Broad H3K4me3 is associated with increased transcription elongation and enhancer activity at tumor-suppressor genes

Chen, Kaifu, Chen, Zhong, Wu, Dayong, Zhang, Lili, Lin, Xueqiu, Su, Jianzhong, Rodriguez, Benjamin, Xi, Yuanxin, Xia, Zheng, Chen, Xi, Shi, Xiaobing, Wang, Qianben, Li, Wei·2015·Nature Genetics
DOI 10.1038/ng.3385

Cited by (387)

Items 301–387 of 387

  1. Different E-box binding transcription factors, similar neuro-developmental defects: ZEB2 (Mowat-Wilson syndrome) and TCF4 (Pitt-Hopkins syndrome)
    Lize Meert, Judith C. Birkhoff, Andrea Conidi, Raymond A. Poot, Danny Huylebroeck · 2022 · Rare Disease and Orphan Drugs Journal
  2. EpiAlign: an alignment-based bioinformatic tool for comparing chromatin state sequences
    Xinzhou Ge, Haowen Zhang, Lingjue Xie, Wei Vivian Li, Soo Bin Kwon, Jingyi Jessica Li · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
  3. accuEnhancer: Accurate enhancer prediction by integration of multiple cell type data with deep learning
    Yi‐An Tung, Wen-Tse Yang, Tsung-Ting Hsieh, Yu‐Chuan Chang, June‐Tai Wu, Yen‐Jen Oyang, Chien‐Yu Chen · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  4. Flnc: Machine Learning Improves the Identification of Novel Full-length Long Noncoding RNAs from RNA Sequencing Data Without Transcriptional Initiation Profiles
    Zixiu Li, Peng Zhou, Euijin Kwon, Katherine A. Fitzgerald, Zhiping Weng, Chan Zhou · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  5. Specificity Guides Interpretation: On H3K4 Methylation at Enhancers and Broad Promoters
    Rohan N. Shah, Alexander J. Ruthenburg · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  6. Broad H3K4me3 Domain Is Associated with Spatial Coherence during Mammalian Embryonic Development
    Xuan Cao, Terry Ma, Rong Fan, Guo‐Cheng Yuan · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  7. CXXC-finger protein 1 associates with FOXP3 to stabilize homeostasis and suppressive functions of regulatory T cells
    Xiaoyu Meng, Yezhang Zhu, Kuai Liu, Yuxi Wang, Xiaoqian Liu, Chenxin Liu, Yan Jun Zeng, Shuai Wang, Xianzhi Gao, Xin Shen et al. · 2024 · eLife
  8. Targeting SLC7A11-mediated cysteine metabolism for the treatment of trastuzumab resistant HER2 positive breast cancer
    Yijia Hua, Ningjun Duan, Chunxiao Sun, Fan Yang, Min Tian, Yanting Sun, Shuhan Zhao, Jue Gong, Qian Liu, Xiang Huang et al. · 2025 · eLife
  9. Tissular chromatin-state cartography based on double-barcoded DNA arrays that capture unloaded PA-Tn5 transposase
    Maria Grazia Mendoza-Ferri, Gwendoline Lozachmeur, Maximilien Duvina, Laetitia Perret, Didier Merciris, Anne Gigout, Marco Antonio Mendoza-Parra · 2025 · Genome Research
  10. Acetylation of H3K115 is associated with fragile nucleosomes at CpG island promoters and active regulatory sites
    Yatendra Kumar, Dipta Sengupta, Elias T. Friman, Robert Scott Illingworth, Manon Soleil, Zheng Fan, Hua Wang, Kristian Helin, Matthieu Gérard, Wendy A. Bickmore · 2025 · eLife
  11. Stress Induced Signaling Pathways in Burkitt’s Lymphoma Play Novel Mechanisms in Fate Determination and Pathogenesis of Germinal Center-Derived B-Lymphomas
