Pioneer Transcription Factors Target Partial DNA Motifs on Nucleosomes to Initiate Reprogramming

Soufi, Abdenour, Garcia, Meilin Fernandez, Jaroszewicz, Artur, Osman, Nebiyu, Pellegrini, Matteo, Zaret, Kenneth S.·2015·Cell
DOI 10.1016/j.cell.2015.03.017

Cited by (780)

Items 701–780 of 780

  1. Research progress on chemical reprogramming for inducing human pluripotent stem cells
    Lin Cheng, Hongkui Deng · 2025 · Scientia Sinica Vitae
  2. Lin28-Mediated Gene Regulatory Loops Synchronize Developmental Transitions Throughout Organogenesis and Oncogenesis
    Indhujah Thevarajan, Maria F. Osuna, Sonia Fuentes Lewey, Eustolia Sauceda, Sayra Briseno, Caylah Griffin, Ba Reun Kim, R. Grant Rowe, Edroaldo Lummertz da Rocha, Jihan K. Osborne · 2025 · SSRN Electronic Journal
  3. Reprogramming Mechanisms and Application Prospects of Induced Pluripotent Stem Cells
    Zijia Liu · 2025 · Journal of Clinical Medicine Research
  4. Genetic regulation within cellular stress response pathways
    Jhos Dufflart · 2022
  5. Systematic DNA nicking reveals the structural logic of protein recognition
    Yumi Minyi Yao, Michael O’Hagan, Karn Onoon, Lihee Givon, Shelly Hamer-Rogotner, Raul Salinas, Naama Kessler, Orly Dym, Tanadet Pipatpolkai, Maria A. Schumacher et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  6. The SMARCA5–DMRT1 Pioneer Complex Establishes Epigenetic Priming to Direct Male Germline Development
    Yuka Kitamura, Yasuhisa Munakata, Hironori Abe, Mengwen Hu, Satoyo Oya, Shanmathi Murugesan, Mahnoor Rizwan, Shawna P. Katz, David J. Picketts, Richard M. Schultz et al. · 2025 · Research Square
  7. MNase stratification reveals heterogeneous 5hmC in naive B cells
    Michael Hsu, Heng-Yi Chen, Fang-Yun Lay, Qin Ma, Benjamin Delatte, Chan‐Wang Jerry Lio · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  8. HAND2 invades nucleolar condensates to pioneer lineage-specific cardiac pacemaker gene programs
    Kartik Kulkarni, Gabriella M. Quinn, Jared Gabriel L. Dela Rosa, Sean C. Goetsch, Vrushali Pandit, Lin Wang, Akane Sakaguchi, Sushama Sivakumar, Nikhil V. Munshi · 2025 · Nature Communications
  9. Solution structure of the Sox2 DNA-binding domain reveals conformational selection in DNA binding
    Andrea Orsetti, Jonathan Slejfer, Satine Ha, Damian I Kevelam, Jan Tekkelenburg, Tjitske van Duijn, Anni Leppäkoski, Aren Sedrakyan, Ákos Szilagyi, Raymond D. Schellevis et al. · 2025 · Nucleic Acids Research
  10. Cohesin facilitates nucleosome invasion by transcription factors
    Shane D Stoeber, Hengye Chen, Ruo-Wen Chen, Courtney Smith, Samuel Becker, Sarah Vinson, Michael Guy Poirier, Lu Bai · 2026 · Science Advances
  11. Repurposed macroH2A Chromatin Landscapes Guide Cellular Reprogramming
    Dimitrios Valakos, Antonis Kokkalis, Eleftheria Klagkou, Alexander Polyzos, Giannis Vatsellas, Dimitris Thanos · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  12. Leukemic Transdifferentiation: From Pathological Plasticity to Dendritic Cell-Based Immunotherapy
    Joanna Dubis, Aleksander Czogalla, Kazimierz Kuliczkowski, Aleksander F. Sikorski · 2025 · Biomedicines
  13. Additional file 14 of Chromatin accessibility profiling in Neurospora crassa reveals molecular features associated with accessible and inaccessible chromatin
    Aileen R. Ferraro, Ameri, Abigail J., Zefu Lu, Masayuki Kamei, Schmitz, Robert J., Lewis, Zachary A. · 2021 · Figshare
  14. Additional file 1 of Chromatin accessibility profiling in Neurospora crassa reveals molecular features associated with accessible and inaccessible chromatin
    Aileen R. Ferraro, Ameri, Abigail J., Zefu Lu, Masayuki Kamei, Schmitz, Robert J., Lewis, Zachary A. · 2021 · Figshare
  15. Additional file 1 of Methylome-based cell-of-origin modeling (Methyl-COOM) identifies aberrant expression of immune regulatory molecules in CLL
