the past, insertion of the RNA-labelling cassette at specific gene loci has been a major hurdle. Here, we present a CRISPR/Cas9- ... ...

Abstract	The MS2 system is a powerful tool for investigating transcription dynamics at the single molecule directly in live cells. In the past, insertion of the RNA-labelling cassette at specific gene loci has been a major hurdle. Here, we present a CRISPR/Cas9-based approach to insert an MS2 cassette with selectable marker at the start of the 3' untranslated region of any coding gene. We demonstrate applicability of our approach by tagging RNA of the stem cell transcription factor Esrrb in mouse embryonic stem cells. Using quantitative fluorescence microscopy we determine the number of nascent transcripts at the Esrrb locus and the fraction of cells expressing the gene. We find that upon differentiation towards epiblast-like cells, expression of Esrrb is down-regulated in an increasing fraction of cells in a binary manner.
MeSH term(s)	Animals ; CRISPR-Cas Systems ; Cells, Cultured ; Gene Editing/methods ; Mice ; Mouse Embryonic Stem Cells/metabolism ; RNA, Messenger/analysis ; RNA, Messenger/chemistry ; RNA, Messenger/metabolism ; Single Molecule Imaging/methods
Chemical Substances	RNA, Messenger
Language	English
Publishing date	2018-09-12
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1066584-5
ISSN	1095-9130 ; 1046-2023
ISSN (online)	1095-9130
ISSN	1046-2023
DOI	10.1016/j.ymeth.2018.09.004
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Article: A CRISPR/Cas9 platform for MS2-labelling of single mRNA in live stem cells

Spille, Jan-Hendrik / Micca Hecht / Valentin Grube / Won-ki Cho / Choongman Lee / Ibrahim I. Cissé

Methods. 2019 Jan. 15, v. 153

2019

Abstract	The MS2 system is a powerful tool for investigating transcription dynamics at the single molecule directly in live cells. In the past, insertion of the RNA-labelling cassette at specific gene loci has been a major hurdle. Here, we present a CRISPR/Cas9-based approach to insert an MS2 cassette with selectable marker at the start of the 3′ untranslated region of any coding gene. We demonstrate applicability of our approach by tagging RNA of the stem cell transcription factor Esrrb in mouse embryonic stem cells. Using quantitative fluorescence microscopy we determine the number of nascent transcripts at the Esrrb locus and the fraction of cells expressing the gene. We find that upon differentiation towards epiblast-like cells, expression of Esrrb is down-regulated in an increasing fraction of cells in a binary manner.
Keywords	embryonic stem cells ; fluorescence microscopy ; genes ; loci ; messenger RNA ; mice ; transcription factors
Language	English
Dates of publication	2019-0115
Size	p. 35-45.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	1066584-5
ISSN	1095-9130 ; 1046-2023
ISSN (online)	1095-9130
ISSN	1046-2023
DOI	10.1016/j.ymeth.2018.09.004
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Article: Clinical Experience with Use of Remdesivir in the Treatment of Severe Acute Respiratory Syndrome Coronavirus 2: a Case Series.

Lee, Choongman / Ahn, Mi Young / Byeon, Kyeongmin / Choi, Jae Phil / Hahm, Chorom / Kim, Hyeonmok / Kim, Suhyun / Kim, Tae Ho / Oh, JungKyun / Oh, Dong Hyun

Infection & chemotherapy

2020 Volume 52, Issue 3, Page(s) 369–380

Abstract: Background: A novel antiviral agent, remdesivir (RDV), is a promising candidate treatment for coronavirus disease 2019 (COVID-19) in the absence of any proven therapy.: Materials and methods: This retrospective case series included 10 patients with a ...

