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101. An XPC-PARP axis links ALC1-mediated chromatin remodeling to global genome DNA damage repair

Author

González-Prieto, Román [0000-0001-8997-2321], González-Prieto, Román, Blessing, Charlotte, Apelt, Katja, Heuvel, Diana van den, González-Leal, Claudia, Rother, Magdalena B., Woude, Melanie van der, Yifrach, Adi, Parnas, Avital, Shah, Rashmi G., Kuo, Tia Tyrsett, Boer, Daphne E. C., Cai, Jin, Kragten, Angela, Kim, Hyun-Suk, Schärer, Orlando D., Vertegaal, Alfred C. O., Shah, Girish M., Adar, Sheera, Lans, Hannes, Attikum, Haico van, Ladurner, Andreas G., Luijsterburg, Martijn, González-Prieto, Román [0000-0001-8997-2321], González-Prieto, Román, Blessing, Charlotte, Apelt, Katja, Heuvel, Diana van den, González-Leal, Claudia, Rother, Magdalena B., Woude, Melanie van der, Yifrach, Adi, Parnas, Avital, Shah, Rashmi G., Kuo, Tia Tyrsett, Boer, Daphne E. C., Cai, Jin, Kragten, Angela, Kim, Hyun-Suk, Schärer, Orlando D., Vertegaal, Alfred C. O., Shah, Girish M., Adar, Sheera, Lans, Hannes, Attikum, Haico van, Ladurner, Andreas G., and Luijsterburg, Martijn

Abstract

Cells employ global genome DNA damage repair (GGR) to eliminate a broad spectrum of DNA lesions, including those induced by UV light. The lesion-recognition factor XPC initiates repair of helix-distorting DNA lesions, but binds inefficiently to lesions that cause poor helix distortion. How such difficult-to-repair lesions are detected in chromatin is unknown. Here, we identify the poly-(ADP-ribose) polymerases PARP1 and PARP2 as constitutive interactors of XPC. The close interaction between these proteins results in the PARylation of XPC at UV lesions, and an XPC-dependent stimulation of the poly-(ADP-ribose) response, which facilitates the recruitment of the poly-(ADP-ribose)-dependent chromatin remodeler ALC1. Both ALC1 and in particular PARP2 are required for the efficient clearing of difficult-to-repair DNA lesions. Our study offers key insights into the molecular mechanisms of GGR by revealing a molecular bookmarking system, which primes chromatin containing difficult-to-repair DNA lesions for efficient repair.

Published
2022

102. XPC–PARP complexes engage the chromatin remodeler ALC1 to catalyze global genome DNA damage repair

Author

National Institutes of Health (US), Netherlands Organization for Scientific Research, German Research Foundation, Dutch Cancer Society, European Research Council, International Cancer Genome Consortium, Israel Science Foundation, National Cancer Institute (US), Université Laval, Natural Sciences and Engineering Research Council of Canada, Israel Cancer Research Fund, Israel Cancer Association USA, Dutch Research Council, Blessing, Charlotte, Apelt, Katja, Heuvel, Diana van den, González-Leal, Claudia, Rother, Magdalena B., Woude, Melanie van der, González-Prieto, Román, Yifrach, Adi, Parnas, Avital, Shah, Rashmi G., Kuo, Tia Tyrsett, Boer, Daphne E. C., Cai, Jin, Kragten, Angela, Kim, Hyun-Suk, Schärer, Orlando D., Vertegaal, Alfred C. O., Shah, Girish M., Adar, Sheera, Lans, Hannes, Attikum, Haico van, Ladurner, Andreas G., Luijsterburg, Martijn S., National Institutes of Health (US), Netherlands Organization for Scientific Research, German Research Foundation, Dutch Cancer Society, European Research Council, International Cancer Genome Consortium, Israel Science Foundation, National Cancer Institute (US), Université Laval, Natural Sciences and Engineering Research Council of Canada, Israel Cancer Research Fund, Israel Cancer Association USA, Dutch Research Council, Blessing, Charlotte, Apelt, Katja, Heuvel, Diana van den, González-Leal, Claudia, Rother, Magdalena B., Woude, Melanie van der, González-Prieto, Román, Yifrach, Adi, Parnas, Avital, Shah, Rashmi G., Kuo, Tia Tyrsett, Boer, Daphne E. C., Cai, Jin, Kragten, Angela, Kim, Hyun-Suk, Schärer, Orlando D., Vertegaal, Alfred C. O., Shah, Girish M., Adar, Sheera, Lans, Hannes, Attikum, Haico van, Ladurner, Andreas G., and Luijsterburg, Martijn S.

Abstract

Cells employ global genome nucleotide excision repair (GGR) to eliminate a broad spectrum of DNA lesions, including those induced by UV light. The lesion-recognition factor XPC initiates repair of helix-destabilizing DNA lesions, but binds poorly to lesions such as CPDs that do not destabilize DNA. How difficult-to-repair lesions are detected in chromatin is unknown. Here, we identify the poly-(ADP-ribose) polymerases PARP1 and PARP2 as constitutive interactors of XPC. Their interaction results in the XPC-stimulated synthesis of poly-(ADP-ribose) (PAR) by PARP1 at UV lesions, which in turn enables the recruitment and activation of the PAR-regulated chromatin remodeler ALC1. PARP2, on the other hand, modulates the retention of ALC1 at DNA damage sites. Notably, ALC1 mediates chromatin expansion at UV-induced DNA lesions, leading to the timely clearing of CPD lesions. Thus, we reveal how chromatin containing difficult-to-repair DNA lesions is primed for repair, providing insight into mechanisms of chromatin plasticity during GGR.