    Wierzbinska, Justyna A., Toth, Reka, Naveed Ishaque, Karsten Rippe, Mallm, Jan-Philipp, Lara C. Klett, Daniel Mertens, Zenz, Thorsten, Hielscher, Thomas, Marc Seifert et al. · 2020 · Figshare
  16. Additional file 1 of SOX2 interacts with hnRNPK to modulate alternative splicing in mouse embryonic stem cells
    Huang, Yanlan, Yuxuan Liu, Mingyi Pu, Zhang, Yuli, Qiang Cao, Senru Li, Yuanjie Wei, Hou, Linlin · 2024 · Figshare
  17. Additional file 2 of SeATAC: a tool for exploring the chromatin landscape and the role of pioneer factors
    Wuming Gong, Nikita Dsouza, Garry, Daniel J. · 2024 · Figshare
  18. Additional file 2 of SOX2 interacts with hnRNPK to modulate alternative splicing in mouse embryonic stem cells
    Huang, Yanlan, Yuxuan Liu, Mingyi Pu, Zhang, Yuli, Qiang Cao, Senru Li, Yuanjie Wei, Hou, Linlin · 2024 · Figshare
  19. Additional file 5 of Chromatin accessibility profiling in Neurospora crassa reveals molecular features associated with accessible and inaccessible chromatin
    Aileen R. Ferraro, Ameri, Abigail J., Zefu Lu, Masayuki Kamei, Schmitz, Robert J., Lewis, Zachary A. · 2021 · Figshare
  20. Additional file 11 of Methylome-based cell-of-origin modeling (Methyl-COOM) identifies aberrant expression of immune regulatory molecules in CLL
    Wierzbinska, Justyna A., Toth, Reka, Naveed Ishaque, Karsten Rippe, Mallm, Jan-Philipp, Lara C. Klett, Daniel Mertens, Zenz, Thorsten, Hielscher, Thomas, Marc Seifert et al. · 2020 · Figshare
  21. Additional file 2 of CRAG: de novo characterization of cell-free DNA fragmentation hotspots in plasma whole-genome sequencing
    Zhou, Xionghui, Zheng, Haizi, Fu, Hailu, Dillehay McKillip, Kelsey L., Susan M. Pinney, Yaping Liu · 2024 · Figshare
  22. Additional file 1 of An interpretable bimodal neural network characterizes the sequence and preexisting chromatin predictors of induced transcription factor binding
    Divyanshi Srivastava, Begüm Aydın, Esteban O. Mazzoni, Shaun Mahony · 2021 · Figshare
  23. Additional file 1 of CRAG: de novo characterization of cell-free DNA fragmentation hotspots in plasma whole-genome sequencing
    Zhou, Xionghui, Zheng, Haizi, Fu, Hailu, Dillehay McKillip, Kelsey L., Susan M. Pinney, Yaping Liu · 2024 · Figshare
  24. Additional file 3 of Chromatin accessibility profiling in Neurospora crassa reveals molecular features associated with accessible and inaccessible chromatin
    Aileen R. Ferraro, Ameri, Abigail J., Zefu Lu, Masayuki Kamei, Schmitz, Robert J., Lewis, Zachary A. · 2021 · Figshare
  25. Additional file 4 of Chromatin accessibility profiling in Neurospora crassa reveals molecular features associated with accessible and inaccessible chromatin
    Aileen R. Ferraro, Ameri, Abigail J., Zefu Lu, Masayuki Kamei, Schmitz, Robert J., Lewis, Zachary A. · 2021 · Figshare
  26. Additional file 3 of A quantitative metric of pioneer activity reveals that HNF4A has stronger in vivo pioneer activity than FOXA1
    Hansen, Jeffrey L., Barak A. Cohen · 2022 · Figshare
  27. Additional file 1 of A quantitative metric of pioneer activity reveals that HNF4A has stronger in vivo pioneer activity than FOXA1
    Hansen, Jeffrey L., Barak A. Cohen · 2022 · Figshare
  28. Additional file 6 of Chromatin accessibility profiling in Neurospora crassa reveals molecular features associated with accessible and inaccessible chromatin
    Aileen R. Ferraro, Ameri, Abigail J., Zefu Lu, Masayuki Kamei, Schmitz, Robert J., Lewis, Zachary A. · 2021 · Figshare
  29. Additional file 3 of An interpretable bimodal neural network characterizes the sequence and preexisting chromatin predictors of induced transcription factor binding
    Divyanshi Srivastava, Begüm Aydın, Esteban O. Mazzoni, Shaun Mahony · 2021 · Figshare