Abstract	Background: A novel antiviral agent, remdesivir (RDV), is a promising candidate treatment for coronavirus disease 2019 (COVID-19) in the absence of any proven therapy. Materials and methods: This retrospective case series included 10 patients with a clinically and laboratory confirmed diagnosis of severe COVID-19 pneumonia who had received RDV for 5 days (n = 5) or 10 days (n = 5) in the Phase III clinical trial of RDV (GS-US-540-5773) conducted by Gilead Sciences. The clinical and laboratory data for these patients were extracted. Results: One patient in the 10-day group received RDV for only 5 days because of nausea and elevated liver transaminases. No patient had respiratory comorbidity. Seven patients had bilateral lesions and three had unilateral lesions on imaging. All patients had received other medications for COVID-19, including lopinavir/ritonavir and hydroxychloroquine, before administration of RDV. Five patients required supplemental oxygen and one required mechanical ventilation. All patients showed clinical and laboratory evidence of improvement. Half of the patients developed elevated liver transaminases and three had nausea. There were no adverse events exceeding grade 2. Conclusion: Our experience indicates that RDV could be a therapeutic option for COVID-19. A well-designed randomized controlled clinical trial is now needed to confirm the efficacy of RDV in patients with COVID-19.
Keywords	covid19
Language	English
Publishing date	2020-07-23
Publishing country	Korea (South)
Document type	Journal Article
ZDB-ID	2573798-3
ISSN	2093-2340
ISSN	2093-2340
DOI	10.3947/ic.2020.52.3.369
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Article ; Online: Selective Detection of Single-Stranded DNA Molecules Using a Glass Nanocapillary Functionalized with DNA.

Youn, Yeoan / Lee, Choongman / Kim, Joo Hyoung / Chang, Young Wook / Kim, Dug Young / Yoo, Kyung-Hwa

Analytical chemistry

2016 Volume 88, Issue 1, Page(s) 688–694

Abstract: We describe glass nanocapillaries with single-stranded DNA molecules (ssDNA) covalently attached to the capillary surface. These DNA-functionalized nanocapillaries selectively facilitate the translocation of target ssDNA that is complementary to the ... ...

Abstract	We describe glass nanocapillaries with single-stranded DNA molecules (ssDNA) covalently attached to the capillary surface. These DNA-functionalized nanocapillaries selectively facilitate the translocation of target ssDNA that is complementary to the probe ssDNA. In addition, the complementary target ssDNA exhibits an event duration time longer than that of the noncomplementary target ssDNA. The temperature dependence measurements of translocation events show that the longer duration time is a result of an interaction between probe and target ssDNA and is dependent on the base pair binding strength. These results demonstrate that single-base mismatch transport selectivity can be achieved using the DNA-functionalized nanocapillaries.
MeSH term(s)	DNA, Single-Stranded/analysis ; DNA, Single-Stranded/chemistry ; Glass/chemistry ; Humans ; Nanotubes/chemistry ; Temperature
Chemical Substances	DNA, Single-Stranded
Language	English
Publishing date	2016-01-05
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.5b02540
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Article: Low Income as a Vulnerable Factor to the Effect of Noise on Insomnia.

Park, Choongman / Sim, Chang Sun / Sung, Joo Hyun / Lee, Jiho / Ahn, Joon Ho / Choe, Young Min / Park, Jangho

Psychiatry investigation

2018 Volume 15, Issue 6, Page(s) 602–612

Abstract: Objective: The present study aimed to examine the potential mediating effect of income level on the association between noise exposure and insomnia.: Methods: 706 individuals were evaluated in conjunction with 2014 noise map data from Seoul, South ... ...

Abstract	Objective: The present study aimed to examine the potential mediating effect of income level on the association between noise exposure and insomnia. Methods: 706 individuals were evaluated in conjunction with 2014 noise map data from Seoul, South Korea. Cross-sectional analysis was performed to examine differences in noise level according to household income, while three separate logistic regression models were used to examine factors influencing insomnia. Odds ratios (ORs) were calculated after adjusting for depression, anxiety, auditory acuity and noise sensitivity in the first model. Analyses were adjusted for sociodemographic variables in the second model, lifestyle factors and medical illnesses in the third model. Results: Noise level was significantly associated with an increased risk of insomnia in the low-income group, although no such association was observed in the high-income group. Groups exposed to >60 dB of noise (Lden; day-evening-night equivalent) exhibited a 1.79-fold increase in the incidence of insomnia relative to those exposed to <50 dB. The result was significant after adjusting sociodemographic variables, although not significant when adjusted for lifestyle factors and medical illnesses. Conclusion: Individuals with low income may be more vulnerable to the deleterious effects of noise exposure on health. Various aspects including income should be considered to ascertain the influence of noise on insomnia.
Language	English
Publishing date	2018-06-07
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.2018.01.14
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