Published
2022

103. Anomalous Defect Dependence of Thermal Conductivity in Epitaxial WO 3 Thin Films

Author

Massachusetts Institute of Technology. Department of Materials Science and Engineering, Massachusetts Institute of Technology. Department of Mechanical Engineering, Ning, Shuai, Huberman, Samuel C., Ding, Zhiwei, Nahm, Ho‐Hyun, Kim, Yong‐Hyun, Kim, Hyun‐Suk, Chen, Gang, Ross, Caroline A., Massachusetts Institute of Technology. Department of Materials Science and Engineering, Massachusetts Institute of Technology. Department of Mechanical Engineering, Ning, Shuai, Huberman, Samuel C., Ding, Zhiwei, Nahm, Ho‐Hyun, Kim, Yong‐Hyun, Kim, Hyun‐Suk, Chen, Gang, and Ross, Caroline A.

Published
2022

104. Oxide thin-film transistors based on i-line stepper process for high PPI displays.

Author

Park, Ji-Min, Jang, Seong Cheol, Lee, Seoung Min, Kang, Min-Ho, Chung, Kwun-Bum, and Kim, Hyun-Suk

Subjects
TRANSISTORS, INDIUM gallium zinc oxide, HIGH resolution imaging, IMAGE registration, INDUSTRIAL electronics, ELECTRONIC industries
Abstract

Indium-gallium-zinc-oxide (IGZO) thin-film transistors (TFTs) with a 1 um channel length were successfully fabricated by i-line lithography with a stepper process, resulting in high throughput. The a-IGZO TFT with a channel length of 1 μm exhibits high mobility of 8.77 cm2/Vs with an on/off current ratio of >3 × 1010. The stepper lithography process is capable of defect-free patterning given its precise layer-to-layer alignment and high image resolutions of the types required for large-area high-PPI displays. Consequently, IGZO TFTs can be fabricated on an 8-inch wafer with only minor electrical property deviations in the turn-on voltage, mobility, and on/off ratio. These results indicate that i-line lithography with a stepper process is a promising process for use in cutting-edge large-area electronics industries. [ABSTRACT FROM AUTHOR]

Published
2023
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120. Two Interaction Surfaces between XPA and RPA Organize the Preincision Complex in Nucleotide Excision Repair

Author

Kim, Mihyun, primary, Kim, Hyun Suk, additional, D’Souza, Areetha, additional, Gallagher, Kaitlyn, additional, Jeong, Eunwoo, additional, Topolska-Wos, Agnieszka, additional, Le Meur, Kateryna Ogorodnik, additional, Tsai, Chi-Lin, additional, Tsai, Miaw-Sheue, additional, Kee, Minyong, additional, Tainer, John A., additional, Yeo, Jung-Eun, additional, Chazin, Walter J., additional, and Schärer, Orlando D., additional

Published
2022
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123. Halide Double Perovskite-Based Efficient Mechanical Energy Harvester and Storage Devices for Self-Charging Power Unit

Author

Yoon, Soon-Gil, primary, Ippili, Swathi, additional, Kim, Jong Heon, additional, Jella, Venkatraju, additional, Behera, Subhashree, additional, Vuong, Van-Hoang, additional, Jung, Jang-Su, additional, Cho, Yujang, additional, Ahn, Jaewan, additional, Kim, Il-Doo, additional, Chang, Yun Hee, additional, and Kim, Hyun-Suk, additional

Published
2022
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129. Optimization of Solid-Phase Extraction of a Degradation Product of Novichok (A234) and Its Application to Environmental Samples.

Author

Lee, Jin Young, Shin, Ji Young, and Kim, Hyun Suk

Subjects
SOLID phase extraction, ENVIRONMENTAL sampling, CHEMICAL weapons, SOIL sampling, DETECTION limit, SAND, CHEMICAL preconcentration
Abstract