  30. Additional file 2 of Chromatin accessibility profiling in Neurospora crassa reveals molecular features associated with accessible and inaccessible chromatin
    Aileen R. Ferraro, Ameri, Abigail J., Zefu Lu, Masayuki Kamei, Schmitz, Robert J., Lewis, Zachary A. · 2021 · Figshare
  31. Additional file 2 of An interpretable bimodal neural network characterizes the sequence and preexisting chromatin predictors of induced transcription factor binding
    Divyanshi Srivastava, Begüm Aydın, Esteban O. Mazzoni, Shaun Mahony · 2021 · Figshare
  32. Additional file 1 of SeATAC: a tool for exploring the chromatin landscape and the role of pioneer factors
    Wuming Gong, Nikita Dsouza, Garry, Daniel J. · 2024 · Figshare
  33. Additional file 13 of Chromatin accessibility profiling in Neurospora crassa reveals molecular features associated with accessible and inaccessible chromatin
    Aileen R. Ferraro, Ameri, Abigail J., Zefu Lu, Masayuki Kamei, Schmitz, Robert J., Lewis, Zachary A. · 2021 · Figshare
  34. Pioneer Transcription Factors Differentially Co-opt Bcl11a and Bcl11b to orchestrate Reprogramming
    Aneta Trajkova, Emile Zakiev, Maria Grazia Mendoza-Ferri, Ines Messahli, M. Ruel, Imène Krossa, Yann Tapponnier, E. Dejonckere, Emma Hunter, Léo Claret et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  35. Chromosome-naïve global networks of initiators of hybrid assembly pathways of endogenous multiprotein complexes
    Gennadi V. Glinsky · 2026 · Research Square
  36. An inducible system to study the regulatory functions of GSX2 in human lateral ganglionic eminence-like progenitors
    Edward Farrow, Smitha Rao, Simon J. Y. Han, Xuyao Chang, Cindy Huynh, Samantha A. Brugmann, Hee‐Woong Lim, Jason H. Tchieu, Kenneth Campbell, Brian A. Gebelein · 2026 · Developmental Biology
  37. Systematic comparison of estimates of transcription factor activity by ATAC-seq and multiplexed reporter assays
    Max Trauernicht, Vinícius H. Franceschini-Santos, H. Yücel, Teodora Filipovska, B. van Steensel · 2026 · bioRxiv
  38. SoxB1-mediated chromatin remodeling promotes sensory neuron differentiation in planarians
    Mallory L. Cathell, Mohamad A Auwal, Sarai Alvarez Zepeda, Kelly G. Ross, Ricardo M. Zayas · 2026 · Genetics
  39. Parallel profiling of genome mutations and multiple chromatin modalities in single cells by scNanoCT&ATAC-seq
    Xiaoying Fan, Dan Su, Zhuobin Lin, Lin Guang Luo, Enze Deng, Qingpei Huang, Wenxin Xu, Zhihua Guo, Zhixiang Zuo · 2026 · Research Square
  40. TFG p. G269V Mutation Disrupts Motor Neuron Function in iPSC ‐Derived Models via Wnt Signaling Dysregulation
    Zhiqiang Mu, Jielin Wang, Tian Xiao, Kun Chen, Xinyu Chen, Qiurong Liu, Jiahui Huang, Yuanbo Li, Jing Chen, Yuanming Wu et al. · 2026 · Journal of Neurochemistry
  41. Early Reprogramming Intermediates Enable Direct Neuronal Conversion Via NGN2
    Silvia Angiolillo, Wei Qin, Alessia Gesualdo, Roberta Frison, Nicola Elvassore, Cecilia Laterza, Onelia Gagliano · 2026 · Journal of Molecular Neuroscience
  42. Counteracting FOX proteins epigenetically control the herpesvirus lytic-latent balance
    Yuhang Xiang, Xiyuan Yang, Juncheng Zhang, Fujun Hou, Yue Cheng Deng, Hui Fu, Hyung Suk Oh, Qiongyan Wang, Siyu Chen, Zeyu Sun et al. · 2026 · Nature Communications
  43. Distinct DNA-binding syntax and chromatin remodeling capacities of bHLH transcription factors in cell differentiation, reprogramming and cancer
    Xabier de Martin, Joel Martínez-Miralles, Serafima Beletskaya, Adrià Navarro, Jan Izquierdo, Baldomero Oliva, Gabriel Santpere · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  44. Role of SoxE transcription factors in development and disease
    Merin Lawrence, Gerhard Schlosser · 2026 · Developmental Dynamics
  45. Pioneer factor BmFoxA modulates temporal gene regulatory networks via promoter selectivity in Bombyx mori
