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ChIP-seq

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Discovering unknown human and mouse transcription factor binding sites and their characteristics from ChIP-seq data
Chun-Ping Yu, Chen-Hao Kuo, Chase W. Nelson, Chi-An Chen, Zhi Thong Soh, Jinn-Jy Lin, Ru-Xiu Hsiao, Chih-Yao Chang, and Wen-Hsiung Li

PNAS May 18, 2021 118 (20) e2026754118; https://doi.org/10.1073/pnas.2026754118
Open Access
Comparative analysis of embryo proper and suspensor transcriptomes in plant embryos with different morphologies
Min Chen, Jer-Young Lin, Xiaomeng Wu, Nestor R. Apuya, Kelli F. Henry, Brandon H. Le, Anhthu Q. Bui, Julie M. Pelletier, Shawn Cokus, Matteo Pellegrini, John J. Harada, and Robert B. Goldberg

PNAS February 9, 2021 118 (6) e2024704118; https://doi.org/10.1073/pnas.2024704118
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Epigenetic competition reveals density-dependent regulation and target site plasticity of phosphorothioate epigenetics in bacteria
Xiaolin Wu, Bo Cao, Patricia Aquino, Tsu-Pei Chiu, Chao Chen, Susu Jiang, Zixin Deng, Shi Chen, Remo Rohs, Lianrong Wang, James E. Galagan, and Peter C. Dedon

PNAS June 23, 2020 117 (25) 14322-14330; first published June 9, 2020. https://doi.org/10.1073/pnas.2002933117
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A parallelized, automated platform enabling individual or sequential ChIP of histone marks and transcription factors
Riccardo Dainese, Vincent Gardeux, Gerard Llimos, Daniel Alpern, Jia Yuan Jiang, Antonio Carlos Alves Meireles-Filho, and Bart Deplancke

PNAS June 16, 2020 117 (24) 13828-13838; first published May 27, 2020. https://doi.org/10.1073/pnas.1913261117
Open Access
Transcription factor profiling reveals molecular choreography and key regulators of human retrotransposon expression
Xiaoji Sun, Xuya Wang, Zuojian Tang, Mark Grivainis, David Kahler, Chi Yun, Paolo Mita, David Fenyö, and Jef D. Boeke

PNAS June 12, 2018 115 (24) E5526-E5535; first published May 25, 2018. https://doi.org/10.1073/pnas.1722565115
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Genome-wide use of high- and low-affinity Tbrain transcription factor binding sites during echinoderm development
Gregory A. Cary, Alys M. Cheatle Jarvela, Rene D. Francolini, and Veronica F. Hinman

PNAS June 6, 2017 114 (23) 5854-5861; first published June 5, 2017. https://doi.org/10.1073/pnas.1610611114
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Estrogen receptor α wields treatment-specific enhancers between morphologically similar endometrial tumors
Marjolein Droog, Ekaterina Nevedomskaya, Gwen M. Dackus, Renske Fles, Yongsoo Kim, Harry Hollema, Marian J. Mourits, Petra M. Nederlof, Hester H. van Boven, Sabine C. Linn, Flora E. van Leeuwen, Lodewyk F. A. Wessels, and Wilbert Zwart

PNAS February 21, 2017 114 (8) E1316-E1325; first published February 6, 2017. https://doi.org/10.1073/pnas.1615233114
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Histone arginine methylation in cocaine action in the nucleus accumbens
Diane M. Damez-Werno, HaoSheng Sun, Kimberly N. Scobie, Ningyi Shao, Jaclyn Rabkin, Caroline Dias, Erin S. Calipari, Ian Maze, Catherine J. Pena, Deena M. Walker, Michael E. Cahill, Ramesh Chandra, Amy Gancarz, Ezekiell Mouzon, Joseph A. Landry, Hannah Cates, Mary-Kay Lobo, David Dietz, C. David Allis, Ernesto Guccione, Gustavo Turecki, Paola Defilippi, Rachael L. Neve, Yasmin L. Hurd, Li Shen, and Eric J. Nestler

PNAS August 23, 2016 113 (34) 9623-9628; first published August 9, 2016. https://doi.org/10.1073/pnas.1605045113
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Functional and mechanistic studies of XPC DNA-repair complex as transcriptional coactivator in embryonic stem cells
Claudia Cattoglio, Elisa T. Zhang, Ivan Grubisic, Kunitoshi Chiba, Yick W. Fong, and Robert Tjian

PNAS May 5, 2015 112 (18) E2317-E2326; first published April 21, 2015. https://doi.org/10.1073/pnas.1505569112
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CHD8 regulates neurodevelopmental pathways associated with autism spectrum disorder in neural progenitors
Aarathi Sugathan, Marta Biagioli, Christelle Golzio, Serkan Erdin, Ian Blumenthal, Poornima Manavalan, Ashok Ragavendran, Harrison Brand, Diane Lucente, Judith Miles, Steven D. Sheridan, Alexei Stortchevoi, Manolis Kellis, Stephen J. Haggarty, Nicholas Katsanis, James F. Gusella, and Michael E. Talkowski

PNAS October 21, 2014 111 (42) E4468-E4477; first published October 7, 2014. https://doi.org/10.1073/pnas.1405266111

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