Topoisomerase 3b facilitates piRNA biogenesis to promote transposon silencing and germ cell development

Authors: Lee, Seung Kyu ¹, Shen, Weiping ¹, Wen, William ¹, Joo, Yuyoung ¹, Xue, Yutong ¹, Park, Aaron ¹, Qiang, Amy ¹, Su, Shuaikun ¹, Zhang, Tianyi ¹, Zhang, Megan ¹, Fan, Jinshui ¹, Zhang, Yongqing ¹, De, Supriyo ¹, Gainetdinov, Ildar ², Sharov, Alexei ¹, Maragkakis, Manolis ¹, Wang, Weidong ^{1, 3, ∗}

Source: In Cell Reports 22 April 2025 44(4)

SUMOylation controls Hu antigen R posttranscriptional activity in liver cancer

Authors: Lachiondo-Ortega, Sofia ^{1, 30}, Rejano-Gordillo, Claudia M. ^{1, 2, 3, 30}, Simon, Jorge ^{1, 4}, Lopitz-Otsoa, Fernando ¹, C. Delgado, Teresa ¹, Mazan-Mamczarz, Krystyna ⁵, Goikoetxea-Usandizaga, Naroa ¹, Zapata-Pavas, L. Estefanía ¹, García-del Río, Ana ⁶, Guerra, Pietro ⁷, Peña-Sanfélix, Patricia ¹, Hermán-Sánchez, Natalia ⁸, Al-Abdulla, Ruba ^{9, 10}, Fernandez-Rodríguez, Carmen ¹, Azkargorta, Mikel ^{4, 11}, Velázquez-Cruz, Alejandro ¹², Guyon, Joris ^{13, 14}, Martín, César ³, Zalamea, Juan Diego ¹⁵, Egia-Mendikute, Leire ⁶, Sanz-Parra, Arantza ¹, Serrano-Maciá, Marina ¹, González-Recio, Irene ¹, Gonzalez-Lopez, Monika ¹⁶, Martínez-Cruz, Luis Alfonso ¹, Pontisso, Patrizia ⁷, Aransay, Ana M. ¹⁶, Barrio, Rosa ¹⁷, Sutherland, James D. ¹⁷, Abrescia, Nicola G.A. ^{15, 18}, Elortza, Félix ^{4, 11}, Lujambio, Amaia ^{19, 20, 21, 22}, Banales, Jesus M. ^{4, 18, 23, 24}, Luque, Raúl M. ⁸, Gahete, Manuel D. ⁸, Palazón, Asís ^{6, 18}, Avila, Matias A. ^{4, 25, 26}, G. Marin, Jose J. ^{4, 27}, De, Supriyo ⁵, Daubon, Thomas ²⁸, Díaz-Quintana, Antonio ¹², Díaz-Moreno, Irene ¹², Gorospe, Myriam ⁵, Rodríguez, Manuel S. ²⁹, Martínez-Chantar, María Luz ^{1, 4, 31, ∗}

Source: In Cell Reports 26 March 2024 43(3)

Cerebrospinal fluid exploratory proteomics and ketamine metabolite pharmacokinetics in human volunteers after ketamine infusion

Authors: Moaddel, Ruin ^{1, 5, ∗}, Farmer, Cristan A. ², Yavi, Mani ², Kadriu, Bashkim ², Zhu, Min ¹, Fan, Jinshui ¹, Chen, Qinghua ¹, Lehrmann, Elin ¹, Fantoni, Giovanna ¹, De, Supriyo ¹, Mazucanti, Caio H. ¹, Acevedo-Diaz, Elia E. ², Yuan, Peixiong ², Gould, Todd D. ^{3, 4}, Park, Lawrence T. ², Egan, Josephine M. ¹, Ferrucci, Luigi ¹, Zarate, Carlos A., Jr. ²

Source: In iScience 15 December 2023 26(12)

A hyper-quiescent chromatin state formed during aging is reversed by regeneration

Authors: Yang, Na, Occean, James R., Melters, Daniël P., Shi, Changyou, Wang, Lin, Stransky, Stephanie, Doyle, Maire E., Cui, Chang-Yi, Delannoy, Michael, Fan, Jinshui, Slama, Eliza, Egan, Josephine M., De, Supriyo, Cunningham, Steven C., de Cabo, Rafael, Sidoli, Simone, Dalal, Yamini, Sen, Payel

Source: In Molecular Cell 18 May 2023 83(10):1659-1676

Spatial transcriptomics of the aging mouse brain reveals origins of inflammation in the white matter.