    Quan Zhang, Yueting Sun, Ruoxuan Zhang, Peikun Tang, Qingyou Xia · 2026 · Insect Biochemistry and Molecular Biology
  46. SnakeHichipTF reveals transcription factor logic underlying enhancer-promoter wiring in the human brain
    Jiang Tan, Yuqing Wu, Richard Head, Yidan Sun · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  47. Endogenous Sox2 expression is essential for Atoh1-induced hair cell addition and regeneration in the mouse utricle
    Yu-Tong Yang, Jingying Guo, Jun-Yi Xu, Wei- Su, Ming-yu Hao, Ting Zhang, S S Gong, Guopeng Wang · 2026 · Neuroscience
  48. Identification et analyse d'éléments cis-régulateurs impliqués dans les mécanismes de régulation transcriptionnelle des gènes au cours de la cardiogénèse chez la drosophile
    Denis Seyres · 2015 · theses.fr (ABES)
  49. Hépatocytes différenciés à partir de cellules souches pluripotentes induites : modèle pour la thérapie cellulaire et génique autologue de l'hémophilie B et modèle préclinique chez le primate
    Eléanor Luce · 2017 · theses.fr (ABES)
  50. The role of Chd7 & Chd8 chromatin remodelers in oligodendrogenesis and (re)myelination
    Corentine Marie · 2017 · theses.fr (ABES)
  51. Analysis of the composition and the function of oocyte-specific TBP2-containing transcription machinery during mouse oogenesis
    Changwei Yu · 2018 · theses.fr (ABES)
  52. Applying Systems Biology and Multi-layered Profiling Towards a Comprehensive Understanding of Cell Aging
    José Américo Nabuco Leva Ferreira de Freitas · 2020 · theses.fr (ABES)
  53. Tools to analyze single-particle tracking data in mammalian cells
    Maxime Woringer · 2019 · theses.fr (ABES)
  54. Mécanismes moléculaires et cellulaires des processus de différenciation et de plasticité cellulaire pour la formation des adipocytes
    Hélène Leménager · 2019 · theses.fr (ABES)
  55. Molecular basis of 3D chromatin organization in Arabidopsis thaliana & Solanum lycopersicum during development and in response to stress
    Ying Huang · 2022 · theses.fr (ABES)
  56. Investigating the role of the centromeric histone variant CENP-A in cancer
    Charlène Renaud-Pageot · 2024 · theses.fr (ABES)
  57. Dual regulation of chemical stress-induced DDI2/3 expression by a transcription factor Fzf1 and nucleosome in Saccharomyces cerevisiae
    Ying Du, Aiyang Lin, Joshua A.R. Brown, LeAnn J. Howe, Wei Xao · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  58. BPabZIP, a new bZIP protein motif that promotes binding near, and displacement of, nucleosomes
    Desiree Tillo, Victor B. Zhurkin, Aleksey Porollo, Stewart R. Durell, Hayley K. Hesse, Matthew R. Hass, Phillip J. Dexheimer, Leah Claire Kottyan, Matthew T. Weirauch, Charles Vinson · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  59. Somatic cell reprogramming into stem cells: approaches, mechanisms, and therapeutic applications
    Zhuo-Er Liao, Zuping He · 2026 · Asian Journal of Andrology
  60. Distinct associations of pioneer factor Ascl1-E12a with nucleosomes drive changes in cell fate
    Bing‐Rui Zhou, Edgar Luzete-Monteiro, Jingchao Zhang, Naomi Takenaka, Hsin‐Yao Tang, Meilín Fernández García, Mariel Coradin, Megan Frederick, Greg Donahue, Benjamin Garcia et al. · 2026 · Molecular Cell
  61. Intrinsic DNA codes govern distinct modes of nucleosome-transcription factor interactions
    Christopher W Carson, Sheethal Umesh Nagalakshmi, Image Adhikari, Julia M. Freewoman, Joseph R. Pizzi, Prakyat Prakash, Feng Cui · 2026 · Nature Communications
  62. CitRWP directly activates CsDAZ3 to promote somatic embryogenesis in Citrus
    Yin Zhou, Xietian Song, Nan Wang, Zhen Yu Cao, Siqi Zhang, Zongzhou Xie, Lijun Chai, Xiao‐Meng Wu, Qiang Xu, Junli Ye et al. · 2026 · New Phytologist
  63. Nucleosomes as active platforms for pioneer factor action