    Santosh Kumar Gothwal, Jacqueline H. Barlow · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  12. Metabolic Regulation of Histone Methylation
    Samantha J. Mentch · 2017 · eCommons (Cornell University)
  13. The Role of RNF40 mediated H2B monoubiquitination in transcription
    Wanhua Xie · 2017 · eDiss (Georg-August-Universität Göttingen)
  14. Integrative Machine Learning and Network Mining Models for the Inference of Regulatory Elements and Interactions in Human Cells
    Asa Thibodeau · 2018 · OpenCommons at University of Connecticut (University of Connecticut)
  15. Dynamics and Topology of Human Transcribed Cis -regulatory Elements
    Shigeki Hirabayashi, Shruti Bhagat, Yu Matsuki, Yujiro Takegami, Takuya Uehata, Ai Kanemaru, Masayoshi Itoh, Kotaro Shirakawa, Akifumi Takaori‐Kondo, Osamu Takeuchi et al. · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
  16. Epigenetic Control of Mesenchymal-Epithelial Interactions Directs Gastrointestinal Development
    Ryan Smith · 2018 · TSpace (University of Toronto)
  17. The role of TET1 and TET1ALT in cancer
    Charly Ryan Good · 2017 · TUScholarShare (Temple University)
  18. Global and Gene-specific Transcriptional Responses to Acute Stress
    Harry Fischl, Tom Brown, Andrew Angel, Jane Mellor · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  19. The role of histone 2B monoubiquitination (H2Bub1) in HER2-driven mammary carcinoma
    Evangelos Prokakis · 2021
  20. Peer Review #2 of "Computational inference of H3K4me3 and H3K27ac domain length (v0.1)"
    2016 · PeerJ
  21. Peer Review #2 of "Computational inference of H3K4me3 and H3K27ac domain length (v0.2)"
    2016 · PeerJ
  22. Peer Review #1 of "Computational inference of H3K4me3 and H3K27ac domain length (v0.2)"
    2016 · PeerJ
  23. Linking Enhancer to Epigenetics: New Way to Think About Human Diseases
    Zhuojuan Luo, Chengqi Lin · 2019 · Springer eBooks
  24. Peer Review #1 of "Computational inference of H3K4me3 and H3K27ac domain length (v0.1)"
    2016 · PeerJ
  25. Loss of the Ash2l subunit of histone H3K4 methyltransferase complexes promotes chromatin compaction at promoters
    Mirna Barsoum, Alexander T. Stenzel, Agnieszka Bochyńska, Chao‐Chung Kuo, Roksaneh Sayadi-Boroujeni, Philip Bussmann, Juliane Lüscher‐Firzlaff, Ivan G. Costa, Bernhard Lüscher · 2022 · Research Square
  26. Long-read genome assemblies reveals a cis -regulatory landscape associated with phenotypic divergence in two sister Siniperca fishes
    Guangxian Tu, Qi Chen, Xinshuang Zhang, Ruirun Jiang, Long Zhang, Cheng-Jun Lai, Zhuyue Yan, Yanrong Lv, Shaoping Weng, Li Zhang et al. · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  27. Heterozygous Kmt2d loss diminishes enhancers to render medulloblastoma cells vulnerable to combinatory inhibition of lysine demethylation and oxidative phosphorylation
    Shilpa S. Dhar, Calena J. Brown, Ali Rizvi, Lauren Reed, Sivareddy Kotla, Constantin Zod, Janak Abraham, Jun‐ichi Abe, Veena Rajaram, Kaifu Chen et al. · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  28. Epigenetic modulation of cancer stem cells in vitro 3D models