Authors: Wang, Lin, Cui, Chang-Yi, Lee, Christopher T., Bodogai, Monica, Yang, Na, Shi, Changyou, Irfanoglu, Mustafa O., Occean, James R., Afrin, Sadia, Sarker, Nishat, McDevitt, Ross A., Lehrmann, Elin, Abbas, Shahroze, Banskota, Nirad, Fan, Jinshui, De, Supriyo, Rapp, Peter, Biragyn, Arya, Benjamini, Dan, Maragkakis, Manolis

Source: Nature Communications; 4/4/2025, Vol. 16 Issue 1, p1-21, 21p

Subject Terms: WHITE matter (Nerve tissue), MYELOID cells, TRANSCRIPTOMES, COMPLEMENT activation, TRANSCRIPTION factors

Interplay between CTCF-binding and CTCF-lacking regulatory elements in generating an architectural stripe at the Igh locus.

Authors: Ma, Fei, Ollikainen, Noah, Du, Hansen, Braikia, Fatima Zohra, Cui, Nina, Bianchi, Aisha Haley, Dunn, Christopher, Nguyen, Cuong, Fan, Jinshui, De, Supriyo, Sen, Ranjan, Qiu, Xiang

Source: Nature Communications; 3/3/2025, Vol. 16 Issue 1, p1-15, 15p

Subject Terms: IMMUNOGLOBULIN heavy chains, GENETIC regulation, GENETIC transcription, LIFE sciences, ARCHITECTURAL details

Loss of HNRNPK During Cell Senescence Linked to Reduced Production of CDC20.

Authors: Shin, Chang Hoon, Rossi, Martina, Mazan-Mamczarz, Krystyna, Martindale, Jennifer L., Munk, Rachel, Pal, Apala, Piao, Yulan, Fan, Jinshui, De, Supriyo, Abdelmohsen, Kotb, Gorospe, Myriam

Source: Molecular & Cellular Biology; 2025, Vol. 45 Issue 3, p129-141, 13p

Subject Terms: CELL cycle proteins, INHIBITION of cellular proliferation, RNA-binding proteins, CELL division, RNA analysis

DNA methylation signatures reveal that distinct combinations of transcription factors specify human immune cell epigenetic identity

Authors: Roy, Roshni, Ramamoorthy, Senthilkumar, Shapiro, Benjamin D., Kaileh, Mary, Hernandez, Dena, Sarantopoulou, Dimitra, Arepalli, Sampath, Boller, Sören, Singh, Amit, Bektas, Arsun, Kim, Jaekwan, Moore, Ann Zenobia, Tanaka, Toshiko, McKelvey, Julia, Zukley, Linda, Nguyen, Cuong, Wallace, Tonya, Dunn, Christopher, Wersto, Robert, Wood, William, Piao, Yulan, Becker, Kevin G., Coletta, Christopher, De, Supriyo, Sen, Jyoti Misra, Battle, Alexis, Weng, Nan-ping, Grosschedl, Rudolf, Ferrucci, Luigi, Sen, Ranjan

Source: In Immunity 9 November 2021 54(11):2465-2480

Genome‐wide transcriptome differences associated with perceived discrimination in an urban, community‐dwelling middle‐aged cohort.

Authors: Pacheco, Natasha L., Noren Hooten, Nicole, Wu, Sharon F., Mensah‐Bonsu, Maame, Zhang, Yongqing, Chitrala, Kumaraswamy Naidu, De, Supriyo, Mode, Nicolle A., Ezike, Ngozi, Beatty Moody, Danielle L., Zonderman, Alan B., Evans, Michele K.

Source: FASEB Journal; Feb2025, Vol. 39 Issue 3, p1-18, 18p

Impact of state-level labour law reforms in India: an empirical analysis.

Authors: Debroy, Bibek¹ (AUTHOR), De, Supriyo² (AUTHOR) supriyode2000@gmail.com, Aditya¹ (AUTHOR), Dudani, Chirag¹ (AUTHOR), K. R., Jayasimha¹ (AUTHOR)

Source: Journal of the Asia Pacific Economy. Sep2024, p1-29. 29p. 15 Illustrations.

Subject Terms: *Labor laws, *Labor contracts, *Labor disputes, *Business size, Law reform

Geographic Terms: India

A new robust and fragile scheme based on chaotic maps and dwt for medical image security.

Authors: De, Supriyo¹, Bhaumik, Jaydeb², Giri, Debasis³, Das, Ashok Kumar⁴, iitkgp.akdas@gmail.com

Source: Multimedia Tools & Applications; Mar2023, Vol. 82 Issue 8, p11753-11792, 40p

Identification of senescent cell subpopulations by CITE‐seq analysis.