    Di Niu, Wulan Deng · 2026 · Molecular Cell
  64. Klf4 overexpression remodels chromatin to reprogram late retinal progenitors toward a retinal ganglion cell-like fate
    Viviane M. Oliveira-Valença, Jacqueline M. Roberts, Fei Chang, Alejandra Bosco, Monica L. Vetter, Mariana S. Silveira · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  65. Bovine α-herpesvirus 1 replication and immediate early transcription unit 1 promoter are jointly stimulated by glucocorticoid receptor and DNA-dependent ATPases
    Fouad S. El-mayet, Mike St. Clair, Brooke Costello, Jeffery B. Ostler, Clinton Jones · 2026 · Journal of General Virology
  66. Effect of nuclear electrostatic potential on the nucleoplasmic distribution of histones and nucleosome stability
    Yuqi Guo, Fei He, Xin Dai, Jiaying Yu, Yixuan Li, Fenfang Li, Cheng‐han Yu, Ying Wai Chan, Andrew W. Holle, Esteban Hoijman et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  67. Broad-stroke regulation by DNA sequence-specific transcription factors
    Zachary Bigelow, Sergei Nechaev · 2026 · Biochemistry and Cell Biology
  68. Cooperation of transposable elements to endow global networks of initiators of hybrid assembly pathways of endogenous multiprotein complexes
    Gennadi V. Glinsky · 2026 · Frontiers in Cellular and Infection Microbiology
  69. Krüppel-like Factor 4 and Glucocorticoid Receptor Cooperatively Transactivate the Bovine Alphaherpesvirus 1 (BoHV-1) Infected Cell Protein 0 (bICP0) Early Promoter
    Hafez Sadeghi, Vanessa Claire Santos, Clinton Jones · 2026 · Viruses
  70. DPF3a couples H3K36me2-dependent chromatin remodeling to genome architecture during myogenesis
    Ming Yu, Jingdong Xue, Qi Zhang, Yixuan Pan, Min Hao, Mingqian Hu, Meiyang Liu, Yuqian Feng, Yanhua Yao, Mengyuan Peng et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  71. KLF4/MLL3 complex axis drives NRBP2 transcription to eliminate acute myeloid leukemia cells
    Meng Yang, Ting Lu, Yicheng He, Cong Chen, Yifei Wang, Guohuan Sun, Yawei Zheng, Jiaxin Qin, Jiali Ye, Xiaowei Xie et al. · 2026 · Leukemia
  72. Dual regulation of chemical stress-induced DDI2/3 expression by a transcription factor Fzf1 and nucleosome in Saccharomyces cerevisiae
    Ying Du, Aiyang Lin, Joshua AR Brown, LeAnn J. Howe, Wei Xiao · 2026 · eLife
  73. Dual regulation of chemical stress-induced DDI2/3 expression by a transcription factor Fzf1 and nucleosome in Saccharomyces cerevisiae
    Ying Du, Aiyang Lin, Joshua AR Brown, LeAnn J. Howe, Wei Xiao · 2026 · eLife
  74. A transcription factor by any other name - function beyond DNA binding and transactivation
    Christina Maria Schuh, Joshua M. Brickman · 2026 · EMBO Reports
  75. Multiscale Energy Landscapes of DNA and Chromatin: From Base-Pair Dynamics to Genome Organization
    Gargi Gautam, Arnab Bhattacherjee · 2026
  76. From Primary Cells to Organoids: Expanding the Biological Relevance of In Vitro Cellular Models
    Fengyan Deng, Yan Wang, Luciana Andrea Castellano, Chongbei Zhao · 2026 · Cells
  77. ETV2 functions as a pioneer factor and regulates endothelial progenitor cell proliferation
    Nicole M. Recka, Daniel James Garry · 2026 · Cell Cycle
  78. Integration by parts: The multi-layered mechanisms of cis-regulatory control
    Jake Cornwall-Scoones, James Briscoe, M. Joaquina Delàs · 2026 · Molecular Cell
  79. Endothelial exosomes remodel chromatin accessibility and superenhancer in cancer cells to promote liver metastatic colonization
    Bei Jin, Shenglan Liu, Hongke Huang, Luo Yang, Dong Wei, Wei Dai, Jingfeng Zhou, Yun Wang, Ping Zhang, Qianyun Ye et al. · 2026 · Signal Transduction and Targeted Therapy
  80. Histone modifications directly modulate transcription factor binding to nucleosomes
    Luca Mariani, Martha L. Bulyk · 2026 · bioRxiv (Cold Spring Harbor Laboratory)