    Jayanta Das, John H. Stella, Myra Saunders, Naphtalie Joassaint, McKenna Dawes, Beanca Ellis, Oneilia Yearde, Rose Mary Stiffin, Marilyn Sherman, Madhumita Das et al. · 2023 · Elsevier eBooks
  29. JMJD6 promotes radioresistance of non-small cell lung cancer via epigenetic regulation of EHF
    Manni Wang, Siyuan Chen, Xuemei He, Aqu Alu, Qiang Pu, Xiawei Wei · 2023 · Research Square
  30. Transglutaminase 2-Mediated Histone H3Q5 Serotonylation: A Selective Epigenetic Regulator Driving Cell Proliferation and Migration in Colorectal Cancer
    Yuting Liu, Yu Yu, Dan Li, Yating Sun, Jingxian Wu, Wanhua Xie · 2024 · Research Square
  31. A Type-2 Fuzzy Logic-Based Explainable Artificial Intelligence for the Prediction of Enhancers
    Khizra Maqsood, Hani Hagras, Nicolae Radu Zabet · 2024 · IEEE International Conference on Fuzzy Systems (FUZZ-IEEE)
  32. CXXC-finger protein 1 associates with FOXP3 to stabilize homeostasis and suppressive functions of regulatory T cells
    Xiaoyu Meng, Yezhang Zhu, Kuai Liu, Yuxi Wang, Xiaoqian Liu, Chenxin Liu, Yan Jun Zeng, Shuai Wang, Xianzhi Gao, Xin Shen et al. · 2024 · eLife
  33. Nutrigenomics and Parkinson's disease
    Khairiah Razali, Khaled Algantri, Su Peng Loh, Shi-Hui Cheng, Wael M.Y. Mohamed · 2024 · Elsevier eBooks
  34. Targeting SLC7A11-mediated cysteine metabolism for the treatment of trastuzumab resistant HER2 positive breast cancer
    Yijia Hua, Ningjun Duan, Chunxiao Sun, Fan Yang, Min Tian, Yanting Sun, Shuhan Zhao, Jue Gong, Qian Liu, Xiang Huang et al. · 2025 · eLife
  35. Machine Learning-based Prediction of the Long-term Stability of Chinese Hamster Ovary Cells due to Epigenetic Changes
    Pedro Seber, Richard D. Braatz · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  36. CXXC-finger protein 1 associates with FOXP3 to stabilize homeostasis and suppressive functions of regulatory T cells
    Xiaoyu Meng, Yezhang Zhu, Kuai Liu, Yuxi Wang, Xiaoqian Liu, Chenxin Liu, Yan Jun Zeng, Shuai Wang, Xianzhi Gao, Xin Shen et al. · 2025 · eLife
  37. Erlotinib induces 3D genome rearrangements in lung cancer cells activating tumor suppressor genes through FOXA2-bound Epromoters
    Guruprasadh Swaminathan, Julio Cordero, Stefan Günther, Johannes Graumann, Thomas W Braun, Gergana D. Dobreva, Guillermo Barreto · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  38. WDR-5 exhibits H3K4 methylation-independent activity during embryonic development in C. elegans
    Nurulhafizah Binti Samsudin, Siyao Wang, Kate Fisher, Gino B Poulin · 2026 · Epigenetics & Chromatin
  39. Acetylation of H3K115 is associated with fragile nucleosomes at CpG island promoters and active regulatory sites
    Yatendra Kumar, Dipta Sengupta, Elias T. Friman, Robert Scott Illingworth, Manon Soleil, Zheng Fan, Hua Wang, Kristian Helin, Matthieu Gérard, Wendy A. Bickmore · 2025 · eLife
  40. Chemical reprogramming of fibroblasts into retinal pigment epithelium cells for vision restoration
    Sha-Sha Li, Hui Liu, Shao-Hui Pan, Zhengbiao Zhu, Shun Zhang, Jia-Hang Li, Ying-Hao Yao, Xinyu Wang, Na Gao, Xiao-Yu Liu et al. · 2025 · Nature Communications
  41. Additional file 1 of Whole-genome landscape of histone H3K4me3 modification during sperm cell lineage development in tomato
