ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation

Citations

Cited by:

1. Timothy D. Arthur & Jennifer P. Nguyen & Agnieszka D’Antonio-Chronowska & Hiroko Matsui & Nayara S. Silva & Isaac N. Joshua & André D. Luchessi & William W. Young Greenwald & Matteo D’Antonio & Martin, 2024. "Complex regulatory networks influence pluripotent cell state transitions in human iPSCs," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
2. Nicholas Sim & Jean-Michel Carter & Kamalakshi Deka & Benita Kiat Tee Tan & Yirong Sim & Suet-Mien Tan & Yinghui Li, 2024. "TWEAK/Fn14 signalling driven super-enhancer reprogramming promotes pro-metastatic metabolic rewiring in triple-negative breast cancer," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
3. Shengen Shawn Hu & Lin Liu & Qi Li & Wenjing Ma & Michael J. Guertin & Clifford A. Meyer & Ke Deng & Tingting Zhang & Chongzhi Zang, 2022. "Intrinsic bias estimation for improved analysis of bulk and single-cell chromatin accessibility profiles using SELMA," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
4. Zhenhui Zhong & Yafei Wang & Ming Wang & Fan Yang & Quentin Angelo Thomas & Yan Xue & Yaxin Zhang & Wanlu Liu & Yasaman Jami-Alahmadi & Linhao Xu & Suhua Feng & Sebastian Marquardt & James A. Wohlschl, 2022. "Histone chaperone ASF1 mediates H3.3-H4 deposition in Arabidopsis," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
5. Dhurjhoti Saha & Solomon Hailu & Arjan Hada & Junwoo Lee & Jie Luo & Jeff A. Ranish & Yuan-chi Lin & Kyle Feola & Jim Persinger & Abhinav Jain & Bin Liu & Yue Lu & Payel Sen & Blaine Bartholomew, 2023. "The AT-hook is an evolutionarily conserved auto-regulatory domain of SWI/SNF required for cell lineage priming," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
6. Joyce J. Thompson & Daniel J. Lee & Apratim Mitra & Sarah Frail & Ryan K. Dale & Pedro P. Rocha, 2022. "Extensive co-binding and rapid redistribution of NANOG and GATA6 during emergence of divergent lineages," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
7. Aditya Kshirsagar & Svetlana Maslov Doroshev & Anna Gorelik & Tsviya Olender & Tamar Sapir & Daisuke Tsuboi & Irit Rosenhek-Goldian & Sergey Malitsky & Maxim Itkin & Amir Argoetti & Yael Mandel-Gutfre, 2023. "LIS1 RNA-binding orchestrates the mechanosensitive properties of embryonic stem cells in AGO2-dependent and independent ways," Nature Communications, Nature, vol. 14(1), pages 1-21, December.
8. Qi Wang & Jerry Antone & Eric Alsop & Rebecca Reiman & Cory Funk & Jaroslav Bendl & Joel T. Dudley & Winnie S. Liang & Timothy L. Karr & Panos Roussos & David A. Bennett & Philip L. Jager & Geidy E. S, 2024. "Single cell transcriptomes and multiscale networks from persons with and without Alzheimer’s disease," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
9. Arthur S. Lee & Lauren J. Ayers & Michael Kosicki & Wai-Man Chan & Lydia N. Fozo & Brandon M. Pratt & Thomas E. Collins & Boxun Zhao & Matthew F. Rose & Alba Sanchis-Juan & Jack M. Fu & Isaac Wong & X, 2024. "A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders," Nature Communications, Nature, vol. 15(1), pages 1-26, December.
10. Baohua Tan & Linjun Hong & Liyao Xiao & Jiajin Wu & Geyan Lu & Shanshan Wang & Langqing Liu & Enqin Zheng & Gengyuan Cai & Zicong Li & Ting Gu & Zhenfang Wu, 2025. "Rewiring of 3D chromatin topology orchestrates transcriptional reprogramming in muscle fiber-type specification and transformation," Nature Communications, Nature, vol. 16(1), pages 1-18, December.
11. Yuyan Cheng & Yuqin Yin & Alice Zhang & Alexander M. Bernstein & Riki Kawaguchi & Kun Gao & Kyra Potter & Hui-Ya Gilbert & Yan Ao & Jing Ou & Catherine J. Fricano-Kugler & Jeffrey L. Goldberg & Zhigan, 2022. "Transcription factor network analysis identifies REST/NRSF as an intrinsic regulator of CNS regeneration in mice," Nature Communications, Nature, vol. 13(1), pages 1-22, December.
12. Atsuki Kawamura & Kazuki Fujii & Kota Tamada & Yoshifumi Abe & Kenta Nitahara & Tomoya Iwasaki & Sho Yagishita & Kenji F. Tanaka & Toru Takumi & Keizo Takao & Masaaki Nishiyama, 2025. "Duplication of the autism-related gene Chd8 leads to behavioral hyperactivity and neurodevelopmental defects in mice," Nature Communications, Nature, vol. 16(1), pages 1-19, December.
13. Tao Zhu & Chunjiao Xia & Ranran Yu & Xinkai Zhou & Xingbing Xu & Lin Wang & Zhanxiang Zong & Junjiao Yang & Yinmeng Liu & Luchang Ming & Yuxin You & Dijun Chen & Weibo Xie, 2024. "Comprehensive mapping and modelling of the rice regulome landscape unveils the regulatory architecture underlying complex traits," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