There have been no detailed investigations regarding solid-phase-extraction (SPE) optimization and screening for the degradation products of ethyl (1-(diethylamino)ethylidene)phosphoramidofluoridate (A234) in various environmental samples. Therefore, as a first step in the selective SPE of the degradation products of A234, we optimized the SPE adsorption and extraction parameters for the A234 degradation product ethylhydrogen (1-(diethylamino)ethylidene)phosphoramidate (cpd 1). Among various SPE cartridges, the Si cartridge (500 mg, 3 mL) selectively extracted cpd 1 using an elution volume of 4 mL of 25% H2O in acetonitrile, which eliminated most interference without cpd 1 loss during loading and washing. In addition, the sorbent capacity is also critical in the adsorption of cpd 1. The Si cartridge (500 mg, 3 mL) retained cpd 1 in the concentration range 1–10 µg/mL. The linearity of detector response of cpd 1 in deionized H2O was studied in the range of 1.0–100 ng/mL and showed good linearity with γ2 ranging from 0.9979 to 0.996. The limits of detection for cpd 1 are 10 ng/mL in the product-scan mode and 100 ng/mL in the full-scan mode. Also, after we optimized the SPE method, we validated the precision and accuracy of the Si-cartridge extraction method in real soil samples with diverse concentrations. The precision ranged from 2.5% to 5.3%. This newly developed SPE is applicable to the analysis of a degradation product of Novichok A234 in various environmental matrices, such as water, soil and sand, in the Organization for the Prohibition of Chemical Weapons (OPCW) proficiency test and unknown samples collected from suspected sites. [ABSTRACT FROM AUTHOR]

Published
2023
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131. Highly Reliable Cell Characteristics with CSOB(Channel-hole Sidewall ONO Butting) Scheme for 7th Generation 3D-NAND

Author

Kang, Jin-kyu, primary, Lee, Jaeduk, additional, Yim, Yongsik, additional, Park, Sejun, additional, Kim, Hyun Suk, additional, Cho, Eun Suk, additional, Kim, Taehun, additional, Lee, Jung Hoon, additional, Kim, Joon, additional, Lee, Raeyoung, additional, Lim, Junhee, additional, Hur, Sunghoi, additional, Ahn, Su Jin, additional, and Song, Jaihyuk, additional

Published
2021
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140. 게임 이용이 청소년의 정신건강과 학업성적에 미치는 영향: 동적 패널 데이터 분석

Author

Lee， Eun-Ju, Soonwook Choi, and Kim， Hyun Suk

Abstract

본 연구는 청소년 게임 이용자 패널 데이터를 활용하여 게임 이용이 정신건강과 학업성적에 미치는 영향을 검증했다. 먼저 정신건강 관련, 게임을 많이 이용할수록 우울감과 공격성이 줄어들었고, 그럴수록 다시 게임 이용은 증가하는 상호적 강화작용 패턴을 발견했다. 불안의 경우, 게임 이용이 불안을 낮추는 일방향적 효과만이 존재했고 게임 이용과 고독감은 유의한 관계를 보이지 않았다. 이러한 결과는 선호 게임 유형(혼자 vs. 게임에서 만난 사람들과 함께 vs. 오프라인 친구들과 함께 하는 게임)이나 대인관계 특성(부모와의 의사소통, 교사 지지, 친구 지지)에 따라 달라지지 않았다. 다음으로 게임 이용은 학업성적에 긍정적 영향을 미쳤지만, 성적은 게임 이용에 영향을 주지 않았다. 게임 이용이 성적에 미치는 효과는 공부시간이나 정신건강 변인들에 의해 매개되지 않았다. 추가분석 결과, 데이터 분석방법에 따라(종단분석 vs. 횡단분석) 게임 효과에 대한 상반된 결론이 도출됨을 확인했다. 구체적으로 횡단분석 결과가 게임에 대한 대중적 우려와 대체로 일치했는데, 이는 방법론적으로 더욱 엄정한 게임 효과 연구가 필요함을 시사한다.

Published
2019
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147. An antisite defect mechanism for room temperature ferroelectricity in orthoferrites

Author

Massachusetts Institute of Technology. Department of Materials Science and Engineering, Massachusetts Institute of Technology. Department of Nuclear Science and Engineering, Ning, Shuai, Kumar, Abinash, Klyukin, Konstantin, Cho, Eunsoo, Kim, Jong Heon, Su, Tingyu, Kim, Hyun-Suk, LeBeau, James M, Yildiz, Bilge, Ross, Caroline A, Massachusetts Institute of Technology. Department of Materials Science and Engineering, Massachusetts Institute of Technology. Department of Nuclear Science and Engineering, Ning, Shuai, Kumar, Abinash, Klyukin, Konstantin, Cho, Eunsoo, Kim, Jong Heon, Su, Tingyu, Kim, Hyun-Suk, LeBeau, James M, Yildiz, Bilge, and Ross, Caroline A

Abstract

AbstractSingle-phase multiferroic materials that allow the coexistence of ferroelectric and magnetic ordering above room temperature are highly desirable, motivating an ongoing search for mechanisms for unconventional ferroelectricity in magnetic oxides. Here, we report an antisite defect mechanism for room temperature ferroelectricity in epitaxial thin films of yttrium orthoferrite, YFeO3, a perovskite-structured canted antiferromagnet. A combination of piezoresponse force microscopy, atomically resolved elemental mapping with aberration corrected scanning transmission electron microscopy and density functional theory calculations reveals that the presence of YFe antisite defects facilitates a non-centrosymmetric distortion promoting ferroelectricity. This mechanism is predicted to work analogously for other rare earth orthoferrites, with a dependence of the polarization on the radius of the rare earth cation. Our work uncovers the distinctive role of antisite defects in providing a mechanism for ferroelectricity in a range of magnetic orthoferrites and further augments the functionality of this family of complex oxides for multiferroic applications.

Published
2021

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