    Yunyun Song, Chang, Zhikai, Yixuan Feng, Tai Wang, Lingtong Liu · 2024 · Figshare
  42. Additional file 6 of Whole-genome landscape of histone H3K4me3 modification during sperm cell lineage development in tomato
    Yunyun Song, Chang, Zhikai, Yixuan Feng, Tai Wang, Lingtong Liu · 2024 · Figshare
  43. Additional file 7 of Chromatin profiling and state predictions reveal insights into epigenetic regulation during early porcine development
    Sarah M. Innis, Ryan A. Cabot · 2024 · Figshare
  44. Additional file 6 of Chromatin profiling and state predictions reveal insights into epigenetic regulation during early porcine development
    Sarah M. Innis, Ryan A. Cabot · 2024 · Figshare
  45. Additional file 1 of Chromatin profiling and state predictions reveal insights into epigenetic regulation during early porcine development
    Sarah M. Innis, Ryan A. Cabot · 2024 · Figshare
  46. Additional file 8 of Whole-genome landscape of histone H3K4me3 modification during sperm cell lineage development in tomato
    Yunyun Song, Chang, Zhikai, Yixuan Feng, Tai Wang, Lingtong Liu · 2024 · Figshare
  47. Additional file 1 of Efficient chromatin profiling of H3K4me3 modification in cotton using CUT&Tag
    Xiaoyuan Tao, Feng Shouli, Zhao, Ting, Xueying Guan · 2020 · Figshare
  48. Additional file 1 of Multimodal epigenetic sequencing analysis (MESA) of cell-free DNA for non-invasive colorectal cancer detection
    Li, Yumei, Xu, Jianfeng, Chaorong Chen, Lu, Zhenhai, 万德森, Diange Li, Jason Sheng Li, Allison J. Sorg, Curt C. Roberts, Shivani Mahajan et al. · 2024 · Figshare
  49. Additional file 4 of Whole-genome landscape of histone H3K4me3 modification during sperm cell lineage development in tomato
    Yunyun Song, Chang, Zhikai, Yixuan Feng, Tai Wang, Lingtong Liu · 2024 · Figshare
  50. Additional file 2 of Multimodal epigenetic sequencing analysis (MESA) of cell-free DNA for non-invasive colorectal cancer detection
    Li, Yumei, Xu, Jianfeng, Chaorong Chen, Lu, Zhenhai, 万德森, Diange Li, Jason Sheng Li, Allison J. Sorg, Curt C. Roberts, Shivani Mahajan et al. · 2024 · Figshare
  51. Additional file 4 of Chromatin profiling and state predictions reveal insights into epigenetic regulation during early porcine development
    Sarah M. Innis, Ryan A. Cabot · 2024 · Figshare
  52. Additional file 3 of Chromatin profiling and state predictions reveal insights into epigenetic regulation during early porcine development
    Sarah M. Innis, Ryan A. Cabot · 2024 · Figshare
  53. Additional file 1 of An explainable artificial intelligence approach for decoding the enhancer histone modifications code and identification of novel enhancers in Drosophila
    Wolfe, Jareth C., Mikheeva, Liudmila A., Hani Hagras, Nicolae Radu Zabet · 2021 · Figshare
  54. Additional file 2 of Whole-genome landscape of histone H3K4me3 modification during sperm cell lineage development in tomato
    Yunyun Song, Chang, Zhikai, Yixuan Feng, Tai Wang, Lingtong Liu · 2024 · Figshare
  55. Additional file 5 of Chromatin profiling and state predictions reveal insights into epigenetic regulation during early porcine development