14. Kathleen Shah & Muralidhara Rao Maradana & M. Joaquina Delàs & Amina Metidji & Frederike Graelmann & Miriam Llorian & Probir Chakravarty & Ying Li & Mauro Tolaini & Michael Shapiro & Gavin Kelly & Chr, 2022. "Cell-intrinsic Aryl Hydrocarbon Receptor signalling is required for the resolution of injury-induced colonic stem cells," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
15. Pin Lyu & Maria Iribarne & Dmitri Serjanov & Yijie Zhai & Thanh Hoang & Leah J. Campbell & Patrick Boyd & Isabella Palazzo & Mikiko Nagashima & Nicholas J. Silva & Peter F. Hitchcock & Jiang Qian & Da, 2023. "Common and divergent gene regulatory networks control injury-induced and developmental neurogenesis in zebrafish retina," Nature Communications, Nature, vol. 14(1), pages 1-21, December.
16. Akihiko Fukagawa & Natsuko Hama & Yasushi Totoki & Hiromi Nakamura & Yasuhito Arai & Mihoko Saito-Adachi & Akiko Maeshima & Yoshiyuki Matsui & Shinichi Yachida & Tetsuo Ushiku & Tatsuhiro Shibata, 2023. "Genomic and epigenomic integrative subtypes of renal cell carcinoma in a Japanese cohort," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
17. Moritz Binder & Raphael E. Szalat & Srikanth Talluri & Mariateresa Fulciniti & Hervé Avet-Loiseau & Giovanni Parmigiani & Mehmet K. Samur & Nikhil C. Munshi, 2024. "Bone marrow stromal cells induce chromatin remodeling in multiple myeloma cells leading to transcriptional changes," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
18. Denis Torre & Nancy J. Francoeur & Yael Kalma & Ilana Gross Carmel & Betsaida S. Melo & Gintaras Deikus & Kimaada Allette & Ron Flohr & Maya Fridrikh & Konstantinos Vlachos & Kent Madrid & Hardik Shah, 2023. "Isoform-resolved transcriptome of the human preimplantation embryo," Nature Communications, Nature, vol. 14(1), pages 1-23, December.
19. Felicia Lazure & Rick Farouni & Korin Sahinyan & Darren M. Blackburn & Aldo Hernández-Corchado & Gabrielle Perron & Tianyuan Lu & Adrien Osakwe & Jiannis Ragoussis & Colin Crist & Theodore J. Perkins , 2023. "Transcriptional reprogramming of skeletal muscle stem cells by the niche environment," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
20. Pascal Hunold & Giulia Pizzolato & Nadia Heramvand & Laura Kaiser & Giulia Barbiera & Olivia Ray & Roman Thomas & Julie George & Martin Peifer & Robert Hänsel-Hertsch, 2025. "DynaTag for efficient mapping of transcription factors in low-input samples and at single-cell resolution," Nature Communications, Nature, vol. 16(1), pages 1-15, December.
21. Takeshi Katsuda & Jonathan H. Sussman & Kenji Ito & Andrew Katznelson & Salina Yuan & Naomi Takenaka & Jinyang Li & Allyson J. Merrell & Hector Cure & Qinglan Li & Reyaz Ur Rasool & Irfan A. Asangani , 2024. "Cellular reprogramming in vivo initiated by SOX4 pioneer factor activity," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
22. Zhuo Ma & Xiaofei Zhang & Wen Zhong & Hongyan Yi & Xiaowei Chen & Yinsuo Zhao & Yanlin Ma & Eli Song & Tao Xu, 2023. "Deciphering early human pancreas development at the single-cell level," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
23. Helen Ray-Jones & Chak Kei Sung & Lai Ting Chan & Alexander Haglund & Pavel Artemov & Monica Della Rosa & Luminita Ruje & Frances Burden & Roman Kreuzhuber & Anna Litovskikh & Eline Weyenbergh & Zoï B, 2025. "Genetic coupling of enhancer activity and connectivity in gene expression control," Nature Communications, Nature, vol. 16(1), pages 1-26, December.
24. Chao Yang & Mahesh Bachu & Yong Du & Caroline Brauner & Ruoxi Yuan & Marie Dominique Ah Kioon & Giancarlo Chesi & Franck J. Barrat & Lionel B. Ivashkiv, 2022. "CXCL4 synergizes with TLR8 for TBK1-IRF5 activation, epigenomic remodeling and inflammatory response in human monocytes," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
25. Chao He & Siteng Bi & Yuqi Li & Chengxiang Song & Heping Zhang & Xintong Xu & Qiang Li & Sulaiman Saeed & Wei Chen & Chunjie Zhao & Caixia Lan & Handong Su & Hailiang Mao & Wenhao Yan, 2024. "Dynamic atlas of histone modifications and gene regulatory networks in endosperm of bread wheat," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
26. Xiaowei Bian & Minna Piipponen & Zhuang Liu & Lihua Luo & Jennifer Geara & Yongjian Chen & Traimate Sangsuwan & Monica Maselli & Candice Diaz & Connor A. Bain & Evelien Eenjes & Maria Genander & Micha, 2024. "Epigenetic memory of radiotherapy in dermal fibroblasts impairs wound repair capacity in cancer survivors," Nature Communications, Nature, vol. 15(1), pages 1-20, December.