Authors: Abdelmohsen, Kotb, Mazan‐Mamczarz, Krystyna, Munk, Rachel, Tsitsipatis, Dimitrios, Meng, Qiong, Rossi, Martina, Pal, Apala, Shin, Chang Hoon, Martindale, Jennifer L., Piao, Yulan, Fan, Jinshui, Yanai, Hagai, De, Supriyo, Beerman, Isabel, Gorospe, Myriam

Source: Aging Cell; Nov2024, Vol. 23 Issue 11, p1-14, 14p

Subject Terms: CELL populations, CELL cycle, IONIZING radiation, CD26 antigen, CD54 antigen, CELLULAR aging

FUS-Mediated Inhibition of Myogenesis Elicited by Suppressing TNNT1 Production.

Authors: Ji, Eunbyul, Pandey, Poonam R., Martindale, Jennifer L., Yang, Xiaoling, Yang, Jen-Hao, Tsitsipatis, Dimitrios, Shin, Chang Hoon, Piao, Yulan, Fan, Jinshui, Mazan-Mamczarz, Krystyna, Banskota, Nirad, De, Supriyo, Gorospe, Myriam

Source: Molecular & Cellular Biology; 2024, Vol. 44 Issue 9, p391-409, 19p

Subject Terms: GENE expression, RNA-binding proteins, MYOGENESIS, GENETIC translation, SKELETAL muscle

Does governing law affect bond spreads?

Authors: Ratha, Dilip, De, Supriyo, Kurlat, Sergio

Source: In Emerging Markets Review September 2018 36:60-78

Sequential Enhancer Sequestration Dysregulates Recombination Center Formation at the IgH Locus

Authors: Qiu, Xiang, Kumari, Gita, Gerasimova, Tatiana, Du, Hansen, Labaran, Lawal, Singh, Amit, De, Supriyo, Wood, William H., III, Becker, Kevin G., Zhou, Weiqiang, Ji, Hongkai, Sen, Ranjan

Source: In Molecular Cell 5 April 2018 70(1):21-33

Gene body DNA hydroxymethylation restricts the magnitude of transcriptional changes during aging.

Authors: Occean, James R., Yang, Na, Sun, Yan, Dawkins, Marshall S., Munk, Rachel, Belair, Cedric, Dar, Showkat, Anerillas, Carlos, Wang, Lin, Shi, Changyou, Dunn, Christopher, Bernier, Michel, Price, Nathan L., Kim, Julie S., Cui, Chang-Yi, Fan, Jinshui, Bhattacharyya, Moitrayee, De, Supriyo, Maragkakis, Manolis, de Cabo, Rafael

Source: Nature Communications; 7/28/2024, Vol. 15 Issue 1, p1-22, 22p

Increased PTCHD4 expression via m⁶A modification of PTCHD4 mRNA promotes senescent cell survival.

Authors: Rossi, Martina, Banskota, Nirad, Shin, Chang Hoon, Anerillas, Carlos, Tsitsipatis, Dimitrios, Yang, Jen-Hao, Munk, Rachel, Martindale, Jennifer L, Yang, Xiaoling, Piao, Yulan, Mazan-Mamczarz, Krystyna, Fan, Jinshui, Lehrmann, Elin, Lam, Kwan-Wood Gabriel, De, Supriyo, Abdelmohsen, Kotb, Gorospe, Myriam

Source: Nucleic Acids Research; 7/8/2024, Vol. 52 Issue 12, p7261-7278, 18p

Cockayne syndrome group A and B proteins converge on transcription-linked resolution of non-B DNA

Authors: Scheibye-Knudsen, Morten, Tseng, Anne, Jensen, Martin Borch, Scheibye-Alsing, Karsten, Fang, Evandro Fei, Iyama, Teruaki, Bharti, Sanjay Kumar, Marosi, Krisztina, Froetscher, Lynn, Kassahun, Henok, Eckley, David Mark, Maul, Robert W., Bastian, Paul, De, Supriyo, Ghosh, Soumita, Nilsen, Hilde, Goldberg, Ilya G., Mattson, Mark P., Wilson, David M., Brosh, Robert M., Gorospe, Myriam, Bohr, Vilhelm A.

Source: Proceedings of the National Academy of Sciences of the United States of America, 2016 Nov 01. 113(44), 12502-12507.

Access URL: https://www.jstor.org/stable/26472307

A secure image encryption scheme based on three different chaotic maps.

Authors: De, Supriyo¹, Bhaumik, Jaydeb², Giri, Debasis³

Source: Multimedia Tools & Applications; Feb2022, Vol. 81 Issue 4, p5485-5514, 30p

Extremely Long-Range Chromatin Loops Link Topological Domains to Facilitate a Diverse Antibody Repertoire

Authors: Montefiori, Lindsey, Wuerffel, Robert, Roqueiro, Damian, Lajoie, Bryan, Guo, Changying, Gerasimova, Tatiana, De, Supriyo, Wood, William, Becker, Kevin G., Dekker, Job, Liang, Jie, Sen, Ranjan, Kenter, Amy L.

Source: In Cell Reports 2 February 2016 14(4):896-906