    Sarah M. Innis, Ryan A. Cabot · 2024 · Figshare
  56. Additional file 2 of An explainable artificial intelligence approach for decoding the enhancer histone modifications code and identification of novel enhancers in Drosophila
    Wolfe, Jareth C., Mikheeva, Liudmila A., Hani Hagras, Nicolae Radu Zabet · 2021 · Figshare
  57. Additional file 1 of Epigenomic landscape of enhancer elements during Hydra head organizer formation
    Puli Chandramouli Reddy, Akhila Gungi, Suyog Ubhe, Sanjeev Galande · 2020 · Figshare
  58. Additional file 3 of Whole-genome landscape of histone H3K4me3 modification during sperm cell lineage development in tomato
    Yunyun Song, Chang, Zhikai, Yixuan Feng, Tai Wang, Lingtong Liu · 2024 · Figshare
  59. Additional file 1 of TADsplimer reveals splits and mergers of topologically associating domains for epigenetic regulation of transcription
    Wang, Guangyu, Qingshu Meng, Bo Xia, Zhang, Shuo, Lv, Jie, Zhao, Dongyu, Li, Yanqiang, Wang, Xin, Zhang, Lili, John P. Cooke et al. · 2020 · Figshare
  60. Additional file 2 of TADsplimer reveals splits and mergers of topologically associating domains for epigenetic regulation of transcription
    Wang, Guangyu, Qingshu Meng, Bo Xia, Zhang, Shuo, Lv, Jie, Zhao, Dongyu, Li, Yanqiang, Wang, Xin, Zhang, Lili, John P. Cooke et al. · 2020 · Figshare
  61. Additional file 2 of Chromatin profiling and state predictions reveal insights into epigenetic regulation during early porcine development
    Sarah M. Innis, Ryan A. Cabot · 2024 · Figshare
  62. Additional file 5 of Whole-genome landscape of histone H3K4me3 modification during sperm cell lineage development in tomato
    Yunyun Song, Chang, Zhikai, Yixuan Feng, Tai Wang, Lingtong Liu · 2024 · Figshare
  63. Additional file 7 of Whole-genome landscape of histone H3K4me3 modification during sperm cell lineage development in tomato
    Yunyun Song, Chang, Zhikai, Yixuan Feng, Tai Wang, Lingtong Liu · 2024 · Figshare
  64. Homozygous Deletion of the Epigenetic Regulator PHF20 in Individuals With Neurodevelopmental Disorder
    Shira Yanovsky‐Dagan, Hongwen Xuan, Jonathan Rips, Emuna Paz‐Ebstein, Talia Baer, Shira Gross, Ayala Frumkin, Xiaobing Shi, Tamar Harel · 2025 · Human Mutation
  65. Acetylation of H3K115 is detected associated with fragile nucleosomes at CpG island promoters and active regulatory sites
    Yatendra Kumar, Dipta Sengupta, Elias T. Friman, Robert Scott Illingworth, Manon Soleil, Zheng Fan, Hua Wang, Kristian Helin, Matthieu Gérard, Wendy A. Bickmore · 2026 · eLife
  66. Regulation of wing growth in vivo by the histone demethylase dLSD1
    Manuela Texier · 2018 · theses.fr (ABES)
  67. Décryptage de dynamiques épigénomiques au cours de la thymopoïèse et de la spermatogenèse en appliquant une méthodologie de recherche reproductible à des données de séquençage à haut débit
    Guillaume Charbonnier · 2019 · theses.fr (ABES)
  68. Rôle dual de PPARγ dans les tumeurs de la vessie
    Laure Coutos-Thévenot · 2019 · theses.fr (ABES)
  69. Bio-Geochemistry of ovarian cancer : Role of selenium nanoparticles in treatment and copper isotopes in detection of ovarian cancer.
    Benoît Toubhans · 2020 · theses.fr (ABES)
  70. L’hétérochromatine duale H3K9me3/H3K36me3 dépendante de SETDB1 et des NSDs assure l’expression des gènes en maintenant les enhancers inactifs
    Amandine Barral · 2021 · theses.fr (ABES)
  71. Deregulation of alternative promoter usage in T-acute lymphoblastic leukemia
    José David Abad Flores · 2021 · theses.fr (ABES)
  72. Histone mark remodeling in cancer: an enhancer-centered perspective
    Jiyoon Park, 전진하, Sujeong Gim, Chan Chung · 2026 · Genes & Genomics
  73. CASER: A semi-supervised model with multi-omics data integration prioritizes cancer-associated epigenetic regulator genes
    Hao Li, Chaohuan Lin, Liyu Liu, Jie Lyu, Zhen Feng · 2026 · PLoS Computational Biology
  74. The signaling upstream of DOT1L-mediated H3K79 methylation
    Chu Chen, Di Wu, Canran Lv, Peng Zhu, Zihao Chen, Q Li, Junming Li, Jie Yang, Jing Zhang · 2026 · Epigenomics
  75. Epigenetic and 3D Genome Changes Drive Primary Trastuzumab Resistance in HER2+ Breast Cancer
    Ningjun Duan, Yijia Hua, Zhengxing Zhou, Nan Jin, Wei Li, Yongmei Yin · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  76. CFP1 promotes B cell class switch recombination through the regulation of S region germline transcription and proliferation
    Gong, Yanan Zhao, Yalin Yang, Yimiao Lu, Jingning Bai, Meiling Liu, Yanhao Chen, Bo Zhao, Ruizhi Zhou, Chun Chen et al. · 2026 · iScience
  77. Mixed lineage leukemia 1 regulates haemocyte proliferation by affecting histone H3 lysine 4 trimethylation during immune priming of Eriocheir sinensis
    Xinyu Zhao, Xue Qiao, Xiaoyu Gu, Yuqing Zeng, Yiqing Wang, Mengjia Chen, Lingling Wang, Linsheng Song · 2026 · International Journal of Biological Macromolecules
  78. DNA methylation and chromatin modifications-updates based on chromatin modifiers
    Zahra Sepehri, Tasnim H. Beacon, Fadumo D.S. Osman, Sanzida Jahan, James Davie · 2026 · Elsevier eBooks
  79. G4 DNA potentiates KDM2B phase separation to couple transcriptional repression with immune remodeling in hepatocellular carcinoma
    Wanxiang Xiong, Xiuhui Shi, Shixiang Pan, Hairui Li, Guang Yang, Chunxu Wang, Yufeng Liu, Mingyou Xu, Boyu Chen, Ruyi Liu et al. · 2026 · Cancer Letters
  80. Epigenetic and 3D Genome Changes Drive Primary Trastuzumab Resistance in HER2+ Breast Cancer
    Ningjun Duan, Yijia Hua, Zhengxing Zhou, Nan Jin, Wei Li, Yongmei Yin · 2026 · eLife
  81. Epigenetic and 3D Genome Changes Drive Primary Trastuzumab Resistance in HER2+ Breast Cancer
    Ningjun Duan, Yijia Hua, Zhengxing Zhou, Nan Jin, Wei Li, Yongmei Yin · 2026 · eLife
  82. Metabolic regulation and cardiac regeneration
    Shanthi L. Davé, Alexander Y. Payumo · 2026 · Elsevier eBooks
  83. TAL1 is indispensable in ETV2-primed human endothelial cell fate determination
    Yun Zhao, M J Sun, Zixuan Hong, Jingkun Yi, Donglin Yu, Xiaojing Ma, Liangliang Tian, Yi Hong, Lijun Sun, Xiaoxia Li et al. · 2026 · Science Advances
  84. KMT2E recruitment by H3 serotonylation regulates neurodevelopmental chromatin dynamics
    Jennifer C. O’Chan, Benjamin H. Weekley, Celi Yang, Min Chen, Ashley M. Cunningham, Sohini Dutta, Winnie Chen, Rasika R. Iyer, Newaz I. Ahmed, Bulent Cetin et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  85. Role of HIF1α in FXR-mediated protection and anti-inflammatory macrophage polarization in parenteral nutrition-associated cholestasis
    Swati Ghosh, Michael W. Devereaux, David J. Orlicky, Karim Christian El Kasmi, Ronald J. Sokol · 2026 · Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease
  86. The role of histone modification in epigenetic regulation of gene expression and cell specification
    Carlo Maria Di Liegro, Gabriella Schiera, Italia Di Liegro · 2026 · Handbook of clinical neurology
  87. Genome‐Wide and Multi‐Omics Analysis Identified DNA‐Interacting Circular RNA circFOXK2 as MLL1 Regulator for Histone H3K4 Methylation in Pancreatic Ductal Adenocarcinoma
    Chi Hin Wong, Jessica Jazmin Peña-Paladines, Sum Yin Valerie Leung, Ka‐Fai To, Ksh Chok, Yangchao Chen · 2026 · Advanced Science